Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)

[JCGiron]

Use this form to register a new ontology with the OBO Foundry. Please read the instructions provided here:
http://obofoundry.org/docs/NewOntologyRegistrationInstructions.html

Ontology title

Ontology for the Anatomy of the Insect SkeletoMuscular system

Requested ID space

AISM

Ontology location

https://github.com/insect-morphology/aism

Contact person

Name: Jennifer Girón
Email address: entiminae@gmail.com
GitHub username: JCGiron

Issue tracker

https://github.com/insect-morphology/aism/issues

Ontology license

• CC0 (public domain)
• CC-BY (version 3 or later)
• Other: please specify

Available ontology formats

owl, obo, jason

What domain is the ontology intended to cover?

Insect anatomy

Related OBO Foundry ontologies

CL, PATO, CARO, BSPO, RO, UBERON

Intended use/related projects

Multispecies insect anatomy ontologies are used as bases for robust knowledge bases for specific anatomical terms (Yoder et al. 2010, HAO Portal), improve the accessibility of morphology descriptions (Balhoff et al. 2014), and are useful for improving the modeling of discrete morphological characters in phylogenetic context (Tarasov 2019a, 2019b).

There are two major reasons why insects are poorly represented amongst multispecies anatomy ontologies: lack of a base insect anatomy ontology and the lack of infrastructure to build such resource.

The ontology for the Anatomy of the Insect SkeletoMuscular system contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system in insect biodiversity research. The cuticle is the product of the single layer epithelium and mirrors changes in the morphology of this single sheet (like a blanket). This ontology serves as a root ontology for other multispecies insect anatomy ontologies.
This ontology repository was created using the Ontology Development Kit.

Data source

Additional comments or remarks

[zhengj2007]

Discussed on 2021-04-20 call.

@matentzn will look at it and reply soon.

[matentzn]

Hey @JCGiron! Aside from the above comments, could you please fill in the following metadata record which will be used by the OBO Foundry website? Note that the values shown are just examples, for example something like aism, cohm, mondo (it does not have to be four letters). your_domain_like_for_example_anatomy could be simply anatomy, and the license should be whatever your actual license is. An example can be found here, but you really only need to fill in the metadata mentioned here. You can copy the below, and make a new comment with the correct information pertaining to your ontology. Thank you!

id: aism
title: The Title Of Your Ontology
contact:
  email: email@example.com
  label: Your Name
description: Some one sentence description of your ontology.
domain: anatomy
homepage: https://github.com/YOURORG/your_repo
products:
  - id: yourfourletterid.owl
  - id: yourfourletterid.obo
dependencies:
  - id: ro
  - id: otheroboontology
tracker: https://github.com/YOURORG/your_repo/issues
license:
  url: http://creativecommons.org/licenses/by/3.0/
  label: CC-BY
usages:
  - user: http://website.of.the.project.using.my.ontology.com
    description: A short description how the project above is using my ontology

[JCGiron]

Of course!

id: aism
title: Ontology for the Anatomy of the Insect SkeletoMuscular system
contact:
  email: entiminae@gmail.com
  label: Jennifer C. Girón
description: The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.
domain: insect anatomy
homepage: https://github.com/insect-morphology/aism
products:
  - id: aism.owl
  - id: aism.obo
dependencies:
  - id: ro
  - id: uberon
  - id: caro
  - id: pato
  - id: bfo
  - id: bspo
tracker: https://github.com/insect-morphology/aism/issues
license:
  url: https://creativecommons.org/licenses/by/4.0/
  label: CC-BY
usages:
  - user: https://github.com/insect-morphology/colao
    description: The AISM is serving as the baseline for the beetle anatomy ontology. 
  - user: https://github.com/insect-morphology/lepao
    description: The AISM is serving as the baseline for the anatomy ontology for butterflies and moths. 

[matentzn]

Thank you @JCGiron

before I will review the contents of AISM, would you be able to address the problems on the OBO dashboard:
https://obofoundry.github.io/obo-nor.github.io/dashboard/index.html

Feel free to contact me on slack if you have problems with this. Ideally this will be all green before we start looking at it in more depth, but at least there should not be any "red" :) Thank you!

[matentzn]

(you can ping me to refresh the dashboard results any time you like!)

[JCGiron]

The newly released version (v2021-04-22) has corrected most of the reported issues.

[matentzn]

Thank you @JCGiron

Format:

• Great job on fixing the dashboard issues. Syntactically, your ontology is in great shape, and my comments in this regard are really only there to make a good thing better.
• Suggestions (non-critical, i.e. not necessary to address for OBO acceptance):
  • You are a poster-child (amazing) of attribution, and make a lot of use of the cd:contributor tag, which I love. To really make the most out of this annotation, I would suggest you use orcids instead of strings to uniquely identify each contributor (as you do in the ontology metadata). so rather than the jgiron string in : is_a: AISM:0000063 {http://purl.org/dc/elements/1.1/contributor="jgiron"} ! appendage segment you use your orcid.
  • your use of AISM:0000171 for a subset is a bit non-standard, but I don't think its wrong. Check out how other ontologies like Uberon and CL name and manage these tags if you want to align, but maybe its ok as is.
  • There is no point in having AISM:00000000 if you don't use it!
• Main problems of AISM (need to be addressed before acceptance):
  • Your ontology is incoherent (there are unsatisfiable classes). This happens most likely due to the fact that ELK 0.4.3, the reasoner you are using for your classification of the release, cannot understand all the axioms you are using. You need to use HermiT instead - which is terribly slow, but if you need to use axioms more complex, then you have no choice. I debugged it a bit (find me on slack to help you how you can do it yourself in the future), and the root of the problem is the fact that the bearer of relation has as a range restriction specifically dependent continuant. So if you say something like: "bearer of conjunctiva", and "conjunctive cant be an independent continuant (violating BFO). See this intimidating beast:
    
    Maybe all you need to do is review your uses of bearer of and make sure they always point to PATO qualities only - but I have not gotten that far (all I know is that if you remove the range restriction from the "bearer of" relation, your ontology becomes consistent).
  • Your ontology is a bit overmodelled - if you asked @cmungall he would use the word "rococo" to denote axiomatisation that is complex (he exaggerates sometimes, but the basic rule of thumb is: Use intersection ("and") and existential restriction ("some") in a reasonable way, but avoid all other constructs unless they are necessary for your computational use case. For example, saying that "unporous sensillum" has part exactly 1 pore canal might be true - but its very hard computationally. In fact, it violates some weird role-hierarchy constraint in OWL, so its not even legal (you cant use a non simple, i.e. transitive, axiom together with "exactly 1").
  • Two of your axioms violate the OWL spec (these need to be deleted or changed to some):

<owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/AISM_0000131"/>
        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
        <owl:annotatedTarget>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
                <owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
                <owl:onClass rdf:resource="http://purl.obolibrary.org/obo/AISM_0000177"/>
            </owl:Restriction>
        </owl:annotatedTarget>
        <dc:contributor>imiko</dc:contributor>
    </owl:Axiom>

and

    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/AISM_0000130"/>
        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
        <owl:annotatedTarget>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
                <owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
                <owl:onClass rdf:resource="http://purl.obolibrary.org/obo/AISM_0000177"/>
            </owl:Restriction>
        </owl:annotatedTarget>
        <dc:contributor>imiko</dc:contributor>
    </owl:Axiom>

Once you have addressed these issues, we will have an anatomy ontology engineer review your modelling, and that should be it! I am pretty confident we get this sorted.

All best and find me on slack if you need help!

[JCGiron]

We revised and fixed the critical problems indicated above. The newly released version (v2021-04-26) incorporated these changes.

[matentzn]

Thank you @JCGiron I can confirm now - all the coherency issues are addressed. We will conduct an anatomy axiom pattern review now to give you some feedback!

[dosumis]

Hi @JCGiron - great to see this work reaching fruition! I remember discussing much of this with Istvan back in 2012.

The following is just feedback and does not effect your acceptance into the obo-library:

In general I think the patternization makes a lot of sense, especially on the leaf nodes. I particularly like your use of relative position (adjacent_to and continuous_with, encircles) e.g. I love your patterns for sternites and tergites.

And that I can visualise connections like this:

It might be useful to consider turning these patterns into DOSDP templates

Places where you might improve:

1. As far as I can tell, you don't use any inference to build your classification (aism-base.owl has no equivalentClass axioms), but there are places where it would be relatively trivial to add equivalentClass axioms to drive this e.g. defining abdominal sternites & tergites by their location.
2. I can see what you're trying to do with the definitions of conjuctiva, sclerite, etc, but the logic doesn't quite do the work you need it to do e.g. conjunctiva "The region of the insect cuticle that is more flexible than the neighboring sclerite(s) (sclerite(s) that the conjunctiva is continuous with)."
   
   I think what you're trying to say here is that the thickness and flexibility of a region of cuticle relative to its neighbouring regions is what defines conjunctiva, but the axioms just say that conjunctiva is thinner and more flexible than some sclerite. You might be able to get what you want by using Self restriction, but I think it's worth asking what the use cases are for axiomatising in the first place. Can this useful be used to drive inferred classification or clear query use cases? If not you might consider dropping the axioms in this case and relying on your perfectly good text definition.
3. You use not in quite a lot in ways that are not usable by the ELK reasoner & I couldn't get HermiT (which could use them) to complete. You may want to consider whether you need this expressiveness.
4. Something odd appears to be going on with imports - e.g. the Uberon import pulls in lots of vertebrate specific terms. It might be worth trying to track down why this is (@matentzn should be able to help).
5. @Clare72 is editor of the Drosophila Anatomy Ontology. It might be useful to get her take on the ontology if she has time, esp wrt potential alignment issues with DAO (FBbt). One obvious place I can see potential for alignment issues is around the treatment of sensilla, which DAO models as cell cluster organs (including neuron, socket, 'seta', glial cell), whereas you use the term to refer to the seta alone. Another potential problem area for alignment - terms named for some major part of an insect body that actually refer to just the integument of the structure:
   . This pattern is quite pervasive, but only really affects labels, so it might best be fixed at the level of mappings & in combination with some system for recording longer labels that clarify meaning.

[matentzn]

Congratulations, AISM was cleared for inclusion in the OBO Foundry at our OBO Operations Call yesterday. :)

Next steps:

1. @JCGiron please make a pull request with the desired metatada (here is an example)
2. After that, please make a pull request with your purl config (you can use the one in src/metadata if you used ODK), example here.

Let me know if you need more help!

[JCGiron]

Thank you, @matentzn!
I just created both pull requests, although I'm not entirely sure if I created the files in the appropriate places.

[matentzn]

Almost, I fixed it for you here: https://github.com/OBOFoundry/purl.obolibrary.org/pull/760/files
So you can close the one you did :)

[JCGiron]

Thank you, @matentzn!

Is there anything else I should do now?

[matentzn]

No, that's it! It will take a while for all the technical issues to permeate through all the system, unless you are in a rush.

[JCGiron]

Thanks!, no rush. I was just wondering because of the "submitter action needed" tag still on. We'll wait!

[matentzn]

This issue can be closed now!