all_entities_Publication
Return all instances of the Publication entity.
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:
all_entities_Publication -a would retrieve all entities of type Publication and include all fields in the entities in the output.
Related entities
The Publication entity has the following relationship links:
Command-Line Options
- -a
-
Return all fields.
- -h
-
Display a list of the fields available for use.
- -fields field-list
-
Choose a set of fields to return. Field-list is a comma-separated list of strings. The following fields are available:
- title
- link
- pubdate
Output Format
The standard output is a tab-delimited file. It consists of the input file with an extra column added for each requested field. Input lines that cannot be extended are written to stderr.