WormBase-Caltech Weekly Calls May 2016

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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?


  • 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
  • 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")


  • 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



  • 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, after Wen changes the source files to include the data

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

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
  • Created a wiki page for the in-house discussion, will bring in other mods once we have a clear understanding of what we want to do and what we need

May 26, 2016

Gene Name Changes widget on WB homepage

  • Should go live for WS253 (this weekend)
  • Will display changes to gene names
  • Will make a blog post to announce

UMOD call next week: Phenotype curation

  • Will discuss data associations made at each MOD
  • Will discuss genetic entities annotated with phenotypes (genotypes, alleles, RNAi reagents)
  • Will discuss use of phenotype ontologies vs. entity-quality PATO annotations
  • Should consider/dicsuss environment/condition
  • Chris will contact other presenters with topic guide

UMOD weekly curator call

  • Could be a forum for summarizing working group discussions

Biological Ontologies & BioCreative meeting

  • http://icbo.cgrb.oregonstate.edu/
  • August 1-4, 2016
  • Oregon State University
  • Chris Mungall will give tutorial on ontology development
  • Raymond has been in contact with Chris about cell ontology
  • Raymond has been trying to "owl-ize" the anatomy ontology
  • We could gain advantages by using OWL format for our ontologies
  • We want to understand OWL and Protege
  • We'll want to create a UMOD ontology working group

TAGC coloring book

  • Have worm facts incorporated
  • Need to include rat info
  • Cost depends on publisher
  • Up to 30 pages, currently
  • Including data for 7 MODs

NHGRI meeting

  • NIH people are happy about UMOD collaboration
  • Question: what are we NOT going to do?
  • What needs fundraising? e.g. neural circuits, metabolite curation
  • Short term: create working groups and discuss
  • Micropublications, GSA pipeline, author interactions/community annotation, toxicology; new ventures to think about as UMOD
  • WB curators can develop it and then share with others
  • Do MODs curate from bio-archives (preprints)? No, only peer-reviewed articles


  • BioCaddie trying to develop new DataMed, data indexing
  • Micropublications could be indexed by DataMed and/or PubMed
  • What are requirements for PubMed? Need to collect some minimum number of publications (~50-100?) intitally
  • Indexing by Google Scholar?
  • 3-year projection; where do we want it to be?

Curation methods

  • How to various MODs curate? by paper vs. by datatype?
  • Will we need to move to a paper-by-paper curation approach? Not necessarily
  • What is the curation tool of the future? Needs to be flexible
  • How many core yet independent databases will be in use?
  • Over time we may migrate over to some other system

WS253 in Datomic

  • Datomic query tool available