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| [[WormBase-Caltech_Weekly_Calls_September_2015|September]] | | [[WormBase-Caltech_Weekly_Calls_September_2015|September]] |
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− | | + | [[WormBase-Caltech_Weekly_Calls_October_2015|October]] |
− | == October 1, 2015 ==
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− | === Micropublications ===
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− | * General discussion on DOI handling for micropublications and using the ?Paper model
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− | * Project started with expression pattern submissions
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− | * Micropublications were displayed on ?Expr_pattern pages on WormBase/WormBook
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− | * We do currently assign a DOI to these URLs/pages
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− | * 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
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− | * Daniela has requested changes to ?Expr_pattern model to accommodate micropublication
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− | ** So many of the tags were shared (or could be shared) with the ?Paper class
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− | * If micropublications will be indexed by MEDLINE, we could use our standard paper pipeline to capture paper data
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− | ** Any lag in indexing is likely negligible (~1 day)
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− | * 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
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− | | |
− | === Community Curation paper ===
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− | * Due at end of October
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− | * Daniela communicating with Mary Ann; should micropublications be mentioned?
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− | * Database issue that is published concurrently with the BioCurator meeting
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− | * Hopefully we have some feedback by the time we need to make revisions (end of January)
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− | * E-mails to authors for concise description and allele-phenotype will go out today/soon
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− | === WS251 citace upload tomorrow ===
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− | | |
− | === Community editing of concise descriptions ===
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− | * Would like community to edit manually-written and automated gene descriptions
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− | * Would be nice to have a link to the concise description form from gene overview/existing description
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− | * Same for allele-phenotype form
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− | | |
− | === Traveling to labs ===
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− | * Soliciting community contributions AND providing user help/guidance
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− | * Need to emphasize the importance of MODs and why they need support
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− | * We should cater our discussions to what the labs specifically work on
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− | * Could start with 2-4 days of trial; half-day at campuses
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− | * Needs to be short talk/seminar (not an hour, much shorter)
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− | * Should we go to local/area meetings
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− | * Will likely be effective to have one-on-one discussions with PIs, lab members
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− | == October 8, 2015 ==
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− | === Soliciting community curation ===
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− | * Juancarlos, Ranjana and Chris working on a pipeline to e-mail authors
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− | * Will try to automate as much as possible
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− | * Will avoid e-mailing authors that have already been AFP e-mailed in the last 3 months
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− | * Juancarlos writing scripts to generate list of valid papers with relevant e-mail information
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− | * Would be good to parse corresponding author and first author from paper XMLs, but publishers are not uniform in their format
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− | | |
− | === SObA in Cytoscape ===
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− | * Juancarlos working on adapting SObA to Cytoscape
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− | * Would allow zooming in for details, zooming out to hide details
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− | | |
− | === Help Desk query ===
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− | * Looking for all mutations in a Million Mutation strain
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− | * Currently, large queries on website point users to FTP site, but without direction
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− | * Would be good to provide more clear directions to users (point to specific file)
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− | * We used to have a mechanism for users to download a flat file for large datasets, but missing now
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− | | |
− | === Community Curation paper ===
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− | * Will wait for the right time to write, after feedback, etc.
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− | * Biocurator meeting is in April, by which time we will hopefully have good results to present (talk/poster/workshop).
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− | | |
− | === Cell Ontology project ===
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− | * Didn't get funding on first round application
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− | * However, may get funded through GO
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− | * Species agnostic, but tries to draw connections between human and C. elegans cell types
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− | * Example, human epithelial cells using FGF/Wnt etc. connected to C. elegans epithelial cells using FGF/Wnt etc.
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− | | |
− | === Micropublications ===
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− | * WormBook gets indexed by NCBI/PubMed
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− | * We want micropublications to be indexed
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− | * Marie-Anne Felix asked about species descriptions
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− | * We have a micropublication form for expression data; can we build for other data types?
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− | * Data in form does not, currently, read into Postgres
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− | * Would be good to automatically generate a PDF
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− | == October 15, 2015 ==
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− | === VPC annotations ===
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− | * Expression pattern data will be incorporated into concise descriptions.
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− | * 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..).
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− | * This applies to Gene expression, Gene regulation, Phenotype classes -possibly others.
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− | * 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)
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− | * Ranjana will open a ticket about it.
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− | * 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)
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− | | |
− | ===Obsolete terms===
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− | * For ontology terms that become obsolete we should implement a system to notify curators, in the same fashion as GO operates:
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− | * e-mail curators when a term becomes obsolete
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− | * have a check in place: when curators submit their files a script would alert them in case they contain obsolete terms
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− | | |
− | ===Male annotations===
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− | We should think of a general way on how to handle annotations to male vs hermaphrodite
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− | == October 22, 2015 ==
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− | | |
− | === Submit Data webpage ===
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− | * Reviewed feedback for NAR paper suggests we user guidelines for large data submissions available.
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− | * propose a new Widget on the Submit Data page.
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− | | |
− | === New SObA phenotype based on Cytoscape ===
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− | * daf-3 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000899>
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− | * daf-2 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000898>
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− | | |
− | Compared to the GraphViz version
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− | daf-2 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898>
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− | Cytoscape advantage
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− | 1. Ability to zoom in place; zoom level controls showing/hiding texts.
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− | 2. More node-specific information and action is displayed in graph.
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− | 3. Newer technology; active development; used by web team already.
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− | disadvantage
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− | 1. Not as much QA available on-line.
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− | 2. Different idiosyncracies.
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− | 3. Perhaps not as stable.
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− | | |
− | * Not clear that Cytoscape is (or can be) as good as the current, developed GraphViz view
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− | * 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
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− | * Plan is to go live with what we have in 2 months
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− | | |
− | === Citace upload ===
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− | * Official upload to Hinxton on Friday December 4th
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− | * Local citace upload to Wen on Tuesday December 1st, 10am
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− | | |
− | === Community curation e-mails ===
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− | * Would be good to automate the creation of the e-mail
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− | * Still just working out the details & logistics
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− | == October 29, 2015 ==
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− | | |
− | === AGENDA ===
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− | ==== New SObA phenotype based on Cytoscape ====
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− | * daf-3 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000899>
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− | * daf-2 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000898>
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− | | |
− | Comments:
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− | * would it be possible to space out a little more the legend from the primary graph? (Daniela)
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− | * pluralize 'allele' (Daniela)
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− | * Allele phenotype filter (Karen)
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− | * Show Gene and Allele names (Karen)
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− | | |
− | === MINUTES ===
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− | | |
− | ==== Condition class microarray tag ====
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− | * User asked for microarray data with a specific genotype
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− | * Wen needs to write a script for each of these types of inquires
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− | * Wen proposes a new tag in the ?Condition class to indicate that annotations using the ?Condition object were for microarray experiments
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− | * This way, Wen can perform a simpler query of the database to get condition-specific data
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− | ==== SObA in Cytoscape ====
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− | * Looks good
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− | * Slight drawback compared to GraphViz in terms of node and edge layout
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− | * Probably wiser to go ahead with Cytoscape for various reasons
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− | * Hopefully we can optimize display in the future
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− | * Would like to add filtering options in future display
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− | * How easy is it to extend the SObA graph to other classes/ontologies?
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− | ** Reasonably easy, but each case has specific needs
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− | ** Some classes, like Anatomy annotations, may require a pre-slimmed display with an option to drill down into the datad
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− | | |
− | ==== Itai Yanai data ====
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− | * Daniela received developmental timing RNASeq data set from Itai Yanai
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− | * The data has been made into .ACE file for upload
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− | | |
− | ==== Micropublications ====
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− | * WormBook will have a "data" article type
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− | * Will make announcements about micropublications on the WormBase homepage, when ready
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− | * Hopefully micropublications will enter into WormBase through the normal ?Paper class pipeline
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− | * Wen: Several (5 or 6) microarray data sets in GEO that don't have publications (and probably won't)
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− | ** Would be good to contact these authors to ask if they want to micropublish
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− | * PDFs may or may not be made for each article
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− | * Asking/will ask NLM if we need added tags for proper indexing
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− | * How do we minimize the cost of publishing? Standardization?
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− | ** One data type at a time, requiring minimum information standards (MIME), as in GEO
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− | * What about minireviews based on, or informing, WormBase processes/topics?
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− | | |
− | ==== Funding supplements ====
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− | * Common APIs for Intermine in the cloud (for 6 different MODs)
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− | * Textpresso in the cloud
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− | | |
− | ==== Concise descriptions for other species ====
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− | * We can take non-elegans species large-scale expression data (?Expression_cluster data) and inform concise description for relevant non-elegans genes
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− | ==== Modeling biological events ====
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− | * Looking at large-scale cell division timing data
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− | * Should we consider a generic modeling of biological events (independent of ?Life_stage)
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− | * Would capture timing information for experiments at instance level (specific experiments from specific paper) using ~primary data
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− | * How to achieve inter-comparability between datasets? Not sure yet, need to think about for future. Will probably require intelligent abstraction of data
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− | | |
− | ==== Community curation e-mailing ====
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− | * Allele-phenotype e-mails have gone out for 55 papers starting October 1st
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− | ** 10 form submissions in response
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− | ** 5 e-mail responses
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− | * Juancarlos developing form & tracker for Chris and Ranjana's pipelines
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− | * Soon should be able to send e-mails to authors in matter of seconds
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