Ontology meeting 2014-07-10

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Attendees: Jane, Paola, Harold, Heiko, Chris, DavidH, DavidOS, Tanya

Minutes: Tanya

GOC meeting in Barcelona

Could we please discuss participation of EBI folks with the PIs if Judy and/or Paul are on the call. July 16th is the deadline for discounted hotel booking. 

  8 need to come from EBI, funding issues need sorting out.

SIG flash talk

Paola added her comments. Need feedback from others too, esp. re. presentation of moving to OWL/Protege workflow. 

  DavidH and Harold gave feedback directly to Judy. Did anyone do the Protege/OWL slide?  Judy has a slide and accompanying text.

biological phase

We talked last year about adding a 'biological phase' term as a direct subclass of 'biological process'.

This would be for the cell cycle phases, but other subclasses might be:

  • menstrual cycle phase
  • estrous cycle phase
  • others? [Paola suggests 'hair cycle phase']
Definition: A distinct period or stage in a biological process or cycle.

In annotation extensions, we would use happens_during between BPs and biological phases

'biological phase' would be disjoint with other biological processes 

 Try biological phase child of biological process and see what happens.

Should we worry about what type of BFO occurrent it is? temporal_region or occurrent? 

  Definitely occurrents, a temporal subdivision of a parent process, suggests a part_of relationship to that parent process.

We may want to define the cell cycle processes by their start and end processes. 

  JANE: add term with parentage and definition as proposed.

(Related) Processes vs Phases

We need to break the link, see: https://sourceforge.net/p/geneontology/ontology-requests/10988/ 

 Jane will do this.

Milestones for tickets

Please can everyone who has ontology tickets assigned to them make sure a milestone is added (this is the submitting group). Val needs these.

update on cell type logical definitions - chris

muscle cell issues

  • DOS did a lot of work with satellite cells which he can summarize

the following need to be reconciled with CL:

  • GO:0014716 ! satellite cell asymmetric division involved in skeletal muscle regeneration
  • GO:0014719 ! satellite cell activation
  • GO:0014813 ! satellite cell commitment
  • GO:0014816 ! satellite cell differentiation
  • GO:0014817 ! satellite cell fate specification
  • GO:0014818 ! satellite cell fate determination
  • GO:0014833 ! satellite cell asymmetric division
  • GO:0014834 ! satellite cell maintenance involved in skeletal muscle regeneration
  • GO:0014841 ! satellite cell proliferation
  • GO:0014901 ! satellite cell activation involved in skeletal muscle regeneration
  DavidOS will make some edits in CL and GO to align the ontologies.  There is something tricky about stem cells that needs picking apart to reconcile
  CL and GO.

other

How are these classes different? Note that mesenchymal cells in CL are already classified as (multi-fate) stem cells. 

[Term]
id: GO:0072497
name: mesenchymal stem cell differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal stem cell. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." [CL:0002452, GOC:BHF]
is_a: GO:0048863  ! stem cell differentiation

[Term]
id: GO:0048762
name: mesenchymal cell differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types." [GOC:dph, GOC:jid]
is_a: GO:0048863  ! stem cell differentiation
relationship: part_of GO:0060485 ! mesenchyme development
intersection_of: GO:0030154  ! cell differentiation
intersection_of: results_in_acquisition_of_features_of CL:0000134

CL:0002452 was merged into 'mesenchymal cell' 

  Need to 'split' mesenchymal cell and mesenchymal stem cell in CL.

timeline for uberon logical defs

  Chris will add first set for X development terms. No templates for now.

OWLTooling

  Point of contention: How to hide subsets or all of the cached links (implementation details). Should be worked out.
  Timeline for plugin?:  hard to estimate right now, this has more components (GUI esp) than previous ones

Website

Can we do better for ontology work on the new website? http://geneontology.org/page/download-ontology 

  Add file with GO term id:GO term mapping. Used to be created by a cronjob on Amelia's machine. Should be able to recreate this using
  Jenkins.

Post-translational modifications

Have we decided whether these are functions or processes? 

  Some involve single enzymatic activities. Some involve more than one enzymatic activity.  Have starts and ends and add examples and use comment field.
  Harold to look into better definition for glycosylation.  Do this incrementally for post-tsl modifications.
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