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Campaign to annotate ontology root terms with IAO:0000700
The annotation property has ontology root term (IAO:0000700) is used to annotate onto an ontology what its root terms are. This is usually more specific than owl:Thing
or upper-level BFO terms, since these are typically the super-classes of the terms in each ontology that are actually being curated in the ontology itself.
Goals
- Annotate OBO Foundry ontologies using IAO:0000700
Benefits
- the Ontology Lookup Service uses this to help better display ontologies
- this will be generally useful for things like alignment with COB since it makes it easier to figure out where the work will be
Example Contributions
- Example pull request on an OWL file: https://github.com/DiseaseOntology/SymptomOntology/pull/12
- Open the OWL file in Protege
- Add an annotation property http://purl.obolibrary.org/obo/IAO_0000700 if not already available
- Apply it (TODO add screenshots)
- Example pull request on an OBO file: https://github.com/The-Sequence-Ontology/SO-Ontologies/pull/604.
- Open the OBO file
- You can directly add
property_value: IAO:0000700 PREFIX:XXXXXXX
before the first[Term]
standza like in https://github.com/cthoyt/SO-Ontologies/blob/a1fc22a8be4e07c65d726b30d5c54e989b4a6275/so-edit.obo#L22-L25
See https://cthoyt.github.io/cob-root-analysis for charts of the upper parts of several ontologies
Template Contribution Text
Related to https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2149
## What This PR Does
Applies the annotation property [has ontology root term (IAO:0000700)](http://purl.obolibrary.org/obo/IAO_0000700) at the the ontology level to list the following terms from this ontology as "root terms":
1. PREFIX:XXXXXXX
2. ...
## Why this is helpful
- the Ontology Lookup Service uses this to help better display ontologies
- if any of the terms mentioned above are ever aligned with an upper ontology like BFO, it still will be the thing shown on OLS as the "root"
- this will be generally useful for things like alignment with COB since it makes it easier to figure out what are the upper level terms in this ontology are
Related Discussions
- https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1365#issuecomment-729996711
- https://github.com/OBOFoundry/COB/issues/214
Big supporter of this. If I get a checklist of all anatomy and phenotype ontologies that don't have IAO:700 on them I will get cracking.
the following ontologies in "anatomy and development" and "phenotype" domains do not have root terms annotated. See https://cthoyt.github.io/cob-root-analysis for images of the upper parts of all of these ontologies to help with curation. Generated with code at https://github.com/cthoyt/cob-root-analysis
domain | prefix | repository | image |
---|---|---|---|
anatomy and development | aism | https://github.com/insect-morphology/aism | |
anatomy and development | amphx | https://github.com/EBISPOT/amphx_ontology | |
anatomy and development | bspo | https://github.com/obophenotype/biological-spatial-ontology | |
anatomy and development | bto | https://github.com/BRENDA-Enzymes/BTO | |
anatomy and development | caro | https://github.com/obophenotype/caro | |
anatomy and development | clao | https://github.com/luis-gonzalez-m/Collembola | |
anatomy and development | clo | https://github.com/CLO-Ontology/CLO | |
anatomy and development | clyh | https://github.com/EBISPOT/clyh_ontology | |
anatomy and development | colao | https://github.com/insect-morphology/colao | |
anatomy and development | cteno | https://github.com/obophenotype/ctenophore-ontology | |
anatomy and development | ddanat | https://github.com/dictyBase/migration-data | |
anatomy and development | ddpheno | https://github.com/obophenotype/dicty-phenotype-ontology | |
anatomy and development | ecao | https://github.com/echinoderm-ontology/ecao_ontology | |
anatomy and development | emapa | https://github.com/obophenotype/mouse-anatomy-ontology | |
anatomy and development | fao | https://github.com/obophenotype/fungal-anatomy-ontology | |
anatomy and development | hao | https://github.com/hymao/hao | |
anatomy and development | hom | https://github.com/BgeeDB/homology-ontology | |
anatomy and development | hsapdv | https://github.com/obophenotype/developmental-stage-ontologies | |
anatomy and development | lepao | https://github.com/insect-morphology/lepao | |
anatomy and development | ma | https://github.com/obophenotype/mouse-anatomy-ontology | |
anatomy and development | mfmo | https://github.com/RDruzinsky/feedontology | |
anatomy and development | mmusdv | https://github.com/obophenotype/developmental-stage-ontologies | |
anatomy and development | oarcs | https://github.com/aszool/oarcs | |
anatomy and development | olatdv | https://github.com/obophenotype/developmental-stage-ontologies | |
anatomy and development | pdumdv | https://github.com/obophenotype/developmental-stage-ontologies | |
anatomy and development | plana | https://github.com/obophenotype/planaria-ontology | |
anatomy and development | po | https://github.com/Planteome/plant-ontology | |
anatomy and development | poro | https://github.com/obophenotype/porifera-ontology | |
anatomy and development | spd | https://github.com/obophenotype/spider-ontology | |
anatomy and development | xao | https://github.com/xenopus-anatomy/xao | |
anatomy and development | zfa | https://github.com/cerivs/zebrafish-anatomical-ontology | |
anatomy and development | zfs | https://github.com/cerivs/zebrafish-anatomical-ontology | |
phenotype | apo | https://github.com/obophenotype/ascomycete-phenotype-ontology | |
phenotype | flopo | https://github.com/flora-phenotype-ontology/flopoontology | |
phenotype | oba | https://github.com/obophenotype/bio-attribute-ontology | |
phenotype | omp | https://github.com/microbialphenotypes/OMP-ontology | |
phenotype | pcl | https://github.com/obophenotype/provisional_cell_ontology | |
phenotype | phipo | https://github.com/PHI-base/phipo | |
phenotype | planp | https://github.com/obophenotype/planarian-phenotype-ontology | |
phenotype | ppo | https://github.com/PlantPhenoOntology/PPO | |
phenotype | to | https://github.com/Planteome/plant-trait-ontology | |
phenotype | uo | https://github.com/bio-ontology-research-group/unit-ontology | |
phenotype | vt | https://github.com/AnimalGenome/vertebrate-trait-ontology | |
phenotype | xpo | https://github.com/obophenotype/xenopus-phenotype-ontology | |
phenotype | zp | https://github.com/obophenotype/zebrafish-phenotype-ontology |
I made a table to help track the progress:
Repository | Finished? | PR Link |
---|---|---|
aism |
|
https://github.com/insect-morphology/aism/issues/67 |
amphx |
|
https://github.com/EBISPOT/amphx_ontology/pull/5 |
bspo |
|
https://github.com/obophenotype/biological-spatial-ontology/pull/41 |
bto |
|
https://github.com/BRENDA-Enzymes/BTO/pull/23 |
caro |
|
|
clao |
|
https://github.com/luis-gonzalez-m/Collembola/issues/3 |
clo |
|
|
clyh |
|
|
colao |
|
|
cteno |
|
|
ddanat |
|
|
ddpheno |
|
|
ecao |
|
|
emapa |
|
https://github.com/obophenotype/mouse-anatomy-ontology/pull/122 |
fao |
|
|
hao |
|
|
hom |
|
|
hsapdv |
|
https://github.com/obophenotype/developmental-stage-ontologies/pull/82 |
lepao |
|
|
ma |
|
https://github.com/obophenotype/mouse-anatomy-ontology/pull/122 |
mfmo |
|
|
mmusdv |
|
https://github.com/obophenotype/developmental-stage-ontologies/pull/82 |
oarcs |
|
|
olatdv |
|
https://github.com/obophenotype/developmental-stage-ontologies/pull/82 |
pdumdv |
|
https://github.com/obophenotype/developmental-stage-ontologies/pull/82 |
plana |
|
|
po |
|
|
poro |
|
|
so |
|
https://github.com/The-Sequence-Ontology/SO-Ontologies/pull/604 |
spd |
|
|
symp |
|
https://github.com/DiseaseOntology/SymptomOntology/pull/12 |
xao |
|
https://github.com/xenopus-anatomy/xao/pull/60 |
zfa |
|
https://github.com/cerivs/zebrafish-anatomical-ontology/pull/166 |
zfs |
|
https://github.com/cerivs/zebrafish-anatomical-ontology/pull/166 |
apo |
|
|
flopo |
|
https://github.com/flora-phenotype-ontology/flopoontology/issues/11 |
oba |
|
|
omp |
|
|
pcl |
|
|
phipo |
|
|
planp |
|
|
ppo |
|
|
to |
|
|
trans |
|
https://github.com/DiseaseOntology/PathogenTransmissionOntology/commit/62905e2b2fc4b333b14ee21e5922aac5e8193780 |
uo |
|
|
vt |
|
|
xpo |
|
https://github.com/obophenotype/xenopus-phenotype-ontology/pull/158 |
zp |
|