WormBase-Caltech Weekly Calls August 2020

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