Ontology meeting 2013-05-02

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Minutes: Becky

Attendees:

  • Paola
  • Jane
  • Becky
  • Harold
  • Heiko
  • Chris


Links report including cell types

See report at http://build.berkeleybop.org/job/build-go-assert-inferences/23/artifact/assert-report.txt

Was there any discussion on this at the latest CL call? Did Alex provide any feedback outside the call? In general, are there areas of the CL that we should be more 'wary' of? Media:cl-assert-report-alex.txt

Chris: try and fix problems as close to the source as possible for the inversion problems (where CL has inverted hierarchy compared to GO (e.g. fix CL or GO). If you can't do that, remove the logical definition until you can.

Alex only looked at the immune system cell types. Generally, get CL to look at the problem (add item to CL tracker), and then go with what they decide. Have item on GO tracker that points to CL tracker.

Chris to look at CL xps with obsolete classes (see below)



(Feasibility and strategy for) providing hard links from apoptosis terms to the apoptosis curation manual on the wiki

In particular, linking to annotation examples in the apoptosis curation manual. Stemming from apoptosis project & discussion - Pascale suggested this at the GOC meeting, other curators also asked.


Need to decide where in the GO term the link would go. Makes most sense to go in the comment. Suggested text: For annotation guidance, see [wiki link].

Problem is manual overhead of maintaining and updating the wiki pages. It would work if the headings in the wiki are of the same syntax (GO ID followed by GO term name) but it's a headache to maintain. One option to make the updating easier is just to link to the generic apoptosis curation manual page.

Also the problem of which GO browsers would be able to display and hyperlink this information.

Apoptosis curation manual is [here]

Q: How can we add this link to ALL terms under cell death? Need a job/script that propagates it through the obo file.

AI: Paola to put in JIRA issue for this. We'd need to run the script periodically (as part of the release) to check the comment has been propagated t any new terms. Need to consider whether we want to propagate the comment over 'regulates' relationships.

AI: Jane to find out what Rachael and Tony are already doing on this front.


Templates for regulation of biological qualities

For creating 'regulation of biological trait/quality' terms in TermGenie, do we need to come up with our own mini-ontology of traits?

Stems from SF on sperm motility

This now exists in [[1]]

AI: Chris to look through the initial bbq file and remove the dodgy ones that aren't traits.


Template for receptor activities

Seems we missed these with the chemical xps. They're complicated because mechanism and substrate are often combined, but we should be easily able to make templates for some. The pattern should be the same as binding. Has there been an obol pass on these?

Looks quite straight forward.

  • Bring in protein ontology for receptors that have a protein substrate.
  • Bring in CHEBI for receptors that have a chemical substrate

AI: Becky to look through this file for errors/anomalies.


CL xps with obsolete classes

We have added the CL to the XP validation, during that OORT found a number of XPs using obsolete classes. This is the full list and the orginal log can be found here.

  • Obsolete class CL:0000282 'trichome' in axiom: EquivalentClasses(GO:0048629 'trichome patterning' ObjectIntersectionOf(GO:0007389 'pattern specification process' ObjectSomeValuesFrom(occurs_in 'occurs in' CL:0000282 'trichome')) )
  • Obsolete class CL:0000284 'companion cell' in axiom: EquivalentClasses(GO:0048758 'companion cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000284 'companion cell')) )
  • Obsolete class CL:0000668 'obsolete parenchymal cell' in axiom: EquivalentClasses(GO:0048760 'parenchymal cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000668 'obsolete parenchymal cell')) )
  • Obsolete class CL:0000299 'trichoblast' in axiom: EquivalentClasses(GO:0048764 'trichoblast maturation' ObjectIntersectionOf(GO:0021700 'developmental maturation' ObjectSomeValuesFrom(results_in_maturation_of 'results in maturation of' CL:0000299 'trichoblast')) )
  • Obsolete class CL:0000294 'sieve cell' in axiom: EquivalentClasses(GO:0048756 'sieve cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000294 'sieve cell')) )
  • Obsolete class CL:0000620 'zoospore' in axiom: EquivalentClasses(GO:0075239 'zoospore formation' ObjectIntersectionOf(GO:0048646 'anatomical structure formation involved in morphogenesis' ObjectSomeValuesFrom(results_in_formation_of 'results in formation_of' CL:0000620 'zoospore')) )
  • Obsolete class CL:0000280 'generative cell' in axiom: EquivalentClasses(GO:0055047 'generative cell mitosis' ObjectIntersectionOf(GO:0007067 'mitosis' ObjectSomeValuesFrom(occurs_in 'occurs in' CL:0000280 'generative cell')) )
  • Obsolete class CL:0000616 'sporangiospore' in axiom: EquivalentClasses(GO:0034300 'sporangiospore formation' ObjectIntersectionOf(GO:0048646 'anatomical structure formation involved in morphogenesis' ObjectSomeValuesFrom(results_in_formation_of 'results in formation_of' CL:0000616 'sporangiospore')) )
  • Obsolete class CL:0000282 'trichome' in axiom: EquivalentClasses(GO:0010090 'trichome morphogenesis' ObjectIntersectionOf(GO:0009653 'anatomical structure morphogenesis' ObjectSomeValuesFrom(results_in_morphogenesis_of 'results in morphogenesis of' CL:0000282 'trichome')) )
  • Obsolete class CL:0000332 'atrichoblast' in axiom: EquivalentClasses(GO:0010056 'atrichoblast fate specification' ObjectIntersectionOf(GO:0001708 'cell fate specification' ObjectSomeValuesFrom(results_in_specification_of 'results_in_specification_of' CL:0000332 'atrichoblast')) )
  • Obsolete class CL:0000299 'trichoblast' in axiom: EquivalentClasses(GO:0010057 'trichoblast fate specification' ObjectIntersectionOf(GO:0001708 'cell fate specification' ObjectSomeValuesFrom(results_in_specification_of 'results_in_specification_of' CL:0000299 'trichoblast')) )
  • Obsolete class CL:0000299 'trichoblast' in axiom: EquivalentClasses(GO:0010054 'trichoblast differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000299 'trichoblast')) )
  • Obsolete class CL:0000332 'atrichoblast' in axiom: EquivalentClasses(GO:0010055 'atrichoblast differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000332 'atrichoblast')) )
  • Obsolete class CL:0000292 'guard cell' in axiom: EquivalentClasses(GO:0010052 'guard cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000292 'guard cell')) )
  • Obsolete class CL:0000282 'trichome' in axiom: EquivalentClasses(GO:0010026 'trichome differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000282 'trichome')) )
  • Obsolete class CL:0000292 'guard cell' in axiom: EquivalentClasses(GO:0010377 'guard cell fate commitment' ObjectIntersectionOf(GO:0045165 'cell fate commitment' ObjectSomeValuesFrom(results_in_commitment_to 'results in commitment to' CL:0000292 'guard cell')) )
  • Obsolete class CL:0000262 'guard mother cell' in axiom: EquivalentClasses(GO:0010444 'guard mother cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000262 'guard mother cell')) )
  • Obsolete class CL:0000292 'guard cell' in axiom: EquivalentClasses(GO:0010441 'guard cell development' ObjectIntersectionOf(GO:0032502 'developmental process' ObjectSomeValuesFrom(results_in_development_of results_in_development_of CL:0000292 'guard cell')) )
  • Obsolete class CL:0000292 'guard cell' in axiom: EquivalentClasses(GO:0010442 'guard cell morphogenesis' ObjectIntersectionOf(GO:0009653 'anatomical structure morphogenesis' ObjectSomeValuesFrom(results_in_morphogenesis_of 'results in morphogenesis of' CL:0000292 'guard cell')) )
  • Obsolete class CL:0000248 'microsporocyte' in axiom: EquivalentClasses(GO:0010480 'microsporocyte differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000248 'microsporocyte')) )
  • Obsolete class CL:0000288 'synergid' in axiom: EquivalentClasses(GO:0010198 'synergid death' ObjectIntersectionOf(GO:0008219 'cell death' ObjectSomeValuesFrom(occurs_in 'occurs in' CL:0000288 'synergid')) )
  • Obsolete class CL:0000262 'guard mother cell' in axiom: EquivalentClasses(GO:0010235 'guard mother cell cytokinesis' ObjectIntersectionOf(GO:0051301 'cell division' ObjectSomeValuesFrom(occurs_in 'occurs in' CL:0000262 'guard mother cell')) )
  • Obsolete class CL:0005016 'apical cell' in axiom: EquivalentClasses(GO:0010654 'apical cell fate commitment' ObjectIntersectionOf(GO:0045165 'cell fate commitment' ObjectSomeValuesFrom(results_in_commitment_to 'results in commitment to' CL:0005016 'apical cell')) )
  • Obsolete class CL:0000276 'sclerenchyma cell' in axiom: EquivalentClasses(GO:0014001 'sclerenchyma cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000276 'sclerenchyma cell')) )
  • Obsolete class CL:0000280 'generative cell' in axiom: EquivalentClasses(GO:0022619 'generative cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000280 'generative cell')) )
  • Obsolete class CL:0000296 'vegetative cell' in axiom: EquivalentClasses(GO:0022620 'vegetative cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000296 'vegetative cell')) )
  • Obsolete class CL:0000537 'antipodal cell' in axiom: EquivalentClasses(GO:0009557 'antipodal cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000537 'antipodal cell')) )
  • Obsolete class CL:0000250 'megaspore' in axiom: EquivalentClasses(GO:0009554 'megasporogenesis' ObjectIntersectionOf(GO:0032502 'developmental process' ObjectSomeValuesFrom(results_in_development_of results_in_development_of CL:0000250 'megaspore')) )
  • Obsolete class CL:0000252 'microspore' in axiom: EquivalentClasses(GO:0009556 'microsporogenesis' ObjectIntersectionOf(GO:0032502 'developmental process' ObjectSomeValuesFrom(results_in_development_of results_in_development_of CL:0000252 'microspore')) )
  • Obsolete class CL:0000288 'synergid' in axiom: EquivalentClasses(GO:0009563 'synergid differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000288 'synergid')) )
  • Obsolete class CL:0000254 'egg cell' in axiom: EquivalentClasses(GO:0009560 'embryo sac egg cell differentiation' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000254 'egg cell')) )
  • Obsolete class CL:0000522 'spore' in axiom: EquivalentClasses(GO:0030435 'sporulation resulting in formation of a cellular spore' ObjectIntersectionOf(GO:0030154 'cell differentiation' ObjectSomeValuesFrom(results_in_acquisition_of_features_of 'results in acquisition of features of' CL:0000522 'spore')) )