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- Pulled out papers that mention "unpublished" and "data not shown"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- Have "unpublished" data mentioned in one paper later published in another?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- Another approach could check how many chapters from PhD theses are unpublished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- Check BioArchive, how much is still unpublished 5 years out?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- Any published reports about how much unpublished data there is?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