Difference between revisions of "WormBase-Caltech Weekly Calls"

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

Revision as of 17:54, 19 November 2015

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings


2015 Meetings

January

February

March

April

May

June

July

August

September

October


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

Micropublications

  • 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

WormBook

  • 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

Micropublications

  • Should go into PubMed Central

Allele descriptions

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

SObA

  • 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 (esp. with Cytoscape) on same page, e.g. Interactions widget (w/Cytoscape viewer)
    • Updated javascript 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