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| | [[WormBase-Caltech_Weekly_Calls_July_2020|July]] | | [[WormBase-Caltech_Weekly_Calls_July_2020|July]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_August_2020|August]] |
| − | ==August 6th, 2020==
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| − | ===Experimental conditions data flow into Alliance===
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| − | *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)
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| − | *We use the WB Molecule CV for Inducers and Modifiers in disease annotation
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| − | *Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
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| − | *So for data flow into Alliance:
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| − | **In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
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| − | **Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
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| − | * How do we handle genetic sex? Part of condition?
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| − | ** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
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| − | ** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
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| − | | |
| − | | |
| − | == August 13, 2020 ==
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| − | | |
| − | === Species in Postgres and ACEDB/Datomic ===
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| − | * Want to dump "Affected By Pathogen" fields in Phenotype OA and RNAi OA
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| − | * Want to be sure that what gets dumped aligns with species loaded into ACEDB
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| − | * Currently one species annotated not in WS277: Streptococcus gallolyticus subsp. gallolyticus
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| − | * We currently have multiple Postgres tables for storing species lists:
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| − | ** pap_species_index (used by "Affected By Pathogen" fields, AFP); Kimberly uses to assign species to papers and occasionally adds new ones
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| − | ** obo_name_ncbitaxonid
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| − | ** obo_name_taxon (original, smaller list)
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| − | ** h_pap_species_index (history for pap_species_index)
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| − | * How do species get loaded into ACEDB? Dumps from Postgres? Which table(s)?
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| − | * WS277 has 7,906 species (1,936 have no NCBI Taxon ID)
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| − | * Kimberly has occasionally uploaded a species.ace file in the context of GO curation; but Hinxton otherwise handles it; should ask them
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| − | * New species are associated with paper objects, but otherwise no additional data for those species come from Caltech
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| − | * 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?
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| − | | |
| − | === WS279 Citace upload ===
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| − | * When is it happening? Not sure; not on release schedule right now
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| − | | |
| − | === SOLR server security (IMSS) ===
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| − | * IMSS network security blocked network on our server due to its open SOLR web access.
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| − | * Part of AMIGO stack, very old version, drives our ontology browser directly, SObA, Enrichment tools indirectly.
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| − | * Added some firewall/URL filter and IMSS opens up the network (for now). IMSS still gripes about its service is open to the world.
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| − | | |
| − | === Alzheimer's disease portal ===
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| − | * Supplement grant awarded to Alliance for an Alzheimer's disease portal
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| − | * Could involve automated/concise descriptions, interactions, etc.
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| − | * Could establish useful pipelines that could be reused in other contexts
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| − | | |
| − | | |
| − | ==August 20th, 2020==
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| − | | |
| − | === Handling sex (male/hermaphrodite) in Expression ===
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| − | * In Alliance Expression group, talking about how to handle sex in expression annotations
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| − | * In WB, will start collecting sex in a separate field (rather than integrated into ontology terms)
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| − | * Daniela will capture sexually dimorphic expression in remarks/comments
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| − | * Will eventually figure out how to handle/display at the Alliance
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| − | * Daniela will go back to existing annotations to fix data retroactively
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| − | | |
| − | === Alliance webinars ===
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| − | * We won't present at Caltech BBE retreat
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| − | * Maybe we can present later in the academic year
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| − | | |
| − | === WormBase build ===
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| − | * WS277 took about 3 months
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| − | * If this is a general change (we need 3 months for each build), then we should reconsider our release schedule
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| − | * This was largely due to technical issues at EBI out of our control
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| − | * Really helpful for curators to know when we can expect to have to upload; maybe sliding schedule doesn't work for CIT
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| − | * Proposal: Take 3 months for the next two releases and readjust in the new year; Wen will email Hinxton
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| − | | |
| − | | |
| − | ==August 27th, 2020==
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| − | | |
| − | === Textpresso knockout allele counter ===
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| − | * Ann Rougvie asked if Textpresso could pull out references to knockout alleles (from deletion project) in C. elegans literature
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| − | * Valerio has a tool setup for the analysis
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| − | | |
| − | === OA bug; joinkeys with multiple entries ===
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| − | * Stumbled on while querying the app_anatomy
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| − | * Turns out there are several PG joinkeys associated with multiple entries (should only ever be one)
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| − | * Only latest entry shows up in OA; often there is one entry (single term or list) plus additional blank entries
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| − | * Blank entries could be latest and so show up in OA and in Postgres queries
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| − | * Not clear where the problem originated; maybe some script to populate the OA
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| − | * Karen: would be good to have an immediate report of such instances after they occur
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| − | * 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)
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| − | * Looking at timestamps can give a clue
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| − | ** for app_anatomy, the issues only occurred in 2008 and a few in 2010
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| − | ** Also, if timestamps are very close to each other for many entries, likely a script is doing it
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| − | * Action item: clean up data and then Juancarlos will make cronjob to check for the issue every day going forward
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| − | | |
| − | === SObA Graph ===
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| − | * New spacing parameters set to make nodes appear closer together; makes default view more readable
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| − | * Can we move the SObA graph to the bottom of the widget? Users may want to see primary data in the table first
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| − | * Graph can take time to load
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| − | * Could hide the SObA graph by default with a button/icon to allow users to open it
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