Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
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 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
 +
= 2020 Meetings =
  
= 2019 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
 
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
 
 
 
 
== June 6, 2019 ==
 
 
 
=== New SObA graphs ===
 
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
 
 
 
=== Phenotype association file format ===
 
* May be best to leave the format as is
 
* There are problems; paper IDs keep switching columns
 
* Would need to revisit the reasoning for why we do it that way
 
* When will the Alliance produce a similar/replacement file? Not sure
 
 
 
=== Phenotype requests ===
 
* Sent out 1140 emails on May 30
 
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
 
* 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
 
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
== June 13, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
=== IWM ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* 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 ===
+
== June 4, 2020 ==
* 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 ===
+
=== Citace (tentative) upload ===
* Andy Golden will meet with Ranjana and Chris at IWM to discuss
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Andy asked about protocol pages at WormBase?
+
* Citace upload to Hinxton on Friday, July 10th
* Paul: Bioprotocols and Protocols IO
 
* Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
 
  
 +
=== Caltech reopening ===
 +
* Paul looking to get plan approved
 +
* People that want to come to campus need to watch training video
 +
* Masks available in Paul's lab
 +
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 +
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 +
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 +
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 +
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
==June 27th, 2019==
+
=== Nameserver ===
===IWM 2019===
+
* Nameserver was down
* Impressions, analysis, feedback from Users etc etc
+
* CIT curators would still like to have a single form to interact with
* Anatomy term synonym search
+
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
** User pointed out that "RnB" search returns 0 results; GitHub ticket made to index anatomy synonyms
+
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
* Ciliated neurons
+
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
** User pointed out that male ciliated neurons are missing as a subclass of term "ciliated neuron"; GitHub ticket made, easy fix
+
* Hinxton is pulling in CGC strains, how often?
* Import of 22G and 26G RNAs
+
* Caltech could possibly get a block of IDs
** Spoke to Julie Claycomb
 
** These are short RNAs transcribed by RNA-dependent RNA Polymerase (RdRP) off of mRNA molecules
 
** Should these be instantiated as gene objects in WormBase? Julie argues that these are not genes
 
*** Should these just be transcript objects? Would they be linked to a gene? Or maybe also to any transcripts from which they could be derived?
 
** Many map uniquely to the genome, but some map in multiple locations
 
* Ranjana & Chris spoke with Andy Golden
 
** Andy and his lab will submit phenotype and disease data as they become available (likely pre-publication); we will likely point to a consortium as source until paper is published
 
** There is still a strong need for cross-species variant mapping/visualization
 
* miRNA binding sites
 
** User asked at workshop and at booth; can we show miRNA binding sites in JBrowse? We would need to collect the data
 
** There are many sources of miRNA-target interactions, some experimental, most predicted
 
*** Chris compiled [https://docs.google.com/spreadsheets/d/19-txXrGi-ROFuByyLnQYvWbKl3o12KZON56qto3MN6g/edit?usp=sharing list of interaction databases] for Alliance interactions working group
 
  
===Giving disease model annotations a stable identifier===
+
=== Alliance SimpleMine ===
*Currently disease model annotations get a temporary ID at the time of dump,
+
* Any updates? 3.1 feature freeze is tomorrow
<pre style="white-space: pre-wrap;
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
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?
 

Latest revision as of 00:09, 5 June 2020

Previous Years

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GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January

February

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call