Categorisation scheme for OBO ontologies

matentzn commented 4 years ago

To move forward on the recurring issues of grouping OBO ontologies into some useful macroscopic categories/domains, there were a few proposals:

@zhengj2007 Proposal
My proposal (which I did not-knowing that @zhengj2007 had worked on one)
@nataled ("using COB")

Aspects of this have been discussed here (Portal pages), here (Failed links to group pages) and here (in the context of the revision of the "scope" principle). I would like to suggest this:

We have a small set (~10) of fixed domains to choose from.
Every ontology picks exactly one domain.
We have a more open-ended set of tags (optional field in metadata). Here, ontology devs can group their ontologies more deeply. Having this field will preclude any discussion about “I want more than one tag”.

My suggestion to start with is this and iterate over it together:

upper
anatomy and development
health
phenotype
experiments
environment
biochemistry
metabolomics and nutrition
biological systems
other

I looked at what values are currently used in the domain metadata field across OBO ontology metadata entries, and sorted those into these proposed categories.

Note that there are, of course, other possible categorisation schemes - starting from taxon (ontologies pertaining to plants, humans etc). Also @nataled point of simply using COB would be an option, but I think that domains that would be most useful are more like topics (Health, Biochemistry, Anatomy and Development etc) than concepts ("disease", "anatomical entity"), at least most of the time. I think that annotation with COB terms would be useful as well - maybe under a new element called coverage, that allows multiple elements. Also, the point here is to present some sensible high level groupings to the user, to help them to find relevant ontologies faster. I can see OLS picking this up as well.

cmungall commented 4 years ago

Using COB wouldn't work as a cardinality 1 field as so many ontologies are spread over multiple upper levels

mellybelly commented 4 years ago

I like the list as proposed. Agree ontologies should have ability to list more than one category. I like the idea of having a category view in the landing page, it would make it easier for newcomers to see what content we have.

ddooley commented 4 years ago

Re, "metabolomics and nutrition" the cluster of food related ontologies here also has a domain space of agriculture (production), diet and other food related things. Wondering about capturing that in a single topic?

matentzn commented 4 years ago

@mellybelly The above suggestion was, to be precise, to assign a single domain, and than allow an arbitrary number of category tags; the single primary domain should serve as a rough grouping for the OBO ontology overview table.. Otherwise you would have the same ontology appear multiple times in the overview, which would blow up its size (its already too long).

@ddooley Do you have any suggestion for a name of that category?

ddooley commented 4 years ago

perhaps:"agriculture, diet, metabolomics and nutrition"

matentzn commented 4 years ago

OK new working version:

- upper
- anatomy and development
- health
- phenotype
- experiments
- environment
- biochemistry
- agriculture, diet, metabolomics and nutrition
- biological systems
- other

mellybelly commented 4 years ago

I like this a lot, except I find agriculture a bit too different from diet, metabolomics and nutrition, which I do think go together. I also wonder if we need a tag that is something more like 'social' or 'information artifact' for things like CRO, OOST, and OMRSE. Or these would go in other? Feels weird to have an 'other'; would anyone use that category for filtering?

matentzn commented 3 years ago

I would imagine someone that does not find the category the need not filtering on category at all.. And there are the tags that could be used for filtering; the alternative is to see "Other" as temporary and try to categorise everything in it..

@ddooley Whats your opinion on having:

- agriculture
- diet, metabolomics and nutrition

ddooley commented 3 years ago

Sure, and I presume people can multi-select?

matentzn commented 3 years ago

Yeah this was not so much about the UI itself, but I am sure, if we used this in the UI, multiple select would definitely be possible! New list:

- upper
- anatomy and development
- health
- phenotype
- experiments
- environment
- biochemistry
- agriculture
- diet, metabolomics and nutrition
- biological systems
- other

ddooley commented 3 years ago

@pbuttigieg maybe you want "environment" to be "natural and built environment" ? Or a separate "anthroposphere"? The human-made infrastructure that so much research has a context in.

yongqunh commented 3 years ago

I think we can include "Microbiology" (which may include virology, bacteriology, parasitology, etc. )

matentzn commented 3 years ago

Sure:

- upper
- anatomy and development
- health
- phenotype
- experiments
- environment
- biochemistry
- microbiology
- agriculture
- diet, metabolomics and nutrition
- biological systems
- other

yongqunh commented 3 years ago

Great. Thanks!

matentzn commented 3 years ago

https://docs.google.com/document/d/1fitsa5ZWKR_fidG0zC_eQIZDhmPXDpkG_oiql6nCDRo/edit?usp=sharing

matentzn commented 3 years ago

This is how the new categories would look like:

new category    ontology    old domain
agriculture agro    agronomy
anatomy and development aeo anatomy
anatomy and development amphx   anatomy
anatomy and development bila    anatomy
anatomy and development bspo    anatomy
anatomy and development bto anatomy
anatomy and development caro    anatomy
anatomy and development ceph    anatomy
anatomy and development cl  cells
anatomy and development clyh    anatomy
anatomy and development cteno   anatomy
anatomy and development ddanat  anatomy
anatomy and development ddpheno anatomy
anatomy and development ecao    anatomy
anatomy and development ehdaa2  anatomy
anatomy and development emap    anatomy
anatomy and development emapa   anatomy
anatomy and development fao anatomy
anatomy and development fbbt    Drosophilid anatomy
anatomy and development fbdv    development
anatomy and development fma anatomy
anatomy and development hao anatomy
anatomy and development ma  anatomy
anatomy and development mfmo    anatomy
anatomy and development mfo anatomy
anatomy and development oarcs   anatomy
anatomy and development plana   anatomy
anatomy and development po  anatomy and development
anatomy and development poro    anatomy
anatomy and development spd anatomy
anatomy and development tads    anatomy
anatomy and development tao anatomy
anatomy and development tgma    anatomy
anatomy and development uberon  anatomy
anatomy and development vsao    anatomy
anatomy and development wbbt    anatomy
anatomy and development xao anatomy
anatomy and development zfa anatomy
anatomy and development zfs anatomy
biochemistry    chebi   biochemistry
biochemistry    cheminf biochemistry
biochemistry    chiro   biochemistry
biochemistry    gno glycan structure
biochemistry    lipro   lipids
biochemistry    mod proteins
biochemistry    mro Major Histocompatibility Complex
biochemistry    pr  proteins
biochemistry    resid   proteins
biochemistry    rnao    molecular structure
biochemistry    sbo biochemistry
biological systems  geno    genotype-to-phenotype associations
biological systems  nbo behavior
biological systems  pw  biological process
biological systems  sibo    behavior
biological systems  upa pathways
diet, metabolomics and nutrition    fideo   diet, metabolomics and nutrition
environment ecocore ecological functions, ecological interactions
environment ecto    environment
environment envo    environment
environment eo  environment
environment miro    environment
environment pco collections of organisms
environment zeco    environment
experiments eco experiments
experiments fbbi    imaging experiments
experiments mco experimental conditions
experiments mi  experiments
experiments mo  experiments
experiments ms  MS experiments
experiments ncro    experiments
experiments nmr experiments
experiments obi experiments
experiments ornaseq experiments
experiments peco    experimental conditions
experiments sep provenance
experiments sepio   scientific claims, evidence
health  aero    health
health  apollo_sv   health
health  chmo    health
health  cmo clinical
health  cvdo    health
health  dinto   health
health  doid    disease
health  dron    health
health  exo health
health  flu health
health  genepio health
health  ido health
health  idomal  health
health  mf  health
health  mfoem   health
health  mfomd   health
health  mmo clinical
health  mondo   disease
health  mpath   health
health  mpio    health
health  oae adverse events, health
health  obib    health
health  ogms    medicine
health  ohd health
health  omiabis health
health  omrse   medicine
health  ontoneo biomedical, health
health  oostt   health
health  pdro    health
health  symp    disease
health  trans   disease
health  vo  health
health  xco clinical
other   bco biodiversity collections
other   cro scholarly contribution roles
other   ero resources
other   eupath  functional genomics, population biology, clinical epidemiology, and microbiomes
other   fbcv    
other   fbsp    taxonomy
other   fobi    metabolomics and nutrition
other   foodon  food
other   fovt    vertebrate traits
other   gecko   cohort studies
other   go  biology
other   hancestro   ancestry
other   iao information
other   kisao   algorithms
other   labo    clinical documentation
other   maxo    stuff
other   ncbitaxon   taxonomy
other   nomen   biological nomenclature
other   obcs    statistics
other   omo ontology term annotation
other   ons nutrition, nutritional studies, nutrition professionals
other   psdo    learning systems
other   pso plant disease and abiotic stress
other   so  biological sequence
other   stato   statistics
other   swo software
other   taxrank taxonomy
other   tto taxonomy
other   txpo    toxicity
other   wbls    developemental life stage
other   xlmod   MS cross-linker reagents
phenotype   apo phenotype
phenotype   dpo phenotype
phenotype   flopo   phenotype
phenotype   fypo    phenotype
phenotype   hp  phenotype
phenotype   micro   phenotype
phenotype   mp  phenotype
phenotype   oba phenotype
phenotype   omp phenotype
phenotype   pato    phenotype
phenotype   phipo   phenotype
phenotype   planp   phenotype
phenotype   ppo plant phenotypes
phenotype   to  phenotype
phenotype   uo  phenotype
phenotype   wbphenotype phenotype
phenotype   xpo phenotype
phenotype   zp  phenotype
upper   bfo upper
upper   cob upper
upper   ro  relations

nataled commented 3 years ago

I took a quick crack at the 'other' category to see if (1) new categories could be created; or (2) the given ontology can perhaps fit into an existing category. The latter assignments are prefixed with a '?'

The new categories are organisms/populations/taxonomy, information/documentation/metadata (I only used the first word for brevity). Proposed names and assignments should be reviewed/revised, as these suggestions were based purely on the name of the ontology and not any review of its actual content. Any remaining 'other' were grouped into sets for which I did not come up with a name. Again, these need review.

organisms bco biodiversity collections organisms eupath functional genomics, population biology, clinical epidemiology, and microbiomes organisms fbsp taxonomy organisms gecko cohort studies organisms hancestro ancestry organisms ncbitaxon taxonomy organisms taxrank taxonomy organisms tto taxonomy information iao information information labo clinical documentation information nomen biological nomenclature information omo ontology term annotation information psdo learning systems other cro scholarly contribution roles (PERHAPS 'information'?) other ero resources (PERHAPS 'information'?) other pso plant disease and abiotic stress (PERHAPS 'health'?)

other1 kisao algorithms other1 obcs statistics other1 stato statistics other1 swo software

other fbcv
other go biology other maxo stuff other ons nutrition, nutritional studies, nutrition professionals

?anatomy and development wbls developemental life stage ?biochemistry so biological sequence ?biochemistry txpo toxicity ?biochemistry xlmod MS cross-linker reagents ?diet, metabolomics, and nutrition fobi metabolomics and nutrition ?diet, metabolomics, and nutrition foodon food ?phenotype fovt vertebrate traits

matentzn commented 3 years ago

This is great, thank you @nataled

I updated the list to accommodate your suggestions, I made one change: (plant disease and abiotic stress under agronomy rather than health) and classified the "other" category (GO under biological systems, maxo under health and ons under diets). I made a pull request to put fbcv under organisms.

Here is the updated list:

Category: anatomy and development

domain	ontology	category
anatomy	aeo	anatomy and development
anatomy	amphx	anatomy and development
anatomy	bila	anatomy and development
anatomy	bspo	anatomy and development
anatomy	bto	anatomy and development
anatomy	caro	anatomy and development
anatomy	ceph	anatomy and development
cells	cl	anatomy and development
anatomy	clyh	anatomy and development
anatomy	cteno	anatomy and development
anatomy	ddanat	anatomy and development
anatomy	ddpheno	anatomy and development
anatomy	ecao	anatomy and development
anatomy	ehdaa2	anatomy and development
anatomy	emap	anatomy and development
anatomy	emapa	anatomy and development
anatomy	fao	anatomy and development
Drosophilid anatomy	fbbt	anatomy and development
development	fbdv	anatomy and development
anatomy	fma	anatomy and development
anatomy	hao	anatomy and development
anatomy	ma	anatomy and development
anatomy	mfmo	anatomy and development
anatomy	mfo	anatomy and development
anatomy	oarcs	anatomy and development
anatomy	plana	anatomy and development
anatomy and development	po	anatomy and development
anatomy	poro	anatomy and development
anatomy	spd	anatomy and development
anatomy	tads	anatomy and development
anatomy	tao	anatomy and development
anatomy	tgma	anatomy and development
anatomy	uberon	anatomy and development
anatomy	vsao	anatomy and development
anatomy	wbbt	anatomy and development
developemental life stage	wbls	anatomy and development
anatomy	xao	anatomy and development
anatomy	zfa	anatomy and development
anatomy	zfs	anatomy and development

Category: health

domain	ontology	category
health	aero	health
health	apollo_sv	health
health	chmo	health
clinical	cmo	health
health	cvdo	health
health	dinto	health
disease	doid	health
health	dron	health
health	exo	health
health	flu	health
health	genepio	health
health	ido	health
health	idomal	health
stuff	maxo	health
health	mf	health
health	mfoem	health
health	mfomd	health
clinical	mmo	health
disease	mondo	health
health	mpath	health
health	mpio	health
adverse events, health	oae	health
health	obib	health
medicine	ogms	health
health	ohd	health
health	omiabis	health
medicine	omrse	health
biomedical, health	ontoneo	health
health	oostt	health
health	pdro	health
disease	symp	health
disease	trans	health
health	vo	health
clinical	xco	health

Category: phenotype

domain	ontology	category
phenotype	apo	phenotype
phenotype	dpo	phenotype
phenotype	flopo	phenotype
vertebrate traits	fovt	phenotype
phenotype	fypo	phenotype
phenotype	hp	phenotype
phenotype	micro	phenotype
phenotype	mp	phenotype
phenotype	oba	phenotype
phenotype	omp	phenotype
phenotype	pato	phenotype
phenotype	phipo	phenotype
phenotype	planp	phenotype
plant phenotypes	ppo	phenotype
phenotype	to	phenotype
phenotype	uo	phenotype
phenotype	wbphenotype	phenotype
phenotype	xpo	phenotype
phenotype	zp	phenotype

Category: biochemistry

domain	ontology	category
biochemistry	chebi	biochemistry
biochemistry	cheminf	biochemistry
biochemistry	chiro	biochemistry
glycan structure	gno	biochemistry
lipids	lipro	biochemistry
proteins	mod	biochemistry
Major Histocompatibility Complex	mro	biochemistry
proteins	pr	biochemistry
proteins	resid	biochemistry
molecular structure	rnao	biochemistry
biochemistry	sbo	biochemistry
biological sequence	so	biochemistry
toxicity	txpo	biochemistry
MS cross-linker reagents	xlmod	biochemistry

Category: experiments

domain	ontology	category
experiments	eco	experiments
imaging experiments	fbbi	experiments
experimental conditions	mco	experiments
experiments	mi	experiments
experiments	mo	experiments
MS experiments	ms	experiments
experiments	ncro	experiments
experiments	nmr	experiments
experiments	obi	experiments
experiments	ornaseq	experiments
experimental conditions	peco	experiments
provenance	sep	experiments
scientific claims, evidence	sepio	experiments

Category: organisms

domain	ontology	category
biodiversity collections	bco	organisms
functional genomics, population biology, clinical epidemiology, and microbiomes	eupath	organisms
taxonomy	fbsp	organisms
cohort studies	gecko	organisms
ancestry	hancestro	organisms
taxonomy	ncbitaxon	organisms
taxonomy	taxrank	organisms
taxonomy	tto	organisms

Category: environment

domain	ontology	category
ecological functions, ecological interactions	ecocore	environment
environment	ecto	environment
environment	envo	environment
environment	eo	environment
environment	miro	environment
collections of organisms	pco	environment
environment	zeco	environment

Category: information

domain	ontology	category
scholarly contribution roles	cro	information
resources	ero	information
information	iao	information
clinical documentation	labo	information
biological nomenclature	nomen	information
ontology term annotation	omo	information
learning systems	psdo	information

Category: biological systems

domain	ontology	category
genotype-to-phenotype associations	geno	biological systems
biology	go	biological systems
behavior	nbo	biological systems
biological process	pw	biological systems
behavior	sibo	biological systems
pathways	upa	biological systems

Category: diet, metabolomics and nutrition

domain	ontology	category
diet, metabolomics and nutrition	fideo	diet, metabolomics and nutrition
metabolomics and nutrition	fobi	diet, metabolomics and nutrition
food	foodon	diet, metabolomics and nutrition
nutrition, nutritional studies, nutrition professionals	ons	diet, metabolomics and nutrition

Category: information technology

domain	ontology	category
algorithms	kisao	information technology
statistics	obcs	information technology
statistics	stato	information technology
software	swo	information technology

Category: upper

domain	ontology	category
upper	bfo	upper
upper	cob	upper
relations	ro	upper

Category: agriculture

domain	ontology	category
agronomy	agro	agriculture
plant disease and abiotic stress	pso	agriculture

Category: other

domain	ontology	category
None	fbcv	other

matentzn commented 3 years ago

The way I would like to proceed with this is to

replace the current domain in the yaml config files with the new category (keeping the element named domain) and then introducing a new element tags where we add the old domain.

For example:

OLD fbbt.md

id: fbbt
domain: Drosophilid anatomy

becomes:

id: fbbt
domain: anatomy and development
tags:
  - Drosophilid anatomy

@jamesaoverton you think this makes sense?

jamesaoverton commented 3 years ago

@matentzn Yes, I like that approach.

matentzn commented 3 years ago

Alright, thank you! Note to self: After the next OBO operations call, I will make a pull request with the necessary changes.

matentzn commented 2 years ago

Final update of ontology categories 2022:

domain	ontology	category
diet, metabolomics and nutrition	cdno	diet, metabolomics and nutrition
diet, metabolomics and nutrition	fideo	diet, metabolomics and nutrition
metabolomics and nutrition	fobi	diet, metabolomics and nutrition
food	foodon	diet, metabolomics and nutrition
nutritional epidemiology, observational studies, dietary surveys	one	diet, metabolomics and nutrition
nutrition, nutritional studies, nutrition professionals	ons	diet, metabolomics and nutrition

domain	ontology	category
digital evolution, a branch of Artificial Life.	ontoavida	other

Implementation:

https://github.com/OBOFoundry/OBOFoundry.github.io/pull/1810

jonquet commented 2 years ago

@matentzn

What's the point in creating a bunch of other ambiguous keywords... What about:

upper
anatomy and development => http://purl.bioontology.org/ontology/MESH/D000715 and http://purl.bioontology.org/ontology/MESH/D015509
health
phenotype => http://purl.bioontology.org/ontology/MESH/D010641
experiments
environment => http://purl.bioontology.org/ontology/MESH/D004777
biochemistry => http://purl.bioontology.org/ontology/MESH/D001671
microbiology => http://purl.bioontology.org/ontology/MESH/D008829
agriculture => http://purl.bioontology.org/ontology/MESH/D000383
diet, metabolomics and nutrition => http://purl.bioontology.org/ontology/MESH/D004032, http://purl.bioontology.org/ontology/MESH/D055432 and http://purl.bioontology.org/ontology/MESH/D052756
biological systems
other => REMOVE THIS ONE! other is not a tag, but a placeholder for future problems ...

Some are missing, but I am sure you got my point ;)

By the way BioPortal offers also such high concepts topics => http://data.bioontology.org/categories that are used to tag the ontologies. Problem, they do not come from a standard reference thesaurus (such as MeSH) that would unambiguously define the topic).

Then the md files will get a good old RDF triple :

http://purl.obolibrary.org/obo/fbbt.owl dcterms:subject http://purl.bioontology.org/ontology/MESH/D000715

matentzn commented 2 years ago

@jonquet I am all for using standard vocabularies. I am fine with thinking in this direction, but I must say, this issue has been around for so many years now, and so often discussed, I would rather just merge this PR and make a new issue for mapping the categories to controlled vocabularies. There are so many implications, like:

Do we really want to use MESH as a controlled vocabulary for the topics?
Do we really after 3 years open up the discussion again and on domains that cover multiple topics? E.g. diet, metabolomics and nutrition: Why do I have to use 3 MESH terms rather than one simple string?
The fact that they are ambiguous is deliberate - many ontologies really do not fall all that clearly into one such domain/category, so vague is, in this case, good. It is really just about a simple prima facie grouping on the website.
Your mapping is what I consider COB should be doing - if we can, in the future, link every ontology to the COB upper terms they deal with, we can get the same effect..

I am happy to be convinced otherwise, but we are replacing 60 vague topics here with 15 less vague ones and QC that ensures they will be the only ones moving forward. Small iterations!

Re: other, I am fine to get rid of that, in favour of an "artificial life" category..

EDIT: "other" category removed.

alanruttenberg commented 2 years ago

experiments -> investigations or some other synonym. 1) Experiments is ambiguous as to whether the ontology is an experiment or subject matter is experiment 2) Not all investigations are experiments

matentzn commented 2 years ago

experiments -> investigations or some other synonym.

@jamesaoverton @bpeters42 What do you think about @alanruttenbergs suggestion? A longer name like "experiments and investigations" is also fine.

bpeters42 commented 2 years ago

I also prefer 'investigations'. And I very much agree with Nico's point otherwise about getting this merged with these 'good enough' categories, and hopefully work towards getting these into COB - where we can actually test if terms are in the declared scope or not.

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experiments -> investigations or some other synonym.

@jamesaoverton https://github.com/jamesaoverton @bpeters42 https://github.com/bpeters42 What do you think about @alanruttenbergs suggestion? A longer name like "experiments and investigations" is also fine.

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matentzn commented 2 years ago

[x] Nico to rename experiments to investigations before merging

jonquet commented 2 years ago

@matentzn I am mostly worried in being able to store an information that a machine can understand/parse and that is encoded in a standard way. I agree with your step by step approach. Indeed, it's already a great work the whole group is doing these days in harmonizing the metadata. Having this PR removed the "other" category is also a big step ;) one day or another this field would have created trouble to someone ;)

matentzn commented 2 years ago

Great @jonquet, thanks for the feedback!

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