WormBase-Caltech Weekly Calls

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May 5, 2015

Tissue enrichment tool

• Some slight modifications have been made
• Raymond/Juancarlos request testing
• Made adjustments to gene name handling
• Tool could go live for the next release
• Data will remain frozen at WS252

Gene summaries

• Paul asked Norbert about gene descriptions
• FB has been getting good community response for contributing gene descriptions
• Automation still sounds like the right way to go
• Ranjana will look at summaries at other MOD sites

Phenotype display

• MGI/MGD had a graph display of phenotype ontology (Paul S.)
• Made phenotype ontology slim for the summary heatmaps
• How do all of the MODs display phenotypes?

Progress reports

• Curators can write a paragraph on innovation
  • Community curation (report numbers)
  • WOBr
  • SObA
  • Automated descriptions
  • Micropublications

Curation pipeline comparisons

• Would be nice to compare how MODs prioritize curation, triage papers, etc.
• How many MODs curate paper-by-paper (for all datatypes at once) vs. our method, by datatype?
  • WB & MGI curate by datatype, most others by paper (for all datatypes)
• How are all MODs doing in terms of paper coverage?
  • Do we need more manual effort, more automation? How much, given cost of each?

SPELL

• SGD uses SPELL but does not develop

May 12, 2016

Communication tools for umod teams

• Mike Cherry set up Stanford umod-project- email lists for the different umod groups, PIs, software developers, and curators
  • umod-project-curation@lists.stanford.edu
  • https://mailman.stanford.edu/mailman/listinfo/umod-project-curation
  • note: if you signup for a digest, you will receive e-mails from the list on a different time scale than people who didn't choose 'digest'
• Slack is back, download the app and look umod-project. You can also visit https://umod-project.slack.com/.
  • Browse the channels and join the ones that you want.
  • Create any new channel, it seems there is no limit to the channels that can be created.
• Suzi Lewis will be setting up a github account for project tracking and wiki pages

Human Disease working group meeting

• Next Monday and Tuesday, in Kerckhoff 024
• Curators will review data models for human disease at each site
• Brainstorming session for future plans
• Possibility of molecule-disease interactions ("exacerbated by", "ameliorated by")

Metabolomics

• Wen came across metabolic profiling papers while looking for proteomics papers
• Wen will send to Karen, who is managing metabolites as part of molecule class
• BIGG database, a new metabolite database (http://bigg.ucsd.edu/)

Progress Report

• Send Paul progress report blurbs in next week (by Thursday)

Cross MOD call

• Reviewed FlyBase and Rat Genome Database this week
• Will review SGD and MGI next week
• Suzi Lewis asking about Intermine instances; what can Mine do that the Base cannot, and vice versa?
• Other MODs have more fully functional and fully populated InterMine instances
• Agenda and Minutes: http://bit.ly/1NXuBVD
• Schedule and Topic signup: http://bit.ly/243UNL2

FraqMine/SimpleMine

• http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/fraqmine.cgi
• We want to make the tool available to users, maybe under Tools menu
• Will need to discuss with Todd (Paul sending email)

Micropublications

• BioCADDIE developers are currently working on indexing datasets requested by the NIH for inclusion in a June 30 Prototype test. After then they will reach out to us to look into the WormData (micropublication) indexing.

May 19, 2016

Dead genes in FraqMine?

• User asked for gene IDs for dead genes from list of sequence IDs
• FraqMine/SimpleMine does not currently accept/return dead genes
• Juancarlos will make changes to script to add an additional column indicating that a gene is dead

Community curation request delay

• Currently we wait 3 months before sending additonal community curation requests to authors
• Considering making delay only 1 month or less; opinions?
• Most annotations come within a week of a request
• One month is probably good
• Should we send list of alleles to lab heads with annotated phenotypes?
• Show community curated alleles/annotations on WB homepage?
• Show top 20 community curators on WB homepages?
• Make use of the "Activity" widget on homepage? Replace random page with community contributions?

Citace upload

• June 28th, 10am

uMOD Phenotype call

• Today 11am Pacific
• Join BlueJeans call: https://bluejeans.com/626771895
• To be discussed at NHGRI meeting next Monday & Tuesday

Distinctions between Human Disease curation and Phenotype curation?

• WB and other MODs have been curating phenotype and human disease separately
• Some consider phenotypes and disease as the same (Monarch perspective)
• We should consider the extent to which these overlap and are distinct

Human Disease meeting

• People are looking for commonalities
• Disease Ontology is a good starting point of commonality
• Agreement to curate experimental models
• UMOD Disease portal: search for a gene and get links to each individual MOD
• DBs should serve a disease data file
  • WB has gene-disease association file
• Sources of disease files: OMIM, Medic(?), etc.
• MIM-to-gene file
• Query tools: what should they look like? What kind of results?
  • Simple table views as results
• UMOD disease detail report page ideas
• Want to consider relations to molecules/chemicals ("modifiers")
  • Exacerbates, ameliorates, is a therapeutic for
• Drug-induced models
• Disease strains/genotypes, how to handle
• Should disease curation expand to capturing alleles/genotypes/strains?
  • We can, going forward

Objectifying Genotypes

• Increasingly, we are encountering needs to objectify genotypes
• We have strain objects, although strains are not always specified in papers
• We could potentially create strain objects that are named according to a paper ID
• This would enable us to capture certain phenotype and genetic interaction annotations
• We need to consider a strain's phenotype in relation to a control strain
• We already annotate phenotypes to transgenes while specifying the gene (in the transgene) that causes the phenotype
• It will be good for WB cuartors to hear from other MODs about how they handle this
• We can reconvene after today's phenotype call and focus on this discussion for future cross-MOD calls