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OBOFoundry / COB

An experimental ontology containing key terms from Open Biological and Biomedical Ontologies (OBO)
https://obofoundry.github.io/COB
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Integrate 'organism' #6

Closed jamesaoverton closed 5 years ago

jamesaoverton commented 6 years ago

OBI:0100026 organism was never in OBI scope but was required for various tasks. It's defined as equivalent to Viruses or Bacteria or Archaea or Eukaryota.

I think NCBITaxon:131567 cellular organism is more recent. Its three subclasses are Bacteria, Archaea, and Eukaryota -- Viruses are not included.

I know that @bpeters42 has some thoughts on this.

cmungall commented 6 years ago

Definition is a bit circular but I think this does the trick: http://purl.obolibrary.org/obo/CARO_0001010

Note you need one more axiom to make things link up: https://github.com/obophenotype/caro/issues/15

bpeters42 commented 6 years ago

Yes, I would use the OBI term and change the logical definition to refer to cellular organism +virus + viroid rather than the three subtypes (bacteria, eukaryote, archae), exactly like in the CARO term Chris points to.

Question will be what the label should be. I am very much in favor of keeping it as 'organism'. If this will upset too many people, We can switch to something like 'generalized organism'.

On Fri, Sep 21, 2018 at 11:44 AM Chris Mungall notifications@github.com wrote:

Definition is a bit circular but I think this does the trick: http://purl.obolibrary.org/obo/CARO_0001010

Note you need one more axiom to make things link up: obophenotype/caro#15 https://github.com/obophenotype/caro/issues/15

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zhengj2007 commented 6 years ago

+1 Bjoern

cmungall commented 6 years ago

isn't OBI an odd place for this to live?

I'm 50-50 on name. On the one hand, we tend to err on the side of ugliness to prevent confusion. On the other, I especially don't like long union clauses. If the consensus is for short name then let's change it in CARO -- then would it make sense to import from CARO?

cmungall commented 6 years ago

Note: need 'organism' to use in domain/range for biotic interaction relations in https://github.com/oborel/obo-relations/pull/261

bpeters42 commented 6 years ago

The OBI term is widely used across OBO ontologies. It is definitely not a good home, but I would argue that neither is CARO. NCBITaxon would be the best one. But we are trying to get away from that concept anyway, especially with the core, so why not give OBI a bit of credit for creating a term that others found widely useful? Part of that usefulness is the short label, which especially for a 'core', where we are trying to educate people and make them less scared of ontologies. I agree completely that the long union clauses are especially ugly. That is why I proposed 'generalized organism' as a compromise.

On Tue, Sep 25, 2018 at 8:35 PM Chris Mungall notifications@github.com wrote:

Note: need 'organism' to use in domain/range for biotic interaction relations in oborel/obo-relations#261 https://github.com/oborel/obo-relations/pull/261

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cmungall commented 6 years ago

No criticism intended, just looking for the best long term home.

NCBITaxon is a good choice, except thus far we have treated this as a direct syntactic transform. See the docs on http://obofoundry.org/ontology/ncbitaxon.html

On the one hand I'd like to do some additional processing, e.g. depluralizing terms, but that would be a big break from our process so far (maybe it's time). We have also strictly adhered to the numeric part of the URI corresponding to a numeric identifier in the source ncbi taxonomy database. It gets a bit odd if we start minting our own URIs with the NCBITaxon prefix. First we have to choose a number that is guaranteed not to clash ('0'? Random 10 digit number?). Even then it's a recipe for sowing confusion...

cmungall commented 6 years ago

We could just ask ncbi to add a taxon node for organism, they are our chosen authority here.

The foreseeable objection is that this may seen as a commitment about phylogenetic relationship of viruses in relationship to cellular organisms

mcourtot commented 6 years ago

I would strongly prefer not to mint new ID using someone else's prefix - if we really need new terms and NCBI taxonomy doesn't want to add them then the only compromise I can think of is adding them in the NCBITaxon file but with another prefix (something like OBOTaxon or else) so they'd be available but clearly not created/supported by NCBI.

I like the idea of asking NCBI to add an organism that includes cellular organisms + virus + viroid - should we try that and advise if they're reluctant? @cmungall do you know the right person to ask?

nataled commented 6 years ago

Perhaps NCBITaxon:1 ("root") would somewhat fit for the ID? True, the ontology does include non-organism things outside the scope of what we're looking for (such as plasmids), but since that's already the case maybe we can let it slide? Or, if additional processing is going to happen anyway, such terms can be removed.

zhengj2007 commented 6 years ago

@mcourtot "I like the idea of asking NCBI to add an organism that includes cellular organisms + virus + viroid".

I like this idea too. One more question, in this case, shall we deprecated OBI: organism?

bpeters42 commented 6 years ago

Can we please stick to one task at a time? I don't want the core work to depend on getting NCBI taxonomy folks to create something (they have not been responsive in the past). We have a perfectly fine term in OBI that is in wide use. We should request an equivalent term from the NCBI taxonomy, and make an editor note on the OBI term. If that gets made, yes, we should obsolete the OBI term, but we should not wait on any of this to happen right now.

On Wed, Sep 26, 2018 at 10:49 AM jie zheng notifications@github.com wrote:

@mcourtot https://github.com/mcourtot "I like the idea of asking NCBI to add an organism that includes cellular organisms + virus + viroid".

I like this idea too. One more question, in this case, shall we deprecated OBI: organism?

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mcourtot commented 6 years ago

Proposal is

  1. use the OBI term and change the logical definition to refer to cellular organism +virus + viroid. Add editor note on OBI term with details of the request in 2. We will keep 'organism' label for now.
  2. request new organism term from NCBI - when/if created advise about deprecating the OBI term
cstoeckert commented 6 years ago

+1

From: Melanie Courtot notifications@github.com Reply-To: OBOFoundry/Experimental-OBO-Core reply@reply.github.com Date: Thursday, September 27, 2018 at 11:42 AM To: OBOFoundry/Experimental-OBO-Core Experimental-OBO-Core@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [OBOFoundry/Experimental-OBO-Core] Integrate 'organism' (#6)

Proposal is

  1. use the OBI term and change the logical definition to refer to cellular organism +virus + viroid. Add editor note on OBI term with details of the request in 2. We will keep 'organism' label for now.
  2. request new organism term from NCBI - when/if created advise about deprecating the OBI term

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zhengj2007 commented 6 years ago

+1 Melanie's proposal

cmungall commented 6 years ago

Alternate proposal

  1. use the CARO class but relabel to 'organism'
  2. request new organism term from NCBI - when/if created advise about deprecating the CARO term

This just seems to make sense. organisms are anatomical entities, CARO is an upper-level anatomical entity ontology with root class 'anatomical entity'. OBI is an ontology of biomedical investigations, organisms exist independent of biomedical investigations. Full credit to OBI for providing the term since 2009 but we need to move forwards with a more sensible modularization strategy.

Another issue is that the OBI class explicitly makes no commitment to start/end, and explicitly says this is out of scope; the editor note says "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms'), 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI." - for anatomy ontology use cases there needs to be ontological commitment.

bpeters42 commented 6 years ago

To be frank, the caro definition is complete crap. And I strongly doubt that there is consensus that organisms are a kind of anatomical entities. Try to propose it as a parent to ncbi... but i will once again say ok to this so that we can move on.

On Thu, Sep 27, 2018, 5:32 PM Chris Mungall notifications@github.com wrote:

Alternate proposal

  1. use the CARO class but relabel to 'organism'
  2. request new organism term from NCBI - when/if created advise about deprecating the CARO term

This just seems to make sense. organisms are anatomical entities, CARO is an upper-level anatomical entity ontology with root class 'anatomical entity'. OBI is an ontology of biomedical investigations, organisms exist independent of biomedical investigations. Full credit to OBI for providing the term since 2009 but we need to move forwards with a more sensible modularization strategy.

Another issue is that the OBI class explicitly makes no commitment to start/end, and explicitly says this is out of scope; the editor note says "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms'), 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI." - for anatomy ontology use cases there needs to be ontological commitment.

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bpeters42 commented 6 years ago

It looks like the next RO release is pushing for the CARO class to be the new 'organism'. As I said, I will no longer object to it. But then I would very much want to change that class to make it not less embarrassing

Currently: label: "organism or virus or viroid". definition: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle."

Problems:

Suggestion: Replace with the imperfect elucidation in OBI, dropping the 'living' part to stop the virus haters: "A material entity such as an animal, plant, bacteria or virus or viroid, that is capable of replicating or reproducing, growth and maintenance in the right environment."

mellybelly commented 6 years ago

Most definitions of organism do not include viruses and viroids. There is of course a whole body of literature arguing about how to define organism. I don't think we should spend a lot more time on this - an enormous effort was spent during the creation of these terms in CARO and other ontologies already and many decades more generally ;-).

I don't think this presence of this class/class label is a matter of being a virus hater. We do need a union class, and this is reason it was created, quite the opposite of being a virus hater.

I don't think 'organism' by itself as a label works as most organismal biologists use this term in exclusion of viruses and viroids and are very likely to use it incorrectly. I don't love 'generalized organism' but would be ok with that given that it is at least a flag that it might mean something more than simply 'organism'. I am also fine with keeping the union label.

Agree we should have definitions for organism, species.

Agree the text definition of 'anatomical entity' is not consistent with the intent, we can readily fix this. An 'anatomical entity' should be part of a 'cellular organism'. Most anatomists would likely argue that viral parts are not anatomical entities, though this poses less of an issue for misuse than the organism one above. Will make a ticket.

There are many 'organism' classes in the obo library, we should indeed clean them up, they all mean slightly different things in different ontologies: http://www.ontobee.org/search?ontology=&keywords=organism&submit=Search+terms

What is the current QA/clean up process for potential duplicate entities across OBO? We will be happy to help reconcile but would like to do so using standard process or otherwise help make a standard process.

bpeters42 commented 6 years ago

This thread is part of an attempt of a cleanup process for duplicate shared entities across OBO. Yes, there are many other ontologies that define 'organism', the one in OBI being by far the most used (26 vs. 16 for CARO in the page you linked to). My sligthly angry tone comes from being asked to drop yet another OBI term that we spent a lot of time getting right. But it sounds like you are willing to fix CARO, and then we will adopt that in the OBO-Core, and eventually use it to replace the OBI term, and others.

To be concrete, everyone please comment if you agree or object to the below. I took OBIs definition, cut out even more of the potentially controversial bits (viruses don't really 'grow'), and added what I think we are really after, namely the presence of DNA or RNA (to exclude prions and other crap)

Label: 'generalized organism' Elucidation: "A material entity such as an animal, plant, bacteria, virus or viroid that is capable of replicating or reproducing in the right environment, and that includes genetic information encoded in nucleic acids to do so."

Feel free to disagree, but then propose alternative definitions.

cmungall commented 6 years ago

Just to add general noise and confusion, my position is at odds with everyone... but I have extreme confidence we are converging.

I like names used by scientists. I may be in the minority but I favor using "organism" in the broad sense to include viruses.

I am against both boolean names and adjectives like "generalized" or the elsewhere proposed extended organism. I slightly prefer the boolean name (though I really dislike boolean names or disjunctive OWL definitions) as a non-ontologist can intuit the meaning, whereas "generalized" is too much like ontologese (and doesn't really work on the instance level).

Using organism inclusively is simple, intuitive, and reflects a general conceptual unity amongst its subclasses. I don't see a major risk in curator misuse, there is some risk in that scientists who use the term more restrictedly might attack us for this... but show me an area where this isn't the case. I don't think there is an upper level term in any ontology I work on that isn't controversial. We can of course include obo foundry unique labels, usage notes, logical axioms, and synonyms as well of course.

Both OBI and CARO terms are the product of excellent yet poorly rewarded work by multiple expert people volunteering time. Nevertheless we have to test this work against other communities and be open to revisiting things. On the CARO side, I know we started with a very FMA/BFO philosophy mandate and have gradually moved more towards a more humane ontology, and we should be open to further evolution in that direction.

I think there will also be some shuffling of classes around as part of COREification, and we should have modularity in mind rather than ownership.

Re: definition. I am happy to go with either CARO's clade-based definitions or with OBI's direct definition. However, for the clade-based definitions, there need to be some PURLs for the clade individuals themselves. And then we still have to define those PURLs. On balance it seems simpler to define directly.

I like Bjoern's definition. I mildly prefer moving "such as" clauses to definition gloss (and making it stronger: explicitly stating membership). But currently there is nothing in it that firmly excludes either transposons and possibly even somatic cells. I would like to see "genome" in the definition (although this puts us at risk of circularity (and will need exception clauses for chimeras etc)).

cmungall commented 6 years ago

FWIW:

  is_a GO:0051704 ! multi-organism process
   is_a GO:0044419 ! interspecies interaction between organisms
    is_a GO:0044403 ! symbiosis, encompassing mutualism through parasitism
     is_a GO:0016032 ! viral process ***

If we make the grouping class label something other than "organism" we should give a heads up on the GO tracker and request GO change to either "multi-generalized organism process" or "multi cellular-organism or virus process".

mellybelly commented 6 years ago

Ok, lots to think about!

Please everyone, we all have put in a lot of volunteer time and it is exactly the goal of OBO to bring together diverse perspectives into a unified view of biology. No one "owns" content, and it is a basic premise of OBO that one is open to evolution of content to support conceptual alignment. I do think the community is not well tracking all of this hard work though, if one is not attending the RO meeting its a bit opaque - just as an aside it would be good to write an update soon to obo-discuss. You might get more helpers that way too (for example I would be happy to compare and contrast any of the organism/anatomy related duplicates to try to come up with consensus and best placement).

Regarding the above.

I too like the names used by scientists. That is why I don't like the use of 'organism' to mean things that most biologists don't consider organisms ;-). TBH the fact that biologists have not really converged on a label for the union class is very likely why NCBI taxon never had it either. We CAN change this now, but how to do so without confusing or offending? Sometimes labels do need to evolve. What we think of now as a gene is not the same as when that term was originally coined. I don't love 'generalized organism' either but at least is is a flag that it means something different the generally assumed definition of organism. I guess I am willing to be overridden, but lets please better understand consequences if we do want to do that as we are just one small community and we will not change a large community of biologists' mind about such things with one OBO label. Perhaps a poll? Would be good to ask NCBI, EOL and other phylogenetic groups what sorts of requests and suggestions they have gotten.

I like Bjoern's definition too, edits in response to Chris' comments: "A material entity that is prokaryote (e.g. bacteria, archaea), eukaroyte (e.g. animal, plant, fungus), virus, or viroid and is capable of replicating or reproducing in the right environment, and that includes genetic information encoded in nucleic acids to do so."

Not sure about how to include genome.

I would disagree with the GO hierarchy.... In my mind not all viral processes are 'interspecies interaction between organisms' nor 'symbiosis, encompassing mutualism through parasitism'.

bpeters42 commented 6 years ago

I like Melissa's edited definition. I think 'genetic information encoded in nucleic acids to do so' captures what 'genome' would entail without becoming circular.

Regarding label I also had as my first choice 'organism' which in my part of biological (immunology, virology) would be accepted by most to include viruses. I am fine with the two other labels as well ('generalized organism' or 'cellular organism, virus or viroid'). We can totally do a vote, and include the other two as alternative labels.

On Sun, Oct 21, 2018 at 12:34 PM Melissa Haendel notifications@github.com wrote:

Ok, lots to think about!

Please everyone, we all have put in a lot of volunteer time and it is exactly the goal of OBO to bring together diverse perspectives into a unified view of biology. No one "owns" content, and it is a basic premise of OBO that one is open to evolution of content to support conceptual alignment. I do think the community is not well tracking all of this hard work though, if one is not attending the RO meeting its a bit opaque - just as an aside it would be good to write an update soon to obo-discuss. You might get more helpers that way too (for example I would be happy to compare and contrast any of the organism/anatomy related duplicates to try to come up with consensus and best placement).

Regarding the above.

I too like the names used by scientists. That is why I don't like the use of 'organism' to mean things that most biologists don't consider organisms ;-). TBH the fact that biologists have not really converged on a label for the union class is very likely why NCBI taxon never had it either. We CAN change this now, but how to do so without confusing or offending? Sometimes labels do need to evolve. What we think of now as a gene is not the same as when that term was originally coined. I don't love 'generalized organism' either but at least is is a flag that it means something different the generally assumed definition of organism. I guess I am willing to be overridden, but lets please better understand consequences if we do want to do that as we are just one small community and we will not change a large community of biologists' mind about such things with one OBO label. Perhaps a poll? Would be good to ask NCBI, EOL and other phylogenetic groups what sorts of requests and suggestions they have gotten.

I like Bjoern's definition too, edits in response to Chris' comments: "A material entity that is prokaryote (e.g. bacteria, archaea), eukaroyte (e.g. animal, plant, fungus), virus, or viroid and is capable of replicating or reproducing in the right environment, and that includes genetic information encoded in nucleic acids to do so."

Not sure about how to include genome.

I would disagree with the GO hierarchy.... In my mind not all viral processes are 'interspecies interaction between organisms' nor 'symbiosis, encompassing mutualism through parasitism'.

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mellybelly commented 6 years ago

Also, (cellular) organism is viewed by anatomists as the root of the anatomical partonomy, so is by definition an anatomical entity (though most anatomists don't use the word entity, thats more of an ontological term).

bpeters42 commented 6 years ago

I would think anatomists restrict themselves to multi-cellular organisms?

On Sun, Oct 21, 2018 at 1:45 PM Melissa Haendel notifications@github.com wrote:

Also, (cellular) organism is viewed by anatomists as the root of the anatomical partonomy, so is by definition an anatomical entity (though most anatomists don't use the word entity, thats more of an ontological term).

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mellybelly commented 6 years ago

There are cellular anatomists, though they largely fall into studies of single-cell or multi-cellular eukaryotes (and not prokaryotes). GO Cellular Component is considered anatomy and therefore has an equivalency axiom in CARO, for example.

bpeters42 commented 6 years ago

'Anatomy' is used in all kinds of contexts, including the 'anatomy of a relationship' and the like. There is plenty of 'viral anatomy' out there. I thought you were using 'anatomy' here as shorthand for the type of stuff that would be covered in a class taught in medical school, or what is part of the anatomy ontologies in the OBO foundry. All of which is multi-cellular organisms.

Our goal is to have an intuitive upper level hierarchy. If I am looking for where to find e.g. MHC molecules, I would look under molecules / molecular complexes or the like, not under 'anatomical entity'.

On Sun, Oct 21, 2018 at 1:55 PM Melissa Haendel notifications@github.com wrote:

There are cellular anatomists, though they largely fall into studies of single-cell or multi-cellular eukaryotes (and not prokaryotes). GO Cellular Component is considered anatomy and therefore has an equivalency axiom in CARO, for example.

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zhengj2007 commented 6 years ago

I like Melissa's edited definition too. Regarding labels, I'd prefer 'organism'.

mellybelly commented 6 years ago

@bpeters42 was just thinking of cellular anatomy - cellular structure and physiology. Things like mitochondria and lysosomes are in GO and are considered cellular anatomy, taught in med school anatomy classes, etc. I don't think most anatomists would consider proteins as anatomy, though obviously there are anatomical structures such as gap junctions that are largely protein complexes and there is a fuzzy line there. We do have the 'gross anatomical part' class to address this issue that was requested by OBI, we can revisit this class too. CARO as an anatomical reference ontology does intend to provide upper level axioms for cellular anatomy of any cell.

bpeters42 commented 6 years ago

On Mon, Oct 22, 2018 at 8:38 AM Melissa Haendel notifications@github.com wrote:

@bpeters42 https://github.com/bpeters42 was just thinking of cellular anatomy - cellular structure and physiology. Things like mitochondria and lysosomes are in GO and are considered cellular anatomy, taught in med school anatomy classes, etc. I don't think most anatomists would consider proteins as anatomy, though obviously there are anatomical structures such as gap junctions that are largely protein complexes and there is a fuzzy line there. We do have the 'gross anatomical part' class to address this issue that was requested by OBI, we can revisit this class too. CARO as an anatomical reference ontology does intend to provide upper level axioms for cellular anatomy of any cell.

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cmungall commented 5 years ago

PR to relabel organism in CARO: https://github.com/obophenotype/caro/pull/17

cmungall commented 5 years ago

Some discussion on organism in OBI, not sure how relevant: https://github.com/obi-ontology/obi/issues/994

bpeters42 commented 5 years ago

The : obi-ontology/obi#994 https://github.com/obi-ontology/obi/issues/994 discussion ended up being more about reasoning / display issues rather than modeling issues.

Thanks for the CARO pull request to relabel organism (obophenotype/caro#17 https://github.com/obophenotype/caro/pull/17). Beyond the relabeling, were you also planning to update the definition to what was discussed in this thread? The last iteration from Melissa, for which there were no specific objections was: "A material entity that is prokaryote (e.g. bacteria, archaea), eukaroyte (e.g. animal, plant, fungus), virus, or viroid and is capable of replicating or reproducing in the right environment, and that includes genetic information encoded in nucleic acids to do so."

If all that is in, I am fine with retiring the OBI term in favor of the CARO term, but of course this is not just up to me. The other alternative being if we migrate it to a common OBO-Core namespace (did we settle on a replacement for 'core'?)

Talk to you tomorrow

On Mon, Feb 11, 2019 at 5:21 PM Chris Mungall notifications@github.com wrote:

Some discussion on organism in OBI, not sure how relevant: obi-ontology/obi#994 https://github.com/obi-ontology/obi/issues/994

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cmungall commented 5 years ago

Yep, I will update the definition in the PR

On Mon, Feb 11, 2019 at 9:58 PM bpeters42 notifications@github.com wrote:

The : obi-ontology/obi#994 https://github.com/obi-ontology/obi/issues/994 discussion ended up being more about reasoning / display issues rather than modeling issues.

Thanks for the CARO pull request to relabel organism (obophenotype/caro#17 https://github.com/obophenotype/caro/pull/17). Beyond the relabeling, were you also planning to update the definition to what was discussed in this thread? The last iteration from Melissa, for which there were no specific objections was: "A material entity that is prokaryote (e.g. bacteria, archaea), eukaroyte (e.g. animal, plant, fungus), virus, or viroid and is capable of replicating or reproducing in the right environment, and that includes genetic information encoded in nucleic acids to do so."

If all that is in, I am fine with retiring the OBI term in favor of the CARO term, but of course this is not just up to me. The other alternative being if we migrate it to a common OBO-Core namespace (did we settle on a replacement for 'core'?)

Talk to you tomorrow

On Mon, Feb 11, 2019 at 5:21 PM Chris Mungall notifications@github.com wrote:

Some discussion on organism in OBI, not sure how relevant: obi-ontology/obi#994 https://github.com/obi-ontology/obi/issues/994

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beckyjackson commented 5 years ago

We have created an 'organism' term with a unique ID, but we are discussing mapping equivalent external terms in #23.