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| − | == February 11, 2016 ==
| + | [[WormBase-Caltech_Weekly_Calls_February_2016|February]] |
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| − | === Postgres data not in ACEDB ===
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| − | * Should we this data get into ACEDB to be converted to Datomic (via the existing pipeline)? Maybe, but only temporarily
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| − | * We will need to learn to model in Datomic to start building curation tools that run off of Datomic
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| − | * Juancarlos has access to Colonnade & trAceView (table maker tool and web interface to view Datomic data like in ACEDB)
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| − | * 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
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| − | * Juancarlos has a few action items to test reading from and writing to Datomic in a simple manner
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| − | * Paper editor may be best form to start Datomic transition, since it doesn't deal with N1-objects changing with N2-other-objects
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| − | * Bulk updates of data not edited through the OA may be another good starting point, as those pipelines will need to change Datomic directly
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| | | | |
| − | === CITace upload ===
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| − | * Upload files to Wen by Tuesday Feb 16, 10am
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| − | === Life stage ontology update === | + | == March 3, 2016 == |
| − | * To accommodate flat worms, will make "worm life stage" root node with "platyhelminth (flatworm)..." and "nematode (roundworm)..." children
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| − | === Timestamps === | + | === Topic 1 === |
| − | * Data in OA's has timestamp history, but all data first imported in bulk has one 'epoch' timestamp
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| − | * Chris looking into older timestamps from older versions of WS/ACEDB
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| − | * 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?)
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| − | * Would be best to have as many original timestamps as possible
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| − | == February 18, 2016 == | + | === Topic 2 === |
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| − | === Automated descriptions === | |
| − | * Plan is to phase-out the manually written descriptions
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| − | * ubc-9 gene had old (2004) manually written description but no automated description (Wen)
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| − | * Eventually we would want all descriptions to be automated; we can't maintain manual descriptions for all genes
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| − | * Kimberly and Ranjana will review older descriptions to see what else can be automated
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| − | | |
| − | === Upload summary ===
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| − | * Wen updated language for each line of the Citace upload summary to be more human readable
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| − | | |
| − | === SObA legend ===
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| − | * Updated SObA legend to include an indicator of what the arrows indicate
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| − | | |
| − | === Transgenome data ===
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| − | * Daniela asking for the data from labs (Mihail Sarov)
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| − | | |
| − | === WS254 upload ===
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| − | * When is the next data upload? End of March? End of April?
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| − | | |
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| − | == February 25, 2016 ==
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| − | | |
| − | === Transgenome project ===
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| − | * Sibyl and Daniela spoke with lab
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| − | * Will setup an API for continuous updates of data
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| − | * ~14,000 constructs (~14,000 genes), ~300 analyzed so far, ~3,000 pictures so far
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| − | * WormBase will receive regular updates of Expr_pattern objects as .ACE
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| − | ** Expr_pattern objects from the project will not be touched locally by WB curators; only using their forms
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| − | * We will get a one-time dump of all transgenes and constructs that we can edit locally
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| − | | |
| − | === Expression cluster anatomy data ===
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| − | * Would like to add anatomy expression data from expression clusters to GAF
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| − | * Using enrichment status for new lines in GAF
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| − | * 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.
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| − | | |
| − | === Timestamps ===
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| − | * Trying to restore time stamps for older annotations that are not accurately captured in Postgres timestamps
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| − | * Wen rebuilding old releases; we only want to restore time stamps for object creation, not detailed attributes
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| − | | |
| − | === Objectifying phenotype annotations ===
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| − | * Chris thinking about objectifying allele-phenotype and transgene-phenotype annotations
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| − | * Would make it easier to query out annotation-specific data
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| − | * Chris and Juancarlos will work to consider future querying difficulties in Datomic
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| − | | |
| − | === Caprica revived ===
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| − | * Running Ubuntu 14
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| − | * Has 20GB memory, could have up to 24GB
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| − | * Could be used for other projects, like testing Datomic
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