Ontology meeting 2022-06-27

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

Editors discussion tickets

Protein processing & specificity (Raymond, Helen)

https://github.com/geneontology/go-ontology/issues/23378 see also notes from last call: Ontology_meeting_2022-06-6

Uberon taxon constraints are too stringent

See https://github.com/geneontology/go-ontology/issues/23445 Do we need to remove the relation 'GO:0110165 cellular anatomical entity' is_a 'CARO_0000000 anatomical entity'?

PR failure

https://github.com/geneontology/go-ontology/pull/23546 - > OK to merge, this is due to a non project member making a PR

Antiporters & specificity

(Pascale): https://github.com/geneontology/go-ontology/issues/23374

• Antiporters reorganization: https://docs.google.com/presentation/d/11-C28wy_quSlbzhyNX0QZaUaZytdCpJkp9XL7vXGutg/edit?usp=sharing

-> OK to start implementing

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

• User requests:
  • proteinogenic amino acid biosynthesis and non-proteinogenic amino acid biosynthesis