WormBase-Caltech Weekly Calls November 2014

November 6, 2014

Cleaning up obsolete life stages

• Old life stages in ACEDB as string name instead of life stage ID
• Have been cleaned up

Updating Curation Status Form

• Textpresso string matches have been included in the form
• Papers flagged as positive by string matching are included as positives for the indicated data type. Curatable papers not flagged are considered flagged negative (so looking at the stats page for "any flagged" will look like all papers have been flagged, if the string flagging method is selected.

Community Annotation Approaches

• Working on tables and forms
• Will be good to reach out to community (Paul's lab and others)
• Need to consider how we handle controlled vocabularies and ontologies
• Need to see how users/community are able to find the appropriate term for each
• Distinguish between publisher-mandated submission and voluntary submission
• We want to take advantage of the existing data submission forms wherever possible
• Idea: include a link to data submission forms from data widgets within the WormBase website
• Chris working with Textpresso to identify ontology terms from paper text for suggestion to community annotators

Construct object submission in OA

• There have been some problems up until yesterday (Nov 5) where the OA wasn't appropriately taking in ?Construct entries
• Curators can work with Juancarlos to pull up annotation history to double check that data was entered properly

November 13, 2014

WormBase chapter in WormBook

• Google Doc here
• Goal to have at least half of the chapters published by the 2015 International C. elegans Meeting
• May need to submit chapters by ~April 2015
• Plan to have first drafts ready by February 2015

Upload schedule

• Models freeze for WS247 on December 6th
• Data upload on Jan 9th, 2015

Community Annotation Form/Table

• We need a good way for users to look up official terms e.g. phenotypes, clones, etc.
• We want a form (web-based, single entry) and a spreadsheet/table (Google, Excel, OpenOffice -> .tsv) with data validation
• Chris will work on RNAi data submission table (Google Doc here)
  • We will require: Author name, author e-mail, paper/publication ID, sequence info (sequence, PCR_Product, Ahringer well location, Vidal well location, WB ?Clone object), Strain AND Genotype, Delivery method, Species, and Phenotype
• We need a way to validate .tsv files so authors can check before official submission (Chris will discuss with Juancarlos)
• Karen will work on Allele-Phenotype data submission spreadsheet/table (form exists, may need updating)
• We may want to enable PATO style annotations for phenotype (in form and spreadsheet)
• We will test these tables/forms with select groups (like Paul's lab)
• Will eventually reach out to worm community and then also publishers
• We should advertise this whenever/wherever possible

SPELL Server

• Wen looking at where to have SPELL hosted

SciReader

• J. Pritchard's http://scireader.org/ made for helping people find the best papers to read

OA problems

• OA has been throwing pop-up errors indicating that data has not been accepted into the form
• Curators have needed to stop curating, note the error message, and reload the OA to check if the data has been entered properly
• Problem seems to have arisen once we moved to the new Tazendra machine
• We may need to log pings to Tazendra to troubleshoot

November 20, 2014

WormBook chapter on WormBase

• Feedback from Martin Chalfie
  • Overview section may be redundant
  • Need a chapter/section on bulk data downloading and querying
  • Probably need a WormMine chapter (but maybe only once we have a dedicated developer?)
• General comment from Martin
  • Very difficult/frustrating to find orthologs from other organisms

RNASeq data

• LOTS of new RNASeq data coming out
• ModSeek - new software to replace SPELL (possibly?)
• FlyBase has a nice visual representation of RNASeq data
  • One problem is the number of different data sets we have

OA data entry problems

• Raymond has been looking into
• Has been some lost data packets through the network
• Raymond had updated device drivers and network cards for Mangolassi and Tazendra

WormBase Ontology Browser (WOBr) issues

• WOBr has been having problems
• Data needs updating for WS245 and WS246

Community Data Entry Tables

• Updated RNAi table draft here
• There is an issue with table performance when data validation columns have >~10,000 possibly entries
• We may have to really limit what we have data validation for
• There are >41,000 strains in WormBase currently; we may want to use a filtered list (e.g. only those with genotype information)
• Group wrote to help desk this morning with RNAi data to submit; will try out table with them and get feedback
• We may want to try other spreadsheet software to check performance: Excel, Cloud-based Excel, Open Office, etc.
• Google Doc spreadsheets can be downloaded as tab-delimited files for parsing by scripts

Waterston PFM dataset

• Xiaodong working on curating now

LEGO curation

• Kimberly working with others on LEGO curation to cross-check different curators efforts