WormBase-Caltech Weekly Calls October 2015

From WormBaseWiki
Jump to navigationJump to search

October 1, 2015


  • General discussion on DOI handling for micropublications and using the ?Paper model
  • Project started with expression pattern submissions
  • Micropublications were displayed on ?Expr_pattern pages on WormBase/WormBook
  • We do currently assign a DOI to these URLs/pages
  • If we put the micro publications in Wormbook shall we request a different DOI? May be enough to request a DOI for WormBook, with just a link to the respective WormBase page
  • Daniela has requested changes to ?Expr_pattern model to accommodate micropublication
    • So many of the tags were shared (or could be shared) with the ?Paper class
  • If micropublications will be indexed by MEDLINE, we could use our standard paper pipeline to capture paper data
    • Any lag in indexing is likely negligible (~1 day)
  • Daniela & Paul asked NLM to change the title of WormBook from "WormBook: An online review of C. elegans biology" to just "WormBook" to accommodate a broader scope; haven't heard back yet

Community Curation paper

  • Due at end of October
  • Daniela communicating with Mary Ann; should micropublications be mentioned?
  • Database issue that is published concurrently with the BioCurator meeting
  • Hopefully we have some feedback by the time we need to make revisions (end of January)
  • E-mails to authors for concise description and allele-phenotype will go out today/soon

WS251 citace upload tomorrow

Community editing of concise descriptions

  • Would like community to edit manually-written and automated gene descriptions
  • Would be nice to have a link to the concise description form from gene overview/existing description
  • Same for allele-phenotype form

Traveling to labs

  • Soliciting community contributions AND providing user help/guidance
  • Need to emphasize the importance of MODs and why they need support
  • We should cater our discussions to what the labs specifically work on
  • Could start with 2-4 days of trial; half-day at campuses
  • Needs to be short talk/seminar (not an hour, much shorter)
  • Should we go to local/area meetings
  • Will likely be effective to have one-on-one discussions with PIs, lab members

October 8, 2015

Soliciting community curation

  • Juancarlos, Ranjana and Chris working on a pipeline to e-mail authors
  • Will try to automate as much as possible
  • Will avoid e-mailing authors that have already been AFP e-mailed in the last 3 months
  • Juancarlos writing scripts to generate list of valid papers with relevant e-mail information
  • Would be good to parse corresponding author and first author from paper XMLs, but publishers are not uniform in their format

SObA in Cytoscape

  • Juancarlos working on adapting SObA to Cytoscape
  • Would allow zooming in for details, zooming out to hide details

Help Desk query

  • Looking for all mutations in a Million Mutation strain
  • Currently, large queries on website point users to FTP site, but without direction
  • Would be good to provide more clear directions to users (point to specific file)
  • We used to have a mechanism for users to download a flat file for large datasets, but missing now

Community Curation paper

  • Will wait for the right time to write, after feedback, etc.
  • Biocurator meeting is in April, by which time we will hopefully have good results to present (talk/poster/workshop).

Cell Ontology project

  • Didn't get funding on first round application
  • However, may get funded through GO
  • Species agnostic, but tries to draw connections between human and C. elegans cell types
  • Example, human epithelial cells using FGF/Wnt etc. connected to C. elegans epithelial cells using FGF/Wnt etc.


  • WormBook gets indexed by NCBI/PubMed
  • We want micropublications to be indexed
  • Marie-Anne Felix asked about species descriptions
  • We have a micropublication form for expression data; can we build for other data types?
  • Data in form does not, currently, read into Postgres
  • Would be good to automatically generate a PDF

October 15, 2015

VPC annotations

  • Expression pattern data will be incorporated into concise descriptions.
  • The annotations done to vulval precursor cells are currently done to the generic (sex-agnostic) term Pn.p (e.g. P5.p, P6.p, etc..).
  • This applies to Gene expression, Gene regulation, Phenotype classes -possibly others.
  • All curators that have annotations to sex-agnostic VPC terms should change their annotations, e.g. P5.p -> P5.p hermaphrodite (going back to the papers)
  • Ranjana will open a ticket about it.
  • Wen will be notified and will help pulling out all the annotations that have been made to those terms (Wen- I can brief you on this)

Obsolete terms

  • For ontology terms that become obsolete we should implement a system to notify curators, in the same fashion as GO operates:
  • e-mail curators when a term becomes obsolete
  • have a check in place: when curators submit their files a script would alert them in case they contain obsolete terms

Male annotations

We should think of a general way on how to handle annotations to male vs hermaphrodite

October 22, 2015

Submit Data webpage

  • Reviewed feedback for NAR paper suggests we user guidelines for large data submissions available.
  • propose a new Widget on the Submit Data page.

New SObA phenotype based on Cytoscape

Compared to the GraphViz version daf-2 <>

Cytoscape advantage

1. Ability to zoom in place; zoom level controls showing/hiding texts.
2. More node-specific information and action is displayed in graph.
3. Newer technology; active development; used by web team already.
1. Not as much QA available on-line.
2. Different idiosyncracies.
3. Perhaps not as stable.
  • Not clear that Cytoscape is (or can be) as good as the current, developed GraphViz view
  • Juancarlos & Raymond will continue to work on Cytoscape view for another month, then we will make a decision as to which version we will go with
  • Plan is to go live with what we have in 2 months

Citace upload

  • Official upload to Hinxton on Friday December 4th
  • Local citace upload to Wen on Tuesday December 1st, 10am

Community curation e-mails

  • Would be good to automate the creation of the e-mail
  • Still just working out the details & logistics

October 29, 2015


New SObA phenotype based on Cytoscape


  • would it be possible to space out a little more the legend from the primary graph? (Daniela)
  • pluralize 'allele' (Daniela)
  • Allele phenotype filter (Karen)
  • Show Gene and Allele names (Karen)


Condition class microarray tag

  • User asked for microarray data with a specific genotype
  • Wen needs to write a script for each of these types of inquires
  • Wen proposes a new tag in the ?Condition class to indicate that annotations using the ?Condition object were for microarray experiments
  • This way, Wen can perform a simpler query of the database to get condition-specific data

SObA in Cytoscape

  • Looks good
  • Slight drawback compared to GraphViz in terms of node and edge layout
  • Probably wiser to go ahead with Cytoscape for various reasons
  • Hopefully we can optimize display in the future
  • Would like to add filtering options in future display
  • How easy is it to extend the SObA graph to other classes/ontologies?
    • Reasonably easy, but each case has specific needs
    • Some classes, like Anatomy annotations, may require a pre-slimmed display with an option to drill down into the datad

Itai Yanai data

  • Daniela received developmental timing RNASeq data set from Itai Yanai
  • The data has been made into .ACE file for upload


  • WormBook will have a "data" article type
  • Will make announcements about micropublications on the WormBase homepage, when ready
  • Hopefully micropublications will enter into WormBase through the normal ?Paper class pipeline
  • Wen: Several (5 or 6) microarray data sets in GEO that don't have publications (and probably won't)
    • Would be good to contact these authors to ask if they want to micropublish
  • PDFs may or may not be made for each article
  • Asking/will ask NLM if we need added tags for proper indexing
  • How do we minimize the cost of publishing? Standardization?
    • One data type at a time, requiring minimum information standards (MIME), as in GEO
  • What about minireviews based on, or informing, WormBase processes/topics?

Funding supplements

  • Common APIs for Intermine in the cloud (for 6 different MODs)
  • Textpresso in the cloud

Concise descriptions for other species

  • We can take non-elegans species large-scale expression data (?Expression_cluster data) and inform concise description for relevant non-elegans genes

Modeling biological events

  • Looking at large-scale cell division timing data
  • Should we consider a generic modeling of biological events (independent of ?Life_stage)
  • Would capture timing information for experiments at instance level (specific experiments from specific paper) using ~primary data
  • How to achieve inter-comparability between datasets? Not sure yet, need to think about for future. Will probably require intelligent abstraction of data

Community curation e-mailing

  • Allele-phenotype e-mails have gone out for 55 papers starting October 1st
    • 10 form submissions in response
    • 5 e-mail responses
  • Juancarlos developing form & tracker for Chris and Ranjana's pipelines
  • Soon should be able to send e-mails to authors in matter of seconds