|
|
Line 41: |
Line 41: |
| [[WormBase-Caltech_Weekly_Calls_September_2018|September]] | | [[WormBase-Caltech_Weekly_Calls_September_2018|September]] |
| | | |
− | | + | [[WormBase-Caltech_Weekly_Calls_October_2018|October]] |
− | == 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 ===
| |
− | * http://34.224.93.60/ 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]
| |