WBConfCall 2012.06.07-Agenda and Minutes
Contents
Agenda
(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?
- Which species?
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
to...
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
?Anatomy_term
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").
Life_stage Model
Daniela proposes to add a name tag to store names after the name to ID switch
?Life _stage Public name UNIQUE Text