Query the entity Publication.
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).
Example:
query_entity_Publication -a
The Publication entity has the following relationship links:
Limit the results to entities where the given field has the given value.
Limit the results to entities where the given field is LIKE (in the sql sense) the given value.
Limit the results to entities where the given field is related to the given value based on the given operator.
The operators supported are as follows. We provide text based alternatives to the comparison operators so that extra quoting is not required to keep the command-line shell from confusing them with shell I/O redirection operators.
Return all fields.
Display a list of the fields available for use.
Choose a set of fields to return. Field-list is a comma-separated list of strings. The following fields are available:
The standard output is a tab-delimited file containing a column for each requested field.
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.