Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Variation not currently connected to phenotype | * Variation not currently connected to phenotype | ||
* Matt R. is working on it | * Matt R. is working on it | ||
+ | |||
+ | == June 23, 2016 == | ||
+ | ===TAGC=== | ||
+ | ====poster==== | ||
+ | *will be at a shared booth with Flybase and SGD | ||
+ | *unclear on the number of posters, it looks like we should have two | ||
+ | ** Large scale gene expression (SPELL) + Pathways | ||
+ | ** Community annotation + Micropublication | ||
+ | NOTE: this meeting is the C. elegans Development, Cell Biology and Gene Expression Topic meeting. | ||
+ | |||
+ | |||
+ | ====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 |
Revision as of 21:25, 22 June 2016
Contents
Previous Years
2016 Meetings
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
June 23, 2016
TAGC
poster
- will be at a shared booth with Flybase and SGD
- unclear on the number of posters, it looks like we should have two
- Large scale gene expression (SPELL) + Pathways
- Community annotation + Micropublication
NOTE: this meeting is the C. elegans Development, Cell Biology and Gene Expression Topic meeting.
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