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 ==
+
[[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
 
  
 +
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
  
== June 13, 2019 ==
 
  
=== IWM ===
+
== December 5, 2019 ==
* 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 ===
+
=== New interaction Venn diagram tool ===
* Paul attended
+
* [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions]
* Alliance publicity was discussed
+
* Venn diagram shows how various interactors have multiple interaction types with a common focus gene
* SAB likes the Alliance orthology features
+
* For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
* Working on topics: displaying papers and data
+
* Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
* Pathways: discussion about best approach
+
* Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
* Metabolic engineering
+
* Request: could there be a toggle to include/exclude high-throughput interactions?
* Meta data about RNASeq data
+
* Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
** SPELL tool, basically only tool of its kind available; need new tools
+
* Request: Change the wording "Browse selection" to something like "View/analyze gene list"
* Species-specific proteins: how best to find them? HMMs (Jackhammer)?
+
* Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?  
  
=== Concise descriptions ===
+
=== New round of phenotype requests ===
* Progress being made within the Alliance to update the automated concise gene descriptions
+
* GMail really throttling email sending
* We will still accept manually written descriptions and display them in parallel with automated descriptions
+
* Chris will reach out to Google/GMail to see if we can:
 +
** A) get a clear explanation about what their restrictions are and how they work and
 +
** B) see if we can get a paid plan to help expedite the email process (see how much cost)
  
=== Micropublications ===
+
=== Aligning interaction data with GO and GO-CAM ===
* If people are requesting manually written gene descriptions, they could submit a microreview
+
* The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
* Concern was expressed about how to handle a really high throughput of submissions:
+
* Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
** Daniela: Working towards automating as much of the processing pipeline as possible
+
* Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
+
** Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
** Not getting lots of submissions yet, probably won't be inundated in the near future
+
* Chris and Kimberly will meet to discuss further
** 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 ===
+
=== Short SObA talk at Alliance meeting ===
* Andy Golden will meet with Ranjana and Chris at IWM to discuss
+
* Raymond prepared to give short talk on SObA to the Alliance group
* 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)
 
  
 
+
=== Single cell data visualization tool ===
==June 27th, 2019==
+
* Eduardo will present to Paul's lab meeting tomorrow
===IWM 2019: Feedback from Users===
+
* Will discuss at Alliance expression working group pre-meeting
* Anatomy term synonym search
 
** User pointed out that "RnB" search returns 0 results; GitHub ticket made to index anatomy synonyms
 
* Ciliated neurons
 
** User pointed out that male ciliated neurons are missing as a subclass of term "ciliated neuron"; GitHub ticket made, easy fix
 
* Import of 22G and 26G RNAs
 
** 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
 
* Ontology aware diffs of annotations (gene1 expression vs. gene2 expression)
 
* Promoter sequence in experimental constructs
 
* Workshop went well
 
** Next time, maybe have people bring laptops and follow along; be more interactive
 
** We could do webinars, for WormMine for example, allow people to work along with the presentation
 
*** Do other MODs/groups do webinars? How have they been? Useful?
 
** Competing with other workshops during the IWM
 
** Can focus on new, less-used features for webinars, tutorial videos
 
* Hawaiian genome in JBrowse
 
* Had internet stability issues at UCLA; can we get a local, dedicated WiFi?
 
* Next meeting (2021) will likely be in Europe (Cambridge UK?)
 
* User at cGal workshop asked about tissue-specific promoters/transgenes
 
** Have ~30 drivers and ~30 effectors; will WB take them in unpublished? Could make BioRChiv preprint (quick, before peer-review) and/or micropublication (after peer-review)
 
 
 
=== TAGC meeting ===
 
* Next April (2020)
 
* Alliance representation needed
 
 
 
===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?
 
* Need to ask Kevin, Hinxton; what are the other implications for maintaining and generating persistent, unique IDs
 
 
 
=== Anatomy ontology issues ===
 
* Currently, "intestinal muscle" is considered "part of" intestine
 
** User asked for intestinally expressed genes; using WOBr would also retrieve genes in intestinal muscle
 
** David Hall confirmed that instestinal muscle cells are not part of intestine
 
** Maybe we can change to: "intestinal muscle" part_of "alimentary system"
 
* Currently, "amphid process" is considered "part of" each type of amphid neuron like AWC, AFD, etc.
 
** Problem is that users looking in WOBr for AWC-expressed genes will be given genes expressed in ANY amphid process regardless of which cell
 
** Propose to change to: "amphid process" part_of "amphid neuron" only
 

Latest revision as of 21:08, 5 December 2019

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2019 Meetings

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December 5, 2019

New interaction Venn diagram tool

  • daf-16 interactions
  • Venn diagram shows how various interactors have multiple interaction types with a common focus gene
  • For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
  • Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
  • Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
  • Request: could there be a toggle to include/exclude high-throughput interactions?
  • Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
  • Request: Change the wording "Browse selection" to something like "View/analyze gene list"
  • Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?

New round of phenotype requests

  • GMail really throttling email sending
  • Chris will reach out to Google/GMail to see if we can:
    • A) get a clear explanation about what their restrictions are and how they work and
    • B) see if we can get a paid plan to help expedite the email process (see how much cost)

Aligning interaction data with GO and GO-CAM

  • The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
  • Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
  • Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
    • Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
  • Chris and Kimberly will meet to discuss further

Short SObA talk at Alliance meeting

  • Raymond prepared to give short talk on SObA to the Alliance group

Single cell data visualization tool

  • Eduardo will present to Paul's lab meeting tomorrow
  • Will discuss at Alliance expression working group pre-meeting