WormBase-Caltech Weekly Calls

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October 1, 2015

Micropublications

• 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

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.

Micropublications

• 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

• daf-3 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000899>
• daf-2 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000898>

Compared to the GraphViz version daf-2 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898>

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.
disadvantage
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

AGENDA

New SObA phenotype based on Cytoscape

• daf-3 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000899>
• daf-2 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000898>

Comments:

• 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)

MINUTES

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

Micropublications

• 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