Difference between revisions of "WormBase-Caltech Weekly Calls"
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=== Expression cluster anatomy/life-stage data === | === Expression cluster anatomy/life-stage data === | ||
− | * Would like to add anatomy | + | * Would like to add anatomy expression data from expression clusters to GAF |
* Using enrichment status for new lines in 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) | + | * 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 === | === Timestamps === |
Revision as of 23:09, 25 February 2016
Contents
Previous Years
2016 Meetings
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
Timestamps
- 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/life-stage 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