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| | [[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]] | | [[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]] |
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| | [[WormBase-Caltech_Weekly_Calls_November_2018|November]] | | [[WormBase-Caltech_Weekly_Calls_November_2018|November]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_December_2018|December]] |
| − | == December 6, 2018 ==
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| − | | |
| − | === SObA for disease (& other ontology?) annotations ===
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| − | * Next Alliance all-hands call in February, present SObA for Skunkworks (innovation talks)?
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| − | * SObA top-slicing (summary view) gets tricky; Raymond looking into better solutions, if available
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| − | * SObA summary could be redundant with ribbon? SObA would provide dynamic, trimmed nodes
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| − | | |
| − | === Worm phenotype ontology ===
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| − | * Meeting today at 12pm Pacific, 3pm Eastern
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| − | * In process of adding back obsolete terms to the ontology
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| − | * Question about "has_obo_namespace" attribute; not required for ODK process; used by WB pipelines?
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| − | | |
| − | === ISB Meeting, Cambridge, UK, April 2019 ===
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| − | * Abstracts from WB?
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| − | ** New Author First Pass - Daniela, Valerio, Kimberly, et al.
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| − | ** Automated gene descriptions - Ranjana, gene description working group
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| − | | |
| − | === GO expression data using Uberon anatomy terms ===
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| − | * Some GO curators curating C. elegans expression annotations (from synapse annotation project) to Uberon anatomy terms, not WBbt terms
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| − | * Kimberly will look into enforcing Noctua editor to use C. elegans anatomy ontology when creating C. elegans annotations
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| − | * Can possibly perform automated mapping if appropriate cross-references exist
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| − | * Kimberly has already found annotations to inappropriate Uberon terms
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| − | | |
| − | | |
| − | == December 13, 2018 ==
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| − | | |
| − | === Protege Tutorial ===
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| − | * Doodle poll open: https://doodle.com/poll/kn49rd3rggymn68g
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| − | * Please fill out poll if you are interested in attending
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| − | * Resources available
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| − | ** here (right-click and Save As): https://www.dropbox.com/s/6fygtby4x6d2t0r/ProtegeShortCourse.zip?dl=0
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| − | ** and here: https://protege.stanford.edu/shortcourse/201810/resources.html
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| − | | |
| − | === Updates to Gene Regulation OA ===
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| − | * Removed two unused fields/tables: Trans-regulator Seq and Trans-regulated Seq
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| − | * (In progress) Now a single field for anatomy, life stage, and subcellular localization (SCL) (as opposed to a set of each for each type of regulation result)
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| − | * May require ?Interaction model change if anatomy, lifestage, and/or SCL to be annotated without a result type
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| − | | |
| − | === Micropublication workshop IWM 2019 ===
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| − | * Micropublication group will apply for a workshop
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| − | * If they get it they will need a tiny (~5 min) slot in the general WB
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| − | | |
| − | === RNAi uniquely_mapped tags ===
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| − | * User pointed out that an RNAi object in WormMine was not flagged as "Uniquely mapped"
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| − | * Turns out that the current RNAi mapping pipeline does not add a "Uniquely_mapped" tag
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| − | * All existing tags are coming from older RNAi objects in CitaceMinus
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| − | * Chris working on .ACE file to delete all of these tags from CitaceMinus
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| − | * Chris will upload the .ACE file to citpub@spica in the Data_for_midbuild directory for Wen
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| − | | |
| − | === Worm wiring & Worm Atlas ===
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| − | * Todd and Raymond meeting this afternoon
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| − | * Chris will join
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| − | * 2pm Pacific time
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| − | | |
| − | === WS270 upload ===
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| − | * Jan 11th upload to Hinxton
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| − | * Tuesday, January 8th citace upload 10am
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| − | | |
| − | === Alliance grant renewal ===
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| − | * Send Paul drafts for working group updates before next Thursday Dec 20, just to give him a heads up on content
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| − | * Paul currently working off All-Hands meeting presentations
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| − | | |
| − | === Alliance vs. MODs efficiencies ===
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| − | * Compare user pipelines for getting info like:
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| − | ** for a human disease gene, what are the phenotypes in model organisms?
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| − | * What are the best work products of the Alliance so far?
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| − | ** Expression ribbon
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| − | ** Orthology
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| − | ** Molecular interactions? Good to have nicer interface, consolidation of data; no automated comparative tools yet, but can get equivalent results with some clicking
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| − | ** How to best measure impact?
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| − | | |
| − | === Noctua imports ===
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| − | * Can we export/duplicate a Noctua model to apply to a different gene?
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| − | * Can export in GPAD or GAF
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| − | * Want to seed Noctua models with MOD data; efficient, large scale import
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| − | | |
| − | == December 20, 2018 ==
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| − | | |
| − | === Authors, Papers, Meeting Abstracts ===
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| − | *https://github.com/WormBase/website/issues/6802
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| − | *Authors on older (i.e. 2000) meeting abstracts don't always have associated WBPerson objects
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| − | **Anything we can/should do about this?
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| − | *Author on some older abstracts are also listed First Name Last Name as opposed to Last Name, First Name
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| − | **This results in display errors - Todd and Sibyl will try to fix this
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| − | **Any way to fix the source data via script?
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| − | *Can meeting abstracts be added to TPC?
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| − | *Some WB users are still using the old Textpresso. Put a message on that site that it will soon be retired?
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| − | **The old Textpresso site is what comes up first in a Google search for 'textpresso'.
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| − | *Other suggestions from Jonathan:
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| − | **Having the possibility to restrict a search to a given field (e.g. title) and being able to rank the different columns in the results (i.e. by journal or year, etc, not just Doc score) would be welcome.
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