Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
== June 6, 2019 ==
 
  
=== New SObA graphs ===
+
== July 11th, 2019 ==
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
 
  
=== Phenotype association file format ===
+
=== Alliance all hands meeting ===
* May be best to leave the format as is
+
* Raymond: would be interested in discussing ontologies and their usage in the Alliance
* There are problems; paper IDs keep switching columns
+
** Phenotype, anatomy ontologies, GO, etc.
* Would need to revisit the reasoning for why we do it that way
+
** Ontology browsers, SObA
* When will the Alliance produce a similar/replacement file? Not sure
 
  
=== Phenotype requests ===
+
=== IWM workshop ===
* Sent out 1140 emails on May 30
+
* Videos ready for upload
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
+
* Wen and Raymond now have access to outreach@wormbase.org account; will upload videos
* 21 papers flagged as not having phenotypes
 
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
 
  
 
+
=== Protocol videos ===
== June 13, 2019 ==
+
* Wen met Craig Mello at the IWM; he is interested in putting up microinjection videos online; linkable from WormBase?
 
+
* Can make each video a Video Weblog so people can make comments, etc.
=== IWM ===
 
* Coordinating transportation of swag boxes to Pauley Pavilion
 
* Workshop on Saturday June 22, from 1pm to 2:30pm
 
* Saturday morning micropublication breakfast 7:30 - 8:30am
 
* Workshop
 
** Presenters: it may be best to present as use cases rather than a research project
 
** Chris will cover SimpleMine for Wen
 
** Chris: won't do live demo; only screenshots, maybe some video
 
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
 
* Paul's talk
 
** Cover Alliance
 
** New features
 
*** SObA (for new data)
 
*** Complete for protein-protein interactions
 
*** RNASeq tools
 
*** Updated automated gene concise descriptions?
 
** Phenotype community curation
 
*** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
 
** Author First Pass
 
** Micropublication
 
 
 
=== SGD SAB ===
 
* Paul attended
 
* Alliance publicity was discussed
 
* SAB likes the Alliance orthology features
 
* Working on topics: displaying papers and data
 
* Pathways: discussion about best approach
 
* Metabolic engineering
 
* Meta data about RNASeq data
 
** SPELL tool, basically only tool of its kind available; need new tools
 
* Species-specific proteins: how best to find them? HMMs (Jackhammer)?
 
 
 
=== Concise descriptions ===
 
* Progress being made within the Alliance to update the automated concise gene descriptions
 
* We will still accept manually written descriptions and display them in parallel with automated descriptions
 
 
 
=== Micropublications ===
 
* If people are requesting manually written gene descriptions, they could submit a microreview
 
* Concern was expressed about how to handle a really high throughput of submissions:
 
** Daniela: Working towards automating as much of the processing pipeline as possible
 
** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
 
** Not getting lots of submissions yet, probably won't be inundated in the near future
 
** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
 
* Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
 
 
 
=== Undiagnosed Disease Network data ===
 
* Andy Golden will meet with Ranjana and Chris at IWM to discuss
 
* Andy asked about protocol pages at WormBase?
 
* Paul: Bioprotocols and Protocols IO
 
* Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
 
 
 
 
 
==June 27th, 2019==
 
===IWM 2019===
 
*Impressions, analysis, feedback from Users etc etc
 
 
 
===Giving disease model annotations a stable identifier===
 
*Currently disease model annotations get a temporary ID at the time of dump,
 
<pre style="white-space: pre-wrap;
 
white-space: -moz-pre-wrap;
 
white-space: -pre-wrap;
 
white-space: -o-pre-wrap;
 
word-wrap: break-word">
 
Disease_model_annotation : "00000004"
 
Disease_term "DOID:0050833"
 
Disease_of_species "Homo sapiens"
 
Variation "WBVar00275555"
 
Disease_relevant_gene "WBGene00011559"
 
Inferred_gene "WBGene00011559"
 
Association_type "is_implicated_in"
 
Evidence_code "IMP"
 
Genetic_sex "hermaphrodite"
 
Paper_evidence "WBPaper00035924"
 
Database "OMIM" "gene" "613891 "
 
Database "OMIM" "disease" "258900"
 
Curator_confirmed "WBPerson324"
 
Date_last_updated "2017-04-24"
 
</pre>
 
*Would like to institute stable identifiers across releases, so the plan is to call these objects, 'WBDisease_annotation:<number>', so then the above identifier would become 'WBDisease_annotation:00000004', or 'WBDiseaseannot:00000004' or 'WBDiseaseAnnot:00000004'
 
*ID convention--is underscore allowed?
 
*Is 'WBDisease_annotation:00000004' too long for acedb?
 

Revision as of 14:01, 15 July 2019

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July 11th, 2019

Alliance all hands meeting

  • Raymond: would be interested in discussing ontologies and their usage in the Alliance
    • Phenotype, anatomy ontologies, GO, etc.
    • Ontology browsers, SObA

IWM workshop

  • Videos ready for upload
  • Wen and Raymond now have access to outreach@wormbase.org account; will upload videos

Protocol videos

  • Wen met Craig Mello at the IWM; he is interested in putting up microinjection videos online; linkable from WormBase?
  • Can make each video a Video Weblog so people can make comments, etc.