README file

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

PRO file is in OBO 1.2 format and should be opened with OBO Edit 1.1 or higher. The editor can be downloaded from http://www.oboedit.org/index.html.


The ontology follows the structure: 

Root level -> protein
Family level -> translation product of an evolutionarily-related gene family 
Gene level -> translation product of a specific gene 
Sequence level -> translation product of a specific processed transcript
Modification level -> 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.


Changes from Release 2.1

The relation and cross-reference to other ontologies are now in the PRO association tab delimited file (PAF.txt). Therefore, the “comment:” and the “xref:” field do not contain GO, SO or MOD information.
Only xref for databases that are the source for defining the class are kept in the ontology. This is the case for  PIRSF, PANTHER, PFAM and MIM.

PAF.txt for release 3.0
All the annotation of the PRO terms is now in the PAF.txt file (more documentation for this format is in the PAF guidelines.pdf file. 

The file format comprises 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.

Minor changes
The definition for isoforms as “a translation product of a processed transcript of a given gene” has been slightly modified to “a translation product of a mature transcript of a given gene” based on the definition of SO:0000233 mature_transcript that applies both to Eukaryotes and Prokaryotes.

The release version was added in the remark line.