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| | [[WormBase-Caltech_Weekly_Calls_October_2015|October]] | | [[WormBase-Caltech_Weekly_Calls_October_2015|October]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_November_2015|November]] |
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| − | == November 5, 2015 ==
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| − | === IEA GO Annotations informating descriptions for non-elegans === | + | == December 3, 2015 == |
| − | * Some non-elegans genes have confident-sounding descriptions, about localization for example; likely not manual
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| − | * Will make sure automated descriptions handle IEA's appropriately
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| | | | |
| − | === Wen using Textpresso machine to build SPELL === | + | === Topic 1 === |
| − | * Athena was taking 48 hours to build SPELL (4GB max memory allotted)
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| − | * Textpresso machine took 24 hours (8GB memory allotted)
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| − | * Maybe we can use Textpresso machine for future builds
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| − | * SPELL java program running on Athena (alloted 4GB out of 6GB)
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| − | * Can monitor Athena memory usage; check for any memory leaks
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| − | | |
| − | === Community Curation Tracker CGI ===
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| − | * Purpose: To automate many steps of the e-mailing process to authors requesting community curation and to track those papers for which we've sent e-mails
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| − | * There is a "Ready" form and a "Tracker" form; "Ready" for generating list of papers to e-mail about, "Tracker" to track the status of papers that have already been e-mailed about
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| − | * Wiki documentation at: http://wiki.wormbase.org/index.php/Contacting_the_Community#Community_Contact_.26_Curation_Tracker_CGI
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| − | * Sandbox CGI located at: http://mangolassi.caltech.edu/~postgres/cgi-bin/community_curation_tracker.cgi
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| − | * EMAIL FUNCTIONALITY IS LIVE: please note!
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| − | * Allele-phentoype("New mutant" datatype) CGI is live on Tazendra
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| − | * Concise description version will be cloned from the New Mutant CGI and modified as needed
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| − | | |
| − | === SObA Graphs for phenotype ===
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| − | * Juancarlos will transfer code tomorrow, if there are no change requests before then
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| − | * Existing feature requests will be added to future releases of SObA
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| − | | |
| − | === Micropublications ===
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| − | * Daniela spoke with Daniel about having web pages in WormBook style to house micropublications
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| − | | |
| − | === Status of WormBase User Survey? ===
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| − | * Paul sent around paper this morning: http://www.nature.com/nature/journal/v527/n7576_supp/full/527S16a.html
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| − | * What aspects of databases really get used by users?
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| − | * How can we be more efficient with existing curation pipelines?
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| − | * Question of the month on WormBase?
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| − | * We could get user feedback when visiting labs
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| − | | |
| − | === Sending author updates ===
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| − | * Would be nice to have a mechanism to update authors on what has been curated for their paper
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| − | * Could give paper data summaries as well as recent updates to curation for a paper
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| − | | |
| − | === Objectifying/Itemizing annotations from Postgres ===
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| − | * What if we objectified itemized Postgres entries for easier display of all annotations per paper, for example?
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| − | * May require addition of a text field tag to the ?Paper class, for example, that would capture each annotation item for a paper
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| − | * This would be ''in lieu'' of actually objectifying all annotations
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| − | | |
| − | | |
| − | == November 12, 2015 ==
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| − | | |
| − | === Citace upload Dec 1st ===
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| − | | |
| − | === SAB set for Feb 4-5, 2016 ===
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| − | | |
| − | === Concise description form ===
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| − | * URL for listing genes mentioned in a paper
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| − | * Ranjana will send to Kimberly
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| − | | |
| − | === Community curation CGI ===
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| − | * Almost ready for prime time
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| − | * ~155 e-mails sent out for allele-phenotype; ~25-30 responses
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| − | | |
| − | === Scripts for community description form ===
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| − | * James wrote scripts that will need to inform community CGI
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| − | * Ranjana will work with Juancarlos
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| − | | |
| − | === FlyBase text mining ===
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| − | * Text mining for Fly corpus, entity recognition and extraction, esp. for transgenes
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| − | * Need to improve SVM on transgene and allele recognition
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| − | * Textpresso working on tools for FlyBase
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| − | | |
| − | === Phenotype SObA graph ===
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| − | * Making progress towards making the graph a widget on the gene page
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| − | * Still issues to iron out; working with Sibyl
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| − | * Some conflicts with Cytoscape for interactions vs. SObA
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| − | | |
| − | === Data Visualization program opportunity ===
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| − | * Will have to write a grant
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| − | * Would pay for one person, get two with grant
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| − | * Anyone with ideas should consider a proposal
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| − | * Dec 15th deadline
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| − | | |
| − | === WormBook ===
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| − | * Daniel prepared mockup for new web page
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| − | | |
| − | === Biocuration meeting ===
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| − | * Mary Ann working out plans for community curation workshop
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| − | * Does PomBase track their community curation?
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| − | | |
| − | === HT115 vs HT115(DE3) E.coli strains ===
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| − | * Redundant, should probably merge HT115 into HT115(DE3), as the RNAi-host E.coli strain
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| − | | |
| − | === Visualization plans ===
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| − | * Karen e-mailed around older proposal for work with Santiago Lombeyda
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| − | * Original project was to upgrade visualization of pathways and virtual worm in WB page
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| − | | |
| − | | |
| − | == November 19, 2015 ==
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| − | | |
| − | === Community curation ===
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| − | * Community e-mailing for allele-phenotype: 315 e-mails sent, 49 papers curated, 260 community annotations in the Phenotype OA
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| − | * Chris gave Paul list of all sy* alleles and phenotypes
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| − | * Paul going through table to add phenotypes not already in WB
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| − | * Paul using Textpresso and an allele-phenotype worksheet
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| − | * Do we want to create more elaborate forms or parallel forms? Probably parallel forms (in future)
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| − | * How can we assess completeness of curation? Very difficult to automate, currently
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| − | ** Check figures and tables
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| − | ** Ask authors about completeness
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| − | * Publication templates/worksheets? Streamline data submission concurrent with publication
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| − | * Can discuss at SAB in Feb
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| − | * We can send PI's/authors lists of alleles and what phenotypes WB has
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| − | | |
| − | === Working with NCBI ===
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| − | * Interested in Textpresso text-mining and SVM categorizing
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| − | * How might we work with NCBI & PubMed Central to curate? They are willing to run SVM on PMC corpus
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| − | | |
| − | === Minimum information requirements ===
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| − | * RNAi MI seemed bulky and not complete
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| − | * Asks authors for genes targeted, not dsRNA sequence
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| − | * We could write up a paragraph outlining the complaints about the proposed RNAi MI
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| − | * Maybe micropublish the paragraph
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| − | | |
| − | === Micropublications ===
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| − | * Should go into PubMed Central
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| − | | |
| − | === Allele descriptions ===
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| − | * Karen wants to adapt Ranjana and James' automated gene descriptions for alleles
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| − | * Start working on in January
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| − | | |
| − | === SObA ===
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| − | * Juancarlos making progress on integrating into the WB site
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| − | * There are difficulties getting SObA into it's own widget on the gene page
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| − | ** Conflicts with other settings (javascript / cytoscape) on same page, e.g. Interactions widget (w/Cytoscape viewer)
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| − | ** Updated cytoscape.min.js version on Interactions viewer
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| − | | |
| − | === Corresponding author curation ===
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| − | * Juancarlos and Cecilia have worked out a pipeline to capture corresponding authors for each paper
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| − | * Once paper editor changes are decided, can go live
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| − | | |
| − | === WormBook chapters for WormBase ===
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| − | * Each chapter written for users, but we likely want to avoid too much technical jargon
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| − | * We do want transparency
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| − | * We can separate the chapters into less-technical and more-technical, for easier reading
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