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| | = 2017 Meetings = | | = 2017 Meetings = |
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| − | == January 5, 2017 ==
| + | [[WormBase-Caltech_Weekly_Calls_January_2017|January]] |
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| − | === BioCurator meeting ===
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| − | * Who from WormBase will go?
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| − | ** Raymond (SObA), Chris (Community curation), Mary Ann, Wen would like to go
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| − | ** Daniela maybe for micropublication
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| − | | |
| − | === International C. elegans Meeting ===
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| − | * June 2017
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| − | * Whether all WB staff go depends on whether we have an all hands meeting before/after
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| − | * Plenty of things to present; AGR stuff etc.
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| − | | |
| − | === Citace upload ===
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| − | * Prepare files by 10am on Tuesday, Jan 10
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| − | | |
| − | === LEGO curation ===
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| − | * Kimberly working on different C. elegans models
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| − | * Working on several pathways simultaneously
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| − | * Should be in production soon (this year), fully evidenced
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| − | * Full benefit may not be apparent until AGR has LEGO fully integrated
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| − | * Working out how inferred annotations propagate from Noctua/LEGO model to GAF
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| − | * MGI creating many LEGO models
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| − | * How are curators, that went to training, using LEGO?
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| − | * Curation level view may not be amenable to general biologist/user viewing
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| − | * What is the best existing pathway display? WikiPathways? Protege?
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| − | * GO people (Seth, Chris M., Suzi etc.) are working on display, but have limited resources for this
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| − | * Maybe we could work with WikiPathways team?
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| − | * Pathway studio at RGD? Manually generated
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| − | * Should WB have a LEGO call? Yes, probably
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| − | * Curators may need access to Protein2GO for full curation/inference by sequence similarity
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| − | * How do we/should we resolve parallel pipelines for curating cellular component data (Go versus Expression pattern)?
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| − | * How do we accommodate specific versus general processes? E.g. specific versus general cell division
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| − | * We would like a mechanism for a LEGO curator to pull relevant data from GAF
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| − | * We would like curators to focus on pathway perspective of curation, where authors can submit experimental details with a potential automated or semi-automated mechanism to bridge the gap
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| − | | |
| − | === Expression widget ===
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| − | * Daniela and Sibyl working on a more compact display of the expression data widget on gene pages
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| − | * Should we keep subcellular localization in the expression widget? Yes
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| − | | |
| − | === SObA for Gene Ontology ===
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| − | * Raymond and Juancarlos working on
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| − | * First for WormBase, eventually want for AGR
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| − | * For GO data, will have three different roots (for each branch of GO); One DAG for each
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| − | * Could have phenotype graphs from particular perspective, e.g. via anatomy, via life stage, via GO, etc.
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| − | * Would be great to have a comparative view mechanism
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| − | | |
| − | == January 12, 2017 ==
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| − | === Caltech LEGO Call ===
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| − | *Confirm time: Mondays, 11am PST (2pm EST/7pm GMT)
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| − | *Start January 23rd
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| − | *Format?
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| − | **Start with curation of one paper together?
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| − | ***Possible paper: [https://www.ncbi.nlm.nih.gov/pubmed/27881675 The Intestinal Copper Exporter CUA-1 Is Required for Systemic Copper Homeostasis in Caenorhabditis elegans.]
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| − | **Curators then select individual topics?
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| − | | |
| − | === Switching website to run off Datomic ===
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| − | * Juancarlos joining biweekly call on Wednesdays with Adam, Matt, and Sibyl
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| − | * Juancarlos working on Person page widgets currently
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| − | ** Intellectual lineage graph will need to be rewritten in Clojure
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| − | * Web team is working out the file/directory structure to organize widget generation
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| − | * Is the Datomic database denormalized? To what extent? No, not really
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| − | ** This affects how we might eventually write into Datomic from our curation database
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| − | * May be best for Caltech to keep a Postgres curation database in parallel to Datomic (and eventually sync nightly)
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| − | ** This may also be best with AGR as well
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| − | | |
| − | === Biocuration meeting 2017 ===
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| − | * Who's going? Ranjana, Chris, Raymond, Mary Ann, Daniela (if she gets a talk)
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| − | * Ranjana - automated descriptions
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| − | * Raymond - SObA graph
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| − | * Chris - Genetic interactions
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| − | * Mary Ann - Community curation
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| − | * Daniela - Micropublications
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| − | | |
| − | === Community curation presentation on AGR curator call ===
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| − | * Chris and Val Wood presented; minutes are here- [https://docs.google.com/document/d/1PdmdnTduxidxaljExTbalNA4ReyIRsZZmV6U-5ckXiI/edit AGR minutes]
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| − | * WB community curation numbers
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| − | ** 321 papers solicited and community curated (Phenotype OA)
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| − | ** 417 papers community curated in total (Phenotype OA)
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| − | ** 313 unique community curators (Phen OA); average 8 annotations per curator
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| − | ** 64 papers solicited and community curated (RNAi OA)
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| − | ** 74 papers community curated in total (RNAi OA)
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| − | ** 61 unique community curators (RNAi OA); average 16 annotations per curator
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| − | ** 3324 annotations total; 2969 valid and confirmed
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| − | ** 2111 solicitations gone out; 16% response rate
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| − | | |
| − | Val presented some information on how complete contributors were:
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| − | *''1990s were getting 10 annotations/paper, in most recent years are now getting 50 annots/paper (years are publication years)''
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| − | *''Curation quality - users often omit a data type, but for what they do curate, they are generally very accurate, and often request more specific terms''
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| − | | |
| − | Chris suspects ~20% authors are complete in their phenotype curation of their paper.
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| − | | |
| − | === Pulling WB data into LEGO models ===
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| − | * Phenotype data requires a mapping step to map alleles and RNAi to genes
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| − | * How might we crowd source or get low cost curators to curate bulk data? Followed by expert curation for LEGO models
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| − | * May be best for curators to take on specific topics of biology
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| − | | |
| − | | |
| − | == January 19, 2017 ==
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| − | | |
| − | === SObA graph for Gene Ontology ===
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| − | * Juancarlos and Raymond asking for feedback on GO SObA graph
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| − | * Kimberly: Can we create graphs for subsets of annotations (manual vs. automated)?
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| − | ** Raymond: It's doable as a standalone graph, but may be difficult to make an option embedded within the core display
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| − | ** May be a way to display IEA annotations separately from non-IEA annotations
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| − | ** Raymond: Can develop a personal view for Kimberly to visualize manual vs. automated annotations
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| − | * Three root terms for GO, displayed side-by-side in the same graph; root nodes are different sizes and not necessarily displayed aligned
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| − | * May be able to force the root nodes to be the same size
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| − | * May want to show/hide individual roots; doable although unclear how difficult to implement
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| − | * GO function and component are likely to be smaller networks than process
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| − | * Pulling data from GAF into Solr
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| − | * Can this be adopted for the AGR portal? Yes
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| − | | |
| − | === WormBase workshop at 2017 IWM ===
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| − | * Ranjana organizing
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| − | * Discuss ideas with Ranjana
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| − | * Have 1.5 - 2 hours
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| − | * Will want to discuss micropublications and community annotations
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| − | * We haven't had mirrors in a long time: discuss Datomic for people who want to query? Yes, brief announcement
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| − | | |
| − | === User Survey ===
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| − | * We may want user surveys to prepare for grant writing, progress report
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| − | * Could send out to users by May?
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| − | * What to focus on: performance, data types, usability
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| − | * Could have multiple short surveys
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| − | * What one question would we want answers to help with design decisions?
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| − | * Do we want (eventually for AGR) a professional surveyor?
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| − | * Are our services meeting user needs?
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| − | * We can take a closer look at user logs; see what data, widgets, tools used most frequently (least frequently)
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| − | * We could create focus groups to get feedback from users on specific topics (30 minute sessions during poster sessions, for example); maybe at booth? during meal time?
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| − | ** Would want to post a schedule with dedicated locations
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| − | * Could have WormBase hats, brightly colored ;), to indicate to people that we're WormBase staff
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| − | | |
| − | === Disease data display on AGR portal gene page ===
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| − | * Working out a way to drill down from a summary view down to detailed table view
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| − | * Need to make sure it is intuitive and non-jargony for end users
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| − | * Yvonne Bradford drew up some mockups that represent a ribbon or heatmap display of annotations to disease categories for experimental models, etc.
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| − | * We do want a SObA graph; could possibly create a SObA graph that represents annotations to a gene AND all of its orthologs
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| − | | |
| − | === First LEGO call ===
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| − | * This Monday (Jan 23) 11am Pacific
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| − | | |
| − | | |
| − | == January 26, 2017 ==
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| − | | |
| − | === GO-CC annotations to paper term info in OA ===
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| − | * Daniela working on with Juancarlos
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| − | | |
| − | === Disease working group ===
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| − | * Working to finalize the DAF (disease association file)
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| − | * Having extra meeting tomorrow
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| − | * Will then hand over DAF format to Kevin Howe (WB Data Quartermaster)
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| − | * In general, Kevin would prefer AGR files to be generated from the WB build process
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| − | | |
| − | === Expression data working group? ===
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| − | * Daniela asking about an expression working group
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| − | * We don't have one currently, but one could be generated, although it may not make it into AGR portal 0.3, 0.6 or 1.0
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| − | | |
| − | === Coherence, Consistency, and Continuity working group ===
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| − | * Working on a standard for table display in AGR portal
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| − | * Asking for standard functionality
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| − | ** Table filtering, by column
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| − | ** Table sorting, including sort order
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| − | ** Paginated, choosing number of results per page
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| − | ** Download options, tab-delimited and other formats
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| − | ** Link to Intermine, to view, save and manipulate table and lists
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| − | * Currently WormBase has insufficient means to download some lists of results, for example downloading list of RNAi's that cause a lethal phenotype on the "lethal" phenotype page
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| − | ** WB points users to FTP site, without specifying a file or how to parse
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| − | | |
| − | === WormMine vs AGR Intermine ===
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| − | * Is Paulo working on shared/AGR Intermine or just WormMine? We think just WormMine
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| − | * There was an issue with making orthology calls which may have interfered with integrating worm data into common Intermine
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