Difference between revisions of "WormBase-Caltech Weekly Calls"

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

Revision as of 16:11, 3 January 2019