Editor file guide (Retired)
REALLY OUT OF DATE - to be updated
GO editor files
Human edited files are in italic
Imports - and how to request changes
Auto-generated import files, updated nightly. Do not edit.
Files under $ontology:
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
Manually edit this file to import a class from an external ontology
$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_go_imports.dict # Automatically generated from import files
$ontology/editors/oboedit_user.dict # Use dictionary for OBO-Edit. Extend this manually.
$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.
|- database: AGI_LocusCode|
|name: Arabidopsis Genome Initiative|
|description: Comprises TAIR, TIGR and MIPS|
"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:
Moving axioms between ontologies: