Editor file guide

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GO editor files

Human edited files are in italic

$ontology = http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/

Imports - and how to request changes

Auto-generated import files, updated nightly. Do not edit.

Files under $ontology:

extensions/pato_import.owl

extensions/oba_import.owl

extensions/chebi_import.owl

extensions/po_import.owl

extensions/ro_import.owl

extensions/cl_import.owl

extensions/pr_import.owl

extensions/so_import.owl

extensions/uberon_import.owl

extensions/ncbitaxon_import.owl

Editable Ontology files:

$ontology/editors/gene_ontology_write.obo: The main editor's file. Almost everything you'll ever want to edit lives here (see below for exceptions). The master remains in OBO, not OWL, as this allows multiple edits to be automatically reconciled by svn/git/unix merge and for changes to be tracked via diffs. This file also contains instantiated subclassing axioms derived from reasoning. These are all annotated with "'is_inferred: "true". (We plan to move these axioms into an import module).

$ontology/extensions/gorel-edit.obo: This file contains GO specific relations (these have GOREL IDs), and GO-specific annotations on relations ontology relations.

$ontology/extensions/ro_pending.owl: This file contains GO specific relations (these have GOREL IDs). WE ARE REVIEWING THE RELATIONSHIP BETWEEN THIS AND GOREL-EDIT.

$ontology/extensions/x-disjoint.owl: disjointness GCI axioms. All other disjointness axioms live in the main

$ontology/extensions/imports_requests.obo:

Manually edit this file to import a class from an external ontology

Import config

$ontology/editors/oboedit.catalog # Specifies local paths to import files for OBO-Edit

$ontology/editors/catalog-v001.xml # Specifies local paths to import files for Protege, OWLtools

Dictionaries for spell checking (in OBO-Edit)

$ontology/editors/oboedit_allowedrepeats.dict

$ontology/editors/oboedit_go_imports.dict # Automatically generated from import files

$ontology/editors/oboedit_user.dict # Use dictionary for OBO-Edit. Extend this manually.

ID ranges

$ontology/editors/go-idranges.txt: File for specification of reserved ID ranges for GO editors & tools. Edit this file to assign and new range, or a subrange for work in a branch.

Config file (on GitHub)

db-xrefs.yaml: Details of entities from third party resources that can be referenced via xrefs.

Each entry includes:

  • How to refer to the resource in and xref

  • How xrefs can be expanded to make URLs.

  • Entity type

e.g.:

- database: AGI_LocusCode
name: Arabidopsis Genome Initiative
description: Comprises TAIR, TIGR and MIPS
generic_urls:
entity_types:
type_id: SO:0000704
id_syntax: A[Tt][MmCc0-5][Gg][0-9]{5}(\.[0-9]{1})?
url_syntax: http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id]
example_id: AGI_LocusCode:At2g17950
example_url: http://arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950

"AGI_LocusCode:At2g17950" refers to a type of gene from the resource:Arabidopsis Genome Initiative. This entity can be accessed at the URL http://arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950

users.yaml: A list of GO contributors and the initials used to refer to them in xrefs. Includes ORCID ids (where available) and details of permissions to use various GO tools.

Finding where axioms live and moving them between files

How to tell which file an axiom comes from. Float over the axioms and wait for a pop-up box:

Image03.png

Image04.png

Moving axioms between ontologies:

Image05.png


Category:GO Editors