Difference between revisions of "WormBase-Caltech Weekly Calls"
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* WS269 citace upload Tuesday, November 13 | * WS269 citace upload Tuesday, November 13 | ||
* Can we add upload dates to Google calendar for WormBase? | * Can we add upload dates to Google calendar for WormBase? | ||
+ | |||
+ | |||
+ | == October 18, 2018 == | ||
+ | |||
+ | === Upload === | ||
+ | * To Hinxton Nov 16 | ||
+ | * Citace upload to Wen Nov 13 | ||
+ | |||
+ | === Data provenance in WOBr tools === | ||
+ | * Juancarlos and Raymond have been working on | ||
+ | * Awaiting pull request | ||
+ | * Can test: juancarlos.wormbase.org | ||
+ | ** Go to WOBr and test anatomy ontology | ||
+ | ** Now WOBr gene count results show data objects from which the associations come (Expr_pattern and Expression_cluster objects) |
Revision as of 15:48, 18 October 2018
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2018 Meetings
October 4, 2018
SimpleMine
- Automated descriptions will be removed from Postgres/OA
- SimpleMine needed to update where it pulls the automated descriptions from
- Will add expression cluster and automated description columns output (in addition to concise description)
- Added RNAseq FPKM download function for 9 species: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/fpkmmine.cgi
- Added SimpleMine-like topic search: http://tazendra.caltech.edu/%7Eazurebrd/cgi-bin/forms/spellmine.cgi
- Should put the new tools under the WormBase Tools menu
October 11, 2018
Ready for new round of phenotype requests
- Some users are getting confused about the name & email prepopulation based on IP address
- May want to stop autopopulating name and email or autopopulate based on email recipient only (encode in URL sent in email)
- Could we use cookies? Possibly, but may only help if a computer is shared but the browser isn't
- Current autocomplete expects exact match to person primary name; e.g. "Scott Emmons" will not match the official name "Scott Wilson Emmons"
- Maybe we could improve search matching; algorithm from Cecilia/Juancarlos? Elastic search by Valerio?
- Can we capture incomplete sessions? We may be able to learn from them. May be flooded by robot visits? Is it worth going through all the logs/sessions? Info is there if we want to look at it.
- Will go ahead and send emails for only new set of papers (won't resend requests for papers that had emails sent in June/July)
- Maybe go back to papers that already had a request sent at the 6 month time point
- Include other papers in need of curation at bottom of email; possibly, would it turn off users?
Worm Phenotype Ontology
- WPO has a new home on GitHub
- Edits should only be made to the edit file
- Anyone interested in contributing to the WPO should contact Chris for update pipeline info
- Need to make sure that all users of the WPO have the updated link information
Provide provenance in query tools
- Prompted by user question/request
- Specifically in WOBr, Anatomy pages
- WOBr provides genes annotated to term; should provide provenance of each gene and its annotations
- Expression pattern and expression cluster gene lists (in context of Anatomy WOBr); want to provide provenance for this data
- Provenance = an object ID, like "Expr1234" or "WBPaper00032062:age_regulated_genes" with link to relevant page
WOBr disease associations
- Ranjana wondering if WOBr is using updated disease-gene associations
- Gene association file (for disease) being generated by script; likely need to update where the data is coming from
- Ranjana will discuss with Raymond and Kevin
New WormMine superuser
- Now all template queries are owned by a new superuser
- If people are interested in adding or editing templates talk to Chris or Paulo for superuser access
- We were running into login, template ownership, and consistency issues
Next upload Nov 16
- WS269 citace upload Tuesday, November 13
- Can we add upload dates to Google calendar for WormBase?
October 18, 2018
Upload
- To Hinxton Nov 16
- Citace upload to Wen Nov 13
Data provenance in WOBr tools
- Juancarlos and Raymond have been working on
- Awaiting pull request
- Can test: juancarlos.wormbase.org
- Go to WOBr and test anatomy ontology
- Now WOBr gene count results show data objects from which the associations come (Expr_pattern and Expression_cluster objects)