WBConfCall 2018.06.21-Agenda and Minutes

From WormBaseWiki
Jump to navigationJump to search



  • Progress / status of data-type/tools documents
  • Next steps?

WS267 Models

Relations Ontology (RO) Terms

  • ?RO_term proposal sent to models@wormbase list
 ?RO_term Name UNIQUE ?Text
          Status UNIQUE Valid
          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
  • Proposed review and synchronization of all ontology models and tags for WS268

Help Desk