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| | [[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]] | | [[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_2015|2016 Meetings]] |
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| | [[WormBase-Caltech_Weekly_Calls_November_2016|November]] | | [[WormBase-Caltech_Weekly_Calls_November_2016|November]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_December_2016|December]] |
| − | == December 1, 2016 ==
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| − | | |
| − | === Micropublication grant ===
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| − | * Daniela and Karen working on
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| − | * Pulled out papers that mention "unpublished" and "data not shown"
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| − | * Working with Transgenome project and GSA
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| − | * Deadline Dec 15th
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| − | * Proposal for BD2K call, multiple agencies (NHGRI)
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| − | * Focusing on curation process (as opposed to publication process)
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| − | * Have "unpublished" data mentioned in one paper later published in another? Maybe, difficult to know
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| − | * Could sample ~20 papers to check
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| − | * Another approach could check how many chapters from PhD theses are unpublished
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| − | * Could ask authors (source of personal communication) if they've ever published the data
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| − | * Check BioArchive, how much is still unpublished 5 years out?
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| − | * Could be a process where authors cannot say "data not shown" they need to micropublish
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| − | * Any published reports about how much unpublished data there is?
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| − | * What are the numbers for fly, mouse (other organism) papers?
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| − | * Micropublications are something that AGR is interested in
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| − | | |
| − | === GoToMeeting trial ===
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| − | * Allows computer call-in or phone dial in
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| − | * Reasonably priced, but costs add up if many people are dialing in with the toll-free number (8 cents per minute per person)
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| − | * Allows for multiple webcams and screen sharing
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| − | * People generally like it
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| − | | |
| − | === Citace upload ===
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| − | * January 13th, 2017
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| − | | |
| − | | |
| − | == December 8, 2016 ==
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| − | | |
| − | === LinkOut from PubMed paper pages to WormBase paper pages? ===
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| − | *GO recently established link outs from PubMed to AmiGO
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| − | *TAIR links out from PubMed to TAIR paper pages
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| − | *Do this for WB (and AGR)?
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| − | * Can take a look at WB paper pages, maybe clean up, e.g. make less jargony
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| − | | |
| − | === AGR meeting ===
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| − | * Faceted search for data across MODs
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| − | * Goal: Common gene report page
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| − | ** Minimal gene report page by March
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| − | *** gene id, names
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| − | *** gene concise description
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| − | *** gene sequences
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| − | *** gene location/structure
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| − | *** gene orthology
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| − | *** gene-disease connections
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| − | *** gene ontology (go-slim ribbons)
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| − | * AGR use case meeting yesterday discussed outcome of Denver meeting
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| − | ** Figuring out the role of the use case working group with new working groups
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| − | * GO slims - generic or organism-specific? Possibly both; we should see what works
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| − | * Project manager? Maybe
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| − | * Gene descriptions
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| − | ** ZFIN doesn't have them; could we take advantage of automated descriptions?
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| − | | |
| − | === WormBase grant ===
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| − | * Need to submit in May or September
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| − | * What needs to be thought about for the renewal?
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| − | ** Datomic will continue (should be done by new grant cycle)
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| − | ** Curation
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| − | *** What's happening in community annotation?
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| − | **** We can use existing phenotype pipeline
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| − | **** Can encourage bulk data uploads
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| − | *** What data are we curating?
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| − | *** Noctua training and implementation
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| − | *** Disease curation becoming standard
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| − | *** Molecule curation
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| − | *** Physical interaction curation: most DBs farm out; we do our own
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| − | **** Common, basic datatype that could be curated by international curation efforts
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| − | *** Pathway curation
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| − | **** Can we establish automated pipelines to pull in pathway annotations from core data?
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| − | | |
| − | === SObA graphs for gene ontology data ===
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| − | * Raymond & Juancarlos will work on a SObA graph for GO annotations
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| − | * Similar to existing phenotype graph, e.g.: http://www.wormbase.org/species/c_elegans/gene/WBGene00006763#b--10
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| − | | |
| − | | |
| − | == December 15, 2016 ==
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| − | | |
| − | === AGR use case working group ===
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| − | * Members of use case WG will be delegated to smaller working groups to help build the AGR portal gene report page
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| − | * Chris working with disease working group to build a disease widget on a gene report page
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| − | | |
| − | === SObA graphs for gene ontology data ===
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| − | * Raymond and Juancarlos are working on it
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| − | * Have contacted Chris Mungall for advice
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| − | | |
| − | === Gene enrichment analysis ===
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| − | * Raymond working with David Angeles to create more enrichment analysis tools
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| − | * To include GO term and phenotype enrichment analysis (hyper-geometric test)
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