Difference between revisions of "WormBase-Caltech Weekly Calls"
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− | == October | + | == October 29, 2015 == |
=== AGENDA === | === AGENDA === |
Revision as of 19:52, 29 October 2015
Contents
Previous Years
2015 Meetings
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
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.
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