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| [[WormBase-Caltech_Weekly_Calls_May_2019|May]] | | [[WormBase-Caltech_Weekly_Calls_May_2019|May]] |
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| + | [[WormBase-Caltech_Weekly_Calls_June_2019|June]] |
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− | == June 6, 2019 ==
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− | === New SObA graphs === | + | == July 11th, 2019 == |
− | * May put graphs within existing widgets, but don't need to rush to get that ready for IWM
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− | === Phenotype association file format === | + | === Alliance all hands meeting === |
− | * May be best to leave the format as is | + | * Raymond: would be interested in discussing ontologies and their usage in the Alliance |
− | * There are problems; paper IDs keep switching columns | + | ** Phenotype, anatomy ontologies, GO, etc. |
− | * Would need to revisit the reasoning for why we do it that way | + | ** Ontology browsers, SObA |
− | * When will the Alliance produce a similar/replacement file? Not sure | |
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− | === Phenotype requests === | + | === IWM workshop === |
− | * Sent out 1140 emails on May 30 | + | * Videos ready for upload |
− | * Since have received 374 annotations from 54 papers (42 requested, 12 additional) | + | * Wen and Raymond now have access to outreach@wormbase.org account; will upload videos |
− | * 21 papers flagged as not having phenotypes
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− | * Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
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− | | + | === Protocol videos === |
− | == June 13, 2019 ==
| + | * Wen met Craig Mello at the IWM; he is interested in putting up microinjection videos online; linkable from WormBase? |
− | | + | * Can make each video a Video Weblog so people can make comments, etc. |
− | === IWM === | |
− | * Coordinating transportation of swag boxes to Pauley Pavilion
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− | * Workshop on Saturday June 22, from 1pm to 2:30pm
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− | * Saturday morning micropublication breakfast 7:30 - 8:30am
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− | * Workshop
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− | ** Presenters: it may be best to present as use cases rather than a research project
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− | ** Chris will cover SimpleMine for Wen | |
− | ** Chris: won't do live demo; only screenshots, maybe some video
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− | * Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
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− | * Paul's talk
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− | ** Cover Alliance
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− | ** New features
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− | *** SObA (for new data)
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− | *** Complete for protein-protein interactions
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− | *** RNASeq tools
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− | *** Updated automated gene concise descriptions?
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− | ** Phenotype community curation
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− | *** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
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− | ** Author First Pass
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− | ** Micropublication
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− | === SGD SAB ===
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− | * Paul attended
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− | * Alliance publicity was discussed
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− | * SAB likes the Alliance orthology features
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− | * Working on topics: displaying papers and data
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− | * Pathways: discussion about best approach
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− | * Metabolic engineering
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− | * Meta data about RNASeq data
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− | ** SPELL tool, basically only tool of its kind available; need new tools
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− | * Species-specific proteins: how best to find them? HMMs (Jackhammer)?
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− | === Concise descriptions ===
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− | * Progress being made within the Alliance to update the automated concise gene descriptions | |
− | * We will still accept manually written descriptions and display them in parallel with automated descriptions
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− | === Micropubs ===
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− | * If people are requesting manually written gene descriptions, they could submit a microreview
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− | * Concern was expressed about how to handle a really high throughput of submissions:
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− | ** Daniela: Working towards automating as much of the processing pipeline as possible
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− | ** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
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− | ** Not getting lots of submissions yet, probably won't be inundated in the near future
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− | ** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
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