Ontology meeting 2017-05-26: Difference between revisions

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**Terms that use import and export should be clarified wrt the start and end points
**Terms that use import and export should be clarified wrt the start and end points
*How best do we distinguish maintenance vs transport
*How best do we distinguish maintenance vs transport
*This is an area of GO that may be overly complicated
**Localization is mixed with location
**It will be a pretty big job to untangle all of this





Revision as of 12:16, 26 May 2017

Conference Line

Agenda

github Ontology Projects

Discussion points (Pascale):

  1.  NTR RO: 'transports' https://github.com/oborel/obo-relations/issues/161
  2.  Keeping old stanzas as synonyms for merged terms: Could this rule be relaxed? Sometimes the other name is not appropriate.
  3. Otherwise- is it possible to move secondary IDs ? For example "GO:0019060 intracellular transport of viral protein in host cell " (https://github.com/geneontology/go-ontology/issues/13478) has synonyms
    • viral capsid transport in host cell nucleus,
    • intracellular viral protein transport,
    • intracellular viral capsid transport and
    • viral capsid transport in host cell cytoplasm

Presumably the merge was done to the wrong term, these seem like synonyms for 'GO:0075733 intracellular transport of virus'

GOC Meeting

  • Review agenda items

Minutes

  • On call: Chris, David OS, Eric, Harold, Jim, Karen, Kimberly, Moni, Pascale, Suzi, Tanya

Adding 'transport' as a relation in RO

  • The existing relation, 'transports or maintains localization of', may be more than is needed for some terms
  • A simpler 'transport' relation could be added as a child of 'transports of maintains localization of'
    • This would not, presumably, break things
    • We do still need the 'maintains' concept in a parent relation, though
  • There is also import and export and these are not used quite consistently throughout the ontology
    • The high level terms for import and export do not specify from where to where, so are not very useful
    • Terms that use import and export should be clarified wrt the start and end points
  • How best do we distinguish maintenance vs transport
  • This is an area of GO that may be overly complicated
    • Localization is mixed with location
    • It will be a pretty big job to untangle all of this