README file

PRO ontology files are in OBO 1.2 format and should be opened with OBO Edit 2.0 or higher. The editor can be downloaded from http://www.oboedit.org/.
The file pro.obo is a version of the ontology with no implied links. The reasoner has to be "on" to see the correct hierarchy in the OBO Edit.
The file pro_reasoned.obo is a version of the ontology with the implied links already in place. 

As of release 16.0 the official files supplied by PRO use PR: ID space.


Under the class "amino acid chain" there are two terms: "protein" and "proteolytic cleavage products".

Under protein term the ontology is organized in classes as follows: 

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, human, and E. coli (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.
However, there are some terms that are organism specific and in such cases the organism name is displayed in parenthesis, e.g. PR:000025483, delphilin isoform 2 (mouse). In addition, the Category token is preceded by organism-, e.g. Category=organism-gene.

The class GO:0032991 macromolecular complex encompasses complexes composed of protein subunits exclusively, or proteins with other molecules. PRO refers to GO for any existing complex term, but create new PRO terms whenever more specific complexes are needed.

Annotations for PRO terms are 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.

ID mapping files
Each mapping file contains the mappings to various external databases. Mappings are of two types: 
i) exact: The database object is an exact match to the object described by PRO. For example, PR:000026497 describes an isoform of 6-phosphofructokinase type C in human only, which corresponds to UniProtKB:Q01813-1.
ii) is_a: The database object is more specific than the object described by PRO. For example, PR:000026465 describes an isoform of 6-phosphofructokinase type C but in any organism, so UniProtKB:Q01813-1 (human) and UniProtKB:Q9WUA3-1 (mouse) are mapped to this term.

The file promapping.txt is tab-delimited, each line indicating the PRO ID, the database ID, and the type of mapping (is_a or exact). The promapping.obo file contains the same information as promapping.txt, but in OBO format.

-PRO reasoned File-
The pro_reasoned.obo contains the ontology with implied links, then no reasoner is needed to view the ontology. The reasoned terms will contain the statement "implied link automatically realized" in the created is_a relation.
Example:
in pro.obo
[Term]
id: PR:000025257
name: heat shock protein 105 kDa (mouse)
def: "A heat shock protein 105 kDa that is encoded in the genome of mouse." [PRO:DAN]
comment: Category=organism-gene.
xref: UniProtKB:Q61699
intersection_of: PR:000003410 ! heat shock protein 105 kDa
intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus

in pro_reasoned.obo
[Term]
id: PR:000025257
name: heat shock protein 105 kDa (mouse)
def: "A heat shock protein 105 kDa that is encoded in the genome of mouse." [PRO:DAN]
comment: Category=organism-gene.
synonym: "mHSPH1" EXACT PRO-short-label []
xref: UniProtKB:Q61699
is_a: PR:000003410 ! implied link automatically realized ! heat shock protein 105 kDa
is_a: PR:000029032 ! implied link automatically realized ! Mus musculus protein
intersection_of: PR:000003410 ! heat shock protein 105 kDa
intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus

================================================