Encourage repositories to add obofoundry topic

[cthoyt]

After completing #1493, it's now time to do a bit of outreach to the community and ask all of the different members to add the obofoundry topic to their repos. It's pretty simple through the main page for the repository, but in case it's not obvious there's a tutorial here: https://docs.github.com/en/github/administering-a-repository/managing-repository-settings/classifying-your-repository-with-topics.

Methods

I've used the following script https://gist.github.com/cthoyt/95694a05190fc23b997fae62f12f96f1 which generates this table as a summary and also automatically created issues on all of the repos (which get linked back to this one). Note, after a while this triggers the abuse detection in the GitHub API 😆, so I added in a time.sleep(2) to calm it down

Full Table, created at the time of filing the issue

ontology	title	owner	repo	topics	has_obofoundry_topic
bfo	Basic Formal Ontology	BFO-ontology	BFO		False
chebi	Chemical Entities of Biological Interest	ebi-chebi	ChEBI		False
doid	Human Disease Ontology	DiseaseOntology	HumanDiseaseOntology		False
go	Gene Ontology	geneontology	go-ontology	ontology,go,owl,obo,obofoundry,gene-ontology	True
pato	Phenotype And Trait Ontology	pato-ontology	pato	phenotypes,trait-ontology,obo,ontology,units,qualities,quantities,standards,semantic-web	False
po	Plant Ontology	Planteome	plant-ontology		False
pr	PRotein Ontology (PRO)	PROconsortium	PRoteinOntology	obofoundry,biomedical-ontologies,obo,protein-ontology	True
xao	Xenopus Anatomy Ontology	xenopus-anatomy	xao	xenopus-anatomy-ontology,anatomy,ontology,xenopus,xao	False
zfa	Zebrafish anatomy and development ontology	cerivs	zebrafish-anatomical-ontology		False
aeo	Anatomical Entity Ontology	obophenotype	human-developmental-anatomy-ontology		False
agro	Agronomy Ontology	AgriculturalSemantics	agro	agronomy,agriculture,agriculture-research,agronomy-ontology	False
aism	Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)	insect-morphology	aism	ontology,ontology-development-kit,multispecies-anatomy-ontologies,insect-ontology,insect-anatomy-ontologies,insect-anatomy	False
amphx	The Amphioxus Development and Anatomy Ontology	EBISPOT	amphx_ontology		False
apo	Ascomycete phenotype ontology	obophenotype	ascomycete-phenotype-ontology		False
apollo_sv	Apollo Structured Vocabulary	ApolloDev	apollo-sv		False
aro	Antibiotic Resistance Ontology	arpcard	aro		False
bco	Biological Collections Ontology	tucotuco	bco	obofoundry	True
bspo	Biological Spatial Ontology	obophenotype	biological-spatial-ontology	obofoundry	True
bto	BRENDA tissue / enzyme source	BRENDA-Enzymes	BTO		False
caro	Common Anatomy Reference Ontology	obophenotype	caro	obofoundry	True
cdao	Comparative Data Analysis Ontology	evoinfo	cdao	comparative-analysis,phylogenetics,ontology,semantic-web,information-exchange,obofoundry	True
cdno	Compositional Dietary Nutrition Ontology	Southern-Cross-Plant-Science	cdno	ontology,nutrition,obofoundry,owl	True
cheminf	Chemical Information Ontology	semanticchemistry	semanticchemistry	chemistry,ontology,cheminformatics,chemical-information	False
chiro	CHEBI Integrated Role Ontology	obophenotype	chiro		False
chmo	Chemical Methods Ontology	rsc-ontologies	rsc-cmo		False
cido	Coronavirus Infectious Disease Ontology	cido-ontology	cido		False
cio	Confidence Information Ontology	BgeeDB	confidence-information-ontology		False
cl	Cell Ontology	obophenotype	cell-ontology	obofoundry,cell-ontology,ontology,anatomy,cell-types,owl	True
clao	Collembola Anatomy Ontology	luis-gonzalez-m	Collembola	anatomy,hexapod-anatomy,ontology	False
clo	Cell Line Ontology	CLO-Ontology	CLO		False
clyh	Clytia hemisphaerica Development and Anatomy Ontology	EBISPOT	clyh_ontology		False
cmo	Clinical measurement ontology	rat-genome-database	CMO-Clinical-Measurement-Ontology		False
cob	Core Ontology for Biology and Biomedicine	OBOFoundry	COB	obofoundry,owl,upper-ontology	True
cro	Contributor Role Ontology	data2health	contributor-role-ontology	data2health,pea	False
cteno	Ctenophore Ontology	obophenotype	ctenophore-ontology		False
cto	CTO: Core Ontology of Clinical Trials	ClinicalTrialOntology	CTO	ontology,clinical-trials	False
cvdo	Cardiovascular Disease Ontology	OpenLHS	CVDO		False
ddanat	Dictyostelium discoideum anatomy	dictyBase	migration-data		False
ddpheno	Dictyostelium discoideum phenotype ontology	obophenotype	dicty-phenotype-ontology		False
dideo	Drug-drug Interaction and Drug-drug Interaction Evidence Ontology	DIDEO	DIDEO		False
dpo	Drosophila Phenotype Ontology	FlyBase	drosophila-phenotype-ontology	phenotype,ontology,flybase,obofoundry	True
duo	Data Use Ontology	EBISPOT	DUO	obofoundry,ontology,datasets-tagged,biomedical-informatics,biomedical-applications,genomics-data,owl	True
ecao	The Echinoderm Anatomy and Development Ontology	echinoderm-ontology	ecao_ontology		False
eco	Evidence ontology	evidenceontology	evidenceontology		False
ecocore	An ontology of core ecological entities	EcologicalSemantics	ecocore		False
ecto	Environmental conditions, treatments and exposures ontology	EnvironmentOntology	environmental-exposure-ontology	exposure,obo,ontology,owl,health,environment	False
emapa	Mouse Developmental Anatomy Ontology	obophenotype	mouse-anatomy-ontology		False
envo	Environment Ontology	EnvironmentOntology	envo		False
eupath	VEuPathDB ontology	VEuPathDB-ontology	VEuPathDB-ontology	obofoundry	True
exo	Exposure ontology	CTDbase	exposure-ontology		False
fao	Fungal gross anatomy	obophenotype	fungal-anatomy-ontology		False
fbbi	Biological Imaging Methods Ontology	CRBS	Biological_Imaging_Methods_Ontology		False
fbcv	FlyBase Controlled Vocabulary	FlyBase	flybase-controlled-vocabulary	drosophila,flybase,obofoundry,ontology,phenotype,genetics	True
fideo	Food Interactions with Drugs Evidence Ontology	getbordea	fideo		False
flopo	Flora Phenotype Ontology	flora-phenotype-ontology	flopoontology		False
foodon	FOODON	FoodOntology	foodon	obofoundry,ontology,owl,food,agriculture	True
fovt	FuTRES Ontology of Vertebrate Traits	futres	fovt		False
fypo	Fission Yeast Phenotype Ontology	pombase	fypo	fission-yeast,pombase,phenotypes,obofoundry	True
gaz	Gazetteer	EnvironmentOntology	gaz		False
gecko	Genomics Cohorts Knowledge Ontology	IHCC-cohorts	GECKO		False
genepio	Genomic Epidemiology Ontology	GenEpiO	genepio	obofoundry	True
geno	Genotype Ontology	monarch-initiative	GENO-ontology	monarchinitiative,ontology,obofoundry	True
gno	Glycan Naming and Subsumption Ontology (GNOme)	glygen-glycan-data	GNOme		False
hancestro	Human Ancestry Ontology	EBISPOT	ancestro		False
hao	Hymenoptera Anatomy Ontology	hymao	hao	obofoundry,hymenoptera	True
hom	Homology Ontology	BgeeDB	homology-ontology		False
hsapdv	Human Developmental Stages	obophenotype	developmental-stage-ontologies		False
hso	Health Surveillance Ontology	SVA-SE	HSO		False
htn	Hypertension Ontology	aellenhicks	htn_owl		False
iao	Information Artifact Ontology	information-artifact-ontology	IAO		False
iceo	Integrative and Conjugative Element Ontology	ontoice	ICEO		False
ico	Informed Consent Ontology	ICO-ontology	ICO		False
ido	Infectious Disease Ontology	infectious-disease-ontology	infectious-disease-ontology		False
ino	Interaction Network Ontology	INO-ontology	ino		False
labo	clinical LABoratory Ontology	OpenLHS	LABO		False
ma	Mouse adult gross anatomy	obophenotype	mouse-anatomy-ontology		False
maxo	Medical Action Ontology	monarch-initiative	MAxO	monarchinitiative	False
mco	Microbial Conditions Ontology	microbial-conditions-ontology	microbial-conditions-ontology		False
mf	Mental Functioning Ontology	jannahastings	mental-functioning-ontology		False
mfmo	Mammalian Feeding Muscle Ontology	RDruzinsky	feedontology		False
mfoem	Emotion Ontology	jannahastings	emotion-ontology		False
mfomd	Mental Disease Ontology	jannahastings	mental-functioning-ontology		False
mi	Molecular Interactions Controlled Vocabulary	HUPO-PSI	psi-mi-CV		False
miapa	MIAPA Ontology	evoinfo	miapa	minimum-information,information-exchange,standard,phylogenetics	False
micro	Ontology of Prokaryotic Phenotypic and Metabolic Characters	carrineblank	MicrO	ontology,phenomic,prokaryotic-taxonomic-descriptions,microbiology,bioinformatics-databases	False
mmo	Measurement method ontology	rat-genome-database	MMO-Measurement-Method-Ontology		False
mmusdv	Mouse Developmental Stages	obophenotype	developmental-stage-ontologies		False
mod	Protein modification	HUPO-PSI	psi-mod-CV		False
mondo	Mondo Disease Ontology	monarch-initiative	mondo	monarchinitiative,ontology,obofoundry,mondo,disease,disease-classification,owl	True
mop	Molecular Process Ontology	rsc-ontologies	rxno		False
mp	Mammalian Phenotype Ontology	obophenotype	mammalian-phenotype-ontology		False
mpath	Mouse pathology ontology	PaulNSchofield	mpath		False
mpio	Minimum PDDI Information Ontology	MPIO-Developers	MPIO		False
mro	MHC Restriction Ontology	IEDB	MRO		False
ms	Mass spectrometry ontology	HUPO-PSI	psi-ms-CV		False
nbo	Neuro Behavior Ontology	obo-behavior	behavior-ontology	ontology,neuro-behaviour-ontology,behavioural-phenotypes,web-ontology-language,animal-behaviours,obo	False
ncbitaxon	NCBI organismal classification	obophenotype	ncbitaxon	obofoundry,taxonomy,ncbi-taxonomy,ontology	True
ncit	NCI Thesaurus OBO Edition	NCI-Thesaurus	thesaurus-obo-edition		False
ncro	Non-Coding RNA Ontology	OmniSearch	NCRO-Ontology-Files		False
nomen	NOMEN - A nomenclatural ontology for biological names	SpeciesFileGroup	nomen	web-ontology-language,ontology,biological-entities,nomenclature,taxa	False
oae	Ontology of Adverse Events	OAE-ontology	OAE		False
oarcs	Ontology of Arthropod Circulatory Systems	aszool	oarcs		False
oba	Ontology of Biological Attributes	obophenotype	bio-attribute-ontology	obofoundry	True
obcs	Ontology of Biological and Clinical Statistics	obcs	obcs		False
obib	Ontology for Biobanking	biobanking	biobanking		False
ogms	Ontology for General Medical Science	OGMS	ogms		False
ogsf	Ontology of Genetic Susceptibility Factor	linikujp	OGSF		False
ohmi	Ontology of Host-Microbiome Interactions	ohmi-ontology	ohmi		False
ohpi	Ontology of Host Pathogen Interactions	OHPI	ohpi		False
olatdv	Medaka Developmental Stages	obophenotype	developmental-stage-ontologies		False
omiabis	Ontologized MIABIS	OMIABIS	omiabis-dev		False
omit	Ontology for MIRNA Target	OmniSearch	omit		False
omo	OBO Metadata Ontology	information-artifact-ontology	ontology-metadata		False
omp	Ontology of Microbial Phenotypes	microbialphenotypes	OMP-ontology		False
omrse	Ontology of Medically Related Social Entities	ufbmi	OMRSE		False
one	Ontology for Nutritional Epidemiology	cyang0128	Nutritional-epidemiologic-ontologies	ontology,ontology-search,nutrition,epidemiology,data-sharing,dietary-intake,strobe-nut,obofoundry	True
ons	Ontology for Nutritional Studies	enpadasi	Ontology-for-Nutritional-Studies	ontology,nutrition,health,intervention-study,observational-study,metabolomics,food-intake,biomarker,databases,nutritional-studies,diet,obofoundry	True
ontoneo	Obstetric and Neonatal Ontology	ontoneo-project	Ontoneo		False
oostt	Ontology of Organizational Structures of Trauma centers and Trauma systems	OOSTT	OOSTT		False
opl	Ontology for Parasite LifeCycle	OPL-ontology	OPL		False
opmi	Ontology of Precision Medicine and Investigation	OPMI	opmi		False
ornaseq	Ontology of RNA Sequencing	safisher	ornaseq		False
ovae	Ontology of Vaccine Adverse Events	OVAE-Ontology	ovae		False
pco	Population and Community Ontology	PopulationAndCommunityOntology	pco	obofoundry	True
pdro	The Prescription of Drugs Ontology	OpenLHS	PDRO		False
pdumdv	Platynereis Developmental Stages	obophenotype	developmental-stage-ontologies		False
peco	Plant Experimental Conditions Ontology	Planteome	plant-experimental-conditions-ontology		False
phipo	Pathogen Host Interaction Phenotype Ontology	PHI-base	phipo		False
plana	planaria-ontology	obophenotype	planaria-ontology		False
planp	Planarian Phenotype Ontology	obophenotype	planarian-phenotype-ontology		False
poro	Porifera Ontology	obophenotype	porifera-ontology	obofoundry	True
ppo	Plant Phenology Ontology	PlantPhenoOntology	PPO		False
psdo	Performance Summary Display Ontology	Display-Lab	psdo	ontology,obo,owl	False
pso	Plant Stress Ontology	Planteome	plant-stress-ontology		False
pw	Pathway ontology	rat-genome-database	PW-Pathway-Ontology		False
rbo	Radiation Biology Ontology	Radiobiology-Informatics-Consortium	RBO		False
ro	Relation Ontology	oborel	obo-relations	obofoundry	True
rs	Rat Strain Ontology	rat-genome-database	RS-Rat-Strain-Ontology		False
rxno	Name Reaction Ontology	rsc-ontologies	rxno		False
sepio	Scientific Evidence and Provenance Information Ontology	monarch-initiative	SEPIO-ontology	monarchinitiative,evidence,provenance	False
so	Sequence types and features ontology	The-Sequence-Ontology	SO-Ontologies		False
spd	Spider Ontology	obophenotype	spider-ontology		False
stato	The Statistical Methods Ontology	ISA-tools	stato	statistics,ontology,owl	False
swo	Software ontology	allysonlister	swo		False
symp	Symptom Ontology	DiseaseOntology	SymptomOntology		False
taxrank	Taxonomic rank vocabulary	phenoscape	taxrank		False
to	Plant Trait Ontology	Planteome	plant-trait-ontology		False
trans	Pathogen Transmission Ontology	DiseaseOntology	PathogenTransmissionOntology		False
tto	Teleost taxonomy ontology	phenoscape	teleost-taxonomy-ontology		False
uberon	Uberon multi-species anatomy ontology	obophenotype	uberon	obofoundry,uberon,ontology,anatomy,monarchinitiative	True
uo	Units of measurement ontology	bio-ontology-research-group	unit-ontology	ontology,units-of-measurement,obo	False
upheno	Unified phenotype ontology (uPheno)	obophenotype	upheno	obofoundry	True
vo	Vaccine Ontology	vaccineontology	VO		False
vt	Vertebrate trait ontology	AnimalGenome	vertebrate-trait-ontology		False
vto	Vertebrate Taxonomy Ontology	phenoscape	vertebrate-taxonomy-ontology		False
wbbt	C. elegans Gross Anatomy Ontology	obophenotype	c-elegans-gross-anatomy-ontology	obofoundry,caenorhabditis-elegans,anatomy,ontology	True
wbls	C. elegans development ontology	obophenotype	c-elegans-development-ontology	wormbase,nematodes,development,ontology,caenorhabditis-elegans,obofoundry	True
wbphenotype	C. elegans phenotype	obophenotype	c-elegans-phenotype-ontology	ontology,elegans-phenotype-ontology,phenotype-term,caenorhabditis-elegans,phenotype-ontologies,phenotypes,nematodes,obofoundry,elegans	True
xco	Experimental condition ontology	rat-genome-database	XCO-experimental-condition-ontology		False
xlmod	HUPO-PSI cross-linking and derivatization reagents controlled vocabulary	HUPO-PSI	mzIdentML		False
xpo	Xenopus Phenotype Ontology	obophenotype	xenopus-phenotype-ontology	xenopus-phenotype-ontology,phenotype,ontology,xenopus,xpo	False
zeco	Zebrafish Experimental Conditions Ontology	ybradford	zebrafish-experimental-conditions-ontology		False
zfs	Zebrafish developmental stages ontology	cerivs	zebrafish-anatomical-ontology		False
zp	Zebrafish Phenotype Ontology	obophenotype	zebrafish-phenotype-ontology		False
fobi	FOBI	pcastellanoescuder	FoodBiomarkerOntology	ontology,metabolomics,nutrition,biomarkers,foods,knowledge-graph,ontologies	False
gsso	Gender, Sex, and Sexual Orientation (GSSO) ontology	Superraptor	GSSO	gender,ontology,gender-identity,sex,sexuality,gender-diversity	False
hp	Human Phenotype Ontology	obophenotype	human-phenotype-ontology	hpo,ontology,phenotype,phenotyping,ontologies,obo,owl,semantic-web,obofoundry	True
scdo	Sickle Cell Disease Ontology	scdodev	scdo-ontology		False
txpo	Toxic Process Ontology	txpo-ontology	TXPO		False
sibo	Social Insect Behavior Ontology	obophenotype	sibo		False
ceph	Cephalopod Ontology	obophenotype	cephalopod-ontology		False
ehdaa2	Human developmental anatomy, abstract	obophenotype	human-developmental-anatomy-ontology		False
rnao	RNA ontology	BGSU-RNA	rnao		False
upa	Unipathway	geneontology	unipathway		False
bcgo	Beta Cell Genomics Ontology	obi-bcgo	bcgo		False
dinto	The Drug-Drug Interactions Ontology	labda	DINTO		False
eo	Plant Environment Ontology	Planteome	plant-environment-ontology		False
tao	Teleost Anatomy Ontology	obophenotype	uberon	obofoundry,uberon,ontology,anatomy,monarchinitiative	True
vsao	Vertebrate Skeletal Anatomy Ontology-	obophenotype	uberon	obofoundry,uberon,ontology,anatomy,monarchinitiative	True

[mbrochhausen]

Sorry, I should know that, but could you please clarify this sentence:
"Note, after a while this triggers the abuse detection in the GitHub API 😆"
Thanks!

[cthoyt]

@mbrochhausen GitHub rightly protects itself and its users from abuse by looking for fishy people like me who are opening lots of issues programatically in very quick succession. After 15 or 20 issues posted, it started returning a warning that I was abusing the API and should try later.

After I initially posted the comment you're referring to, I realized I could just add a simple rate limit by using time.sleep(2) between each issue creation, which seemed to be enough to avoid further error messages

[mbrochhausen]

Thanks! I appreciate the clarification.

[matentzn]

We (OFOC call today) decided to mandate this softly as part of best practices which are collected here: #1579

Thanks for the suggestion! Great.

[cthoyt]

@matentzn excellent

[cthoyt]

As of right now, 43 of the repositories that I originally pinged two years ago have not responded. I just pinged all 43, tagging their responsible people (this is now possible since in the last two years, I have convinced the OBO community that having the GitHub handle easily accessible for each active ontology is valuable). I suggest that in a few months, we review who remains unresponsive and begin marking ontologies as orphaned/inactive accordingly.

[matentzn]

I suggest that in a few months, we review who remains unresponsive and begin marking ontologies as orphaned/inactive accordingly.

You can always initiate a process like this, but not dealing with a specific issue does not all by itself constitute "inactivity"

[cthoyt]

True, but most of the remaining haven’t committed in the last 3-5 years and haven’t addressed any of the issues or PRs. I would be keen on having a more concrete definition of “inactive” and would hope that it includes any repository that hasn’t committed or responded to issues in the last X years (pick whatever x feels most comfortable)