Ontology meeting 2012-10-04

MINUTES: Tanya

ATTENDEES: Jane, Tanya, David, Chris, Becky, Heiko, Paola

Monthly update: Project Management in JIRA

See http://wiki.geneontology.org/index.php/Ontology_meeting_2012-09-12#Project_Management_in_JIRA

  Reviewed items for September, added comments and new information.  Moved some items to October.

  cellular chemical homeostasis - chemical substance -> chemical entity for xps

BP x CC Localization and Transport XPs

• Loaded go-trunk/ontology/extensions/x-transport_and_localization.owl into Protege (see email thread subject: go/extensions/x-transport-and-localization). The reasoner re-inferred inferences when I removed them, and the XPs made sense.

• Some localization XPs seem to be missing:
  • ribonucleoprotein complex localization
  • spindle pole body localization
  • telomere localization
  • endoplasmic reticulum localization
  • chloroplast localization
  • mitochondrial pyruvate transport
  • plasma membrane pyruvate transport

  Why missed?  Chris checked.  mitochondrial = relational adjective hard to catch. Make tracker 
  item to figure out what's going on.   Add the missing ones.

• What's next? Can these be added to the live GO file?

  Yes, these can be added to the live GO file, gene_ontology_write.obo.

Import and Export

• Where are we up to on the import and export XPs? Previous action item (http://gocwiki.geneontology.org/index.php/Ontology_meeting_2012-09-26#EXPORT_.26_IMPORT) was for Crhis to create import and export relationships as subtypes of 'to' and 'from'. Will keep these broad (omit any transmembrane info).

  Still to do.  Create a JIRA item.

Transport/er activity vs. Transmembrane transport/er activity

  Heiko: Create 'chemical transmembrane transport' and 'chemical transporter activity' templates.

• Most of the remaining plain 'transporter' terms that have transmembrane parentage are 'high/low affinity xxx transport'. These terms are currently direct children of 'xxx transmembrane transport'. The defs all point to the more generic MF, not the one that crosses the membrane.

  Example: high-affinity hexose transport: The directed, high-affinity movement of a hexose into, 
  out of or within a cell, or between cells, by means of some agent such as a transporter or pore. 
  In high affinity transport the transporter is able to bind the solute even if it is only present 
  at very low concentrations.

• • Solution 1: add transmembrane to term string, modify def to say 'across a membrane'

  Solution 2: move terms to more generic parent, add more specific term, look at annotations  
  DO THIS, MORE CONSERVATIVE

• Most of the remaining plain 'transporter activity' terms that have transmembrane parentage are direct children of 'drug transmembrane transporter activity'. The defs all point to the more generic MF, not the one that crosses the membrane.

  Example:  amiloride transporter activity: Enables the directed movement of amiloride of amiloride 
  into, out of or within a cell, or between cells. Amiloride is a potent and specific inhibitor of 
  sodium ion entry into cells. It is used as a potassium-sparing diuretic.

• • Solution 1: add transmembrane to term string, modify def to say 'across a membrane'

  Solution 2: add a new term 'drug transporter activity' as one parent, move them out of the 
  TMM parent directly to copy to transporter activity. [Add TMM child for each specific chemical]

Revisiting Transcription factor catabolism

• GO:0010620 has no XPs: negative regulation of transcription by transcription factor catabolism ; GO:0010620

• In the pre-LEGO era, without making 'TF catabolism' and 'regulation of TF catabolism' terms, we're still struggling to capture the role of the upstream regulators in a pathway that signal to the proteases to degrade the transcription factors.

  Can't fit all the relevant information into col 16. Just create the terms for now and use LEGO later.

GO Meeting Prep

Heiko:

• demo - show list of templates and diversity of terms that can be requested
• Provide background about new templates and what goes into creating a new one.