README file for PRO release 4.1 (05-Feb-2009) The Protein Ontology Consortium--the Protein Information Resource, The Jackson Laboratory, and the Department of Philosophy at the State University of New York at Buffalo--is pleased to announce PRO Release 4.1 (05-Feb-2009). PRO describes the relationships of proteins and protein evolutionary classes, delineates the multiple protein forms of a gene locus (ontology for protein forms), and interconnects existing ontologies. In addition, PRO formally describes protein complexes. Further information is available at http://purl.obolibrary.org/obo/pr. The stable URLs for this release are: http://purl.obolibrary.org/obo/pr/2009-02-05/pr.obo (retrieves release_4.1/pro_nonreasoned.obo) http://purl.obolibrary.org/obo/pr/2009-02-05/pr-asserted.obo (retrieves release_4.1/pro_nonreasoned.obo) It is also possible to retrieve the above release-specific files using the release number in place of the date in the URL (for example, http://purl.obolibrary.org/obo/pr/4.1/pr.obo). The latest version can be retrieved using similar PURLs that lack the /pr/2009-02-05 part (for example, http://purl.obolibrary.org/obo/pr.obo). ===== Files included with this release are: pro_nonreasoned.obo PRO ontology file without reasoning applied; OBO 1.2 format PAF.txt Annotations to PRO terms; tab-delimited promapping.txt Cross-references to external databases; tab-delimited promapping.obo Supplemental file with conversion of promapping.txt to OBO; OBO 1.2 format pro_readme.txt This file pro_release_note.txt Statistics and changes pertinent to this release ===== PAF.txt file format (19 tab-delimited fields) Column Column Title Description 1 PRO_ID PRO identifier, mandatory 2 Object_term Name of the PRO term 3 Object_synonym Other names by which the described object is known 4 Qualifier Flags that modify the interpretation of an annotation 5 Relation Relation to the corresponding annotation. 6 Ontology_ID ID for the corresponding annotation. 7 Ontology_term Term name for the corresponding ontology ID. 8 Interaction_with To indicate binding partner. 9 Evidence_source Pubmed ID or database source for the evidence. 10 Taxon Taxon identifier for the species that the annotation is extracted from. 11 Evidence_code Same as evidence code for GO annotations 12 Inferred_from Use only for evidence code: IPI and ISS for PRO. 13 DB_ID One or more unique identifiers for a single source cited as an authority for the attribution of the ontology term. 14 Protein_region To indicate part of the protein sequence. 15 Modified_residue(s), MOD_ID To indicate the residue(s) that has a post-translational modification and the type of modification. 16 Date Date on which the annotation was made. 17 Assigned_by The database which made the annotation. 18 Equivalent forms List the equivalent form in other organisms. 19 Comments Curator comments, free text. ===== PRO mapping tab-delimited file (promapping.txt) Column Column Title Description 1 -- PRO identifier 2 -- Cross-referenced database object 3 -- Mapping type Mappings can be of two types: i) exact: The database object has the same scope as the object described by PRO. ii) is_a: The database object is more specific than the object described by PRO. In general, database objects specific to an organism will map exactly to the corresponding organism-specific PRO term, while those same database objects will map as is_a to the corresponding organism-generic PRO term. For example, PR:000026465 describes an isoform of 6-phosphofructokinase type C in any organism, so UniProtKB:Q01813-1 (human) and UniProtKB:Q9WUA3-1 (mouse) are mapped to this term.