Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(166 intermediate revisions by 7 users not shown)
Line 35: Line 35:
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
== June 6, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
=== New SObA graphs ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
 
  
=== Phenotype association file format ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
* 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
 
  
  
== June 13, 2019 ==
+
== November 7, 2019 ==
  
=== IWM ===
+
=== WS275 Citace upload ===
* Coordinating transportation of swag boxes to Pauley Pavilion
+
* Maybe Nov 22 upload to Hinxton
* Workshop on Saturday June 22, from 1pm to 2:30pm
+
* CIT curators upload to Spica on Tues Nov 19
* 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 ===
+
=== ?Genotype class ===
* Paul attended
+
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
* Alliance publicity was discussed
+
* Several classes have a "Genotype" tag with text entry
* SAB likes the Alliance orthology features
+
** Strain
* Working on topics: displaying papers and data
+
** 2_point_data
* Pathways: discussion about best approach
+
** Pos_neg_data
* Metabolic engineering
+
** Multi_pt_data
* Meta data about RNASeq data
+
** RNAi
** SPELL tool, basically only tool of its kind available; need new tools
+
** Phenotype_info
* Species-specific proteins: how best to find them? HMMs (Jackhammer)?
+
** Mass_spec_experiment (no data as of WS273)
 +
** Condition
 +
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
 +
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
 +
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
 +
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
 +
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
 +
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
 +
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
 +
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
 +
** Reference to parent strain, like "Parent strain is AG359"
 +
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
 +
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"
  
=== Concise descriptions ===
+
=== Gene comparison SObA ===
* Progress being made within the Alliance to update the automated concise gene descriptions
+
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
* 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 ===
+
== November 14, 2019 ==
* 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)
 
  
 +
=== TAGC meeting ===
 +
* The Allied Genetics Conference next April (2020) in/near Washington DC
 +
* Abstract deadline is Dec 5th
 +
* Alliance has a shared booth (3 adjacent booths)
 +
* Micropublications will have a booth (Karen and Daniela will attend)
 +
* Focus will be on highlighting the Alliance
 +
* Workshop at NLM in days following TAGC about curation at scale (Kimberly attending and chairing session)
  
==June 27th, 2019==
+
=== Alliance all hands meeting ===
===IWM 2019===
+
* Lightning talk topics?
* Impressions, analysis, feedback from Users etc etc
+
** Single cell RNA Seq (Eduardo)
* Anatomy term synonym search
+
** SimpleMine? (Wen)
** User pointed out that "RnB" search returns 0 results; GitHub ticket made to index anatomy synonyms
+
** SObA? (Raymond); still working on multi-species SObA
* Ciliated neurons
+
** Phenotype community curation?
** User pointed out that male ciliated neurons are missing as a subclass of term "ciliated neuron"; GitHub ticket made, easy fix
+
** Micropublications?
* Import of 22G and 26G RNAs
+
** AFP?
** 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
 
** Associated data for now would likely just be protein-RNA interactions (Argonaute-RNA interactions)
 
*** May eventually include phenotype and/or gene ontology (biological process) annotations
 
* 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 general ===
*Currently disease model annotations get a temporary ID at the time of dump,
+
* Alliance needs a curation database
<pre style="white-space: pre-wrap;
+
** A curation working group was proposed
white-space: -moz-pre-wrap;
+
** What needs to happen to get this going?
white-space: -pre-wrap;
+
** Would include text mining tools/resources
white-space: -o-pre-wrap;
+
** Would be good to have something like the curation status form
word-wrap: break-word">
+
** MODs likely have their own special requirements, but there should probably be at least a common minimal set of features
Disease_model_annotation : "00000004"
+
** Variant sequence curation could be a good first start (if all MODs handle their own variant sequence curation) as a common data type
Disease_term "DOID:0050833"
+
* Micropubs pushing data submission forms; might as well house them within the Alliance
Disease_of_species "Homo sapiens"
+
* Would be good to have a common (or individually relevant) AFP form(s) for all Alliance members
Variation "WBVar00275555"
+
** Maybe MOD curators can manage configuration files to indicate what is relevant for their species
Disease_relevant_gene "WBGene00011559"
+
** First priority is to focus on automatically recognizable entities/features from papers
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 19:58, 14 November 2019

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings


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


2019 Meetings

January

February

March

April

May

June

July

August

September

October


November 7, 2019

WS275 Citace upload

  • Maybe Nov 22 upload to Hinxton
  • CIT curators upload to Spica on Tues Nov 19

?Genotype class

  • Working data model document
  • Several classes have a "Genotype" tag with text entry
    • Strain
    • 2_point_data
    • Pos_neg_data
    • Multi_pt_data
    • RNAi
    • Phenotype_info
    • Mass_spec_experiment (no data as of WS273)
    • Condition
  • Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
    • Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
    • Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
    • Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
    • Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
    • Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
    • Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
    • Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
    • Reference to parent strain, like "Parent strain is AG359"
    • Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
    • Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"

Gene comparison SObA


November 14, 2019

TAGC meeting

  • The Allied Genetics Conference next April (2020) in/near Washington DC
  • Abstract deadline is Dec 5th
  • Alliance has a shared booth (3 adjacent booths)
  • Micropublications will have a booth (Karen and Daniela will attend)
  • Focus will be on highlighting the Alliance
  • Workshop at NLM in days following TAGC about curation at scale (Kimberly attending and chairing session)

Alliance all hands meeting

  • Lightning talk topics?
    • Single cell RNA Seq (Eduardo)
    • SimpleMine? (Wen)
    • SObA? (Raymond); still working on multi-species SObA
    • Phenotype community curation?
    • Micropublications?
    • AFP?

Alliance general

  • Alliance needs a curation database
    • A curation working group was proposed
    • What needs to happen to get this going?
    • Would include text mining tools/resources
    • Would be good to have something like the curation status form
    • MODs likely have their own special requirements, but there should probably be at least a common minimal set of features
    • Variant sequence curation could be a good first start (if all MODs handle their own variant sequence curation) as a common data type
  • Micropubs pushing data submission forms; might as well house them within the Alliance
  • Would be good to have a common (or individually relevant) AFP form(s) for all Alliance members
    • Maybe MOD curators can manage configuration files to indicate what is relevant for their species
    • First priority is to focus on automatically recognizable entities/features from papers