Difference between revisions of "WBConfCall 2017-07-20-Agenda and Minutes"
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Line 9: | Line 9: | ||
*Testing needed for: | *Testing needed for: | ||
**construct (Karen - responded) | **construct (Karen - responded) | ||
− | **interaction | + | **interaction (Chris) |
− | **pcr_product | + | **pcr_product (Hinxton) |
− | **phenotype | + | **phenotype (Chris) |
**paper (Kimberly - responded) | **paper (Kimberly - responded) | ||
− | **position_matrix | + | **position_matrix (Raymond) |
− | **pseudogene | + | **pseudogene (Hinxton) |
− | **rearrangment | + | **rearrangment (Raymond, Mary Ann?) |
== Open Help Desk Tickets == | == Open Help Desk Tickets == | ||
*[https://github.com/WormBase/website/issues/5759 Need to get additional Phenotype association data into WormMine] | *[https://github.com/WormBase/website/issues/5759 Need to get additional Phenotype association data into WormMine] | ||
Line 27: | Line 27: | ||
= Minutes = | = Minutes = | ||
− | *On call: Adam, Chris, Daniela, Gary, Juancarlos, Karen, Kevin, Kimberly, Michael P., Paolo, Paul S., Ranjana, Raymond, Scott, Sibyl, Todd | + | *On call: Adam, Chris, Daniela, Gary S., Gary W., Juancarlos, Karen, Kevin, Kimberly, Michael P., Paolo, Paul S., Ranjana, Raymond, Scott, Sibyl, Todd |
== Release Announcements == | == Release Announcements == | ||
*In response to some user feedback at the worm meeting, shall we announce our releases outside of WB staff? | *In response to some user feedback at the worm meeting, shall we announce our releases outside of WB staff? | ||
Line 75: | Line 75: | ||
**Retrofit old release notes? | **Retrofit old release notes? | ||
***For now, won't retrofit, but if needed could be done in the future | ***For now, won't retrofit, but if needed could be done in the future | ||
+ | *Summary: | ||
+ | **WS260 will be delayed until August 25th | ||
+ | **WS261 will be released two month after that | ||
+ | **WS262 will follow the same two-month cycle, but upload will be a week earlier to begin to accommodate the five-week build cycle (may need to re-visit this) | ||
+ | == New Datomic Widgets on Staging == | ||
+ | *Adam needs people to test | ||
+ | *Testing needed for: | ||
+ | **construct (Karen - responded) | ||
+ | **interaction (Chris) | ||
+ | **pcr_product (Hinxton) | ||
+ | **phenotype (Chris) | ||
+ | **paper (Kimberly - responded) | ||
+ | **position_matrix (Raymond) | ||
+ | **pseudogene (Hinxton) | ||
+ | **rearrangment (Raymond, Mary Ann?) | ||
+ | == Open Help Desk Tickets == | ||
+ | *[https://github.com/WormBase/website/issues/5756 Can't find the gene info reported in any of the pa...] | ||
+ | **Kimberly answered - need confirmation from Daniela | ||
+ | **Atomized evidence in automated descriptions | ||
+ | *[https://github.com/WormBase/website/issues/5755 Is there somewhere a good explanation of the features in the genome browser?] | ||
+ | **Gary answered - any more we need to do either with display or explanation? | ||
+ | **Scott will take a look at the ticket to see what might be done here to help, e.g. tutorials | ||
+ | == Genomic Coordinates between Releases == | ||
+ | *Do the coordinates change between releases? | ||
+ | *If there's a new assembly (e.g. different Ce versions), there may be new coordinates | ||
+ | == WormMine Update == | ||
+ | *Paolo has WormMine at the point where new data can be added reliably | ||
+ | *WormMine builds are more reliable, robust, stable | ||
+ | *Paolo will solicit suggestions for other data to add; also feel free to contact him directly | ||
+ | *WS260 will have Strains | ||
+ | *Chris and Paolo going over RNAi data; still a few issues to be worked out here | ||
+ | *Chris is also discussing adding Anatomy and Phenotype ontologies so users can perform is_a descendant queries for these ontologies analogous to what can be done with GO | ||
+ | **For Anatomy, will also want to include part_of searches | ||
+ | **Adding new obo files is actually fairly straightforward, but Paolo is working with InterMine developers to make sure all entities associated with an ontology term can be retrieved | ||
+ | *Other new datasets, e.g. gene classes, expanded variation dataset, have been loaded and it would be really helpful to create new templates as these datasets come in | ||
+ | **Tie new templates into Blog posts to help introduce more people to data mining with InterMine | ||
+ | *Also, embed templates, programmatically, into the respective widgets to give people access to be pre-canned queries | ||
+ | **Build an InterMine widget that could be included anywhere? | ||
+ | ***This was done at an InterMine workshop some time ago and it fairly straightforward | ||
+ | **These could be really helpful for retrieving long lists of data, e.g. all genes with lethal phenotypes | ||
+ | *Are single gene queries better served from Datomic? |
Latest revision as of 16:26, 20 July 2017
Agenda
Release Announcements
- maybe we can restart announcing our releases outside of staff@wormbase
WS260 Website Release
- Possibility to delay WS260 website release to Aug 25 (currently scheduled at Aug 4)?
New Datomic Widgets on Staging
- Testing needed for:
- construct (Karen - responded)
- interaction (Chris)
- pcr_product (Hinxton)
- phenotype (Chris)
- paper (Kimberly - responded)
- position_matrix (Raymond)
- pseudogene (Hinxton)
- rearrangment (Raymond, Mary Ann?)
Open Help Desk Tickets
- Need to get additional Phenotype association data into WormMine
- Paul D. answered, but the user was looking for RNAi data in WormMine - a known issue
- Hello, I'm trying to access a paper c...
- Karen and Paul D. answered - Karen is looking into the construct data
- Can't find the gene info reported in any of the pa...
- Kimberly answered - need confirmation from Daniela
- Is there somewhere a good explanation of the features in the genome browser?
- Gary answered - any more we need to do either with display or explanation?
Minutes
- On call: Adam, Chris, Daniela, Gary S., Gary W., Juancarlos, Karen, Kevin, Kimberly, Michael P., Paolo, Paul S., Ranjana, Raymond, Scott, Sibyl, Todd
Release Announcements
- In response to some user feedback at the worm meeting, shall we announce our releases outside of WB staff?
- Ideas:
- Blog
- Rotate turns on the blog?
- Blog could link to the more detailed report of release statistics
- Rotate authorship between Hinxton and Caltech
- The blog post doesn't have to strictly correspond to the release date, but would record the release date for reference
- Forum
- Mailing lists
- wormbase-announce
- should resurrect the announce list
- Website banner
- Blog
- Whatever we decide, this would need to be initiated by OICR
- Suggestions for release email
- Make the email more of a narrative with a link to the statistics, lists
- For the narrative, capture what has been accomplished, substantially, in the latest release
- Provisional version could be posted for comments
- How critical is it for people to know the exact date the release is made live?
- It is important for people to cite/note versions that they searched
- Is there a REST endpoint for determining exactly when a release went live?
- Todd will look into this; may exist, but if not, can be easily made
WS260 Website Release
- May need to be delayed for three weeks past scheduled date
- Why?
- Datomic database was not available until yesterday
- Datomic database is not available until after the official ACeDB release
- Datomic has only recently been considered formally part of the production cycle
- The web developers need a full development cycle to test Datomic, though
- Also noticing some unresponsiveness on the website
- Would like time to track down and address the problem
- Datomic database was not available until yesterday
- WS261 is nearly done, though
- Should we then delay the upload for WS262 or we will be in perpetual catch-up mode
- Todd suggests we push all releases back
- Kevin proposes a slightly longer, five-week build cycle to accommodate having to build Datomic database, as well as ACeDB
- This proposes that we move the data upload one week ahead; the overall cycle would still be eight weeks
- One week is enough to build Datomic?
- But there are still some problems with the data models in Datomic and we can't predict what these issues might be
- Should the release letter (currently sent out) be coordinated with the ACeDB or Datomic database build?
- Who needs to be alerted to the release?
- Doesn't appear to affect Raymond who use automated SOPs to check ftp site daily
- Ranjana likes to know when the files are available for the automated description pipeline
- Matt implemented a Slack-based reporting system that reports the build stages
- The release notes could be converted to a parseable format, e.g. JSON, that allows people to mine for reports
- Retrofit old release notes?
- For now, won't retrofit, but if needed could be done in the future
- Retrofit old release notes?
- Summary:
- WS260 will be delayed until August 25th
- WS261 will be released two month after that
- WS262 will follow the same two-month cycle, but upload will be a week earlier to begin to accommodate the five-week build cycle (may need to re-visit this)
New Datomic Widgets on Staging
- Adam needs people to test
- Testing needed for:
- construct (Karen - responded)
- interaction (Chris)
- pcr_product (Hinxton)
- phenotype (Chris)
- paper (Kimberly - responded)
- position_matrix (Raymond)
- pseudogene (Hinxton)
- rearrangment (Raymond, Mary Ann?)
Open Help Desk Tickets
- Can't find the gene info reported in any of the pa...
- Kimberly answered - need confirmation from Daniela
- Atomized evidence in automated descriptions
- Is there somewhere a good explanation of the features in the genome browser?
- Gary answered - any more we need to do either with display or explanation?
- Scott will take a look at the ticket to see what might be done here to help, e.g. tutorials
Genomic Coordinates between Releases
- Do the coordinates change between releases?
- If there's a new assembly (e.g. different Ce versions), there may be new coordinates
WormMine Update
- Paolo has WormMine at the point where new data can be added reliably
- WormMine builds are more reliable, robust, stable
- Paolo will solicit suggestions for other data to add; also feel free to contact him directly
- WS260 will have Strains
- Chris and Paolo going over RNAi data; still a few issues to be worked out here
- Chris is also discussing adding Anatomy and Phenotype ontologies so users can perform is_a descendant queries for these ontologies analogous to what can be done with GO
- For Anatomy, will also want to include part_of searches
- Adding new obo files is actually fairly straightforward, but Paolo is working with InterMine developers to make sure all entities associated with an ontology term can be retrieved
- Other new datasets, e.g. gene classes, expanded variation dataset, have been loaded and it would be really helpful to create new templates as these datasets come in
- Tie new templates into Blog posts to help introduce more people to data mining with InterMine
- Also, embed templates, programmatically, into the respective widgets to give people access to be pre-canned queries
- Build an InterMine widget that could be included anywhere?
- This was done at an InterMine workshop some time ago and it fairly straightforward
- These could be really helpful for retrieving long lists of data, e.g. all genes with lethal phenotypes
- Build an InterMine widget that could be included anywhere?
- Are single gene queries better served from Datomic?