Ontology meeting 2014-07-10

Attendees:

Minutes:

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?

Definition: A distinct period or stage in a biological process or cycle.

In AE we would use happens_during between BPs and biological phases

'biological phase' would be disjoint with other biological processes

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

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

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.

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.

SIG flash talk

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

Processes vs Phases

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

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

• We still have a cell vs fiber distinction in GO that is not reflected in CL, see https://sourceforge.net/p/geneontology/ontology-requests/10199/
  • GO:0055013 cardiac muscle cell GO:0048739 development vs cardiac muscle fiber development -- do we have any confidence that curators are picking the right term?

• cardiac ventricle mycotes. https://sourceforge.net/p/geneontology/ontology-requests/10990/

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'

OWLTooling

• PCLO-Man https://docs.google.com/document/d/1xAon78Dc0XBCbisT5RLfmXXbGB4wzaeqVTXK5Zg06MU/edit#
• Update on meeting with Matt

Website

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

Post-translational modifications

Have we decided whether these are functions or processes?