Difference between revisions of "WormBase-Caltech Weekly Calls"

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==August 6th, 2020==
===Experimental conditions data flow into Alliance===
*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 ===
* When is it happening? Not sure; not on release schedule right now
=== 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==
=== Textpresso knockout allele counter ===
* Ann Rougvie asked if Textpresso could pull out references to knockout alleles (from deletion project) in C. elegans literature
* Valerio has a tool setup for the analysis
=== OA bug; joinkeys with multiple entries ===
* Stumbled on while querying the app_anatomy
* Turns out there are several PG joinkeys associated with multiple entries (should only ever be one)
* Only latest entry shows up in OA; often there is one entry (single term or list) plus additional blank entries
* Blank entries could be latest and so show up in OA and in Postgres queries
* Not clear where the problem originated; maybe some script to populate the OA
* Karen: would be good to have an immediate report of such instances after they occur
* 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)
* Looking at timestamps can give a clue
** 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 ===
* New spacing parameters set to make nodes appear closer together; makes default view more readable
* Can we move the SObA graph to the bottom of the widget? Users may want to see primary data in the table first
* Graph can take time to load
* Could hide the SObA graph by default with a button/icon to allow users to open it

Revision as of 15:40, 3 September 2020