WBConfCall 2018.06.07-Agenda and Minutes

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Ontologies in WB

  • Plan is to include RO (and possibly also ECO) for WS267
  • Working on data model for RO led to a discussion at Caltech about how much associated data for each ontology we should include in WB
    • For example, RO also has terms from other ontologies:
    id: GO:0003674
    name: molecular_function
    is_a: BFO:0000015 ! process
    property_value: IAO:0000589 "molecular process" xsd:string
  • And extensive metadata about terms in the form of property_value tags (IAO = Information Artifact Ontology):
    • For example:
    id: BFO:0000050
    name: part of
    def: "a core relation that holds between a part and its whole" []
    property_value: IAO:0000111 "is part of" xsd:string
    property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
    property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
    property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
    property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
    property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at 
    certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
    property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an 
    independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically 
    dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A 
    material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent 
    continuant: use 'bearer of'." xsd:string
    property_value: IAO:0000118 "part_of" xsd:string
    property_value: RO:0001900 RO:0001901
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
    property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
    is_transitive: true
    is_a: RO:0002131 ! overlaps
    inverse_of: BFO:0000051 ! has part
  • For curation, we could import only the BFO and RO ID spaces of RO, but include all of the tag-value pairs (the usage examples might be helpful)
  • For WB, though, we could injest only the BFO and RO ID spaces of RO, and only include in the model: id, name, def, is_a, domain, range, and inverse_of tags
    • We can always link out from WB to pages with more detail on RO terms

modENCODE tracks mapped to older version of genome

  • There are apparently many modENCODE genome browser tracks that are not aligned properly, i.e. they are aligned to an older genome version
  • This can be quite misleading to users who aren't aware of the issue (probably most users)
  • We would like to correct this, but remapping won't be possible in the near term
  • Scott has offered to build a stand alone instance of JBrowse for these tracks
  • We need to assess the extent of the problem: which tracks are affected?