CDMI_EntityAPI
$return = $obj->get_entity_AlignmentTree($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_AlignmentTree fields_AlignmentTree is a reference to a hash where the following keys are defined: id has a value which is a string alignment_method has a value which is a string alignment_parameters has a value which is a string alignment_properties has a value which is a string tree_method has a value which is a string tree_parameters has a value which is a string tree_properties has a value which is a string
An alignment arranges a group of protein sequences so that they match. Each alignment is associated with a phylogenetic tree that describes how the sequences developed and their evolutionary distance. The actual tree and alignment FASTA are stored in separate flat files. The Kbase will maintain a set of alignments and associated trees. The majority of these will be based on protein sequences. We will not have a comprehensive set but we will have tens of thousands of such alignments, and we view them as an imporant resource to support annotation. The alignments/trees will include the tools and parameters used to construct them. Access to the underlying sequences and trees in a form convenient to existing tools will be supported.
It has the following fields:
The name of the program used to produce the alignment.
The parameters given to the program when producing the alignment.
A colon-delimited string of key-value pairs containing additional properties of the alignment.
The name of the program used to produce the tree.
The parameters given to the program when producing the tree.
A colon-delimited string of key-value pairs containing additional properties of the tree.
$return = $obj->query_entity_AlignmentTree($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_AlignmentTree fields_AlignmentTree is a reference to a hash where the following keys are defined: id has a value which is a string alignment_method has a value which is a string alignment_parameters has a value which is a string alignment_properties has a value which is a string tree_method has a value which is a string tree_parameters has a value which is a string tree_properties has a value which is a string
$return = $obj->all_entities_AlignmentTree($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_AlignmentTree fields_AlignmentTree is a reference to a hash where the following keys are defined: id has a value which is a string alignment_method has a value which is a string alignment_parameters has a value which is a string alignment_properties has a value which is a string tree_method has a value which is a string tree_parameters has a value which is a string tree_properties has a value which is a string
$return = $obj->get_entity_AlleleFrequency($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_AlleleFrequency fields_AlleleFrequency is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string position has a value which is an int minor_AF has a value which is a float minor_allele has a value which is a string major_AF has a value which is a float major_allele has a value which is a string obs_unit_count has a value which is an int
An allele frequency represents a summary of the major and minor allele frequencies for a position on a chromosome. It has the following fields:
identifier for this allele in the original (source) database
Specific position on the contig where the allele occurs
Minor allele frequency. Floating point number from 0.0 to 0.5.
Text letter representation of the minor allele. Valid values are A, C, G, and T.
Major allele frequency. Floating point number less than or equal to 1.0.
Text letter representation of the major allele. Valid values are A, C, G, and T.
Number of observational units used to compute the allele frequencies. Indicates the quality of the analysis.
$return = $obj->query_entity_AlleleFrequency($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_AlleleFrequency fields_AlleleFrequency is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string position has a value which is an int minor_AF has a value which is a float minor_allele has a value which is a string major_AF has a value which is a float major_allele has a value which is a string obs_unit_count has a value which is an int
$return = $obj->all_entities_AlleleFrequency($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_AlleleFrequency fields_AlleleFrequency is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string position has a value which is an int minor_AF has a value which is a float minor_allele has a value which is a string major_AF has a value which is a float major_allele has a value which is a string obs_unit_count has a value which is an int
$return = $obj->get_entity_Annotation($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Annotation fields_Annotation is a reference to a hash where the following keys are defined: id has a value which is a string annotator has a value which is a string comment has a value which is a string annotation_time has a value which is a string
An annotation is a comment attached to a feature. Annotations are used to track the history of a feature's functional assignments and any related issues. The key is the feature ID followed by a colon and a complemented ten-digit sequence number.
name of the annotator who made the comment
text of the annotation
date and time at which the annotation was made
$return = $obj->query_entity_Annotation($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Annotation fields_Annotation is a reference to a hash where the following keys are defined: id has a value which is a string annotator has a value which is a string comment has a value which is a string annotation_time has a value which is a string
$return = $obj->all_entities_Annotation($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Annotation fields_Annotation is a reference to a hash where the following keys are defined: id has a value which is a string annotator has a value which is a string comment has a value which is a string annotation_time has a value which is a string
$return = $obj->get_entity_Assay($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Assay fields_Assay is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string assay_type has a value which is a string assay_type_id has a value which is a string
An assay is an experimental design for determining alleles at specific chromosome positions. It has the following fields:
identifier for this assay in the original (source) database
Text description of the type of assay (e.g., SNP, length, sequence, categorical, array, short read, SSR marker, AFLP marker)
source ID associated with the assay type (informational)
$return = $obj->query_entity_Assay($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Assay fields_Assay is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string assay_type has a value which is a string assay_type_id has a value which is a string
$return = $obj->all_entities_Assay($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Assay fields_Assay is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string assay_type has a value which is a string assay_type_id has a value which is a string
$return = $obj->get_entity_AtomicRegulon($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_AtomicRegulon fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string
An atomic regulon is an indivisible group of coregulated features on a single genome. Atomic regulons are constructed so that a given feature can only belong to one. Because of this, the expression levels for atomic regulons represent in some sense the state of a cell. An atomicRegulon is a set of protein-encoding genes that are believed to have identical expression profiles (i.e., they will all be expressed or none will be expressed in the vast majority of conditions). These are sometimes referred to as "atomic regulons". Note that there are more common notions of "coregulated set of genes" based on the notion that a single regulatory mechanism impacts an entire set of genes. Since multiple other mechanisms may impact overlapping sets, the genes impacted by a regulatory mechanism need not all share the same expression profile. We use a distinct notion (CoregulatedSet) to reference sets of genes impacted by a single regulatory mechanism (i.e., by a single transcription regulator).
$return = $obj->query_entity_AtomicRegulon($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_AtomicRegulon fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->all_entities_AtomicRegulon($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_AtomicRegulon fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_entity_Attribute($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Attribute fields_Attribute is a reference to a hash where the following keys are defined: id has a value which is a string description has a value which is a string
An attribute describes a category of condition or characteristic for an experiment. The goals of the experiment can be inferred from its values for all the attributes of interest. It has the following fields:
Descriptive text indicating the nature and use of this attribute.
$return = $obj->query_entity_Attribute($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Attribute fields_Attribute is a reference to a hash where the following keys are defined: id has a value which is a string description has a value which is a string
$return = $obj->all_entities_Attribute($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Attribute fields_Attribute is a reference to a hash where the following keys are defined: id has a value which is a string description has a value which is a string
$return = $obj->get_entity_Biomass($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Biomass fields_Biomass is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a reference to a list where each element is a string
A biomass is a collection of compounds in a specific ratio and in specific compartments that are necessary for a cell to function properly. The prediction of biomasses is key to the functioning of the model. It has the following fields:
last modification date of the biomass data
descriptive name for this biomass
$return = $obj->query_entity_Biomass($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Biomass fields_Biomass is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a reference to a list where each element is a string
$return = $obj->all_entities_Biomass($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Biomass fields_Biomass is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a reference to a list where each element is a string
$return = $obj->get_entity_BiomassCompound($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_BiomassCompound fields_BiomassCompound is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float
A Biomass Compound represents the occurrence of a particular compound in a biomass. It has the following fields:
proportion of the biomass in grams per mole that contains this compound
$return = $obj->query_entity_BiomassCompound($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_BiomassCompound fields_BiomassCompound is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float
$return = $obj->all_entities_BiomassCompound($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_BiomassCompound fields_BiomassCompound is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float
$return = $obj->get_entity_Compartment($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Compartment fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string
A compartment is a section of a single model that represents the environment in which a reaction takes place (e.g. cell wall). It has the following fields:
short abbreviated name for this compartment (usually a single character)
date and time of the last modification to the compartment's definition
common name for the compartment
common modeling ID of this compartment
$return = $obj->query_entity_Compartment($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Compartment fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string
$return = $obj->all_entities_Compartment($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Compartment fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string
$return = $obj->get_entity_Complex($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Complex fields_Complex is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a reference to a list where each element is a string msid has a value which is a string mod_date has a value which is a string
A complex is a set of chemical reactions that act in concert to effect a role. It has the following fields:
name of this complex. Not all complexes have names.
common modeling ID of this complex.
date and time of the last change to this complex's definition
$return = $obj->query_entity_Complex($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Complex fields_Complex is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a reference to a list where each element is a string msid has a value which is a string mod_date has a value which is a string
$return = $obj->all_entities_Complex($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Complex fields_Complex is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a reference to a list where each element is a string msid has a value which is a string mod_date has a value which is a string
$return = $obj->get_entity_Compound($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Compound fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
A compound is a chemical that participates in a reaction. Both ligands and reaction components are treated as compounds. It has the following fields:
primary name of the compound, for use in displaying reactions
shortened abbreviation for the compound name
common modeling ID of this compound
TRUE if this compound is found in most reactions, else FALSE
date and time of the last modification to the compound definition
a electrically neutral formula for the compound
a pH-neutral formula for the compound
atomic mass of the compound
$return = $obj->query_entity_Compound($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Compound fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
$return = $obj->all_entities_Compound($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Compound fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
$return = $obj->get_entity_Contig($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Contig fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
A contig is thought of as composing a part of the DNA associated with a specific genome. It is represented as an ID (including the genome ID) and a ContigSequence. We do not think of strings of DNA from, say, a metgenomic sample as "contigs", since there is no associated genome (these would be considered ContigSequences). This use of the term "ContigSequence", rather than just "DNA sequence", may turn out to be a bad idea. For now, you should just realize that a Contig has an associated genome, but a ContigSequence does not.
ID of this contig from the core (source) database
$return = $obj->query_entity_Contig($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Contig fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
$return = $obj->all_entities_Contig($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Contig fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
$return = $obj->get_entity_ContigChunk($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ContigChunk fields_ContigChunk is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
ContigChunks are strings of DNA thought of as being a string in a 4-character alphabet with an associated ID. We allow a broader alphabet that includes U (for RNA) and the standard ambiguity characters. The notion of ContigChunk was introduced to avoid transferring/manipulating huge contigs to access small substrings. A ContigSequence is formed by concatenating a set of one or more ContigChunks. Thus, ContigChunks are the basic units moved from the database to memory. Their existence should be hidden from users in most circumstances (users are expected to request substrings of ContigSequences, and the Kbase software locates the appropriate ContigChunks).
base pairs that make up this sequence
$return = $obj->query_entity_ContigChunk($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ContigChunk fields_ContigChunk is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
$return = $obj->all_entities_ContigChunk($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ContigChunk fields_ContigChunk is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
$return = $obj->get_entity_ContigSequence($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ContigSequence fields_ContigSequence is a reference to a hash where the following keys are defined: id has a value which is a string length has a value which is an int
ContigSequences are strings of DNA. Contigs have an associated genome, but ContigSequences do not.. We can think of random samples of DNA as a set of ContigSequences. There are no length constraints imposed on ContigSequences -- they can be either very short or very long. The basic unit of data that is moved to/from the database is the ContigChunk, from which ContigSequences are formed. The key of a ContigSequence is the sequence's MD5 identifier.
number of base pairs in the contig
$return = $obj->query_entity_ContigSequence($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ContigSequence fields_ContigSequence is a reference to a hash where the following keys are defined: id has a value which is a string length has a value which is an int
$return = $obj->all_entities_ContigSequence($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ContigSequence fields_ContigSequence is a reference to a hash where the following keys are defined: id has a value which is a string length has a value which is an int
$return = $obj->get_entity_CoregulatedSet($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_CoregulatedSet fields_CoregulatedSet is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int
We need to represent sets of genes that are coregulated via some regulatory mechanism. In particular, we wish to represent genes that are coregulated using transcription binding sites and corresponding transcription regulatory proteins. We represent a coregulated set (which may, or may not, be considered a regulon) using CoregulatedSet.
original ID of this coregulated set in the source (core) database
binding location for this set's transcription factor; there may be none of these or there may be more than one
$return = $obj->query_entity_CoregulatedSet($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_CoregulatedSet fields_CoregulatedSet is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int
$return = $obj->all_entities_CoregulatedSet($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_CoregulatedSet fields_CoregulatedSet is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int
$return = $obj->get_entity_Diagram($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Diagram fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string
A functional diagram describes a network of chemical reactions, often comprising a single subsystem. It has the following fields:
descriptive name of this diagram
content of the diagram, in PNG format
$return = $obj->query_entity_Diagram($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Diagram fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string
$return = $obj->all_entities_Diagram($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Diagram fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string
$return = $obj->get_entity_EcNumber($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_EcNumber fields_EcNumber is a reference to a hash where the following keys are defined: id has a value which is a string obsolete has a value which is an int replacedby has a value which is a string
EC numbers are assigned by the Enzyme Commission, and consist of four numbers separated by periods, each indicating a successively smaller cateogry of enzymes. It has the following fields:
This boolean indicates when an EC number is obsolete.
When an obsolete EC number is replaced with another EC number, this string will hold the name of the replacement EC number.
$return = $obj->query_entity_EcNumber($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_EcNumber fields_EcNumber is a reference to a hash where the following keys are defined: id has a value which is a string obsolete has a value which is an int replacedby has a value which is a string
$return = $obj->all_entities_EcNumber($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_EcNumber fields_EcNumber is a reference to a hash where the following keys are defined: id has a value which is a string obsolete has a value which is an int replacedby has a value which is a string
$return = $obj->get_entity_Experiment($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Experiment fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string
An experiment is a combination of conditions for which gene expression information is desired. The result of the experiment is a set of expression levels for features under the given conditions. It has the following fields:
Publication or lab relevant to this experiment.
$return = $obj->query_entity_Experiment($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Experiment fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string
$return = $obj->all_entities_Experiment($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Experiment fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string
$return = $obj->get_entity_Family($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Family fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string
The Kbase will support the maintenance of protein families (as sets of Features with associated translations). We are initially only supporting the notion of a family as composed of a set of isofunctional homologs. That is, the families we initially support should be thought of as containing protein-encoding genes whose associated sequences all implement the same function (we do understand that the notion of "function" is somewhat ambiguous, so let us sweep this under the rug by calling a functional role a "primitive concept"). We currently support families in which the members are translations of features, and we think of Features as having an associated function. Identical protein sequences as products of translating distinct genes may or may not have identical functions, and we allow multiple members of the same Family to share identical protein sequences. This may be justified, since in a very, very, very few cases identical proteins do, in fact, have distinct functions. We would prefer to reach the point where our Families are sets of protein sequence, rather than sets of protein-encoding Features.
type of protein family (e.g. FIGfam, equivalog)
release number / subtype of protein family
optional free-form description of the family. For function-based families, this would be the functional role for the family members.
FASTA-formatted alignment of the family's protein sequences
$return = $obj->query_entity_Family($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Family fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string
$return = $obj->all_entities_Family($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Family fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string
$return = $obj->get_entity_Feature($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Feature fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
A feature (sometimes also called a gene) is a part of a genome that is of special interest. Features may be spread across multiple DNA sequences (contigs) of a genome, but never across more than one genome. Each feature in the database has a unique ID that functions as its ID in this table. Normally a Feature is just a single contigous region on a contig. Features have types, and an appropriate choice of available types allows the support of protein-encoding genes, exons, RNA genes, binding sites, pathogenicity islands, or whatever.
Code indicating the type of this feature. Among the codes currently supported are "peg" for a protein encoding gene, "bs" for a binding site, "opr" for an operon, and so forth.
ID for this feature in its original source (core) database
Number of base pairs in this feature.
Functional assignment for this feature. This will often indicate the feature's functional role or roles, and may also have comments.
alternative identifier for the feature. These are highly unstructured, and frequently non-unique.
$return = $obj->query_entity_Feature($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Feature fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->all_entities_Feature($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Feature fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_entity_Genome($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Genome fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
The Kbase houses a large and growing set of genomes. We often have multiple genomes that have identical DNA. These usually have distinct gene calls and annotations, but not always. We consider the Kbase to be a framework for managing hundreds of thousands of genomes and offering the tools needed to support compartive analysis on large sets of genomes, some of which are virtually identical. Each genome has an MD5 value computed from the DNA that is associated with the genome. Hence, it is easy to recognize when you have identical genomes, perhaps annotated by distinct groups.
Number of protein encoding genes for this genome.
Number of RNA features found for this organism.
Full genus/species/strain name of the genome sequence.
TRUE if the genome sequence is complete, else FALSE
TRUE if this is a prokaryotic genome sequence, else FALSE
Number of base pairs in the genome sequence.
Number of contigs for this genome sequence.
Domain for this organism (Archaea, Bacteria, Eukaryota, Virus, Plasmid, or Environmental Sample).
Genetic code number used for protein translation on most of this genome sequence's contigs.
Percent GC content present in the genome sequence's DNA.
zero or more strings describing phenotypic information about this genome sequence
MD5 identifier describing the genome's DNA sequence
identifier assigned to this genome by the original source
$return = $obj->query_entity_Genome($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Genome fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
$return = $obj->all_entities_Genome($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Genome fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
$return = $obj->get_entity_Locality($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Locality fields_Locality is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string city has a value which is a string state has a value which is a string country has a value which is a string origcty has a value which is a string elevation has a value which is an int latitude has a value which is an int longitude has a value which is an int lo_accession has a value which is a string
A locality is a geographic location. It has the following fields:
Name or description of the location used as a collection site.
City of the collecting site.
State or province of the collecting site.
Country of the collecting site.
3-letter ISO 3166-1 extended country code for the country of origin.
Elevation of the collecting site, expressed in meters above sea level. Negative values are allowed.
Latitude of the collecting site, recorded as a decimal number. North latitudes are positive values and south latitudes are negative numbers.
Longitude of the collecting site, recorded as a decimal number. West longitudes are positive values and east longitudes are negative numbers.
gazeteer ontology term ID
$return = $obj->query_entity_Locality($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Locality fields_Locality is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string city has a value which is a string state has a value which is a string country has a value which is a string origcty has a value which is a string elevation has a value which is an int latitude has a value which is an int longitude has a value which is an int lo_accession has a value which is a string
$return = $obj->all_entities_Locality($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Locality fields_Locality is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string city has a value which is a string state has a value which is a string country has a value which is a string origcty has a value which is a string elevation has a value which is an int latitude has a value which is an int longitude has a value which is an int lo_accession has a value which is a string
$return = $obj->get_entity_Media($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Media fields_Media is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string type has a value which is a string
A media describes the chemical content of the solution in which cells are grown in an experiment or for the purposes of a model. The key is the common media name. The nature of the media is described by its relationship to its constituent compounds. It has the following fields:
date and time of the last modification to the media's definition
descriptive name of the media
type of the medium (aerobic or anaerobic)
$return = $obj->query_entity_Media($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Media fields_Media is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string type has a value which is a string
$return = $obj->all_entities_Media($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Media fields_Media is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string type has a value which is a string
$return = $obj->get_entity_Model($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Model fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int
A model specifies a relationship between sets of features and reactions in a cell. It is used to simulate cell growth and gene knockouts to validate annotations. It has the following fields:
date and time of the last change to the model data
descriptive name of the model
revision number of the model
string indicating where the model came from (e.g. single genome, multiple genome, or community model)
indicator of whether the model is stable, under construction, or under reconstruction
number of reactions in the model
number of compounds in the model
number of annotations used to build the model
$return = $obj->query_entity_Model($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Model fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int
$return = $obj->all_entities_Model($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Model fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int
$return = $obj->get_entity_ModelCompartment($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ModelCompartment fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float
The Model Compartment represents a section of a cell (e.g. cell wall, cytoplasm) as it appears in a specific model. It has the following fields:
number used to distinguish between different instances of the same type of compartment in a single model. Within a model, any two instances of the same compartment must have difference compartment index values.
description used to differentiate between instances of the same compartment in a single model
pH used to determine proton balance in this compartment
ask Chris
$return = $obj->query_entity_ModelCompartment($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ModelCompartment fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float
$return = $obj->all_entities_ModelCompartment($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ModelCompartment fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float
$return = $obj->get_entity_OTU($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_OTU fields_OTU is a reference to a hash where the following keys are defined: id has a value which is a string
An OTU (Organism Taxonomic Unit) is a named group of related genomes. It has the following fields:
$return = $obj->query_entity_OTU($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_OTU fields_OTU is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->all_entities_OTU($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_OTU fields_OTU is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_entity_ObservationalUnit($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ObservationalUnit fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
An ObservationalUnit is an individual plant that 1) is part of an experiment or study, 2) has measured traits, and 3) is assayed for the purpose of determining alleles. It has the following fields:
Name/ID by which the observational unit may be known by the originator and is used in queries.
Secondary name/ID by which the observational unit may be known and is queried.
ID of the plant that was tested to produce this observational unit. Observational units with the same plant ID are different assays of a single physical organism.
$return = $obj->query_entity_ObservationalUnit($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ObservationalUnit fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
$return = $obj->all_entities_ObservationalUnit($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ObservationalUnit fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
$return = $obj->get_entity_PairSet($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_PairSet fields_PairSet is a reference to a hash where the following keys are defined: id has a value which is a string score has a value which is an int
A PairSet is a precompute set of pairs or genes. Each pair occurs close to one another of the chromosome. We believe that all of the first members of the pairs correspond to one another (are quite similar), as do all of the second members of the pairs. These pairs (from prokaryotic genomes) offer on of the most powerful clues relating to uncharacterized genes/peroteins.
Score for this evidence set. The score indicates the number of significantly different genomes represented by the pairings.
$return = $obj->query_entity_PairSet($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_PairSet fields_PairSet is a reference to a hash where the following keys are defined: id has a value which is a string score has a value which is an int
$return = $obj->all_entities_PairSet($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_PairSet fields_PairSet is a reference to a hash where the following keys are defined: id has a value which is a string score has a value which is an int
$return = $obj->get_entity_Pairing($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Pairing fields_Pairing is a reference to a hash where the following keys are defined: id has a value which is a string
A pairing indicates that two features are found close together in a genome. Not all possible pairings are stored in the database; only those that are considered for some reason to be significant for annotation purposes.The key of the pairing is the concatenation of the feature IDs in alphabetical order with an intervening colon. It has the following fields:
$return = $obj->query_entity_Pairing($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Pairing fields_Pairing is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->all_entities_Pairing($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Pairing fields_Pairing is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_entity_ProbeSet($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ProbeSet fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string
A probe set is a device containing multiple probe sequences for use in gene expression experiments. It has the following fields:
$return = $obj->query_entity_ProbeSet($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ProbeSet fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->all_entities_ProbeSet($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ProbeSet fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_entity_ProteinSequence($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ProteinSequence fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
We use the concept of ProteinSequence as an amino acid string with an associated MD5 value. It is easy to access the set of Features that relate to a ProteinSequence. While function is still associated with Features (and may be for some time), publications are associated with ProteinSequences (and the inferred impact on Features is through the relationship connecting ProteinSequences to Features).
The sequence contains the letters corresponding to the protein's amino acids.
$return = $obj->query_entity_ProteinSequence($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ProteinSequence fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
$return = $obj->all_entities_ProteinSequence($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ProteinSequence fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
$return = $obj->get_entity_Publication($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Publication fields_Publication is a reference to a hash where the following keys are defined: id has a value which is a string title has a value which is a string link has a value which is a string pubdate has a value which is a string
Annotators attach publications to ProteinSequences. The criteria we have used to gather such connections is a bit nonstandard. We have sought to attach publications to ProteinSequences when the publication includes an expert asserting a belief or estimate of function. The paper may not be the original characterization. Further, it may not even discuss a sequence protein (much of the literature is very valuable, but reports work on proteins in strains that have not yet been sequenced). On the other hand, reports of sequencing regions of a chromosome (with no specific assertion of a clear function) should not be attached. The attached publications give an ID (usually a Pubmed ID), a URL to the paper (when we have it), and a title (when we have it).
title of the article, or (unknown) if the title is not known
URL of the article
publication date of the article
$return = $obj->query_entity_Publication($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Publication fields_Publication is a reference to a hash where the following keys are defined: id has a value which is a string title has a value which is a string link has a value which is a string pubdate has a value which is a string
$return = $obj->all_entities_Publication($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Publication fields_Publication is a reference to a hash where the following keys are defined: id has a value which is a string title has a value which is a string link has a value which is a string pubdate has a value which is a string
$return = $obj->get_entity_Reaction($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Reaction fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
A reaction is a chemical process that converts one set of compounds (substrate) to another set (products). It has the following fields:
date and time of the last modification to this reaction's definition
descriptive name of this reaction
common modeling ID of this reaction
abbreviated name of this reaction
displayable formula for the reaction
direction of this reaction (> for forward-only, < for backward-only, = for bidirectional)
$return = $obj->query_entity_Reaction($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Reaction fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
$return = $obj->all_entities_Reaction($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Reaction fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
$return = $obj->get_entity_ReactionRule($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ReactionRule fields_ReactionRule is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float
A reaction rule represents the way a reaction takes place within the context of a complex. It has the following fields:
reaction directionality (> for forward, < for backward, = for bidirectional) with respect to this complex
$return = $obj->query_entity_ReactionRule($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ReactionRule fields_ReactionRule is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float
$return = $obj->all_entities_ReactionRule($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_ReactionRule fields_ReactionRule is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float
$return = $obj->get_entity_Reagent($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Reagent fields_Reagent is a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float
This entity represents a compound as it is used by a specific reaction. A reaction involves many compounds, and a compound can be involved in many reactions. The reagent describes the use of the compound by a specific reaction. It has the following fields:
Number of molecules of the compound that participate in a single instance of the reaction. For example, if a reaction produces two water molecules, the stoichiometry of water for the reaction would be two. When a reaction is written on paper in chemical notation, the stoichiometry is the number next to the chemical formula of the compound. The value is negative for substrates and positive for products.
TRUE if the compound is a cofactor; FALSE if it is a major component of the reaction.
Abstract number that groups this reagent into a compartment. Each group can then be assigned to real compartments when doing comparative analysis.
Number of reagents of this type transported. A positive value implies transport into the reactions default compartment; a negative value implies export to the reagent's specified compartment.
$return = $obj->query_entity_Reagent($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Reagent fields_Reagent is a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float
$return = $obj->all_entities_Reagent($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Reagent fields_Reagent is a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float
$return = $obj->get_entity_Requirement($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Requirement fields_Requirement is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float
A requirement describes the way a reaction fits into a model. It has the following fields:
reaction directionality (> for forward, < for backward, = for bidirectional) with respect to this model
$return = $obj->query_entity_Requirement($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Requirement fields_Requirement is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float
$return = $obj->all_entities_Requirement($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Requirement fields_Requirement is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float
$return = $obj->get_entity_Role($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Role fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
A role describes a biological function that may be fulfilled by a feature. One of the main goals of the database is to assign features to roles. Most roles are effected by the construction of proteins. Some, however, deal with functional regulation and message transmission. It has the following fields:
TRUE if a role is hypothetical, else FALSE
$return = $obj->query_entity_Role($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Role fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
$return = $obj->all_entities_Role($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Role fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
$return = $obj->get_entity_SSCell($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_SSCell fields_SSCell is a reference to a hash where the following keys are defined: id has a value which is a string
An SSCell (SpreadSheet Cell) represents a role as it occurs in a subsystem spreadsheet row. The key is a colon-delimited triple containing an MD5 hash of the subsystem ID followed by a genome ID (with optional region string) and a role abbreviation. It has the following fields:
$return = $obj->query_entity_SSCell($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_SSCell fields_SSCell is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->all_entities_SSCell($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_SSCell fields_SSCell is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_entity_SSRow($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_SSRow fields_SSRow is a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string
An SSRow (that is, a row in a subsystem spreadsheet) represents a collection of functional roles present in the Features of a single Genome. The roles are part of a designated subsystem, and the fids associated with each role are included in the row, That is, a row amounts to an instance of a subsystem as it exists in a specific, designated genome.
This flag is TRUE if the assignment of the molecular machine has been curated, and FALSE if it was made by an automated program.
Region in the genome for which the machine is relevant. Normally, this is an empty string, indicating that the machine covers the whole genome. If a subsystem has multiple machines for a genome, this contains a location string describing the region occupied by this particular machine.
$return = $obj->query_entity_SSRow($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_SSRow fields_SSRow is a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string
$return = $obj->all_entities_SSRow($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_SSRow fields_SSRow is a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string
$return = $obj->get_entity_Scenario($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Scenario fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string
A scenario is a partial instance of a subsystem with a defined set of reactions. Each scenario converts input compounds to output compounds using reactions. The scenario may use all of the reactions controlled by a subsystem or only some, and may also incorporate additional reactions. Because scenario names are not unique, the actual scenario ID is a number. It has the following fields:
Common name of the scenario. The name, rather than the ID number, is usually displayed everywhere.
$return = $obj->query_entity_Scenario($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Scenario fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string
$return = $obj->all_entities_Scenario($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Scenario fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string
$return = $obj->get_entity_Source($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Source fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string
A source is a user or organization that is permitted to assign its own identifiers or to submit bioinformatic objects to the database. It has the following fields:
$return = $obj->query_entity_Source($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Source fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->all_entities_Source($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Source fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_entity_StudyExperiment($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_StudyExperiment fields_StudyExperiment is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string design has a value which is a string originator has a value which is a string
An Experiment is a collection of observational units with one originator that are part of a specific study. An experiment may be conducted at more than one location and in more than one season or year. It has the following fields:
Name/ID by which the experiment is known at the source.
Design of the experiment including the numbers and types of observational units, traits, replicates, sampling plan, and analysis that are planned.
Name of the individual or program that are the originators of the experiment.
$return = $obj->query_entity_StudyExperiment($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_StudyExperiment fields_StudyExperiment is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string design has a value which is a string originator has a value which is a string
$return = $obj->all_entities_StudyExperiment($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_StudyExperiment fields_StudyExperiment is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string design has a value which is a string originator has a value which is a string
$return = $obj->get_entity_Subsystem($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Subsystem fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
A subsystem is a set of functional roles that have been annotated simultaneously (e.g., the roles present in a specific pathway), with an associated subsystem spreadsheet which encodes the fids in each genome that implement the functional roles in the subsystem.
version number for the subsystem. This value is incremented each time the subsystem is backed up.
name of the person currently in charge of the subsystem
descriptive notes about the subsystem
description of the subsystem's function in the cell
TRUE if this is a usable subsystem, else FALSE. An unusable subsystem is one that is experimental or is of such low quality that it can negatively affect analysis.
TRUE if this is a private subsystem, else FALSE. A private subsystem has valid data, but is not considered ready for general distribution.
TRUE if this is a clustering-based subsystem, else FALSE. A clustering-based subsystem is one in which there is functional-coupling evidence that genes belong together, but we do not yet know what they do.
TRUE if this is an experimental subsystem, else FALSE. An experimental subsystem is designed for investigation and is not yet ready to be used in comparative analysis and annotation.
$return = $obj->query_entity_Subsystem($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Subsystem fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
$return = $obj->all_entities_Subsystem($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Subsystem fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
$return = $obj->get_entity_SubsystemClass($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_SubsystemClass fields_SubsystemClass is a reference to a hash where the following keys are defined: id has a value which is a string
Subsystem classes impose a hierarchical organization on the subsystems. It has the following fields:
$return = $obj->query_entity_SubsystemClass($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_SubsystemClass fields_SubsystemClass is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->all_entities_SubsystemClass($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_SubsystemClass fields_SubsystemClass is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_entity_TaxonomicGrouping($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_TaxonomicGrouping fields_TaxonomicGrouping is a reference to a hash where the following keys are defined: id has a value which is a string domain has a value which is an int hidden has a value which is an int scientific_name has a value which is a string alias has a value which is a reference to a list where each element is a string
We associate with most genomes a "taxonomy" based on the NCBI taxonomy. This includes, for each genome, a list of ever larger taxonomic groups.
TRUE if this is a domain grouping, else FALSE.
TRUE if this is a hidden grouping, else FALSE. Hidden groupings are not typically shown in a lineage list.
Primary scientific name for this grouping. This is the name used when displaying a taxonomy.
Alternate name for this grouping. A grouping may have many alternate names. The scientific name should also be in this list.
$return = $obj->query_entity_TaxonomicGrouping($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_TaxonomicGrouping fields_TaxonomicGrouping is a reference to a hash where the following keys are defined: id has a value which is a string domain has a value which is an int hidden has a value which is an int scientific_name has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->all_entities_TaxonomicGrouping($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_TaxonomicGrouping fields_TaxonomicGrouping is a reference to a hash where the following keys are defined: id has a value which is a string domain has a value which is an int hidden has a value which is an int scientific_name has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_entity_Trait($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Trait fields_Trait is a reference to a hash where the following keys are defined: id has a value which is a string trait_name has a value which is a string unit_of_measure has a value which is a string TO_ID has a value which is a string protocol has a value which is a string
A Trait is a phenotypic quality that can be measured or observed for an observational unit. Examples include height, sugar content, color, or cold tolerance. It has the following fields:
Text name or description of the trait
The units of measure used when determining this trait. If multiple units of measure are applicable, each has its own row in the database.
Trait Ontology term ID (http://www.gramene.org/plant-ontology/)
A thorough description of how the trait was collected, and if a rating, the minimum and maximum values
$return = $obj->query_entity_Trait($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Trait fields_Trait is a reference to a hash where the following keys are defined: id has a value which is a string trait_name has a value which is a string unit_of_measure has a value which is a string TO_ID has a value which is a string protocol has a value which is a string
$return = $obj->all_entities_Trait($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Trait fields_Trait is a reference to a hash where the following keys are defined: id has a value which is a string trait_name has a value which is a string unit_of_measure has a value which is a string TO_ID has a value which is a string protocol has a value which is a string
$return = $obj->get_entity_Variant($ids, $fields)
$ids is a reference to a list where each element is a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Variant fields_Variant is a reference to a hash where the following keys are defined: id has a value which is a string role_rule has a value which is a reference to a list where each element is a string code has a value which is a string type has a value which is a string comment has a value which is a string
Each subsystem may include the designation of distinct variants. Thus, there may be three closely-related, but distinguishable forms of histidine degradation. Each form would be called a "variant", with an associated code, and all genomes implementing a specific variant can easily be accessed.
a space-delimited list of role IDs, in alphabetical order, that represents a possible list of non-auxiliary roles applicable to this variant. The roles are identified by their abbreviations. A variant may have multiple role rules.
the variant code all by itself
variant type indicating the quality of the subsystem support. A type of "vacant" means that the subsystem does not appear to be implemented by the variant. A type of "incomplete" means that the subsystem appears to be missing many reactions. In all other cases, the type is "normal".
commentary text about the variant
$return = $obj->query_entity_Variant($qry, $fields)
$qry is a reference to a list where each element is a reference to a list containing 3 items: 0: a string 1: a string 2: a string $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Variant fields_Variant is a reference to a hash where the following keys are defined: id has a value which is a string role_rule has a value which is a reference to a list where each element is a string code has a value which is a string type has a value which is a string comment has a value which is a string
$return = $obj->all_entities_Variant($start, $count, $fields)
$start is an int $count is an int $fields is a reference to a list where each element is a string $return is a reference to a hash where the key is a string and the value is a fields_Variant fields_Variant is a reference to a hash where the following keys are defined: id has a value which is a string role_rule has a value which is a reference to a list where each element is a string code has a value which is a string type has a value which is a string comment has a value which is a string
$return = $obj->get_relationship_AffectsLevelOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Experiment 1: a fields_AffectsLevelOf 2: a fields_AtomicRegulon fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string fields_AffectsLevelOf is a reference to a hash where the following keys are defined: id has a value which is a string level has a value which is an int fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string
This relationship indicates the expression level of an atomic regulon for a given experiment. It has the following fields:
Indication of whether the feature is expressed (1), not expressed (-1), or unknown (0).
$return = $obj->get_relationship_IsAffectedIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_AtomicRegulon 1: a fields_AffectsLevelOf 2: a fields_Experiment fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string fields_AffectsLevelOf is a reference to a hash where the following keys are defined: id has a value which is a string level has a value which is an int fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string
$return = $obj->get_relationship_Aligns($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_AlignmentTree 1: a fields_Aligns 2: a fields_ProteinSequence fields_AlignmentTree is a reference to a hash where the following keys are defined: id has a value which is a string alignment_method has a value which is a string alignment_parameters has a value which is a string alignment_properties has a value which is a string tree_method has a value which is a string tree_parameters has a value which is a string tree_properties has a value which is a string fields_Aligns is a reference to a hash where the following keys are defined: id has a value which is a string begin has a value which is an int end has a value which is an int len has a value which is an int sequence_id has a value which is a string properties has a value which is a string fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
This relationship connects each alignment to its constituent protein sequences. Each alignment contains many protein sequences, and a single sequence can be in many alignments. Parts of a single protein can occur in multiple places in an alignment. The sequence-id field is used to keep these unique, and is the string that represents the sequence in the alignment and tree text. It has the following fields:
location within the sequence at which the aligned portion begins
location within the sequence at which the aligned portion ends
length of the sequence within the alignment
identifier for this sequence in the alignment
additional information about this sequence's participation in the alignment
$return = $obj->get_relationship_IsAlignedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProteinSequence 1: a fields_Aligns 2: a fields_AlignmentTree fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string fields_Aligns is a reference to a hash where the following keys are defined: id has a value which is a string begin has a value which is an int end has a value which is an int len has a value which is an int sequence_id has a value which is a string properties has a value which is a string fields_AlignmentTree is a reference to a hash where the following keys are defined: id has a value which is a string alignment_method has a value which is a string alignment_parameters has a value which is a string alignment_properties has a value which is a string tree_method has a value which is a string tree_parameters has a value which is a string tree_properties has a value which is a string
$return = $obj->get_relationship_AssertsFunctionFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Source 1: a fields_AssertsFunctionFor 2: a fields_ProteinSequence fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string fields_AssertsFunctionFor is a reference to a hash where the following keys are defined: id has a value which is a string function has a value which is a string external_id has a value which is a string organism has a value which is a string gi_number has a value which is an int release_date has a value which is a string fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
Sources (users) can make assertions about protein sequence function. The assertion is associated with an external identifier. It has the following fields:
text of the assertion made about the identifier. It may be an empty string, indicating the function is unknown.
external identifier used in making the assertion
organism name associated with this assertion. If the assertion is not associated with a specific organism, this will be an empty string.
NCBI GI number associated with the asserted identifier
date and time the assertion was downloaded
$return = $obj->get_relationship_HasAssertedFunctionFrom($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProteinSequence 1: a fields_AssertsFunctionFor 2: a fields_Source fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string fields_AssertsFunctionFor is a reference to a hash where the following keys are defined: id has a value which is a string function has a value which is a string external_id has a value which is a string organism has a value which is a string gi_number has a value which is an int release_date has a value which is a string fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_Concerns($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Publication 1: a fields_Concerns 2: a fields_ProteinSequence fields_Publication is a reference to a hash where the following keys are defined: id has a value which is a string title has a value which is a string link has a value which is a string pubdate has a value which is a string fields_Concerns is a reference to a hash where the following keys are defined: id has a value which is a string fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
This relationship connects a publication to the protein sequences it describes. It has the following fields:
$return = $obj->get_relationship_IsATopicOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProteinSequence 1: a fields_Concerns 2: a fields_Publication fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string fields_Concerns is a reference to a hash where the following keys are defined: id has a value which is a string fields_Publication is a reference to a hash where the following keys are defined: id has a value which is a string title has a value which is a string link has a value which is a string pubdate has a value which is a string
$return = $obj->get_relationship_Contains($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_SSCell 1: a fields_Contains 2: a fields_Feature fields_SSCell is a reference to a hash where the following keys are defined: id has a value which is a string fields_Contains is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
This relationship connects a subsystem spreadsheet cell to the features that occur in it. A feature may occur in many machine roles and a machine role may contain many features. The subsystem annotation process is essentially the maintenance of this relationship. It has the following fields:
$return = $obj->get_relationship_IsContainedIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_Contains 2: a fields_SSCell fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_Contains is a reference to a hash where the following keys are defined: id has a value which is a string fields_SSCell is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_Controls($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_Controls 2: a fields_CoregulatedSet fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_Controls is a reference to a hash where the following keys are defined: id has a value which is a string fields_CoregulatedSet is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int
This relationship connects a coregulated set to the features that are used as its transcription factors. It has the following fields:
$return = $obj->get_relationship_IsControlledUsing($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_CoregulatedSet 1: a fields_Controls 2: a fields_Feature fields_CoregulatedSet is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int fields_Controls is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_Describes($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Subsystem 1: a fields_Describes 2: a fields_Variant fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int fields_Describes is a reference to a hash where the following keys are defined: id has a value which is a string fields_Variant is a reference to a hash where the following keys are defined: id has a value which is a string role_rule has a value which is a reference to a list where each element is a string code has a value which is a string type has a value which is a string comment has a value which is a string
This relationship connects a subsystem to the individual variants used to implement it. Each variant contains a slightly different subset of the roles in the parent subsystem. It has the following fields:
$return = $obj->get_relationship_IsDescribedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Variant 1: a fields_Describes 2: a fields_Subsystem fields_Variant is a reference to a hash where the following keys are defined: id has a value which is a string role_rule has a value which is a reference to a list where each element is a string code has a value which is a string type has a value which is a string comment has a value which is a string fields_Describes is a reference to a hash where the following keys are defined: id has a value which is a string fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
$return = $obj->get_relationship_Displays($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Diagram 1: a fields_Displays 2: a fields_Reaction fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string fields_Displays is a reference to a hash where the following keys are defined: id has a value which is a string location has a value which is a rectangle rectangle is a string fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
This relationship connects a diagram to its reactions. A diagram shows multiple reactions, and a reaction can be on many diagrams. It has the following fields:
Location of the reaction's node on the diagram.
$return = $obj->get_relationship_IsDisplayedOn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reaction 1: a fields_Displays 2: a fields_Diagram fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string fields_Displays is a reference to a hash where the following keys are defined: id has a value which is a string location has a value which is a rectangle rectangle is a string fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_Encompasses($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_Encompasses 2: a fields_Feature fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_Encompasses is a reference to a hash where the following keys are defined: id has a value which is a string
This relationship connects a feature to a related feature; for example, it would connect a gene to its constituent splice variants, and the splice variants to their exons. It has the following fields:
$return = $obj->get_relationship_IsEncompassedIn($ids, $from_fields, $rel_fields, $to_fields)
$return = $obj->get_relationship_Formulated($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Source 1: a fields_Formulated 2: a fields_CoregulatedSet fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string fields_Formulated is a reference to a hash where the following keys are defined: id has a value which is a string fields_CoregulatedSet is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int
This relationship connects a coregulated set to the source organization that originally computed it. It has the following fields:
$return = $obj->get_relationship_WasFormulatedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_CoregulatedSet 1: a fields_Formulated 2: a fields_Source fields_CoregulatedSet is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int fields_Formulated is a reference to a hash where the following keys are defined: id has a value which is a string fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_GeneratedLevelsFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProbeSet 1: a fields_GeneratedLevelsFor 2: a fields_AtomicRegulon fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string fields_GeneratedLevelsFor is a reference to a hash where the following keys are defined: id has a value which is a string level_vector has a value which is a countVector countVector is a string fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string
This relationship connects an atomic regulon to a probe set from which experimental data was produced for its features. It contains a vector of the expression levels. It has the following fields:
Vector of expression levels (-1, 0, 1) for the experiments, in sequence order.
$return = $obj->get_relationship_WasGeneratedFrom($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_AtomicRegulon 1: a fields_GeneratedLevelsFor 2: a fields_ProbeSet fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string fields_GeneratedLevelsFor is a reference to a hash where the following keys are defined: id has a value which is a string level_vector has a value which is a countVector countVector is a string fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_HasCompoundAliasFrom($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Source 1: a fields_HasCompoundAliasFrom 2: a fields_Compound fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined: id has a value which is a string alias has a value which is a string fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
This relationship connects a source (database or organization) with the compounds for which it has assigned names (aliases). The alias itself is stored as intersection data. It has the following fields:
alias for the compound assigned by the source
$return = $obj->get_relationship_UsesAliasForCompound($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compound 1: a fields_HasCompoundAliasFrom 2: a fields_Source fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined: id has a value which is a string alias has a value which is a string fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_HasIndicatedSignalFrom($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_HasIndicatedSignalFrom 2: a fields_Experiment fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_HasIndicatedSignalFrom is a reference to a hash where the following keys are defined: id has a value which is a string rma_value has a value which is a float level has a value which is an int fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string
This relationship connects an experiment to a feature. The feature expression levels inferred from the experimental results are stored here. It has the following fields:
Normalized expression value for this feature under the experiment's conditions.
$return = $obj->get_relationship_IndicatesSignalFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Experiment 1: a fields_HasIndicatedSignalFrom 2: a fields_Feature fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string fields_HasIndicatedSignalFrom is a reference to a hash where the following keys are defined: id has a value which is a string rma_value has a value which is a float level has a value which is an int fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_HasMember($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Family 1: a fields_HasMember 2: a fields_Feature fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string fields_HasMember is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
This relationship connects each feature family to its constituent features. A family always has many features, and a single feature can be found in many families. It has the following fields:
$return = $obj->get_relationship_IsMemberOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_HasMember 2: a fields_Family fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_HasMember is a reference to a hash where the following keys are defined: id has a value which is a string fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_HasParticipant($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Scenario 1: a fields_HasParticipant 2: a fields_Reaction fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string fields_HasParticipant is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is an int fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
A scenario consists of many participant reactions that convert the input compounds to output compounds. A single reaction may participate in many scenarios. It has the following fields:
Indicates the type of participaton. If 0, the reaction is in the main pathway of the scenario. If 1, the reaction is necessary to make the model work but is not in the subsystem. If 2, the reaction is part of the subsystem but should not be included in the modelling process.
$return = $obj->get_relationship_ParticipatesIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reaction 1: a fields_HasParticipant 2: a fields_Scenario fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string fields_HasParticipant is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is an int fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string
$return = $obj->get_relationship_HasPresenceOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Media 1: a fields_HasPresenceOf 2: a fields_Compound fields_Media is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string type has a value which is a string fields_HasPresenceOf is a reference to a hash where the following keys are defined: id has a value which is a string concentration has a value which is a float minimum_flux has a value which is a float maximum_flux has a value which is a float fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
This relationship connects a media to the compounds that occur in it. The intersection data describes how much of each compound can be found. It has the following fields:
concentration of the compound in the media
minimum flux of the compound for this media
maximum flux of the compound for this media
$return = $obj->get_relationship_IsPresentIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compound 1: a fields_HasPresenceOf 2: a fields_Media fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float fields_HasPresenceOf is a reference to a hash where the following keys are defined: id has a value which is a string concentration has a value which is a float minimum_flux has a value which is a float maximum_flux has a value which is a float fields_Media is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string type has a value which is a string
$return = $obj->get_relationship_HasProteinMember($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Family 1: a fields_HasProteinMember 2: a fields_ProteinSequence fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string fields_HasProteinMember is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
This relationship connects each feature family to its constituent protein sequences. A family always has many protein sequences, and a single sequence can be found in many families. It has the following fields:
Native identifier used for the protein in the definition of the family. This will be its ID in the alignment, if one exists.
$return = $obj->get_relationship_IsProteinMemberOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProteinSequence 1: a fields_HasProteinMember 2: a fields_Family fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string fields_HasProteinMember is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_HasReactionAliasFrom($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Source 1: a fields_HasReactionAliasFrom 2: a fields_Reaction fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string fields_HasReactionAliasFrom is a reference to a hash where the following keys are defined: id has a value which is a string alias has a value which is a string fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
This relationship connects a source (database or organization) with the reactions for which it has assigned names (aliases). The alias itself is stored as intersection data. It has the following fields:
alias for the reaction assigned by the source
$return = $obj->get_relationship_UsesAliasForReaction($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reaction 1: a fields_HasReactionAliasFrom 2: a fields_Source fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string fields_HasReactionAliasFrom is a reference to a hash where the following keys are defined: id has a value which is a string alias has a value which is a string fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_HasRepresentativeOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_HasRepresentativeOf 2: a fields_Family fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_HasRepresentativeOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string
This relationship connects a genome to the FIGfam protein families for which it has representative proteins. This information can be computed from other relationships, but it is provided explicitly to allow fast access to a genome's FIGfam profile. It has the following fields:
$return = $obj->get_relationship_IsRepresentedIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Family 1: a fields_HasRepresentativeOf 2: a fields_Genome fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string fields_HasRepresentativeOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
$return = $obj->get_relationship_HasResultsIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProbeSet 1: a fields_HasResultsIn 2: a fields_Experiment fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string fields_HasResultsIn is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is an int fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string
This relationship connects a probe set to the experiments that were applied to it. It has the following fields:
Sequence number of this experiment in the various result vectors.
$return = $obj->get_relationship_HasResultsFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Experiment 1: a fields_HasResultsIn 2: a fields_ProbeSet fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string fields_HasResultsIn is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is an int fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_HasSection($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ContigSequence 1: a fields_HasSection 2: a fields_ContigChunk fields_ContigSequence is a reference to a hash where the following keys are defined: id has a value which is a string length has a value which is an int fields_HasSection is a reference to a hash where the following keys are defined: id has a value which is a string fields_ContigChunk is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
This relationship connects a contig's sequence to its DNA sequences. It has the following fields:
$return = $obj->get_relationship_IsSectionOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ContigChunk 1: a fields_HasSection 2: a fields_ContigSequence fields_ContigChunk is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string fields_HasSection is a reference to a hash where the following keys are defined: id has a value which is a string fields_ContigSequence is a reference to a hash where the following keys are defined: id has a value which is a string length has a value which is an int
$return = $obj->get_relationship_HasStep($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Complex 1: a fields_HasStep 2: a fields_ReactionRule fields_Complex is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a reference to a list where each element is a string msid has a value which is a string mod_date has a value which is a string fields_HasStep is a reference to a hash where the following keys are defined: id has a value which is a string fields_ReactionRule is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float
This relationship connects a complex to the reaction rules for the reactions that work together to make the complex happen. It has the following fields:
$return = $obj->get_relationship_IsStepOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ReactionRule 1: a fields_HasStep 2: a fields_Complex fields_ReactionRule is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float fields_HasStep is a reference to a hash where the following keys are defined: id has a value which is a string fields_Complex is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a reference to a list where each element is a string msid has a value which is a string mod_date has a value which is a string
$return = $obj->get_relationship_HasTrait($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ObservationalUnit 1: a fields_HasTrait 2: a fields_Trait fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string fields_HasTrait is a reference to a hash where the following keys are defined: id has a value which is a string value has a value which is a float statistic_type has a value which is a string measure_id has a value which is a string fields_Trait is a reference to a hash where the following keys are defined: id has a value which is a string trait_name has a value which is a string unit_of_measure has a value which is a string TO_ID has a value which is a string protocol has a value which is a string
This relationship contains the measurement values of a trait on a specific observational Unit It has the following fields:
value of the trait measurement
text description of the statistic type (e.g. mean, median)
internal ID given to this measurement
$return = $obj->get_relationship_Measures($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Trait 1: a fields_HasTrait 2: a fields_ObservationalUnit fields_Trait is a reference to a hash where the following keys are defined: id has a value which is a string trait_name has a value which is a string unit_of_measure has a value which is a string TO_ID has a value which is a string protocol has a value which is a string fields_HasTrait is a reference to a hash where the following keys are defined: id has a value which is a string value has a value which is a float statistic_type has a value which is a string measure_id has a value which is a string fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
$return = $obj->get_relationship_HasUnits($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Locality 1: a fields_HasUnits 2: a fields_ObservationalUnit fields_Locality is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string city has a value which is a string state has a value which is a string country has a value which is a string origcty has a value which is a string elevation has a value which is an int latitude has a value which is an int longitude has a value which is an int lo_accession has a value which is a string fields_HasUnits is a reference to a hash where the following keys are defined: id has a value which is a string fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
This relationship associates observational units with the geographic location where the unit is planted. It has the following fields:
$return = $obj->get_relationship_IsLocated($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ObservationalUnit 1: a fields_HasUnits 2: a fields_Locality fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string fields_HasUnits is a reference to a hash where the following keys are defined: id has a value which is a string fields_Locality is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string city has a value which is a string state has a value which is a string country has a value which is a string origcty has a value which is a string elevation has a value which is an int latitude has a value which is an int longitude has a value which is an int lo_accession has a value which is a string
$return = $obj->get_relationship_HasUsage($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compound 1: a fields_HasUsage 2: a fields_BiomassCompound fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float fields_HasUsage is a reference to a hash where the following keys are defined: id has a value which is a string fields_BiomassCompound is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float
This relationship connects a biomass compound specification to the compounds for which it is relevant. It has the following fields:
$return = $obj->get_relationship_IsUsageOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_BiomassCompound 1: a fields_HasUsage 2: a fields_Compound fields_BiomassCompound is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float fields_HasUsage is a reference to a hash where the following keys are defined: id has a value which is a string fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
$return = $obj->get_relationship_HasValueFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Experiment 1: a fields_HasValueFor 2: a fields_Attribute fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string fields_HasValueFor is a reference to a hash where the following keys are defined: id has a value which is a string value has a value which is a string fields_Attribute is a reference to a hash where the following keys are defined: id has a value which is a string description has a value which is a string
This relationship connects an experiment to its attributes. The attribute values are stored here. It has the following fields:
Value of this attribute in the given experiment. This is always encoded as a string, but may in fact be a number.
$return = $obj->get_relationship_HasValueIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Attribute 1: a fields_HasValueFor 2: a fields_Experiment fields_Attribute is a reference to a hash where the following keys are defined: id has a value which is a string description has a value which is a string fields_HasValueFor is a reference to a hash where the following keys are defined: id has a value which is a string value has a value which is a string fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string
$return = $obj->get_relationship_HasVariationIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Contig 1: a fields_HasVariationIn 2: a fields_ObservationalUnit fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string fields_HasVariationIn is a reference to a hash where the following keys are defined: id has a value which is a string position has a value which is an int len has a value which is an int data has a value which is a string data2 has a value which is a string quality has a value which is a float fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
This relationship defines an observational unit's DNA variation from a contig in the reference genome. It has the following fields:
Position of this variation in the reference contig.
Length of the variation in the reference contig. A length of zero indicates an insertion.
Replacement DNA for the variation on the primary chromosome. An empty string indicates a deletion. The primary chromosome is chosen arbitrarily among the two chromosomes of a plant's chromosome pair (one coming from the mother and one from the father).
Replacement DNA for the variation on the secondary chromosome. This will frequently be the same as the primary chromosome string.
Quality score assigned to this variation.
$return = $obj->get_relationship_IsVariedIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ObservationalUnit 1: a fields_HasVariationIn 2: a fields_Contig fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string fields_HasVariationIn is a reference to a hash where the following keys are defined: id has a value which is a string position has a value which is an int len has a value which is an int data has a value which is a string data2 has a value which is a string quality has a value which is a float fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
$return = $obj->get_relationship_Impacts($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Trait 1: a fields_Impacts 2: a fields_Contig fields_Trait is a reference to a hash where the following keys are defined: id has a value which is a string trait_name has a value which is a string unit_of_measure has a value which is a string TO_ID has a value which is a string protocol has a value which is a string fields_Impacts is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string rank has a value which is an int pvalue has a value which is a float position has a value which is an int fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
This relationship contains the best scoring statistical correlations between measured traits and the responsible alleles. It has the following fields:
Name of the study which analyzed the data and determined that a variation has impact on a trait
Rank of the position among all positions correlated with this trait.
P-value of the correlation between the variation and the trait
Position in the reference contig where the trait has an impact.
$return = $obj->get_relationship_IsImpactedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Contig 1: a fields_Impacts 2: a fields_Trait fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string fields_Impacts is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string rank has a value which is an int pvalue has a value which is a float position has a value which is an int fields_Trait is a reference to a hash where the following keys are defined: id has a value which is a string trait_name has a value which is a string unit_of_measure has a value which is a string TO_ID has a value which is a string protocol has a value which is a string
$return = $obj->get_relationship_Includes($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Subsystem 1: a fields_Includes 2: a fields_Role fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int fields_Includes is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is an int abbreviation has a value which is a string auxiliary has a value which is an int fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
A subsystem is defined by its roles. The subsystem's variants contain slightly different sets of roles, but all of the roles in a variant must be connected to the parent subsystem by this relationship. A subsystem always has at least one role, and a role always belongs to at least one subsystem. It has the following fields:
Sequence number of the role within the subsystem. When the roles are formed into a variant, they will generally appear in sequence order.
Abbreviation for this role in this subsystem. The abbreviations are used in columnar displays, and they also appear on diagrams.
TRUE if this is an auxiliary role, or FALSE if this role is a functioning part of the subsystem.
$return = $obj->get_relationship_IsIncludedIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Role 1: a fields_Includes 2: a fields_Subsystem fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int fields_Includes is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is an int abbreviation has a value which is a string auxiliary has a value which is an int fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
$return = $obj->get_relationship_IncludesPart($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_StudyExperiment 1: a fields_IncludesPart 2: a fields_ObservationalUnit fields_StudyExperiment is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string design has a value which is a string originator has a value which is a string fields_IncludesPart is a reference to a hash where the following keys are defined: id has a value which is a string fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
This relationship associates observational units with the experiments that generated the data on them. It has the following fields:
$return = $obj->get_relationship_IsPartOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ObservationalUnit 1: a fields_IncludesPart 2: a fields_StudyExperiment fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string fields_IncludesPart is a reference to a hash where the following keys are defined: id has a value which is a string fields_StudyExperiment is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string design has a value which is a string originator has a value which is a string
$return = $obj->get_relationship_IndicatedLevelsFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProbeSet 1: a fields_IndicatedLevelsFor 2: a fields_Feature fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string fields_IndicatedLevelsFor is a reference to a hash where the following keys are defined: id has a value which is a string level_vector has a value which is a countVector countVector is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
This relationship connects a feature to a probe set from which experimental data was produced for the feature. It contains a vector of the expression levels. It has the following fields:
$return = $obj->get_relationship_HasLevelsFrom($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IndicatedLevelsFor 2: a fields_ProbeSet fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IndicatedLevelsFor is a reference to a hash where the following keys are defined: id has a value which is a string level_vector has a value which is a countVector countVector is a string fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_Involves($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reaction 1: a fields_Involves 2: a fields_Reagent fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string fields_Involves is a reference to a hash where the following keys are defined: id has a value which is a string fields_Reagent is a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float
This relationship connects a reaction to the reagents representing the compounds that participate in it. It has the following fields:
$return = $obj->get_relationship_IsInvolvedIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reagent 1: a fields_Involves 2: a fields_Reaction fields_Reagent is a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float fields_Involves is a reference to a hash where the following keys are defined: id has a value which is a string fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
$return = $obj->get_relationship_IsARequirementIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Model 1: a fields_IsARequirementIn 2: a fields_Requirement fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int fields_IsARequirementIn is a reference to a hash where the following keys are defined: id has a value which is a string fields_Requirement is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float
This relationship connects a model to its requirements. A requirement represents the use of a reaction in a single model. It has the following fields:
$return = $obj->get_relationship_IsARequirementOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Requirement 1: a fields_IsARequirementIn 2: a fields_Model fields_Requirement is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float fields_IsARequirementIn is a reference to a hash where the following keys are defined: id has a value which is a string fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int
$return = $obj->get_relationship_IsAnnotatedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsAnnotatedBy 2: a fields_Annotation fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsAnnotatedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Annotation is a reference to a hash where the following keys are defined: id has a value which is a string annotator has a value which is a string comment has a value which is a string annotation_time has a value which is a string
This relationship connects a feature to its annotations. A feature may have multiple annotations, but an annotation belongs to only one feature. It has the following fields:
$return = $obj->get_relationship_Annotates($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Annotation 1: a fields_IsAnnotatedBy 2: a fields_Feature fields_Annotation is a reference to a hash where the following keys are defined: id has a value which is a string annotator has a value which is a string comment has a value which is a string annotation_time has a value which is a string fields_IsAnnotatedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsAssayOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Assay 1: a fields_IsAssayOf 2: a fields_StudyExperiment fields_Assay is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string assay_type has a value which is a string assay_type_id has a value which is a string fields_IsAssayOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_StudyExperiment is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string design has a value which is a string originator has a value which is a string
This relationship associates each assay with the relevant experiments. It has the following fields:
$return = $obj->get_relationship_IsAssayedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_StudyExperiment 1: a fields_IsAssayOf 2: a fields_Assay fields_StudyExperiment is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string design has a value which is a string originator has a value which is a string fields_IsAssayOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Assay is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string assay_type has a value which is a string assay_type_id has a value which is a string
$return = $obj->get_relationship_IsClassFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_SubsystemClass 1: a fields_IsClassFor 2: a fields_Subsystem fields_SubsystemClass is a reference to a hash where the following keys are defined: id has a value which is a string fields_IsClassFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
This relationship connects each subsystem class with the subsystems that belong to it. A class can contain many subsystems, but a subsystem is only in one class. Some subsystems are not in any class, but this is usually a temporary condition. It has the following fields:
$return = $obj->get_relationship_IsInClass($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Subsystem 1: a fields_IsClassFor 2: a fields_SubsystemClass fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int fields_IsClassFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_SubsystemClass is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_IsCollectionOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_OTU 1: a fields_IsCollectionOf 2: a fields_Genome fields_OTU is a reference to a hash where the following keys are defined: id has a value which is a string fields_IsCollectionOf is a reference to a hash where the following keys are defined: id has a value which is a string representative has a value which is an int fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
A genome belongs to only one genome set. For each set, this relationship marks the genome to be used as its representative. It has the following fields:
TRUE for the representative genome of the set, else FALSE.
$return = $obj->get_relationship_IsCollectedInto($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_IsCollectionOf 2: a fields_OTU fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_IsCollectionOf is a reference to a hash where the following keys are defined: id has a value which is a string representative has a value which is an int fields_OTU is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_IsComposedOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_IsComposedOf 2: a fields_Contig fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_IsComposedOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
This relationship connects a genome to its constituent contigs. Unlike contig sequences, a contig belongs to only one genome. It has the following fields:
$return = $obj->get_relationship_IsComponentOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Contig 1: a fields_IsComposedOf 2: a fields_Genome fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string fields_IsComposedOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
$return = $obj->get_relationship_IsComprisedOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Biomass 1: a fields_IsComprisedOf 2: a fields_BiomassCompound fields_Biomass is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a reference to a list where each element is a string fields_IsComprisedOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_BiomassCompound is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float
This relationship connects a biomass to the compound specifications that define it. It has the following fields:
$return = $obj->get_relationship_Comprises($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_BiomassCompound 1: a fields_IsComprisedOf 2: a fields_Biomass fields_BiomassCompound is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float fields_IsComprisedOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Biomass is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsConfiguredBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_IsConfiguredBy 2: a fields_AtomicRegulon fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_IsConfiguredBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string
This relationship connects a genome to the atomic regulons that describe its state. It has the following fields:
$return = $obj->get_relationship_ReflectsStateOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_AtomicRegulon 1: a fields_IsConfiguredBy 2: a fields_Genome fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string fields_IsConfiguredBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
$return = $obj->get_relationship_IsConsistentWith($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_EcNumber 1: a fields_IsConsistentWith 2: a fields_Role fields_EcNumber is a reference to a hash where the following keys are defined: id has a value which is a string obsolete has a value which is an int replacedby has a value which is a string fields_IsConsistentWith is a reference to a hash where the following keys are defined: id has a value which is a string fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
This relationship connects a functional role to the EC numbers consistent with the chemistry described in the role. It has the following fields:
$return = $obj->get_relationship_IsConsistentTo($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Role 1: a fields_IsConsistentWith 2: a fields_EcNumber fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int fields_IsConsistentWith is a reference to a hash where the following keys are defined: id has a value which is a string fields_EcNumber is a reference to a hash where the following keys are defined: id has a value which is a string obsolete has a value which is an int replacedby has a value which is a string
$return = $obj->get_relationship_IsCoregulatedWith($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsCoregulatedWith 2: a fields_Feature fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsCoregulatedWith is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float
This relationship connects a feature with another feature in the same genome with which it appears to be coregulated as a result of expression data analysis. It has the following fields:
Pearson correlation coefficient for this coregulation.
$return = $obj->get_relationship_HasCoregulationWith($ids, $from_fields, $rel_fields, $to_fields)
$return = $obj->get_relationship_IsCoupledTo($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Family 1: a fields_IsCoupledTo 2: a fields_Family fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string fields_IsCoupledTo is a reference to a hash where the following keys are defined: id has a value which is a string co_occurrence_evidence has a value which is an int co_expression_evidence has a value which is an int
This relationship connects two FIGfams that we believe to be related either because their members occur in proximity on chromosomes or because the members are expressed together. Such a relationship is evidence the functions of the FIGfams are themselves related. This relationship is commutative; only the instance in which the first FIGfam has a lower ID than the second is stored. It has the following fields:
number of times members of the two FIGfams occur close to each other on chromosomes
number of times members of the two FIGfams are co-expressed in expression data experiments
$return = $obj->get_relationship_IsCoupledWith($ids, $from_fields, $rel_fields, $to_fields)
$return = $obj->get_relationship_IsDefaultFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compartment 1: a fields_IsDefaultFor 2: a fields_Reaction fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string fields_IsDefaultFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
This relationship connects a reaction to the compartment in which it runs by default. It has the following fields:
$return = $obj->get_relationship_RunsByDefaultIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reaction 1: a fields_IsDefaultFor 2: a fields_Compartment fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string fields_IsDefaultFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string
$return = $obj->get_relationship_IsDefaultLocationOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compartment 1: a fields_IsDefaultLocationOf 2: a fields_Reagent fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string fields_IsDefaultLocationOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Reagent is a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float
This relationship connects a reagent to the compartment which is its default location during the reaction. It has the following fields:
$return = $obj->get_relationship_HasDefaultLocation($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reagent 1: a fields_IsDefaultLocationOf 2: a fields_Compartment fields_Reagent is a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float fields_IsDefaultLocationOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string
$return = $obj->get_relationship_IsDeterminedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_PairSet 1: a fields_IsDeterminedBy 2: a fields_Pairing fields_PairSet is a reference to a hash where the following keys are defined: id has a value which is a string score has a value which is an int fields_IsDeterminedBy is a reference to a hash where the following keys are defined: id has a value which is a string inverted has a value which is an int fields_Pairing is a reference to a hash where the following keys are defined: id has a value which is a string
A functional coupling evidence set exists because it has pairings in it, and this relationship connects the evidence set to its constituent pairings. A pairing cam belong to multiple evidence sets. It has the following fields:
A pairing is an unordered pair of protein sequences, but its similarity to other pairings in a pair set is ordered. Let (A,B) be a pairing and (X,Y) be another pairing in the same set. If this flag is FALSE, then (A =~ X) and (B =~ Y). If this flag is TRUE, then (A =~ Y) and (B =~ X).
$return = $obj->get_relationship_Determines($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Pairing 1: a fields_IsDeterminedBy 2: a fields_PairSet fields_Pairing is a reference to a hash where the following keys are defined: id has a value which is a string fields_IsDeterminedBy is a reference to a hash where the following keys are defined: id has a value which is a string inverted has a value which is an int fields_PairSet is a reference to a hash where the following keys are defined: id has a value which is a string score has a value which is an int
$return = $obj->get_relationship_IsDividedInto($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Model 1: a fields_IsDividedInto 2: a fields_ModelCompartment fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int fields_IsDividedInto is a reference to a hash where the following keys are defined: id has a value which is a string fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float
This relationship connects a model to the cell compartments that participate in the model. It has the following fields:
$return = $obj->get_relationship_IsDivisionOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ModelCompartment 1: a fields_IsDividedInto 2: a fields_Model fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float fields_IsDividedInto is a reference to a hash where the following keys are defined: id has a value which is a string fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int
$return = $obj->get_relationship_IsExemplarOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsExemplarOf 2: a fields_Role fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsExemplarOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
This relationship links a role to a feature that provides a typical example of how the role is implemented. It has the following fields:
$return = $obj->get_relationship_HasAsExemplar($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Role 1: a fields_IsExemplarOf 2: a fields_Feature fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int fields_IsExemplarOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsFamilyFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Family 1: a fields_IsFamilyFor 2: a fields_Role fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string fields_IsFamilyFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
This relationship connects an isofunctional family to the roles that make up its assigned function. It has the following fields:
$return = $obj->get_relationship_DeterminesFunctionOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Role 1: a fields_IsFamilyFor 2: a fields_Family fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int fields_IsFamilyFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_Family is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsFormedOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_AtomicRegulon 1: a fields_IsFormedOf 2: a fields_Feature fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string fields_IsFormedOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
This relationship connects each feature to the atomic regulon to which it belongs. It has the following fields:
$return = $obj->get_relationship_IsFormedInto($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsFormedOf 2: a fields_AtomicRegulon fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsFormedOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_AtomicRegulon is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_IsFunctionalIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Role 1: a fields_IsFunctionalIn 2: a fields_Feature fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int fields_IsFunctionalIn is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
This relationship connects a role with the features in which it plays a functional part. It has the following fields:
$return = $obj->get_relationship_HasFunctional($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsFunctionalIn 2: a fields_Role fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsFunctionalIn is a reference to a hash where the following keys are defined: id has a value which is a string fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
$return = $obj->get_relationship_IsGroupFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_TaxonomicGrouping 1: a fields_IsGroupFor 2: a fields_TaxonomicGrouping fields_TaxonomicGrouping is a reference to a hash where the following keys are defined: id has a value which is a string domain has a value which is an int hidden has a value which is an int scientific_name has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsGroupFor is a reference to a hash where the following keys are defined: id has a value which is a string
The recursive IsGroupFor relationship organizes taxonomic groupings into a hierarchy based on the standard organism taxonomy. It has the following fields:
$return = $obj->get_relationship_IsInGroup($ids, $from_fields, $rel_fields, $to_fields)
$return = $obj->get_relationship_IsImplementedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Variant 1: a fields_IsImplementedBy 2: a fields_SSRow fields_Variant is a reference to a hash where the following keys are defined: id has a value which is a string role_rule has a value which is a reference to a list where each element is a string code has a value which is a string type has a value which is a string comment has a value which is a string fields_IsImplementedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_SSRow is a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string
This relationship connects a variant to the physical machines that implement it in the genomes. A variant is implemented by many machines, but a machine belongs to only one variant. It has the following fields:
$return = $obj->get_relationship_Implements($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_SSRow 1: a fields_IsImplementedBy 2: a fields_Variant fields_SSRow is a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string fields_IsImplementedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Variant is a reference to a hash where the following keys are defined: id has a value which is a string role_rule has a value which is a reference to a list where each element is a string code has a value which is a string type has a value which is a string comment has a value which is a string
$return = $obj->get_relationship_IsInPair($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsInPair 2: a fields_Pairing fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsInPair is a reference to a hash where the following keys are defined: id has a value which is a string fields_Pairing is a reference to a hash where the following keys are defined: id has a value which is a string
A pairing contains exactly two protein sequences. A protein sequence can belong to multiple pairings. When going from a protein sequence to its pairings, they are presented in alphabetical order by sequence key. It has the following fields:
$return = $obj->get_relationship_IsPairOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Pairing 1: a fields_IsInPair 2: a fields_Feature fields_Pairing is a reference to a hash where the following keys are defined: id has a value which is a string fields_IsInPair is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsInstantiatedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compartment 1: a fields_IsInstantiatedBy 2: a fields_ModelCompartment fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string fields_IsInstantiatedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float
This relationship connects a compartment to the instances of that compartment that occur in models. It has the following fields:
$return = $obj->get_relationship_IsInstanceOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ModelCompartment 1: a fields_IsInstantiatedBy 2: a fields_Compartment fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float fields_IsInstantiatedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string
$return = $obj->get_relationship_IsLocatedIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsLocatedIn 2: a fields_Contig fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsLocatedIn is a reference to a hash where the following keys are defined: id has a value which is a string ordinal has a value which is an int begin has a value which is an int len has a value which is an int dir has a value which is a string fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
A feature is a set of DNA sequence fragments. Most features are a single contiquous fragment, so they are located in only one DNA sequence; however, fragments have a maximum length, so even a single contiguous feature may participate in this relationship multiple times. A few features belong to multiple DNA sequences. In that case, however, all the DNA sequences belong to the same genome. A DNA sequence itself will frequently have thousands of features connected to it. It has the following fields:
Sequence number of this segment, starting from 1 and proceeding sequentially forward from there.
Index (1-based) of the first residue in the contig that belongs to the segment.
Length of this segment.
Direction (strand) of the segment: "+" if it is forward and "-" if it is backward.
$return = $obj->get_relationship_IsLocusFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Contig 1: a fields_IsLocatedIn 2: a fields_Feature fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string fields_IsLocatedIn is a reference to a hash where the following keys are defined: id has a value which is a string ordinal has a value which is an int begin has a value which is an int len has a value which is an int dir has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsModeledBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_IsModeledBy 2: a fields_Model fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_IsModeledBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int
A genome can be modeled by many different models, but a model belongs to only one genome. It has the following fields:
$return = $obj->get_relationship_Models($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Model 1: a fields_IsModeledBy 2: a fields_Genome fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int fields_IsModeledBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
$return = $obj->get_relationship_IsOwnerOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_IsOwnerOf 2: a fields_Feature fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_IsOwnerOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
This relationship connects a genome to the features it contains. Though technically redundant (the information is available from the feature's contigs), it simplifies the extremely common process of finding all features for a genome. It has the following fields:
$return = $obj->get_relationship_IsOwnedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsOwnerOf 2: a fields_Genome fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsOwnerOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
$return = $obj->get_relationship_IsProposedLocationOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compartment 1: a fields_IsProposedLocationOf 2: a fields_ReactionRule fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string fields_IsProposedLocationOf is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string fields_ReactionRule is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float
This relationship connects a reaction as it is used in a complex to the compartments in which it usually takes place. Most reactions take place in a single compartment. Transporters take place in two compartments. It has the following fields:
role of the compartment in the reaction: 'primary' if it is the sole or starting compartment, 'secondary' if it is the ending compartment in a multi-compartmental reaction
$return = $obj->get_relationship_HasProposedLocationIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ReactionRule 1: a fields_IsProposedLocationOf 2: a fields_Compartment fields_ReactionRule is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float fields_IsProposedLocationOf is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string fields_Compartment is a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string
$return = $obj->get_relationship_IsProteinFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProteinSequence 1: a fields_IsProteinFor 2: a fields_Feature fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string fields_IsProteinFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
This relationship connects a peg feature to the protein sequence it produces (if any). Only peg features participate in this relationship. A single protein sequence will frequently be produced by many features. It has the following fields:
$return = $obj->get_relationship_Produces($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsProteinFor 2: a fields_ProteinSequence fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsProteinFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
$return = $obj->get_relationship_IsRealLocationOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ModelCompartment 1: a fields_IsRealLocationOf 2: a fields_Requirement fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float fields_IsRealLocationOf is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string fields_Requirement is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float
This relationship connects a model's instance of a reaction to the compartments in which it takes place. Most instances take place in a single compartment. Transporters use two compartments. It has the following fields:
$return = $obj->get_relationship_HasRealLocationIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Requirement 1: a fields_IsRealLocationOf 2: a fields_ModelCompartment fields_Requirement is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float fields_IsRealLocationOf is a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float
$return = $obj->get_relationship_IsReferencedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_IsReferencedBy 2: a fields_ObservationalUnit fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_IsReferencedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
This relationship associates each observational unit with the reference genome that it will be compared to. All variations will be differences between the observational unit and the reference. It has the following fields:
$return = $obj->get_relationship_UsesReference($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ObservationalUnit 1: a fields_IsReferencedBy 2: a fields_Genome fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string fields_IsReferencedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
$return = $obj->get_relationship_IsRegulatedIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Feature 1: a fields_IsRegulatedIn 2: a fields_CoregulatedSet fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsRegulatedIn is a reference to a hash where the following keys are defined: id has a value which is a string fields_CoregulatedSet is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int
This relationship connects a feature to the set of coregulated features. It has the following fields:
$return = $obj->get_relationship_IsRegulatedSetOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_CoregulatedSet 1: a fields_IsRegulatedIn 2: a fields_Feature fields_CoregulatedSet is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int fields_IsRegulatedIn is a reference to a hash where the following keys are defined: id has a value which is a string fields_Feature is a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsRelevantFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Diagram 1: a fields_IsRelevantFor 2: a fields_Subsystem fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string fields_IsRelevantFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
This relationship connects a diagram to the subsystems that are depicted on it. Only diagrams which are useful in curating or annotation the subsystem are specified in this relationship. It has the following fields:
$return = $obj->get_relationship_IsRelevantTo($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Subsystem 1: a fields_IsRelevantFor 2: a fields_Diagram fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int fields_IsRelevantFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsRepresentedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_TaxonomicGrouping 1: a fields_IsRepresentedBy 2: a fields_ObservationalUnit fields_TaxonomicGrouping is a reference to a hash where the following keys are defined: id has a value which is a string domain has a value which is an int hidden has a value which is an int scientific_name has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsRepresentedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
This relationship associates observational units with a genus, species, strain, and/or variety that was the source material. It has the following fields:
$return = $obj->get_relationship_DefinedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ObservationalUnit 1: a fields_IsRepresentedBy 2: a fields_TaxonomicGrouping fields_ObservationalUnit is a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string fields_IsRepresentedBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_TaxonomicGrouping is a reference to a hash where the following keys are defined: id has a value which is a string domain has a value which is an int hidden has a value which is an int scientific_name has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsRequiredBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reaction 1: a fields_IsRequiredBy 2: a fields_Requirement fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string fields_IsRequiredBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Requirement is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float
This relationship links a reaction to the way it is used in a model. It has the following fields:
$return = $obj->get_relationship_Requires($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Requirement 1: a fields_IsRequiredBy 2: a fields_Reaction fields_Requirement is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float fields_IsRequiredBy is a reference to a hash where the following keys are defined: id has a value which is a string fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
$return = $obj->get_relationship_IsRoleOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Role 1: a fields_IsRoleOf 2: a fields_SSCell fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int fields_IsRoleOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_SSCell is a reference to a hash where the following keys are defined: id has a value which is a string
This relationship connects a role to the machine roles that represent its appearance in a molecular machine. A machine role has exactly one associated role, but a role may be represented by many machine roles. It has the following fields:
$return = $obj->get_relationship_HasRole($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_SSCell 1: a fields_IsRoleOf 2: a fields_Role fields_SSCell is a reference to a hash where the following keys are defined: id has a value which is a string fields_IsRoleOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
$return = $obj->get_relationship_IsRowOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_SSRow 1: a fields_IsRowOf 2: a fields_SSCell fields_SSRow is a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string fields_IsRowOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_SSCell is a reference to a hash where the following keys are defined: id has a value which is a string
This relationship connects a subsystem spreadsheet row to its constituent spreadsheet cells. It has the following fields:
$return = $obj->get_relationship_IsRoleFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_SSCell 1: a fields_IsRowOf 2: a fields_SSRow fields_SSCell is a reference to a hash where the following keys are defined: id has a value which is a string fields_IsRowOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_SSRow is a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string
$return = $obj->get_relationship_IsSequenceOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ContigSequence 1: a fields_IsSequenceOf 2: a fields_Contig fields_ContigSequence is a reference to a hash where the following keys are defined: id has a value which is a string length has a value which is an int fields_IsSequenceOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
This relationship connects a Contig as it occurs in a genome to the Contig Sequence that represents the physical DNA base pairs. A contig sequence may represent many contigs, but each contig has only one sequence. It has the following fields:
$return = $obj->get_relationship_HasAsSequence($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Contig 1: a fields_IsSequenceOf 2: a fields_ContigSequence fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string fields_IsSequenceOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_ContigSequence is a reference to a hash where the following keys are defined: id has a value which is a string length has a value which is an int
$return = $obj->get_relationship_IsSubInstanceOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Subsystem 1: a fields_IsSubInstanceOf 2: a fields_Scenario fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int fields_IsSubInstanceOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string
This relationship connects a scenario to its subsystem it validates. A scenario belongs to exactly one subsystem, but a subsystem may have multiple scenarios. It has the following fields:
$return = $obj->get_relationship_Validates($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Scenario 1: a fields_IsSubInstanceOf 2: a fields_Subsystem fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string fields_IsSubInstanceOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
$return = $obj->get_relationship_IsSummarizedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Contig 1: a fields_IsSummarizedBy 2: a fields_AlleleFrequency fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string fields_IsSummarizedBy is a reference to a hash where the following keys are defined: id has a value which is a string position has a value which is an int fields_AlleleFrequency is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string position has a value which is an int minor_AF has a value which is a float minor_allele has a value which is a string major_AF has a value which is a float major_allele has a value which is a string obs_unit_count has a value which is an int
This relationship describes the statistical frequencies of the most common alleles in various positions on the reference contig. It has the following fields:
$return = $obj->get_relationship_Summarizes($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_AlleleFrequency 1: a fields_IsSummarizedBy 2: a fields_Contig fields_AlleleFrequency is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string position has a value which is an int minor_AF has a value which is a float minor_allele has a value which is a string major_AF has a value which is a float major_allele has a value which is a string obs_unit_count has a value which is an int fields_IsSummarizedBy is a reference to a hash where the following keys are defined: id has a value which is a string position has a value which is an int fields_Contig is a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
$return = $obj->get_relationship_IsSuperclassOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_SubsystemClass 1: a fields_IsSuperclassOf 2: a fields_SubsystemClass fields_SubsystemClass is a reference to a hash where the following keys are defined: id has a value which is a string fields_IsSuperclassOf is a reference to a hash where the following keys are defined: id has a value which is a string
This is a recursive relationship that imposes a hierarchy on the subsystem classes. It has the following fields:
$return = $obj->get_relationship_IsSubclassOf($ids, $from_fields, $rel_fields, $to_fields)
$return = $obj->get_relationship_IsTargetOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ModelCompartment 1: a fields_IsTargetOf 2: a fields_BiomassCompound fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float fields_IsTargetOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_BiomassCompound is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float
This relationship connects a compound in a biomass to the compartment in which it is supposed to appear. It has the following fields:
$return = $obj->get_relationship_Targets($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_BiomassCompound 1: a fields_IsTargetOf 2: a fields_ModelCompartment fields_BiomassCompound is a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float fields_IsTargetOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_ModelCompartment is a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float
$return = $obj->get_relationship_IsTaxonomyOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_TaxonomicGrouping 1: a fields_IsTaxonomyOf 2: a fields_Genome fields_TaxonomicGrouping is a reference to a hash where the following keys are defined: id has a value which is a string domain has a value which is an int hidden has a value which is an int scientific_name has a value which is a string alias has a value which is a reference to a list where each element is a string fields_IsTaxonomyOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
A genome is assigned to a particular point in the taxonomy tree, but not necessarily to a leaf node. In some cases, the exact species and strain is not available when inserting the genome, so it is placed at the lowest node that probably contains the actual genome. It has the following fields:
$return = $obj->get_relationship_IsInTaxa($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_IsTaxonomyOf 2: a fields_TaxonomicGrouping fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_IsTaxonomyOf is a reference to a hash where the following keys are defined: id has a value which is a string fields_TaxonomicGrouping is a reference to a hash where the following keys are defined: id has a value which is a string domain has a value which is an int hidden has a value which is an int scientific_name has a value which is a string alias has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_IsTerminusFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compound 1: a fields_IsTerminusFor 2: a fields_Scenario fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float fields_IsTerminusFor is a reference to a hash where the following keys are defined: id has a value which is a string group_number has a value which is an int fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string
A terminus for a scenario is a compound that acts as its input or output. A compound can be the terminus for many scenarios, and a scenario will have many termini. The relationship attributes indicate whether the compound is an input to the scenario or an output. In some cases, there may be multiple alternative output groups. This is also indicated by the attributes. It has the following fields:
If zero, then the compound is an input. If one, the compound is an output. If two, the compound is an auxiliary output.
$return = $obj->get_relationship_HasAsTerminus($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Scenario 1: a fields_IsTerminusFor 2: a fields_Compound fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string fields_IsTerminusFor is a reference to a hash where the following keys are defined: id has a value which is a string group_number has a value which is an int fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
$return = $obj->get_relationship_IsTriggeredBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Complex 1: a fields_IsTriggeredBy 2: a fields_Role fields_Complex is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a reference to a list where each element is a string msid has a value which is a string mod_date has a value which is a string fields_IsTriggeredBy is a reference to a hash where the following keys are defined: id has a value which is a string optional has a value which is an int type has a value which is a string fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
A complex can be triggered by many roles. A role can trigger many complexes. It has the following fields:
TRUE if the role is not necessarily required to trigger the complex, else FALSE
$return = $obj->get_relationship_Triggers($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Role 1: a fields_IsTriggeredBy 2: a fields_Complex fields_Role is a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int fields_IsTriggeredBy is a reference to a hash where the following keys are defined: id has a value which is a string optional has a value which is an int type has a value which is a string fields_Complex is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a reference to a list where each element is a string msid has a value which is a string mod_date has a value which is a string
$return = $obj->get_relationship_IsUsedAs($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reaction 1: a fields_IsUsedAs 2: a fields_ReactionRule fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string fields_IsUsedAs is a reference to a hash where the following keys are defined: id has a value which is a string fields_ReactionRule is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float
This relationship connects a reaction to its usage in specific complexes. It has the following fields:
$return = $obj->get_relationship_IsUseOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ReactionRule 1: a fields_IsUsedAs 2: a fields_Reaction fields_ReactionRule is a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float fields_IsUsedAs is a reference to a hash where the following keys are defined: id has a value which is a string fields_Reaction is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
$return = $obj->get_relationship_Manages($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Model 1: a fields_Manages 2: a fields_Biomass fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int fields_Manages is a reference to a hash where the following keys are defined: id has a value which is a string fields_Biomass is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a reference to a list where each element is a string
This relationship connects a model to the biomasses that are monitored to determine whether or not the model is effective. It has the following fields:
$return = $obj->get_relationship_IsManagedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Biomass 1: a fields_Manages 2: a fields_Model fields_Biomass is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a reference to a list where each element is a string fields_Manages is a reference to a hash where the following keys are defined: id has a value which is a string fields_Model is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int
$return = $obj->get_relationship_OperatesIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Experiment 1: a fields_OperatesIn 2: a fields_Media fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string fields_OperatesIn is a reference to a hash where the following keys are defined: id has a value which is a string fields_Media is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string type has a value which is a string
This relationship connects an experiment to the media in which the experiment took place. It has the following fields:
$return = $obj->get_relationship_IsUtilizedIn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Media 1: a fields_OperatesIn 2: a fields_Experiment fields_Media is a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string type has a value which is a string fields_OperatesIn is a reference to a hash where the following keys are defined: id has a value which is a string fields_Experiment is a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string
$return = $obj->get_relationship_Overlaps($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Scenario 1: a fields_Overlaps 2: a fields_Diagram fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string fields_Overlaps is a reference to a hash where the following keys are defined: id has a value which is a string fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string
A Scenario overlaps a diagram when the diagram displays a portion of the reactions that make up the scenario. A scenario may overlap many diagrams, and a diagram may be include portions of many scenarios. It has the following fields:
$return = $obj->get_relationship_IncludesPartOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Diagram 1: a fields_Overlaps 2: a fields_Scenario fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string fields_Overlaps is a reference to a hash where the following keys are defined: id has a value which is a string fields_Scenario is a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string
$return = $obj->get_relationship_ParticipatesAs($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compound 1: a fields_ParticipatesAs 2: a fields_Reagent fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float fields_ParticipatesAs is a reference to a hash where the following keys are defined: id has a value which is a string fields_Reagent is a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float
This relationship connects a compound to the reagents that represent its participation in reactions. It has the following fields:
$return = $obj->get_relationship_IsParticipationOf($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Reagent 1: a fields_ParticipatesAs 2: a fields_Compound fields_Reagent is a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float fields_ParticipatesAs is a reference to a hash where the following keys are defined: id has a value which is a string fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
$return = $obj->get_relationship_ProducedResultsFor($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProbeSet 1: a fields_ProducedResultsFor 2: a fields_Genome fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string fields_ProducedResultsFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
This relationship connects a probe set to a genome for which it was used to produce experimental results. In general, a probe set is used for only one genome and vice versa, but this is not a requirement. It has the following fields:
$return = $obj->get_relationship_HadResultsProducedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_ProducedResultsFor 2: a fields_ProbeSet fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_ProducedResultsFor is a reference to a hash where the following keys are defined: id has a value which is a string fields_ProbeSet is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_ProjectsOnto($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_ProteinSequence 1: a fields_ProjectsOnto 2: a fields_ProteinSequence fields_ProteinSequence is a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string fields_ProjectsOnto is a reference to a hash where the following keys are defined: id has a value which is a string gene_context has a value which is an int percent_identity has a value which is a float score has a value which is a float
This relationship connects two protein sequences for which a clear bidirectional best hit exists in known genomes. The attributes of the relationship describe how good the relationship is between the proteins. The relationship is bidirectional and symmetric, but is only stored in one direction (lower ID to higher ID). It has the following fields:
number of homologous genes in the immediate context of the two proteins, up to a maximum of 10
percent match between the two protein sequences
score describing the strength of the projection, from 0 to 1, where 1 is the best
$return = $obj->get_relationship_IsProjectedOnto($ids, $from_fields, $rel_fields, $to_fields)
$return = $obj->get_relationship_Provided($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Source 1: a fields_Provided 2: a fields_Subsystem fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string fields_Provided is a reference to a hash where the following keys are defined: id has a value which is a string fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
This relationship connects a source (core) database to the subsystems it submitted to the knowledge base. It has the following fields:
$return = $obj->get_relationship_WasProvidedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Subsystem 1: a fields_Provided 2: a fields_Source fields_Subsystem is a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int fields_Provided is a reference to a hash where the following keys are defined: id has a value which is a string fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_Shows($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Diagram 1: a fields_Shows 2: a fields_Compound fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string fields_Shows is a reference to a hash where the following keys are defined: id has a value which is a string location has a value which is a rectangle rectangle is a string fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
This relationship indicates that a compound appears on a particular diagram. The same compound can appear on many diagrams, and a diagram always contains many compounds. It has the following fields:
Location of the compound's node on the diagram.
$return = $obj->get_relationship_IsShownOn($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Compound 1: a fields_Shows 2: a fields_Diagram fields_Compound is a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float fields_Shows is a reference to a hash where the following keys are defined: id has a value which is a string location has a value which is a rectangle rectangle is a string fields_Diagram is a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string
$return = $obj->get_relationship_Submitted($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Source 1: a fields_Submitted 2: a fields_Genome fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string fields_Submitted is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
This relationship connects a genome to the core database from which it was loaded. It has the following fields:
$return = $obj->get_relationship_WasSubmittedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_Submitted 2: a fields_Source fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_Submitted is a reference to a hash where the following keys are defined: id has a value which is a string fields_Source is a reference to a hash where the following keys are defined: id has a value which is a string
$return = $obj->get_relationship_Uses($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_Genome 1: a fields_Uses 2: a fields_SSRow fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string fields_Uses is a reference to a hash where the following keys are defined: id has a value which is a string fields_SSRow is a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string
This relationship connects a genome to the machines that form its metabolic pathways. A genome can use many machines, but a machine is used by exactly one genome. It has the following fields:
$return = $obj->get_relationship_IsUsedBy($ids, $from_fields, $rel_fields, $to_fields)
$ids is a reference to a list where each element is a string $from_fields is a reference to a list where each element is a string $rel_fields is a reference to a list where each element is a string $to_fields is a reference to a list where each element is a string $return is a reference to a list where each element is a reference to a list containing 3 items: 0: a fields_SSRow 1: a fields_Uses 2: a fields_Genome fields_SSRow is a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string fields_Uses is a reference to a hash where the following keys are defined: id has a value which is a string fields_Genome is a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
a string
an int
A fid is a "feature id". A feature represents an ordered list of regions from the contigs of a genome. Features all have types. This allows you to speak of not only protein-encoding genes (PEGs) and RNAs, but also binding sites, large regions, etc. The location of a fid is defined as a list of "location of a contiguous DNA string" pieces (see the description of the type "location")
A protein_family is thought of as a set of isofunctional, homologous protein sequences. This is not exactly what other groups have meant by "protein families". There is no hierarchy of super-family, family, sub-family. We plan on loading different collections of protein families, but in many cases there will need to be a transformation into the concept used by Kbase.
The concept of "role" or "functional role" is basically an atomic functional unit. The "function of a protein" is made up of one or more roles. That is, a bifunctional protein with an assigned function of
5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) / Cytidylate kinase (EC 2.7.4.14)
would implement two distinct roles (the "function1 / function2" notation is intended to assert that the initial part of the protein implements function1, and the terminal part of the protein implements function2). It is worth noting that a protein often implements multiple roles due to broad specificity. In this case, we suggest describing the protein function as
function1 @ function2
That is the ' / ' separator is used to represent multiple roles implemented by distinct domains of the protein, while ' @ ' is used to represent multiple roles implemented by distinct domains.
A substem is composed of two components: a set of roles that are gathered to be annotated simultaneously and a spreadsheet depicting the proteins within each genome that implement the roles. The set of roles may correspond to a pathway, a complex, an inventory (say, "transporters") or whatever other principle an annotator used to formulate the subsystem.
The subsystem spreadsheet is a list of "rows", each representing the subsytem in a specific genome. Each row includes a variant code (indicating what version of the molecular machine exists in the genome) and cells. Each cell is a 2-tuple:
[role,protein-encoding genes that implement the role in the genome]
Annotators construct subsystems, and in the process impose a controlled vocabulary for roles and functions.
a reference to a list containing 2 items: 0: a subsystem 1: a variant
a reference to a list where each element is a variant_of_subsystem
a reference to a list where each element is a type_of_fid
In encodings of locations, we often specify strands. We specify the strand as '+' or '-'
A region of DNA is maintained as a tuple of four components:
the contig the beginning position (from 1) the strand the length We often speak of "a region". By "location", we mean a sequence of regions from the same genome (perhaps from distinct contigs).
a reference to a list containing 4 items: 0: a contig 1: a begin 2: a strand 3: a length
a "location" refers to a sequence of regions
a reference to a list where each element is a region_of_dna
a reference to a list where each element is a location
we often need to represent regions or locations as strings. We would use something like
contigA_200+100,contigA_402+188
to represent a location composed of two regions
a reference to a list where each element is a region_of_dna_string
The Kbase stores annotations relating to features. Each annotation is a 3-tuple:
the text of the annotation (often a record of assertion of function) the annotator attaching the annotation to the feature the time (in seconds from the epoch) at which the annotation was attached
a reference to a list containing 3 items: 0: a comment 1: an annotator 2: an annotation_time
The Kbase will include a growing body of literature supporting protein functions, asserted phenotypes, etc. References are encoded as 3-tuples:
an id (often a PubMed ID) a URL to the paper a title of the paper
The URL and title are often missing (but, can usually be inferred from the pubmed ID).
a reference to a list containing 3 items: 0: a string 1: a string 2: a string
a reference to a list containing 2 items: 0: a fid 1: a float
a reference to a list where each element is an annotation
a reference to a list where each element is a pubref
a reference to a list where each element is a role
a reference to a list containing 2 items: 0: a role 1: an optional
a reference to a list where each element is a role_with_flag
a reference to a list where each element is a scored_fid
a reference to a list where each element is a protein
a reference to a list where each element is a function
a reference to a list where each element is a taxonomic_group
a reference to a list where each element is a subsystem
a reference to a list where each element is a contig
a reference to a list where each element is a md5
a reference to a list where each element is a genome
a reference to a list containing 2 items: 0: a fid 1: a fid
a reference to a list where each element is a pair_of_fids
a reference to a list where each element is a protein_family
a float
a reference to a list where each element is a fid
a reference to a list containing 2 items: 0: a variant 1: a reference to a hash where the key is a role and the value is a fids
a reference to a list containing 2 items: 0: a fid 1: a function
a reference to a list where each element is a fid_function_pair
A functionally coupled protein family identifies a family, a score, and a function (of the related family)
a reference to a list containing 3 items: 0: a protein_family 1: a score 2: a function
a reference to a list where each element is a fc_protein_family
We now have a number of types and functions relating to ObservationalUnits (ous), alleles and traits. We think of a reference genome and a set of ous that have measured differences (SNPs) when compared to the reference genome. Each allele is associated with a position on a contig of the reference genome. Prior analysis has associated traits with the alleles that impact them. We are interested in supporting operations that locate genes in the region of an allele (i.e., genes of the reference genome that are in a region containining an allele). Similarly, we wish to locate the alleles that impact a trait, map the alleles to regions, loacte the possibly impacted genes, relate these to subsystems, etc.
a reference to a list where each element is an allele
a reference to a list where each element is a trait
a reference to a list where each element is an ou
a reference to a list containing 2 items: 0: a contig 1: an int
a reference to a list where each element is a string
a reference to a list containing 2 items: 0: a complex 1: an optional
a reference to a list where each element is a complex_with_flag
a reference to a list where each element is a complex
a reference to a list where each element is a reaction
Reactions do not connect directly to roles. Rather, the conceptual model is that one or more roles together form a complex. A complex implements one or more reactions. The actual data relating to a complex is spread over two entities: Complex and ReactionComplex. It is convenient to be able to offer access to the complex name, the reactions it implements, and the roles that make it up in a single invocation.
a reference to a hash where the following keys are defined: complex_name has a value which is a name complex_roles has a value which is a roles_with_flags complex_reactions has a value which is a reactions
a reference to a hash where the following keys are defined: complete has a value which is an int contigs has a value which is an int dna_size has a value which is an int gc_content has a value which is a float genetic_code has a value which is an int pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string taxonomy has a value which is a string genome_md5 has a value which is a string
a reference to a list where each element is a regulon
a reference to a hash where the following keys are defined: regulon_id has a value which is a regulon regulon_set has a value which is a fids tfs has a value which is a fids
a reference to a list where each element is a regulon_data
a reference to a hash where the following keys are defined: feature_id has a value which is a fid genome_name has a value which is a string feature_function has a value which is a string feature_length has a value which is an int feature_publications has a value which is a pubrefs feature_location has a value which is a location
a reference to a list containing 3 items: 0: an id 1: a function 2: a source
a reference to a list where each element is a function_assertion
a reference to a list containing 2 items: 0: an atomic_regulon 1: an atomic_regulon_size
a reference to a list where each element is an atomic_regulon_size_pair
a reference to a list where each element is an atomic_regulon
a reference to a list containing 3 items: 0: a subsystem 1: a variant 2: a role
a reference to a list where each element is a ss_var_role_tuple
a reference to a list containing 2 items: 0: a weight 1: a reference to a hash where the key is a field_name and the value is a string
A correspondence is generated as a mapping of fids to fids. The mapping attempts to map a fid to another that performs the same function. The correspondence describes the regions that are similar, the strength of the similarity, the number of genes in the chromosomal context that appear to "correspond" and a score from 0 to 1 that loosely corresponds to confidence in the correspondence.
a reference to a hash where the following keys are defined: to has a value which is a fid iden has a value which is a float ncontext has a value which is an int b1 has a value which is an int e1 has a value which is an int ln1 has a value which is an int b2 has a value which is an int e2 has a value which is an int ln2 has a value which is an int score has a value which is an int
A close_genomes is used to get a set of relatively close genomes (for each input genome, a set of close genomes is calculated, but the result should be viewed as quite approximate. "how" is a suggestion of which algorithm to use:
0 - default (same genus) 1 - find genomes with the same genus name 2 - use the SSU rRNA, if possible 3 - use a set of "universal proteins", if you can
Up to n genomes will be returned for each input genome.
a reference to a list containing 3 items: 0: an id 1: a comment 2: a sequence
a reference to a list where each element is a seq_triple
a reference to a list where each element is an id
fractions or bits
a reference to a hash where the following keys are defined: existing_reps has a value which is a seq_set order has a value which is a string alg has a value which is an int type_sim has a value which is a string cutoff has a value which is a float
a reference to a hash where the following keys are defined: anchors has a value which is an int brenner has a value which is an int cluster has a value which is an int dimer has a value which is an int diags has a value which is an int diags1 has a value which is an int diags2 has a value which is an int le has a value which is an int noanchors has a value which is an int sp has a value which is an int spn has a value which is an int stable has a value which is an int sv has a value which is an int anchorspacing has a value which is a string center has a value which is a string cluster1 has a value which is a string cluster2 has a value which is a string diagbreak has a value which is a string diaglength has a value which is a string diagmargin has a value which is a string distance1 has a value which is a string distance2 has a value which is a string gapopen has a value which is a string log has a value which is a string loga has a value which is a string matrix has a value which is a string maxhours has a value which is a string maxiters has a value which is a string maxmb has a value which is a string maxtrees has a value which is a string minbestcolscore has a value which is a string minsmoothscore has a value which is a string objscore has a value which is a string refinewindow has a value which is a string root1 has a value which is a string root2 has a value which is a string scorefile has a value which is a string seqtype has a value which is a string smoothscorecell has a value which is a string smoothwindow has a value which is a string spscore has a value which is a string SUEFF has a value which is a string usetree has a value which is a string weight1 has a value which is a string weight2 has a value which is a string
linsi | einsi | ginsi | nwnsi | nwns | fftnsi | fftns (D)
a reference to a hash where the following keys are defined: sixmerpair has a value which is an int amino has a value which is an int anysymbol has a value which is an int auto has a value which is an int clustalout has a value which is an int dpparttree has a value which is an int fastapair has a value which is an int fastaparttree has a value which is an int fft has a value which is an int fmodel has a value which is an int genafpair has a value which is an int globalpair has a value which is an int inputorder has a value which is an int localpair has a value which is an int memsave has a value which is an int nofft has a value which is an int noscore has a value which is an int parttree has a value which is an int reorder has a value which is an int treeout has a value which is an int alg has a value which is a string aamatrix has a value which is a string bl has a value which is a string ep has a value which is a string groupsize has a value which is a string jtt has a value which is a string lap has a value which is a string lep has a value which is a string lepx has a value which is a string LOP has a value which is a string LEXP has a value which is a string maxiterate has a value which is a string op has a value which is a string partsize has a value which is a string retree has a value which is a string thread has a value which is a string tm has a value which is a string weighti has a value which is a string
a reference to a hash where the following keys are defined: muscle_parms has a value which is a muscle_parms_t mafft_parms has a value which is a mafft_parms_t tool has a value which is a string align_ends_with_clustal has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string alignment_method has a value which is a string alignment_parameters has a value which is a string alignment_properties has a value which is a string tree_method has a value which is a string tree_parameters has a value which is a string tree_properties has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string position has a value which is an int minor_AF has a value which is a float minor_allele has a value which is a string major_AF has a value which is a float major_allele has a value which is a string obs_unit_count has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string annotator has a value which is a string comment has a value which is a string annotation_time has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string assay_type has a value which is a string assay_type_id has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string description has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a reference to a list where each element is a string
a reference to a hash where the following keys are defined: id has a value which is a string coefficient has a value which is a float
a reference to a hash where the following keys are defined: id has a value which is a string abbr has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a reference to a list where each element is a string msid has a value which is a string mod_date has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string label has a value which is a string abbr has a value which is a string msid has a value which is a string ubiquitous has a value which is an int mod_date has a value which is a string uncharged_formula has a value which is a string formula has a value which is a string mass has a value which is a float
a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string length has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string source_id has a value which is a string binding_location has a value which is a reference to a list where each element is an int
a reference to a hash where the following keys are defined: id has a value which is a string name has a value which is a string content has a value which is a reference to a list where each element is a string
a reference to a hash where the following keys are defined: id has a value which is a string obsolete has a value which is an int replacedby has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string source has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string release has a value which is a string family_function has a value which is a reference to a list where each element is a string alignment has a value which is a reference to a list where each element is a string
a reference to a hash where the following keys are defined: id has a value which is a string feature_type has a value which is a string source_id has a value which is a string sequence_length has a value which is an int function has a value which is a string alias has a value which is a reference to a list where each element is a string
a reference to a hash where the following keys are defined: id has a value which is a string pegs has a value which is an int rnas has a value which is an int scientific_name has a value which is a string complete has a value which is an int prokaryotic has a value which is an int dna_size has a value which is an int contigs has a value which is an int domain has a value which is a string genetic_code has a value which is an int gc_content has a value which is a float phenotype has a value which is a reference to a list where each element is a string md5 has a value which is a string source_id has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string city has a value which is a string state has a value which is a string country has a value which is a string origcty has a value which is a string elevation has a value which is an int latitude has a value which is an int longitude has a value which is an int lo_accession has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string type has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string version has a value which is an int type has a value which is a string status has a value which is a string reaction_count has a value which is an int compound_count has a value which is an int annotation_count has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string compartment_index has a value which is an int label has a value which is a reference to a list where each element is a string pH has a value which is a float potential has a value which is a float
a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string source_name2 has a value which is a reference to a list where each element is a string plant_id has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string score has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string title has a value which is a string link has a value which is a string pubdate has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string mod_date has a value which is a string name has a value which is a string msid has a value which is a string abbr has a value which is a string equation has a value which is a string reversibility has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float
a reference to a hash where the following keys are defined: id has a value which is a string stoichiometry has a value which is a float cofactor has a value which is an int compartment_index has a value which is an int transport_coefficient has a value which is a float
a reference to a hash where the following keys are defined: id has a value which is a string direction has a value which is a string transproton has a value which is a float proton has a value which is a float
a reference to a hash where the following keys are defined: id has a value which is a string hypothetical has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string curated has a value which is an int region has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string common_name has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string design has a value which is a string originator has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string version has a value which is an int curator has a value which is a string notes has a value which is a string description has a value which is a string usable has a value which is an int private has a value which is an int cluster_based has a value which is an int experimental has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string domain has a value which is an int hidden has a value which is an int scientific_name has a value which is a string alias has a value which is a reference to a list where each element is a string
a reference to a hash where the following keys are defined: id has a value which is a string trait_name has a value which is a string unit_of_measure has a value which is a string TO_ID has a value which is a string protocol has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string role_rule has a value which is a reference to a list where each element is a string code has a value which is a string type has a value which is a string comment has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string level has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string begin has a value which is an int end has a value which is an int len has a value which is an int sequence_id has a value which is a string properties has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string function has a value which is a string external_id has a value which is a string organism has a value which is a string gi_number has a value which is an int release_date has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string location has a value which is a rectangle
a reference to a hash where the following keys are defined: id has a value which is a string level_vector has a value which is a countVector
a reference to a hash where the following keys are defined: id has a value which is a string alias has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string rma_value has a value which is a float level has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string concentration has a value which is a float minimum_flux has a value which is a float maximum_flux has a value which is a float
a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string value has a value which is a float statistic_type has a value which is a string measure_id has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string value has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string position has a value which is an int len has a value which is an int data has a value which is a string data2 has a value which is a string quality has a value which is a float
a reference to a hash where the following keys are defined: id has a value which is a string source_name has a value which is a string rank has a value which is an int pvalue has a value which is a float position has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string sequence has a value which is an int abbreviation has a value which is a string auxiliary has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string representative has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string co_occurrence_evidence has a value which is an int co_expression_evidence has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string inverted has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string ordinal has a value which is an int begin has a value which is an int len has a value which is an int dir has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string type has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string position has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string group_number has a value which is an int
a reference to a hash where the following keys are defined: id has a value which is a string optional has a value which is an int type has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a string gene_context has a value which is an int percent_identity has a value which is a float score has a value which is a float
To install Bio::KBase, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::KBase
CPAN shell
perl -MCPAN -e shell install Bio::KBase
For more information on module installation, please visit the detailed CPAN module installation guide.