Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
(9 intermediate revisions by 2 users not shown)
Line 40: Line 40:
 
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
 
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
 +
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
==August 6th, 2020==
 
  
===Experimental conditions data flow into Alliance===
+
== September 3, 2020 ==
*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
 
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
 
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
 
*So for data flow into Alliance:
 
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
 
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
 
* How do we handle genetic sex? Part of condition?
 
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
 
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
 
 
 
 
 
== August 13, 2020 ==
 
 
 
=== Species in Postgres and ACEDB/Datomic ===
 
* Want to dump "Affected By Pathogen" fields in Phenotype OA and RNAi OA
 
* Want to be sure that what gets dumped aligns with species loaded into ACEDB
 
* Currently one species annotated not in WS277: Streptococcus gallolyticus subsp. gallolyticus
 
* We currently have multiple Postgres tables for storing species lists:
 
** pap_species_index (used by "Affected By Pathogen" fields, AFP); Kimberly uses to assign species to papers and occasionally adds new ones
 
** obo_name_ncbitaxonid
 
** obo_name_taxon (original, smaller list)
 
** h_pap_species_index (history for pap_species_index)
 
* How do species get loaded into ACEDB? Dumps from Postgres? Which table(s)?
 
* WS277 has 7,906 species (1,936 have no NCBI Taxon ID)
 
* Kimberly has occasionally uploaded a species.ace file in the context of GO curation; but Hinxton otherwise handles it; should ask them
 
* New species are associated with paper objects, but otherwise no additional data for those species come from Caltech
 
* It might be useful to have species pages in WB that at least list papers for which we have species associations, maybe include other information?
 
  
 
=== WS279 Citace upload ===
 
=== WS279 Citace upload ===
* When is it happening? Not sure; not on release schedule right now
+
* September 25
 
+
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
=== SOLR server security (IMSS) ===
 
* IMSS network security blocked network on our server due to its open SOLR web access.
 
* Part of AMIGO stack, very old version, drives our ontology browser directly, SObA, Enrichment tools indirectly.
 
* Added some firewall/URL filter and IMSS opens up the network (for now). IMSS still gripes about its service is open to the world.
 
 
 
=== Alzheimer's disease portal ===
 
* Supplement grant awarded to Alliance for an Alzheimer's disease portal
 
* Could involve automated/concise descriptions, interactions, etc.
 
* Could establish useful pipelines that could be reused in other contexts
 
 
 
 
 
==August 20th, 2020==
 
 
 
=== Handling sex (male/hermaphrodite) in Expression ===
 
* In Alliance Expression group, talking about how to handle sex in expression annotations
 
* In WB, will start collecting sex in a separate field (rather than integrated into ontology terms)
 
* Daniela will capture sexually dimorphic expression in remarks/comments
 
* Will eventually figure out how to handle/display at the Alliance
 
* Daniela will go back to existing annotations to fix data retroactively
 
 
 
=== Alliance webinars ===
 
* We won't present at Caltech BBE retreat
 
* Maybe we can present later in the academic year
 
 
 
=== WormBase build ===
 
* WS277 took about 3 months
 
* If this is a general change (we need 3 months for each build), then we should reconsider our release schedule
 
* This was largely due to technical issues at EBI out of our control
 
* Really helpful for curators to know when we can expect to have to upload; maybe sliding schedule doesn't work for CIT
 
* Proposal: Take 3 months for the next two releases and readjust in the new year; Wen will email Hinxton
 
 
 
  
==August 27th, 2020==
+
=== New AFP datatype for curation status form (CSF)? ===
 +
* afp_othergenefunc (to capture gene function other than enzymatic activity)
 +
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
  
=== Textpresso knockout allele counter ===
+
=== GO annotation for description ===
* Ann Rougvie asked if Textpresso could pull out references to knockout alleles (from deletion project) in C. elegans literature
+
* Kimberly will look into 'male tail tip developement' terms for description
* Valerio has a tool setup for the analysis
 
  
=== OA bug; joinkeys with multiple entries ===
+
=== Migrate wobr1 server to AWS ===
* Stumbled on while querying the app_anatomy
+
* SOLR, WOBr, SObA, Enrichment analysis
* Turns out there are several PG joinkeys associated with multiple entries (should only ever be one)
+
* Working with Sibyl on the process
* Only latest entry shows up in OA; often there is one entry (single term or list) plus additional blank entries
+
* Will try migrating wobr1 first, as a test case
* Blank entries could be latest and so show up in OA and in Postgres queries
+
* May eventually move, for example, Tazendra
* Not clear where the problem originated; maybe some script to populate the OA
+
** Will there be drawbacks to doing this?
* Karen: would be good to have an immediate report of such instances after they occur
+
** Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
* Would be good to sort out if the OA has a problem or if there is a script/cronjob that is creating the issues (or some of the issues)
+
* Don't yet know the details of the costs, but we can try and keep track
* Looking at timestamps can give a clue
+
* We should move into WB or Alliance AWS instances (or Stanford)
** for app_anatomy, the issues only occurred in 2008 and a few in 2010
 
** Also, if timestamps are very close to each other for many entries, likely a script is doing it
 
* Action item: clean up data and then Juancarlos will make cronjob to check for the issue every day going forward
 
  
=== SObA Graph ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* New spacing parameters set to make nodes appear closer together; makes default view more readable
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Can we move the SObA graph to the bottom of the widget? Users may want to see primary data in the table first
+
* Meeting will be virtual on Zoom
* Graph can take time to load
+
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
* Could hide the SObA graph by default with a button/icon to allow users to open it
+
* Send topic requests to Chris for the talk
 +
* Current topics:
 +
** Micropublications
 +
** Author First Pass
 +
** Automated Gene Descriptions
 +
** Community Curation
 +
** WB Query Tools
 +
* Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
 +
* If the organizers record the talk, we can post it on the blog and WB YouTube channel

Revision as of 16:57, 3 September 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July

August


September 3, 2020

WS279 Citace upload

  • September 25
  • Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific

New AFP datatype for curation status form (CSF)?

  • afp_othergenefunc (to capture gene function other than enzymatic activity)
  • Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later

GO annotation for description

  • Kimberly will look into 'male tail tip developement' terms for description

Migrate wobr1 server to AWS

  • SOLR, WOBr, SObA, Enrichment analysis
  • Working with Sibyl on the process
  • Will try migrating wobr1 first, as a test case
  • May eventually move, for example, Tazendra
    • Will there be drawbacks to doing this?
    • Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
  • Don't yet know the details of the costs, but we can try and keep track
  • We should move into WB or Alliance AWS instances (or Stanford)

WormBase talk at Boston Area Worm Meeting

  • https://www.umassmed.edu/ambroslab/meetings/bawm/
  • Meeting will be virtual on Zoom
  • Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
  • Send topic requests to Chris for the talk
  • Current topics:
    • Micropublications
    • Author First Pass
    • Automated Gene Descriptions
    • Community Curation
    • WB Query Tools
  • Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
  • If the organizers record the talk, we can post it on the blog and WB YouTube channel