Bio-Chado-Schema

Changes for version 0.05700

re-dumped with latest schema loader devel version
stripped _id suffixes for a number of relationships that still had them. Hopefully the schema loader patch used for this will make it into schema loader releases. List of changed relationship names:
- lib/Bio/Chado/Schema/CellLine/CellLine.pm cell_line_relationship_subject_ids -> cell_line_relationship_subjects cell_line_relationship_object_ids -> cell_line_relationship_objects
- lib/Bio/Chado/Schema/Contact/Contact.pm contact_relationship_object_ids -> contact_relationship_objects contact_relationship_subject_ids -> contact_relationship_subjects
- lib/Bio/Chado/Schema/Cv/Cvterm.pm arraydesign_platformtype_ids -> arraydesign_platformtypes arraydesign_substratetype_ids -> arraydesign_substratetypes cvtermpath_type_ids -> cvtermpath_types cvtermpath_object_ids -> cvtermpath_objects cvtermpath_subject_ids -> cvtermpath_subjects cvtermprop_type_ids -> cvtermprop_types cvtermprop_cvterm_ids -> cvtermprop_cvterms cvterm_relationship_type_ids -> cvterm_relationship_types cvterm_relationship_object_ids -> cvterm_relationship_objects cvterm_relationship_subject_ids -> cvterm_relationship_subjects cvtermsynonym_type_ids -> cvtermsynonym_types cvtermsynonym_cvterm_ids -> cvtermsynonym_cvterms expression_cvterm_cvterm_ids -> expression_cvterm_cvterms expression_cvterm_cvterm_type_ids -> expression_cvterm_cvterm_types phenotype_assay_ids -> phenotype_assays phenotype_attr_ids -> phenotype_attrs phenotype_observable_ids -> phenotype_observables phenotype_cvalue_ids -> phenotype_cvalues protocolparam_unittype_ids -> protocolparam_unittypes protocolparam_datatype_ids -> protocolparam_datatypes
- lib/Bio/Chado/Schema/Genetic/Environment.pm phenotype_comparison_environment2_ids -> phenotype_comparison_environment2s phenotype_comparison_environment1_ids -> phenotype_comparison_environment1s
- lib/Bio/Chado/Schema/Genetic/Genotype.pm phenotype_comparison_genotype1_ids -> phenotype_comparison_genotype1s phenotype_comparison_genotype2_ids -> phenotype_comparison_genotype2s
- lib/Bio/Chado/Schema/Mage/Acquisition.pm acquisition_relationship_subject_ids -> acquisition_relationship_subjects acquisition_relationship_object_ids -> acquisition_relationship_objects
- lib/Bio/Chado/Schema/Mage/Biomaterial.pm biomaterial_relationship_subject_ids -> biomaterial_relationship_subjects biomaterial_relationship_object_ids -> biomaterial_relationship_objects
- lib/Bio/Chado/Schema/Mage/Element.pm element_relationship_object_ids -> element_relationship_objects element_relationship_subject_ids -> element_relationship_subjects
- lib/Bio/Chado/Schema/Mage/Elementresult.pm elementresult_relationship_subject_ids -> elementresult_relationship_subjects elementresult_relationship_object_ids -> elementresult_relationship_objects
- lib/Bio/Chado/Schema/Mage/Quantification.pm quantification_relationship_subject_ids -> quantification_relationship_subjects quantification_relationship_object_ids -> quantification_relationship_objects
- lib/Bio/Chado/Schema/Phenotype/Phenotype.pm phenotype_comparison_phenotype1_ids -> phenotype_comparison_phenotype1s phenotype_comparison_phenotype2_ids -> phenotype_comparison_phenotype2s
- lib/Bio/Chado/Schema/Phylogeny/Phylonode.pm phylonode_relationship_object_ids -> phylonode_relationship_objects phylonode_relationship_subject_ids -> phylonode_relationship_subjects
- lib/Bio/Chado/Schema/Pub/Pub.pm pub_relationship_object_ids -> pub_relationship_objects pub_relationship_subject_ids -> pub_relationship_subjects
- lib/Bio/Chado/Schema/Sequence/Feature.pm feature_genotype_feature_ids -> feature_genotype_features feature_genotype_chromosome_ids -> feature_genotype_chromosomes featureloc_feature_ids -> featureloc_features featureloc_srcfeature_ids -> featureloc_srcfeatures featurepos_feature_ids -> featurepos_features featurepos_map_feature_ids -> featurepos_map_features featurerange_leftendf_ids -> featurerange_leftendfs featurerange_rightstartf_ids -> featurerange_rightstartfs featurerange_rightendf_ids -> featurerange_rightendfs featurerange_leftstartf_ids -> featurerange_leftstartfs featurerange_feature_ids -> featurerange_features feature_relationship_subject_ids -> feature_relationship_subjects feature_relationship_object_ids -> feature_relationship_objects
- lib/Bio/Chado/Schema/Stock/Stock.pm stock_relationship_subject_ids -> stock_relationship_subjects stock_relationship_object_ids -> stock_relationship_objects
new create_with() function for creating new cvterms
more POD tweaking to improve CPAN indexing

Documentation

Bio::Chado::Schema::CellLine

For describing cell lines

Bio::Chado::Schema::Companalysis

Augments sequence module with descriptions of computational analyses and features resulting from those analyses

Bio::Chado::Schema::Composite

A collection of bridge codes that have multiple dependancies so they don't happily go where is most obvious

Bio::Chado::Schema::Contact

model persons, institutes, groups, organizations, etc

Bio::Chado::Schema::Cv

Controlled vocabularies and ontologies

Bio::Chado::Schema::Expression

transcript or protein expression data

Bio::Chado::Schema::General

General purpose tables, including dbxrefs

Bio::Chado::Schema::Genetic

Genotypes and mutant alleles

Bio::Chado::Schema::Library

For describing molecular libraries

Bio::Chado::Schema::Mage

Alternative expression module, based on MAGE model

Bio::Chado::Schema::Map

Non-sequence maps: genetic, radiation hybrid, cytogenetic, etc

Bio::Chado::Schema::Organism

Species data - does not include phylogeny

Bio::Chado::Schema::Phenotype

Entity-attribute-value phenotypic character descriptions

Bio::Chado::Schema::Phylogeny

For representing phylogenetic trees; the trees represent the phylogeny of some some kind of sequence feature (mainly proteins) or actual organism taxonomy trees

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Changes for version 0.05700

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