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| | [[WormBase-Caltech_Weekly_Calls_February_2016|February]] | | [[WormBase-Caltech_Weekly_Calls_February_2016|February]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_March_2016|March]] |
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| − | == March 3, 2016 ==
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| − | === Sentence-level indexing ===
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| − | * Chris playing around with flagging sentences as positive/negative for phenotype and flagging keywords as true or false positives
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| − | * It may be helpful to objectify sentences and generate unambiguous, unique IDs for sentences
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| − | * There will likely be difficulty in unambiguously pulling out sentences from re-processed papers
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| − | * Best identifier would be the sentence itself
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| − | * Sentence 'objects' could be connected to annotations in WB
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| − | | |
| − | === Proteomic datasets ===
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| − | * Wen wants to systematically collect proteomic datasets
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| − | * Many are scattered across different resources
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| − | * Would also help ParaSite to index similar datasets for parasites
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| − | * MESH terms may help identify proteomic papers
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| − | | |
| − | === MOD-human disease collaboration ===
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| − | * FlyBase working on a shared template for curating human disease
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| − | * SGD, ZFIN, MGI, FlyBase, and WormBase meeting at Caltech to discuss
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| − | * One priority is minimizing redundancy of effort
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| − | * There is a common portal for human diseases in progress
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| − | * Should consider Monarch initiative approach
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| − | | |
| − | === AddGene & WB constructs ===
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| − | * Karen working with AddGene to pull in worm reagents (plasmids/constructs)
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| − | * AddGene does want to have better linking to WormBase
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| − | | |
| − | === Metabolomic data ===
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| − | * Can we show chemical structures for metabolites?
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| − | * User (M. Witting) says metabolism people will want monoisotopic masses - these masses aren't available through ChEBI at the moment and it will be a while for them to provide them. Will find a formula and sources files for Juancarlos to implement a calculator in the OA.
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| − | * We already use, sync and collaborate with ChEBI
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| − | | |
| − | == March 10, 2016 ==
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| − | | |
| − | === Adding WormBase-Parasite Paper to the Curation Pipeline (Kimberly) ===
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| − | *Developing new paper editor for Jane and Michael P. to approve parasite papers
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| − | *Adding species information to ALL papers; can be one or more species per paper
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| − | *Would like to then incorporate parasite papers into downstream SVM flagging pipeline and curation status form
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| − | *Species information could be used to keep curation stats clear
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| − | * We should discuss the curation and tracking of non-elegans species on the next site-wide call
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| − | * Might be best to have a separate ParaSite-specific curation status form; depends on use-case
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| − | * We may be able to just add new columns to the curation status form, Caltech vs EBI
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| − | * Michael and Jane want to curate gene function, e.g. GO; not sure what else
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| − | | |
| − | === Dynamo-DB backend for Datomic ===
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| − | * REST-API now switched to dynamodb backend.
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| − | * Juancarlos could set up a form to try Datomic queries
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| − | | |
| − | === WB FAQ page ===
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| − | * Need to request write access from Todd
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| − | * We should find out whether this page is used much. It needs updating considerably.
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| − | | |
| − | | |
| − | == March 17, 2016 ==
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| − | | |
| − | === Xiaodong taking year leave ===
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| − | * Will try working with company in China for a year
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| − | * Xiaodong will start April 15
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| − | * Daniela taking over antibody curation, Chris & Daniela taking over gene regulation and sequence feature
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| − | * Xiaodong will discuss antibodies for disease with Ranjana
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| − | | |
| − | === Tissue enrichment tool (Raymond) ===
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| − | * Should development continue with integration into WormBase? Yes, no one else is doing it
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| − | * GO enrichment tool in Intermine?
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| − | | |
| − | === Text mining: brainstorming ===
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| − | * We can likely explore many more options in terms of text mining
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| − | * All possibly recognizable entities could have data filled and displayed to curators and/or end users
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| − | * What about showing PDF markup from papers in PubMed Central? There is increasing interest in participation
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| − | * We're trying sentence-level SVM for phenotype; will see how that works
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| − | * We can quote papers verbatim in annotations, but should probably use double quotes from now on
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| − | * We'll try to generate putative annotations automatically that can be confirmed or rejected by a curator or author
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| − | | |
| − | | |
| − | == March 24, 2016 ==
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| − | | |
| − | === Outsourcing compute time ===
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| − | * SPELL requires 30 hours with 16GB memory
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| − | * Amazon cloud could offer 244GB memory at $3 per hour
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| − | * We already have an Amazon account
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| − | | |
| − | | |
| − | == March 31, 2016 ==
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| − | | |
| − | === Reagent data submission form (from Nobert Perrimon) ===
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| − | * Data table provided as an example submission of reagent information at point of publication
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| − | * Several reagent types included
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| − | * We may want more specific information, e.g. sequence(s), relevant gene(s)
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| − | * Would we need/want other follow-up tables to fill in more specific information?
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| − | * Genetic variations should be added, including sequence
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| − | * WB curators should draw up a table of minimal information for their data type
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| − | * Chris will clean up and send around table for RNAi data submission
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| − | | |
| − | === Proteomic papers (Wen) ===
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| − | * Searching title for "proteome"
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| − | * ~230 papers total
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| − | * ~187 proteomic papers might be curatable
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| − | * Many may not have expression clusters, but Wen did find new datasets
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