Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Phenotype curators regularly have to deal with difficulties of annotating phenotypes to genes | * Phenotype curators regularly have to deal with difficulties of annotating phenotypes to genes | ||
* One issue is the completeness of the ontology and the regular need for new terms | * One issue is the completeness of the ontology and the regular need for new terms | ||
+ | * We may benefit from a PATO-like annotation approach | ||
+ | * We will create a Phenotype Curation working group which can meet regularly to discuss | ||
+ | |||
+ | |||
+ | === Community annotation === | ||
+ | * We would like to implement a CANTO like tool | ||
+ | * We will establish a Community Annotation working group and a | ||
+ | |||
+ | |||
+ | === Topics name === | ||
+ | * Change name to "Pathways"? Back to "Processes"? |
Revision as of 16:29, 16 October 2014
Contents
Previous Years
2014 Meetings
October 2, 2014
ParaSite infrastructure
- Discussion regarding communication/coordination of curation effort (& data display) between WormBase and ParaSite
- What curation/work will ParaSite be taking over that we (WormBase) can stop doing?
- What ParaSite info would a WormBase user be interested in: e.g. synteny/alignments, genetic maps?
- WB has user tracking and feedback features; will we use the same tools for ParaSite? Who handles ParaSite help desk issues?
- Branding? Similarity/differences in look & feel between ParaSite and WB?
WormBase Use Statistics
- 2012 to 2013: page impressions increased ~8%
Last year WB object numbers
- Will compare WS245 numbers to WS239 (~1 year)
Enzyme Widgets & Metabolic Pathway Integration
- Marian Walhout working on metabolic flux analysis project
- Would like to display data for enzymes on WormBase outlining likely reactions that are catalyzed by the gene product
- We could interface with Reactome and/or MetaCyc/BioCyc
- Was an idea to create an enzyme reaction widget on gene page
- GO molecular function has associations with E.C. numbers
October 9, 2014
Citace upload
- Curators should upload data by end of tomorrow (Friday Oct 10th)
- Wen will upload citace to Hinxton on Wednesday (Oct 15th)
- Will be the last upload of the year (next in January?)
BioCurator Meeting
- http://biocuration2015.tilsi.org/
- April 2015 in China
- Michael and Yuling are going
- Abstract deadline in November?
- Edit by Mary Ann - Paper submission deadline 15th Nov, 2014, Abstract submission deadline 1st Feb, 2015
SAB Review
- Response from SAB
- What are our priorities?
- Expression cluster data mining tools (Wen will work on)
- Community Annotation
- CANTO tool - Val Wood from Pombase gave a talk about CANTO
- We could integrate/use CANTO, but we need to decide how we will implement it (probably implement our own type)
- Used for new, recently released papers only
- Would be good for users to get immediate feedback for their contributions
- A widget on user/person pages showing annotation contributions
- On WormBase homepage, have a very visible widget for top community annotators showing the identities of top users
- Advisors felt that it would be useful to have a table and/or template that users/authors could fill out for their data
- Eventually want to coordinate with publishers to get data submissions as part of the publication process
- Good to have PR in place for the International Worm Meeting
International Worm meeting Workshops
- http://www.genetics-gsa.org/celegans/2015/
- Workshop submission deadline for 2015 meeting is November 13, 2014
- Wen could do workshop on SPELL
- Chris could do WormMine workshop
October 16, 2014
Phenotype annotation
- Phenotype curators regularly have to deal with difficulties of annotating phenotypes to genes
- One issue is the completeness of the ontology and the regular need for new terms
- We may benefit from a PATO-like annotation approach
- We will create a Phenotype Curation working group which can meet regularly to discuss
Community annotation
- We would like to implement a CANTO like tool
- We will establish a Community Annotation working group and a
Topics name
- Change name to "Pathways"? Back to "Processes"?