WormBase-Caltech Weekly Calls March 2015

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March 2015

March 5, 2015

New curation topic for WS249

  • We will do Lipid Metabolism for WS249

Paper ID converter tool

GO data model change

  • Change for WS248
  • More detail with each annotation
  • Pipeline for data incorporation into the build has changed; path goes through Caltech/Postgres for QC
  • Changes to gene association file has implications for automated descriptions
  • Do we want to include PAINT annotations for automated descriptions?
    • Based on phylogenetic evidence codes
    • Yes, could be a great benefit to the automated descriptions
    • New GO annotations include a Panther tree node
    • Should we include both manually annotated data AND PAINT data in automated descriptions equally? Should look at examples and check how we want to handle
  • Clickable (linkable) evidence throughout the description?

International meeting give-aways

  • Worm pick holders (pencil grips) with WormBase logos; can they be printed on?
  • T-shirts and/or hats/caps; personalized for curators

Topic & Regional meeting abstracts

  • Usually we receive the data for these meeting abstracts in a non-standardized format; makes it difficult/time-consuming to parse
  • Would be good to request submissions in standard format
  • Good to maybe go through GSA pipeline?

NIH request for info on sustaining bio-databases

  • NIH requesting info on:
    • best practices
    • collaborations/partnerships
    • efficiency
    • alternative funding sources
      • requiring a DB funding allocation in individual grant applications?
    • medical application
  • What benefit do databases provide?
    • Differential usefulness: transient DBs versus maintained, broader impact DBs
  • Should MODs merge?
  • So much has changed in terms of database and web technology since online bio DBs began
  • Value distinction of manually curated annotations
  • How much redundancy is there between DB effort?
  • How do we assess the value of WormBase (or any DB) for academia and industry?
  • We should assess the scientific value to determine monetary value
    • Promote the benefit of transparency and reproducibility


  • We can introduce the idea at the international meeting
  • May be nice to group all micropublications into a single official publication
  • Maybe use "Gene Expression" journal for gene expression data as a pilot

March 12, 2015

Historical_gene tag

  • Issues came up with layered hash references in ACEDB when converting to Datomic
  • Changing line from "Historical_gene ?Gene #Evidence" to "Historical_gene ?Gene Text"
  • Affects ?Interaction, ?Expr_pattern, ?Antibody, ?Construct, and ?WBProcess

WormBook Chapters

  • Do we want/need a separate chapter/section on the new WormBase Ontology Browser?
    • Maybe only need a few small paragraphs in other relevant chapters, should be sufficient
  • Gene Function & Interaction chapter almost complete
    • Need to finish intro for phenotypes
    • Need to add predicted & regulatory interaction descriptions

Topic OA reminder

  • The 'primary'/'nonprimary' paper status is updated automatically every night by a cron job
  • The "Curation Status Omit" toggle button on TAB 3 was intended to flag nonprimary papers, but is no longer needed for that; only for rare noncuratable, primary, relevant articles (e.g. Methods papers)

Cloud bio-data storage

  • Cloud has potential advantage of distributed colocation; robust for queries, performance etc.

Modeling user-submitted data

  • How should we distinguish user-submitted data from curator-submitted data?
  • Should we distinguish at the data model level, with a new tag for example? Probably only need to apply WBPerson evidence, etc.
  • This issue came up with user-submitted/user-edited concise descriptions
  • The distinction can be made explicit exclusively at the display (web page) level
  • There could be a toggle in the OA to indicate user-submitted data

March 19, 2015

WormBook Chapters

  • Most chapters mostly complete as a draft
  • Paul S. working on introduction
  • Process chapter may not fill a chapter; also pending some website updates
  • Person/author section can be added to nomenclature section

Mapping Bio-Annotations to Process

  • Can we achieve automated mapping of annotations to processes?
  • e.g. phenotype-to-process mapping, site-of-action (cells and genes) mapping to process
  • Some phenotypes are indicative of a process, but some cannot be unambiguously mapped
  • Some processes can be mapped to based on sequence homology (e.g. Wnt signaling) rather than phenotype

GO Physical interactions into WormBase

  • Several (~400) papers in curation status form are considered "curated" for physical interactions via the GO pipeline
  • We would like to import these annotations into WormBase
  • Directionality information has been lost in the GO annotations
  • We want to re-curate the interactions to capture detection method and directionality
  • We could import all interactions in bulk without detection method or directionality with flag indicating a need to re-curate with additional information

Topic curation

  • Reminder for curators to check their lipid metabolism papers
  • Daniela working with web team to create a Pictures widget on Topic pages to display pathway/topic images (with permission)

Interaction-based phenotypes

  • On staging, Sibyl has added an "Interaction-based Phenotypes" table in the Gene page Phenotypes widget
  • This phenotype data is taken exclusively from genetic interaction objects to associate the gene with the phenotype

March 26, 2015

Community submission forms

  • Micropublication
    • People may submit expression data directly, with future citation (e.g. DOI)
    • Data submissions will need to adhere to some criteria providing evidence and reviewed by Paul, Daniela, and some other reviewer
    • Form could be recycled for published data submission
    • Forms remember user e-mails from IP used; makes easier to fill out subsequent submissions
    • Daniela will talk to Daniel about assigning DOIs
    • Can these be indexed by PubMed, etc.? Daniela discussing with Caltech librarians
  • We should focus on promoting/pushing one data type submission so as not to overwhelm the community; focus on others later
  • Concise description forms
    • Want to send automated descriptions (or existing manual descriptions) to users to quality check based on their expert (published) knowledge
    • User will use form to submit edits to descriptions
    • Do we want/need users to stick to automated description format/guidelines?
    • We could have direct links to forms from the Overview widget on gene pages

Funding Supplement Dedicated to Interoperability between MODs

  • Textpresso can be used to create common text mining pipelines across databases
  • Combining concise descriptions or taking advantage of other MOD data
  • Supplement funding application due in April (soon)

Database migration

  • Hope to have a pilot of new databases (Datomic?) done by mid-Fall

Global correlation of RNAseq gene expression data

  • All pairs of genes could have a correlation calculation performed (based on RNAseq) and displayed on WormBase
  • Significant correlations could be a type of interaction/association