WormBase-Caltech Weekly Calls
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Contents
Previous Years
2017 Meetings
October 5, 2017
NAR Paper
- Raymond will send around reviews
Mary Ann's transition
- Cecilia will take over laboratory curation
- Hinxton (Paul Davis) will take over nomenclature work
- Hinxton will take over strain info, Mitani (NBP) alleles, sequence features (large scale)
- Sequence feature curation (literature-based, small-scale) will move to Caltech
- Molecule curation may be split; Hinxton could coordinate with ChEBI; GO-CAM modeling molecules handled at Caltech?
- SOP? Karen wrote Wiki pages for molecule curation; she will look them over and can review with others
- Metabolomics was recent big push (biggest effort needed); need to discuss with Michael Witting
AGR Press Release
- Discussed briefly at AGR all-hands call yesterday
- No one on the call had much info
- Ranjana can post on WB blog on Oct 20th (or earlier?)
- Will ask Stacia
AGR momentum
- AGR disease working group
- Lots going on, a lot of progress, still have much to discuss
- Next need to work out how to pull in new data objects like alleles, strains, genotypes, etc.
- Will need to establish a basic, consensus AGR data model for these data types/objects
- How is AGR disease data display compared to WB/MODs? WB is generally (as are other MODs) ahead of AGR
- Site-visit
- PIs go to D.C. to discuss AGR
- Wen working on lab meeting presentations; will present AGR progress, give tutorial
- Raymond working on methods paper for SObA display
- Raymond will start working on neural functional units with phenotype
Sequence feature curation
- Really need to encourage authors to submit tables with specific sequence feature info
- Need to make the data submission process easy, user-friendly
- Karen looking into it
- Work study jobs for students to curate? May not be preferred job for students
- Temp jobs may be the way to go; but learning curve needs to be very short
WB Person curation/outreach
- Cecilia contacts 1-6 people per week by email
- She can ask for contact info: address, email address, phone #, etc.
- How many persons do we have email addresses for?
- Would be good to establish a 2-way communication with WBPersons
- Should some people be demoted if they don't respond to emails? If they are not worm people?
- We provide options to hide email addresses from WB person page
- What do other MODs do? How extensive is the outreach to the community?
- Cecilia reaches out when affiliations change
- Some journals require use of ORCID IDs; makes identifying authors less ambiguous
- Can ask people to update their intellectual lineage (can show lineage graph)
- Juancarlos will query to see how many people with an email address don't have lineage info
- One email from WB per month is OK
- Can use Twitter more, when we do site visits
October 12, 2017
Strain curation
- Paul Davis will take over strain curation
- Many strains important to disease curation may not have been submitted to CGC, and may not exist in WB
- Ranjana needs a way to create new strains for disease models
- Ranjana will talk to Paul, and will add documentation about the issue
Phenotype data display proposal
- Chris has been working on a new way to display phenotype data
- This will largely depend on the new ?Phenotype_experiment model
- Will hopefully solve a number of issues regarding how phenotype data is currently displayed
- Mockups here: https://docs.google.com/presentation/d/1XvMN16B7RU2yPwjD5p9_TywMj0itln-djEWyGx2IxiQ/edit?usp=sharing
- Goals are:
- Clarify phenotype experiment meta data and provenance
- Indicate when multiple perturbations may be responsible for a phenotype
- Clarify when a non-coding gene is annotated to a phenotype whether the phenotype may actually result from disruption of a protein coding gene
- Clarify when a phenotype results from a mutation that affects the exon(s) of one gene and only an intron of another
- Clarify when a phenotype is a double mutant (or other complex perturbation) phenotype
How we handle/display multiple supporting interactions
- As pointed out by Jae, some interactions appear very strange in the Interactions widget Cytoscape view when there are very many "independent" interactions/observations for a pair of genes
- Example, tax-6 and rcan-1: http://www.wormbase.org/species/c_elegans/gene/WBGene00006527#0-8-10
- We've tried to represent the "confidence" of interactions with thicker edges on the graph, but maybe this needs revisiting
- Should there be a log-based increase in edge thickness, instead of a linear one?
- Maybe evidence from the same paper should be considered as one observation?
Collecting person info
- Could we request personal info when we ask for other info, like author first pass, community curation
- Cecilia can manage feedback/input, and triage/defer issues to relevant curators etc.
- Ask people to confirm current institution, lineage information
- Probably need to keep the request minimal (a single line), so as not to overburden people
- We need to point people to person update form
- We could also do more through the website
October 19, 2017
Site visits, area meetings
- About a 12-15 area and topic meetings next year
- Chris will present at Baltimore Worm Meeting on March 16, 2018
- Many meetings are annual (Topic, Seattle, New York), some bimonthly
- Many of these arrange speakers well ahead of time, 6 months ahead for example
- We should reach out to organizers soon, especially for annual meetings
- We can combine WB, Textpresso, and micropublications
- We can/should customize our talks to research areas of each audience
- Many of the talks are about 40 minutes to 1 hour
Micropublication forms vs. WB data submission forms
- Managing discrepancies still need to be worked out
- Looking at differences of output formats
- Customizable forms? Forms built by curator?
- Karen: aside from paper details/meta data, forms can be the same
Phenotype data display proposal
- Chris has been working on a new way to display phenotype data
- This will largely depend on the new ?Phenotype_experiment model
- Will hopefully solve a number of issues regarding how phenotype data is currently displayed
- Mockups here: https://docs.google.com/presentation/d/1XvMN16B7RU2yPwjD5p9_TywMj0itln-djEWyGx2IxiQ/edit?usp=sharing
- Goals are:
- Clarify phenotype experiment meta data and provenance
- Indicate when multiple perturbations may be responsible for a phenotype
- Clarify when a non-coding gene is annotated to a phenotype whether the phenotype may actually result from disruption of a protein coding gene
- Clarify when a phenotype results from a mutation that affects the exon(s) of one gene and only an intron of another
- Clarify when a phenotype is a double mutant (or other complex perturbation) phenotype
October 26, 2017
GO CAM
- GO CAM models do not go into ACEDB, yet
- Kimberly is working on it
- First, Berkeley group is working on producing correct GPAD files as output
- Work is ongoing for a Cytoscape view of pathways
- Noctua calls on 2nd and 4th Wednesdays of the month; anyone can sit in (ask Kimberly)
- Noctua call minutes on Wiki (Kimberly will send around link)
Site visits
- Wen setup Wiki page: http://wiki.wormbase.org/index.php/Meetings#Upcoming_Meetings
- What's the strategy overall? Are we trying to make all meetings?
- About 15 meetings to go to; would be good if we could make all of these, if possible
- Kimberly will go to New York meeting
- Chris will go to Baltimore meeting
- Boulder, CO meeting; interested in having WB talk; sometime in May
- San Diego meeting in January (Wen out of town); volunteers?
- Chris could do Boston and Worcester meetings
Strains
- Are strains in the nameserver? No, and Hinxton is likely retiring the nameserver soon
- Can curators get access to a tool to request a strain object?
- Juancarlos and Ranjana are working on tool (cronjob) to send request to Paul Davis; within the disease OA
Changes to phenotype form
- We need a mechanism to clarify if multiple perturbations entered in the phenotype form represent multiple single experiments or a single complex genotype experiment
- Will give users the option to indicate which of these two scenarios is the case
- We discussed ways of managing this in a previous WB CIT meeting
- Produced mockups of proposal: https://docs.google.com/presentation/d/1HFVn1anbdCu8pHJW0g27a5AvYLFVMyBy4nnrEdA1wKQ/edit?usp=sharing