WormBase-Caltech Weekly Calls

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November 5, 2015

IEA GO Annotations informating descriptions for non-elegans

  • Some non-elegans genes have confident-sounding descriptions, about localization for example; likely not manual
  • Will make sure automated descriptions handle IEA's appropriately

Wen using Textpresso machine to build SPELL

  • Athena was taking 48 hours to build SPELL (4GB max memory allotted)
  • Textpresso machine took 24 hours (8GB memory allotted)
  • Maybe we can use Textpresso machine for future builds
  • SPELL java program running on Athena (alloted 4GB out of 6GB)
  • Can monitor Athena memory usage; check for any memory leaks

Community Curation Tracker CGI

SObA Graphs for phenotype

  • Juancarlos will transfer code tomorrow, if there are no change requests before then
  • Existing feature requests will be added to future releases of SObA


  • Daniela spoke with Daniel about having web pages in WormBook style to house micropublications

Status of WormBase User Survey?

Sending author updates

  • Would be nice to have a mechanism to update authors on what has been curated for their paper
  • Could give paper data summaries as well as recent updates to curation for a paper

Objectifying/Itemizing annotations from Postgres

  • What if we objectified itemized Postgres entries for easier display of all annotations per paper, for example?
  • May require addition of a text field tag to the ?Paper class, for example, that would capture each annotation item for a paper
  • This would be in lieu of actually objectifying all annotations

November 12, 2015

Citace upload Dec 1st

SAB set for Feb 4-5, 2016

Concise description form

  • URL for listing genes mentioned in a paper
  • Ranjana will send to Kimberly

Community curation CGI

  • Almost ready for prime time
  • ~155 e-mails sent out for allele-phenotype; ~25-30 responses

Scripts for community description form

  • James wrote scripts that will need to inform community CGI
  • Ranjana will work with Juancarlos

FlyBase text mining

  • Text mining for Fly corpus, entity recognition and extraction, esp. for transgenes
  • Need to improve SVM on transgene and allele recognition
  • Textpresso working on tools for FlyBase

Phenotype SObA graph

  • Making progress towards making the graph a widget on the gene page
  • Still issues to iron out; working with Sibyl
  • Some conflicts with Cytoscape for interactions vs. SObA

Data Visualization program opportunity

  • Will have to write a grant
  • Would pay for one person, get two with grant
  • Anyone with ideas should consider a proposal
  • Dec 15th deadline


  • Daniel prepared mockup for new web page

Biocuration meeting

  • Mary Ann working out plans for community curation workshop
  • Does PomBase track their community curation?

HT115 vs HT115(DE3) E.coli strains

  • Redundant, should probably merge HT115 into HT115(DE3), as the RNAi-host E.coli strain

Visualization plans

  • Karen e-mailed around older proposal for work with Santiago Lombeyda
  • Original project was to upgrade visualization of pathways and virtual worm in WB page

November 19, 2015

Community curation

  • Community e-mailing for allele-phenotype: 315 e-mails sent, 49 papers curated, 260 community annotations in the Phenotype OA
  • Chris gave Paul list of all sy* alleles and phenotypes
  • Paul going through table to add phenotypes not already in WB
  • Paul using Textpresso and an allele-phenotype worksheet
  • Do we want to create more elaborate forms or parallel forms? Probably parallel forms (in future)
  • How can we assess completeness of curation? Very difficult to automate, currently
    • Check figures and tables
    • Ask authors about completeness
  • Publication templates/worksheets? Streamline data submission concurrent with publication
  • Can discuss at SAB in Feb
  • We can send PI's/authors lists of alleles and what phenotypes WB has

Working with NCBI

  • Interested in Textpresso text-mining and SVM categorizing
  • How might we work with NCBI & PubMed Central to curate? They are willing to run SVM on PMC corpus

Minimum information requirements

  • RNAi MI seemed bulky and not complete
  • Asks authors for genes targeted, not dsRNA sequence
  • We could write up a paragraph outlining the complaints about the proposed RNAi MI
  • Maybe micropublish the paragraph


  • Should go into PubMed Central

Allele descriptions

  • Karen wants to adapt Ranjana and James' automated gene descriptions for alleles
  • Start working on in January


  • Juancarlos making progress on integrating into the WB site
  • There are difficulties getting SObA into it's own widget on the gene page
    • Conflicts with other settings (javascript / cytoscape) on same page, e.g. Interactions widget (w/Cytoscape viewer)
    • Updated cytoscape.min.js version on Interactions viewer

Corresponding author curation

  • Juancarlos and Cecilia have worked out a pipeline to capture corresponding authors for each paper
  • Once paper editor changes are decided, can go live

WormBook chapters for WormBase

  • Each chapter written for users, but we likely want to avoid too much technical jargon
  • We do want transparency
  • We can separate the chapters into less-technical and more-technical, for easier reading