README file

pro.obo contains the link to the most up-to-date file.

PRO file is in OBO 2.0 format and should be opened with OBO Edit 2.0. The editor can be downloaded from http://www.oboedit.org/index.html.


The ontology follows the structure: 

Root level -> protein
Category=family -> translation product of an evolutionarily-related gene family 
Category=gene -> translation product of a specific gene 
Category=Sequence -> translation product of a specific mature transcript
Category=Modification -> unmodified and cleaved/modified translation product

Common sequence forms in mouse and human (but extensible to other organisms) are considered as a unique term. 
At the sequence level, the translation products of the differently mature transcripts of a gene are referred herein as isoforms, whereas the sequence polymorphisms are referred as sequence variants.


PAF.txt for release 6.0 version 1
All the annotation of the PRO terms is in the PAF.txt file (more documentation for this format is in the PAF guidelines.pdf file). 

The file format comprises 20 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	Modifier		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	Relative_to		Modifiers increased, decreased and altered require an entry in this column to indicate what the change is relative to.
9	Interaction_with	To indicate binding partner. 
10	Evidence_source		Pubmed ID or database source for the evidence. 
11	Evidence_code		Same as evidence code for GO annotations
12	Taxon			Taxon identifier for the species that the annotation is extracted from.
13	Inferred_from		Use only for evidence code: IPI and ISS for PRO. 
14	DB_ID			One or more unique identifiers for a single source cited as an authority for the attribution of the ontology term.
15	Protein_region		To indicate part of the protein sequence.
16	Modified_residue(s), MOD_ID	To indicate the residue(s) that has a post-translational modification and the type of modification. 
17	Date			Date on which the annotation was made.
18	Assigned_by		The database which made the annotation. 
19	Equivalent forms	List the equivalent form in other organisms. 
20	Comments		Curator comments, free text.