|
|
Line 20: |
Line 20: |
| | | |
| | | |
− | == February 11, 2016 ==
| + | [[WormBase-Caltech_Weekly_Calls_February_2016|February]] |
| | | |
− | === 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 === | + | == March 3, 2016 == |
− | * To accommodate flat worms, will make "worm life stage" root node with "platyhelminth (flatworm)..." and "nematode (roundworm)..." children
| |
| | | |
− | === Timestamps === | + | === Topic 1 === |
− | * 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 == | + | === Topic 2 === |
− | | |
− | === 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.
| |
− | | |
− | === Timestamps ===
| |
− | * 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
| |