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


1) IN (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

?Interaction 2

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

Interactor  Rearrangement  ?Rearrangement  XREF  Interactor  #Interactor_info


and accordingly add an "Interactor" tag to the ?Rearrangement model:

Interactor  ?Interaction  XREF  Rearrangement

?Interaction 3

3) IN - (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

Interactor_info hash

4) IN (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


5) IN 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


6) IN 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").


7) IN Life_stage Model

From Daniela: add a name tag to store names after the name to ID switch

?Life _stage

   Public_name UNIQUE Text


8) IN ?PCR_product

Kevin (Both of us were away for the call, but I had this in my model to do list).

   Mapping_primers Left_mapping_primer UNIQUE Text
                                Right_mapping_primer UNIQUE Text

This will allow us to capture the primer sequences that will be used for mapping (in the small number of cases where the connected Oligos do not give sensible mappings to the genome, for whatever reason).


Started with discussion about models All already accepted but most recent one. Michael doesn't see anything that stands out in the Anatomy model but will wait on Paul D. final sign off

Discussion of literature pipeline for other nematodes

Caltech fine with extending it to the other species.

They discussed whether to get them all or just going forward. Structure change for say Brugia would be just going forward since a new gene set is about to be set.

Caltech will start collecting the papers and sort by species then see how it goes.

After seeing how many papers then decide what flag are worth the time invested.

Please fill in or correct any of the above information as I was listen and type at the same time.