WBConfCall 2018.06.21-Agenda and Minutes

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Agenda

SAB

WS267 Models

Relations Ontology (RO) Terms

  • ?RO_term proposal sent to models@wormbase list
 ?RO_term Name UNIQUE ?Text
          Status UNIQUE Valid
                        Obsolete
          Alt_id ?Text
          Definition UNIQUE ?Text
          Synonym Broad ?Text
                  Exact ?Text
                  Narrow ?Text
                  Related ?Text
          Child Instance ?RO_term XREF Instance_of
          Parent Instance_of ?RO_term XREF Instance
          Attribute_of GO_annotation ?GO_annotation XREF Annotation_relation
                       Not_GO_annotation ?GO_annotation XREF Annotation_relation_not 
          Version UNIQUE Text
  • Some questions about the model:
  1. I currently have XREFs between tags in the ?RO_term class and the ?GO _annotation class. Will we eventually want XREFs between all classes that refer to an ?RO_term and the ?RO_term? Do we want/need to create these XREFs at all?
  2. I didn't actually add the tags for Ancestor and Descendant. I'm not clear on how these tag values would get used in the database and/or website and if they are really needed.
  3. All of the relations that will be used between genes and GO terms, i.e. the annotation relations, are present in RO, but all of the relations used in annotation extensions are not. Currently, the only annotation extension relation in the C. elegans annotation file that solely uses RO relations is Molecule_relation. In the ?GO_annotation model, I left the annotation extension relations as Text, but I could update the Molecule_relation to use an ?RO_term. It would be nice if all annotation extension relations eventually found their way into RO or were subsumed by an existing RO term, but I don't have a good sense right now of if and when that will happen.

Ontology Models

  • Desendent -> Descendant - fix for WS267?
  • Proposed review and synchronization of all ontology models and tags for WS268

Help Desk

Minutes

SAB

Data types and tools description documents

  • all documents are ready
  • presentations for project meeting to be uploaded to the shared folder
  • need to choose who will present

Agenda

  • introduction and overview (Paul S): need to mention outreach
  • dataflow and backend: status and plans (Kevin H): Do we need feedback from advisors in specific areas? Possible outline: What is our

infrastructure - issues - needs - curation database - interaction with the db

  • curation: status and plans (Chris G):
 - duration of the talk changed to 45 minutes
 - discuss datatypes and effort for curation with WB/Alliance
  • website: status and plans (Todd H): significant changes to devops will be presented
  • tools and displays: status and plans (multiple presentations)
  • possible additional topics:
 - Kevin could add a 10 minutes talk on parasites. (Paul): "We could try to get some funds for parasites from the US"

Project meeting agenda

  • need two people for each item on the agenda
 - datomic migration (Adam and Matt)
 - interaction and coordination with the Alliance (Kevin and ?)
 - outreach (?)

Relations Ontology

  • XREF between RO terms and GO - shouldn't be a major issue to have them in datomic. (Raymond): Make sure that there are enough query tools for datomic for curators to retrieve XREF information. Should we have them also in acedb? Take home: leave the XREF in datomic for now and do not add new them to acedb.
 - It would be helpful for curators to have a presentation at the SAB on datomic query tools
  • ancestor/descendant tags in RO: it may be useful in the future, but no use cases right now. Add field to link to DB?
  • some relations in the GO annotation extension ontology are not included in RO
 - Use GO_rel type

Help Desk issues

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