Campaign to annotate ontology root terms with IAO:0000700

cthoyt commented 1 year ago

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
1. Open the OWL file in Protege
2. Add an annotation property http://purl.obolibrary.org/obo/IAO_0000700 if not already available
3. Apply it (TODO add screenshots)
Example pull request on an OBO file: https://github.com/The-Sequence-Ontology/SO-Ontologies/pull/604.
1. Open the OBO file
2. 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

matentzn commented 1 year ago

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.

cthoyt commented 1 year ago

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
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

erik-whiting commented 1 year ago

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	- [x]	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	- [x]	https://github.com/DiseaseOntology/SymptomOntology/pull/12
xao	- [x]	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	- [x]	https://github.com/DiseaseOntology/PathogenTransmissionOntology/commit/62905e2b2fc4b333b14ee21e5922aac5e8193780
uo	- [ ]
vt	- [ ]
xpo	- [x]	https://github.com/obophenotype/xenopus-phenotype-ontology/pull/158
zp	- [ ]

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