WormBase-Caltech Weekly Calls October 2018
From WormBaseWikiJump to navigationJump to search
- 1 October 4, 2018
- 2 October 11, 2018
- 3 October 18, 2018
- 4 October 25, 2018
October 4, 2018
- 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)
- 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 for WS269
- 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)
New SPELL server
- New server on Amazon (modifying server SGD uses)
- Raymond, Wen, and Todd working on
- Currently only have an SGD mirror running
- Wen will swap the data later today
- WormBase header link (to WormBase) or only link to Alliance site? We want a unified site for Alliance
- Each MOD would still support their own server for their data (MOD-specific grants support each server, for now)
Alliance expression data
- Anatomy-LifeStage pair required for Alliance expression annotations
- Since many expression pattern annotations don't have both, the missing entity would default to ontology root term
- Need to link anatomy root term to Uberon for ribbon display; root term annotations fall under the "Other" category in the ribbon slim
- Create "Anatomical_part" term to serve as the default "Other"/root term?
- All life-stage-only annotations will fall into anatomy "Other" and flood the list; should these be filtered out?
October 25, 2018
WormBase SPELL on Amazon Web Service
- http://18.104.22.168/ is running WormBase SPELL on WS267, based on the SPELL code supported by SGD. It is more stable and faster than the current Caltech server.
- Waiting for Todd to respond if we can use this site as the official server for WormBase SPELL.
- Also need to get an instance (preferably also from WormBase AWS as a development site of WormBase SPELL.
- Caltech will focus on generating new data instead of SPELL code development.
Linking annotation evidence to Anatomy Ontology Browser
Each gene expression annotation shown on WOBr is linked to the object so that users can more easily examine the evidence. Example