Ontology meeting 2022-07-18

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  • Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
  • Present: Pascale, Karen, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris
  • Regrets: Harold, Paul


Editors discussion tickets

Uberon taxon constraints are too stringent

See https://github.com/geneontology/go-ontology/issues/23445

  • Discussion: Still some problems in Uberon (terms too metazoa-specific, ie mentions that life cycle starts at zygote stage, which is not universally true)

ChEBI documentation edited

(Announcement) New section on External Ontologies https://wiki.geneontology.org/External_ontologies on the ontology documentation page: https://wiki.geneontology.org/Ontology_Development#Ontology_editing_principles

Regulation of a process in another organism

See https://github.com/geneontology/go-annotation/issues/4231 In the 'modulation of process in another organism' branch, we link modulation by viruses/symbiont/other organisms to the 'normal' process branch. The advantage is that we can benefit from the logical reasoning from the 'normal' branch hierarchy This causes two issues:

  1. This is not physiological for the 'host'/'target' organism
  2. Taxon constraints:
    • This prohibits adding taxon constraints for these regulation terms
    • Also prevents from using the 'regulates' relation to calculate taxon constraints, so the work we gain from automatic classification needs to be re-done for taxon constraints

It seems removing the links would not create more work, in fact it would be less, since more processes are NOT targeted by other organisms, so the benefits of having more taxon constraints would outweigh the lack of automatic classification of the multi-species branch AND this is more correct biologically.


  • AI (Pascale) should create a new triad for linking the modulation of a process in another organism-
  • AI (Pascale) Open a RO ticket to make in_taxon over regulates transitive

Ordering of subset/ribbon terms

Easiest would be as an external file - ie a tsv where the term would be in order

For a future call

Glycosylation ontology

Email from Alex Diehl 

Hi Chris, Darren, and Pascale,

Over the past year or so I worked with Ted Groth, a graduate student at the University at Buffalo, and his advisor Sriram Neelameghan, with an ontology Ted built related to enzymes related to glycosylation, GlycoEnzOnto.owl.  My major input has been encouraging Ted to reuse the Gene Ontology as much as possible and teaching him about ontology structure.  What Ted added was expert knowledge of particular pathways of glycosylation that are not represented in GO, and he structured the logical axioms of glycosylation pathway classes to relate them to existing GO BP classes.

At the same time, the ontology includes a large number of individuals which essentially mimic traditional GO annotations for enzymes involved in glycosylation, BP, MF, and CC terms, and another set of individuals that are basically intended to mimic GO-CAM models (that was Ted’s intention).  Ted and Sriram are domain experts, and this work I believe extends both the GO representation of glycosylation pathways and annotation of enzymes involved in those pathways.  The challenge is that Ted did this work influenced by the GO but independently of GO’s existing annotation systems and ontology development.  At this point Ted has defended his dissertation, and I have offered to mediate with GO to see what knowledge might be transferred. Ted and Sriram at one point suggested submitting this work as a separate ontology to the OBO Foundry, but I convinced them the value would be best captured if they worked with GO.

A paper about this work is now available in bioRxiv: https://biorxiv.org/cgi/content/short/2022.06.06.493779v1

and the ontology itself is available on Github: https://github.com/neel-lab/GlycoEnzOnto The Github site is a bit confusing as the 1.0 version is not the current version of the ontology; the most current version of the ontology is in the main branch here: https://raw.githubusercontent.com/neel-lab/GlycoEnzOnto/main/GlycoEnzOnto.owl 

In any case, I would ask your opinions about how we might incorporate Ted’s work into the GO ecosystem.

Thanks,
Alex

Automation

Jim working on scripts that automate more taxon constraints calculations/updates, as well as produce an automated report of terms that match design patterns, so these could be more easily checked

User requests

OK let's implement this - these terms are in ChEBI.

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