WBConfCall 2012.06.07-Agenda and Minutes
(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?
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
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
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
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
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.