Difference between revisions of "WormBase-Caltech Weekly Calls"

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== 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
** https://github.com/obophenotype/c-elegans-phenotype-ontology
* Edits should only be made to the edit file
** https://github.com/obophenotype/c-elegans-phenotype-ontology/blob/master/src/ontology/wbphenotype-edit.owl
* 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 ===
* 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.
[https://juancarlos.wormbase.org/tools/ontology_browser/show_genes?focusTermName=neuron&focusTermId=WBbt:0003681 Example]

Revision as of 15:54, 1 November 2018