WormBase-Caltech Weekly Calls

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February 11, 2016

Postgres data not in ACEDB

  • Should we this data get into ACEDB to be converted to Datomic (via the existing pipeline)? Maybe, but only temporarily
  • We will need to learn to model in Datomic to start building curation tools that run off of Datomic
  • Juancarlos has access to Colonnade & trAceView (table maker tool and web interface to view Datomic data like in ACEDB)
  • For long term, we will want to build a curation tool directly on top of Datomic; will need to model currently un-dumped fields in Datomic
  • Juancarlos has a few action items to test reading from and writing to Datomic in a simple manner
  • Paper editor may be best form to start Datomic transition, since it doesn't deal with N1-objects changing with N2-other-objects
  • Bulk updates of data not edited through the OA may be another good starting point, as those pipelines will need to change Datomic directly

CITace upload

  • Upload files to Wen by Tuesday Feb 16, 10am

Life stage ontology update

  • To accommodate flat worms, will make "worm life stage" root node with "platyhelminth (flatworm)..." and "nematode (roundworm)..." children


  • Data in OA's has timestamp history, but all data first imported in bulk has one 'epoch' timestamp
  • Chris looking into older timestamps from older versions of WS/ACEDB
  • Will be good to clarify how older timestamps will be stored in Datomic going forward (i.e. a timestamp field separate from a Datomic intrinsic timestamp?)
  • Would be best to have as many original timestamps as possible

February 18, 2016

Automated descriptions

  • Plan is to phase-out the manually written descriptions
  • ubc-9 gene had old (2004) manually written description but no automated description (Wen)
  • Eventually we would want all descriptions to be automated; we can't maintain manual descriptions for all genes
  • Kimberly and Ranjana will review older descriptions to see what else can be automated

Upload summary

  • Wen updated language for each line of the Citace upload summary to be more human readable

SObA legend

  • Updated SObA legend to include an indicator of what the arrows indicate

Transgenome data

  • Daniela asking for the data from labs (Mihail Sarov)

WS254 upload

  • When is the next data upload? End of March? End of April?

February 25, 2016

Transgenome project

  • Sibyl and Daniela spoke with lab
  • Will setup an API for continuous updates of data
  • ~14,000 constructs (~14,000 genes), ~300 analyzed so far, ~3,000 pictures so far
  • WormBase will receive regular updates of Expr_pattern objects as .ACE
    • Expr_pattern objects from the project will not be touched locally by WB curators; only using their forms
  • We will get a one-time dump of all transgenes and constructs that we can edit locally

Expression cluster anatomy data

  • Would like to add anatomy expression data from expression clusters to GAF
  • Using enrichment status for new lines in GAF
  • May need more evidence codes to accommodate; Inferred from Expression Pattern (IEP) usage vs. Inferred from Direct Assay (IDA). Kimberly advised IDA is appropriate for gene expression data.


  • Trying to restore time stamps for older annotations that are not accurately captured in Postgres timestamps
  • Wen rebuilding old releases; we only want to restore time stamps for object creation, not detailed attributes

Objectifying phenotype annotations

  • Chris thinking about objectifying allele-phenotype and transgene-phenotype annotations
  • Would make it easier to query out annotation-specific data
  • Chris and Juancarlos will work to consider future querying difficulties in Datomic

Caprica revived

  • Running Ubuntu 14
  • Has 20GB memory, could have up to 24GB
  • Could be used for other projects, like testing Datomic