WBConfCall 2012.06.07-Agenda and Minutes

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(Sorry, I won't be able to make the call. I'm traveling to the Development meeting in Madison and looks like my connection will not overlap). -- Todd

  • Discussion of literature pipeline for other nematodes
    • Which species?
      • should we should extend it to our core species (C.elegans, C.briggsae, C.remanei, C.brenneri, C.japonica)?
      • as we will add B.malayi to the core species, it might be more interesting to curate that (plus there are more papers available)?
    • What paper sets (e.g. all papers going forward vs older papers)?
    • What data flagging pipelines are needed?
    • Downstream curation, i.e. author-person connections?

Models Proposals

Interaction and #Interactor_info Model

1) (Chris) I'd like to add the following tags to the main ?Interaction model:

Unaffiliated_variation   ?Variation
Unaffiliated_transgene   ?Transgene
Unaffiliated_antibody    ?Antibody
Unaffiliated_expr_pattern   ?Expr_pattern

2) (Chris) I'd like to add Rearrangement as a subtag of the "Interactor" tag as such:

Interactor  Rearrangement  ?Rearrangement  #Interactor_info

3) (Chris) Can we make "PCR_interactor" and "Sequence_interactor" in the ?Interaction model NOT unique? Right now they are, and this is posing problems (data is being suppressed/overwritten that shouldn't be). -- from Chris

So, go from:

PCR_interactor UNIQUE ?PCR_product #Interactor_info
Sequence_interactor UNIQUE ?Sequence #Interactor_info


PCR_interactor ?PCR_product #Interactor_info
Sequence_interactor ?Sequence #Interactor_info

4) (Chris) I'd like to add two tags to the #Interactor_info hash:

Intragenic_effector_variation   ?Variation   XREF   Interactor
Intragenic_affected_variation   ?Variation   XREF   Interactor

Transgene Model

(Chris) I'd like to add a "3_UTR" tag to the ?Transgene model as a subtag of "Reporter" as such:

Reporter  3_UTR  ?Gene

Anatomy_term Model

raymond proposes adding four sub tags to ?Anatomy_term model


   Child   Cell_c         ?Anatomy_term     XREF Cell_p
           XUNION_OF_c    ?Anatomy_term     XREF XUNION_OF_p
   Parent  Cell_p         ?Anatomy_term     XREF Cell_c
           XUNION_OF_p    ?Anatomy_term     XREF XUNION_OF_c

the Cell_c/p tags are used to represent parent/child developmental lineage relationship between cells. the XUNION_c/p tags are for anatomy ontology to represent a specific uncertain type of lineage relationship (among nuclei). e.g. "AVFL nucleus" develops from ("P1.aaaa nucleus" XOR "W.aaa nucleus").