Ontology meeting 2013-09-19

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Minutes: Paola

Attendees: Becky, Paola, David H, David OS, Harold, Heiko, Tanya, Jane, Chris

Glycosylation

Stems from an email thread that Chris started. Do we need new terms? See Paola's email.

Discussion:

OK to go with Paola's proposal as a temporary fix. Therefore:

Added new terms: GO:0097502 mannosylation, GO:0097503 sialylation.

Edited def. of GO:0008373 sialyltransferase activity to make it substrate-generic.

Added links: GO:0000030 mannosyltransferase activity part_of GO:0097502 mannosylation, GO:0035268 protein mannosylation is_a GO:0097502 mannosylation, GO:0008373 sialyltransferase activity part_of GO:0097503 sialylation.

We might want to tackle these terms again at a later stage, possibly with the help of biochemistry experts.


High-level disjoints

Stemming from Chris's email:

We use a lot of very specific relations, especially in the development logical defs. These are necessary - if we try and use a more generic relation then the reasoner gets everything tangled.

The specific relations are causing some angst when curators use them in class expressions - they'd prefer a smaller set. I would do, but we need some disjointness axioms first.

Let's say we want to get rid of the ugly transports_or_maintains_localization_of and use a more generic has_input. Seems to make sense - we define things such that the input of a transport process is the cargo. Simple?

consider GO:0015986 ! ATP synthesis coupled proton transport

What's it's input?

It's a subtype of transport, so if the rule is that input for transport is always the cargo, then the input is the proton

It's a subtype of metabolic process, so the input is the thing that is modified - the ATP

The fix here is to get rid of the isa-overloading in the ontology, use a different relation that isa for one of the above paths, make transport and metabolism disjoint. If they are disjoint then we can safely use a broader relation without ambiguity.

There's only a handful of things we'd have to deal with if we were to make transport and metabolism disjoint (receptor internalization too). Remember, you can now do DL queries with Elk so you can just query "transport and metabolic process".

David H I know I've pestered you about this isa overloading in development before, I think this is a higher priority now with more curators ramping up to use these relations.

Discussion:

Chris: let's recommend annotators to just use has_input for now.

As for existing annotations (e.g. MGI), on a case-by-case basis we may replace existing transports_or_maintains_localization_of with has_input.

We may want to discuss this at the pre-GOC meetings.

As an aside, Chris asks why is GO:0015986 ATP synthesis coupled proton transport is_a 'ATP biosynthetic process'?

David H says he'd make it has_part actually.

AI: David to modify the link.


'during'

What's the status of the exisiting 'during' terms in the ontology? We need an xp pattern in cell cycle for cases where the processes overlap temporally but aren't necessarily dependant on one another e.g. regulation of transcription during G1 phase. Use happens_during? What about the existing terms - I think many of these are probably really involved_in. [These two for sure:

GO:1901925 negative regulation of protein import into nucleus during spindle assembly checkpoint

GO:1900199 positive regulation of protein export from nucleus during meiotic anaphase II

and they have exact synonyms "involved in". These ones also have part_of intersections:

GO:0045897 positive regulation of transcription during mitosis

GO:0046018 positive regulation of transcription from RNA polymerase I promoter during mitosis

GO:0046022 positive regulation of transcription from RNA polymerase II promoter during mitosis

GO:0046024 positive regulation of transcription from RNA polymerase III promoter during mitosis

GO:0051037 regulation of transcription during meiosis

GO:0045896 regulation of transcription during mitosis]

Discussion:

David and Tanya have looked for 'during' terms in the past. For transcription during cell cycle, experts said they're really 'during', not 'involved in' (it's just a matter of timing).

Jane: let's tease out the ones that are really 'during' and add appropriate xps using happens_during.

AI: Jane will do this.


DOCUMENTATION FOR NEW WEBSITE

  • Who is dividing up the old pages to distribute to people to rewrite?
  • Who is rewriting what?

Chris: Moni has been doing some excellent work on it, we should all look at it, but the pages are not easy to access now.

AI: Chris to check with Moni and point us to the right links; then we'll come back to this.


Follow-up: Changes to external ontologies

Background here http://wiki.geneontology.org/index.php/Ontology_meeting_2013-09-12#Changes_to_external_ontologies

How do we handle obsoletes/alt_ids in owl so that we can get warnings?

AI: Heiko will work on it.


Follow-up: Equivalent classes for Acid/Base transport and transport activity

Background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-09-05#Equivalent_classes_for_Acid.2FBase_transport_and_transport_activity_.28bumped_from_last_week.29

Bumped to next week.


Follow-up: protein localization to xxx

Have we fixed this? http://wiki.geneontology.org/index.php/Ontology_meeting_2013-09-12#Template_for_.27protein_localization_to_xxx.27_.3F

AI: Chris to fix missing logical defs.


Heart terms - reserved for vertebrate hearts or OK for general use?

Uberon has a general term 'circulatory system organ' as well as 'heart' - comments on these terms say to reserve the term heart for vertebrate heart, using the broader term for invertebrates. But GO only uses the term heart - with invertebrate annotations clustering underneath. Should we add a whole set of more general terms based on Uberon 'circulatory system organ?'

Discussion:

David H: at heart meeting, experts were ok with heart also representing dorsal vessels in Drosophila.

Chris: we should use the GO term 'heart' in logical defs.

David OS: good; we still need a couple of layers for invertebrates.

Chris: in Uberon we have developmental relationships, and we had to have two different anatomical terms because dev. rels. are not the same in invertebrates...

David H: similar situation w. kidney terms.

David OS: we may need another layer of terms if we want to place striated muscle cells appropriately. What do we use as reference? CL is also a bit messy in this area. He's been working on it.

David H: at the time of the heart meeting there was no CL yet, so no-one was really trying to align things... and we weren't using reasoners.

David OS: cardiomyocyte = ok to define according to GO, participates in heart contraction.


single v/s multi-organism processes

We could do with xps for these. Can we say in OWL biological process has_participant exactly 1? Or has_participant >1 ?