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_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