WormBase-Caltech Weekly Calls

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2016 Meetings

January

February

March

April

May


June 23, 2016

TAGC

poster

swag

  • bags from past IWM - how many, how would we get them to Orlando - Sarah ships them?
  • SGD will have bottle openers
  • tattoos?
  • special gifts? SGD will have hats (50); do we have any fly swatters left? If so, how many?
  • coloring book publishing


June 2, 2016

SimpleMine

  • Wen will create ticket to create wormbase.org URL
  • Will go under Tools menu
  • Ranjana will make blog post once it is live

Postgres Timestamps

  • Wen, Chris, and Juancarlos have been working on updating older timestamps for OA entries in Postgres
  • For OA entries generated upon creation of some OA's, the Postgres timestamp is the data of OA creation, not the original data of the object
  • Chris identified all objects from various OAs that had the same initial import timestamp, Wen determined the original ACEDB timestamps for those objects, and Juancarlos is updating the OA entries (curator timestamps) to reflect the object's original timestamp
  • This will be good for consistency going forward and for tracking history of object generation over time

Transgenome project

  • Daniela spoke to developer on project
  • They're fixing/cleaning up data on their end
  • Working on mapping fosmids to latest release of WormBase
  • Probably will import data in a month

UMOD phenotype call yesterday

  • Discussed phenotype data associations
  • Many MODs curate phenotypes to genotype; cannot always make direct, unambiguous associations to a single gene
  • SGD curate to gene, using controlled vocabulary
  • Monarch phenotype data exchange format; can include many levels of detail
  • Common challenge: identifying the single causative agent/mutation

June 9, 2016

SimpleMine

  • Wen will make it work off current (live) release of WormBase
  • Do we want to make it more versatile? Add features to specify information to retrieve (specify columns)?
  • Maybe later, but is sufficient for now
  • WormBase official [URL| <http://www.wormbase.org/tools/mine/simplemine.cgi>]
  • Is there a gene # limit? Will test
  • Wen wants to add WormPep ID column; needs to retrieve all WormPep IDs for a gene

Flagging papers for species

  • Going forward, Kimberly, Jane, and Michael will manually flag papers for species
  • Retroactively, papers will be flagged by scripts
  • ~1000 papers not flagged as C. elegans, but likely mentioned in body of paper; Kimberly reviewing
  • These papers often don't have curatable data

Associating genotypes to phenotypes

  • There is increasing need to annotate phenotypes to complex genotypes (not just single alleles/genes, etc.)
  • MGI captures genotype-to-phenotype connections, but can't always attribute a single causative gene
  • We can capture complex genotype phenotypes in interaction objects, but it may be vague to end users
  • Chris will draw up use cases and generate a data model proposal to accommodate

Topic for next curator call

  • Still being voted on via Slack poll
  • Should Doug and Karen decide topic?
  • We need to define/narrow the topic to cover in one hour
  • What are common/different annotations captured by DBs? What data model/infrastructure changes would be required to come to common ground?
  • Paul S. will discuss with Karen and Doug about topics


June 16, 2016

SimpleMine on WB frontpage?

  • Wen has asked to put it under the Tools menu

Curating phenotypes to complex genotypes

  • Should we objectify phenotype experiments, much like ?RNAi objects
  • This would allow encapsulation of genotype elements and phenotype info
  • Curators could explicitly state causative gene in a transgene, but keep automated mapping for RNAi, alleles, and rearrangements
  • Chris will work on data model
  • This may mean we want to eventually merge the Phenotype OA and the RNAi OA

Datomic queries

  • Variation not currently connected to phenotype
  • Matt R. is working on it