Files in this directory are used for carrying out checks for violations between the implicit species specificity of GO terms and the species of origin of the annotated gene products. 

* report-*.txt - per database report of all taxon violations (see below)

* ncbi_taxon_slim.obo - The NCBI taxonomy slim that we use in-house for trigger editing purposes. 

* taxon_go_triggers.obo - The list of GO terms, and the taxonomic groupings that we suggest that they should be used for. 

* taxon_union_terms.obo - The file of in-house taxonomic groupings that are unions of two or more NCBI taxonomy groupings. 

* taxon_union_materialized.obo - taxon_union_terms.obo, with is_a relationship materialized

* taxon_go_imports.obo - The file that can be called by OBO-Edit to automatically load all of the other files for editing or browsing. 

* taxon_violations.txt - The file listing annotations that currently show inconsistencies (DEPRECATED)


See http://gocwiki.geneontology.org/index.php/Taxon_Main_Page

See the Makefile for the scripts used to generate the files.

Report format:

The columns are

1. GO ID (col 5 in original GAF). E.g. GO:0000311
2. GO Label. E.g. plastid large ribosomal subunit
3. Relationship between GO ID and Taxon ID (e.g. only_in_taxon, never_in_taxon)
4. Taxon ID (e.g. NCBITaxon:33090)
5. Taxon Label (e.g. Viridiplantae)
6. Error class (for now always INVALID)
7. Annotated Taxon ID (e.g. taxon:5833)
8. Annotated Object DB (e.g. GeneDB_Pfalciparum)
9. Annotated Object Local ID
10. PMID from GAF
11. Evidence code from GAF

Cols 1-5 show the taxonomic restriction that was violated (e.g. plastid large ribosomal subunit only_in_taxon viridiplantae)
Cols 6-11 give the important information from the GAF line. 


----------


## What follows below is the procedure that was outlined by Chris in October 2012, but on Oct. 25th 2012 we decided to use the perl script assign-relation-ids.pl rather than manually entering GOTAX IDs. (See http://wiki.geneontology.org/index.php/Ontology_meeting_2012-10-25#FOLLOW-UP:_Taxon_triggers) We still want to keep a copy of this file because it contains useful information; just ignore the section about requesting/using ID ranges. 

Prefix: dc: <http://purl.org/dc/elements/1.1/>
Prefix: rdfs: <http://www.w3.org/2000/01/rdf-schema#>
Prefix: idrange:=<http://purl.obolibrary.org/obo/go/extensions/x-taxon-idrange/>
Prefix: allocatedto:=<http://purl.obolibrary.org/obo/IAO_0000597>
Prefix: iddigits:=<http://purl.obolibrary.org/obo/IAO_0000596>
Prefix: idprefix:=<http://purl.obolibrary.org/obo/IAO_0000599>
Prefix: idsfor:=<http://purl.obolibrary.org/obo/IAO_0000598>
Prefix: comment:=<http://www.w3.org/2000/01/rdf-schema#comment>

Ontology: <http://purl.obolibrary.org/obo/go/extensions/x-taxon-idranges.owl>
  Annotations: 
        idprefix: "http://purl.obolibrary.org/obo/GOTAX_", 
        iddigits: 7, 
        idsfor: "GOTAX",
        dc:title "GO taxon constraints editor ID ranges and protocol documentation"^^xsd:string,
        dc:creator "Chris Mungall"^^xsd:string,
        dc:description "

## Protocol for editing GOTAX

In order to add entries with a GOTAX ID you MUST have an idrange
specified in this file. Request an idrange from one of the editors
listed in this document. Ranges are allocated in blocks. An editor may
have multiple blocks.

## Adding new constraints

Every constraint must have a unique GOTAX ID. IDs must never be
resued. Currently there is no automated checking of this, so it relies
on editors checking themselves.

## Removing constraints

A constraint can never be removed. Previously the protocol was to
comment out using obo comments. For example:

```
    ![Term]
    !id: GO:0007595
    !name: lactation
    !relationship: only_in_taxon NCBITaxon:40674 {id=GOTAX:0000104} ! Mammalia
```

Notw the protocol is to ALSO put the uncommented version in
taxon_go_triggers_obsoleted.obo. In addition, the commented stanza
should remain in the main obo file as a clear visual indication to
editors that the constraint is obsoleted, and to avoid GOTAX id reuse.

## Syntax

Follow previous examples. Make sure you don't introduce additional
characters or whitespace, or remove any. This can break parsing.

## Guidelines

Every constraint MUST have a GOTAX id. Every constraint SHOULD have
some piece of provenance - e.g. a PMID or indication of where the
constraint comes from.

These are added as trailing qualifiers, which are axiom annotations in
OWL.

## Possible future changes

Currently the GOTAX file is a hand-edited obo bridge file. The
x-taxon.owl file is automatically derived from this obo file. In
future, the source file may become OWL.

## Protocol for adding new idranges

This file can be edited in Protege or a text editor

"^^xsd:string

AnnotationProperty: allocatedto:
AnnotationProperty: idprefix:
AnnotationProperty: iddigits: 
AnnotationProperty: idsfor: 
AnnotationProperty: comment: 
AnnotationProperty: dc:title
AnnotationProperty: dc:creator
AnnotationProperty: dc:description

Datatype: idrange:1
Annotations: allocatedto: "GOC:ecd"
EquivalentTo: xsd:integer[> 1 , <= 1000]

Datatype: idrange:2
Annotations: allocatedto: "GOC:tb"
EquivalentTo: xsd:integer[> 1001 , <= 2000]

Datatype: idrange:3
Annotations: allocatedto: "GOC:pr"
EquivalentTo: xsd:integer[> 2001 , <= 3000]

Datatype: idrange:4
Annotations: allocatedto: "GOC:dph"
EquivalentTo: xsd:integer[> 3001 , <= 4000]

Datatype: idrange:5
Annotations: allocatedto: "GOC:jl"
EquivalentTo: xsd:integer[> 4001 , <= 5000]