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]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
== June 6, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
=== New SObA graphs ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* 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_August_2020|August]]
* 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
 
  
 +
== September 3, 2020 ==
  
== June 13, 2019 ==
+
=== WS279 Citace upload ===
 +
* September 25
 +
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
  
=== IWM ===
+
=== New AFP datatype for curation status form (CSF)? ===
* Coordinating transportation of swag boxes to Pauley Pavilion
+
* afp_othergenefunc (to capture gene function other than enzymatic activity)
* Workshop on Saturday June 22, from 1pm to 2:30pm
+
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
* Saturday morning micropublication breakfast 7:30 - 8:30am
+
 
* Workshop
+
=== GO annotation for description ===
** Presenters: it may be best to present as use cases rather than a research project
+
* Kimberly will look into 'male tail tip developement' terms for description
** Chris will cover SimpleMine for Wen
+
 
** Chris: won't do live demo; only screenshots, maybe some video
+
=== Migrate wobr1 server to AWS ===
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
+
* SOLR, WOBr, SObA, Enrichment analysis
* Paul's talk
+
* Working with Sibyl on the process
** Cover Alliance
+
* Will try migrating wobr1 first, as a test case
** New features
+
* May eventually move, for example, Tazendra
*** SObA (for new data)
+
** Will there be drawbacks to doing this?
*** Complete for protein-protein interactions
+
** Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
*** RNASeq tools
+
* Don't yet know the details of the costs, but we can try and keep track
*** Updated automated gene concise descriptions?
+
* We should move into WB or Alliance AWS instances (or Stanford)
** Phenotype community curation
+
 
*** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
+
=== WormBase talk at Boston Area Worm Meeting ===
 +
* https://www.umassmed.edu/ambroslab/meetings/bawm/
 +
* Meeting will be virtual on Zoom
 +
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 +
* Send topic requests to Chris for the talk
 +
* Current topics:
 +
** Micropublications
 
** Author First Pass
 
** Author First Pass
** Micropublication
+
** Automated Gene Descriptions
 +
** Community Curation
 +
** WB Query Tools
 +
* Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
 +
* If the organizers record the talk, we can post it on the blog and WB YouTube channel
 +
 
 +
 
 +
== September 10, 2020 ==
 +
 
 +
=== GO GAF Files ===
 +
* WS278 GO GAF is using the new 2.2 file format
 +
* [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md Specifications]
 +
* GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
 +
* Implications for gene descriptions, but what about other tools, applications at WB?
 +
* Some errors in the current WS278 GAF, but will get fixed soon
 +
** Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed
 +
 
 +
===Disease files on FTP===
 +
*No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
 +
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
 +
 
 +
=== WormBase talk at Worcester Area Worm Meeting ===
 +
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
 +
* 30 minute slot; complementary to BAWM talk?
 +
* WormBase members can attend
 +
 
 +
=== WormBase talk at Boston Area Worm Meeting ===
 +
* https://www.umassmed.edu/ambroslab/meetings/bawm/
 +
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 +
* WormBase members can attend; Zoom link will be sent next Monday
 +
 
 +
=== Worm Anatomy Ontology Fixes ===
 +
* Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
 +
* Assessing the best way to address them
 +
* Would be good to be able to automate some edits; options:
 +
** Use OWL API (need someone proficient in coding with OWL API)
 +
** Convert to OBO, programmatically edit, convert back to OWL?
 +
** Use Cellfie plugin for Protege?
 +
** Should discuss with Nico once we have a sense as to what changes need to be made
 +
 
 +
=== Dead Variations in Postgres ===
 +
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
 +
* Noticed that many transgene names were being included, which can result in false positives for the categories
 +
* Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
 +
* Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
 +
* May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
 +
* We could use pattern matching to filter out transgene names
 +
* Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories
 +
 
 +
=== WS279 Citace Upload ===
 +
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
  
=== 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 ===
+
== September 17, 2020 ==
* 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 ===
+
=== Species errors in CITace ===
* If people are requesting manually written gene descriptions, they could submit a microreview
+
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
* 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 ===
+
=== Webinars ===
* Andy Golden will meet with Ranjana and Chris at IWM to discuss
+
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
* Andy asked about protocol pages at WormBase?
+
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
* Paul: Bioprotocols and Protocols IO
+
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
* Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
+
* Chris and Wen can discuss how to setup
 +
* Should we have people register? Maybe
 +
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
  
 +
=== Transcription factors and regulatory networks ===
 +
* Had another question about TFs, asking for common TFs for a list of genes
 +
* An issue is that the TF binding data we have is in disparate forms, trying to reconcile
 +
* We have a ?Transcription_factor class; it would be good to update and integrate with other related data types
  
==June 27th, 2019==
+
=== Alzheimer's disease portal ===
===IWM 2019: Feedback from Users===
+
* Funding has been awarded for Alzheimer's research
* Anatomy term synonym search
+
* Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
** User pointed out that "RnB" search returns 0 results; GitHub ticket made to index anatomy synonyms
+
* Paul S: Alliance SAB tomorrow; we'll see what the SAB says
* Ciliated neurons
+
* Can look at other resources like RGD disease portals and Reactome disease-related pathway models
** User pointed out that male ciliated neurons are missing as a subclass of term "ciliated neuron"; GitHub ticket made, easy fix
+
* Ruth Lovering is doing some work in this regard
* 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 BioRXiv preprint (quick, before peer-review) and/or micropublication (after peer-review)
 
* Protocols
 
** Would be good to establish (for Alliance/WB) framework for serving protocols maintained by community
 
  
=== TAGC meeting ===
+
=== GO meeting ===
* Next April (2020)
+
* All are welcome to attend
* Alliance representation needed
+
* Will discuss GAF format changes, etc.
 +
* Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
 +
** Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss
  
===Giving disease model annotations a stable identifier===
+
=== New GAF 2.2 file ===
*Currently disease model annotations get a temporary ID at the time of dump,
+
* Kimberly has reviewed and sent feedback to Michael P
<pre style="white-space: pre-wrap;
+
* Valerio would like to stay in the loop to test the new files
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 ===
+
=== Data mining tool comparison sheet ===
* Currently, "intestinal muscle" is considered "part of" intestine
+
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
** User asked for intestinally expressed genes; using WOBr would also retrieve genes in intestinal muscle
+
* Needs an update
** David Hall confirmed that instestinal muscle cells are not part of intestine
+
* Could we make this available to users? A link in the Tools menu?
** Maybe we can change to: "intestinal muscle" part_of "alimentary system"
+
* Is this useful to users? Would they understand it? Maybe be better as a curator resource
* Currently, "amphid process" is considered "part of" each type of amphid neuron like AWC, AFD, etc.
+
* Could this be micropublished?
** Problem is that users looking in WOBr for AWC-expressed genes will be given genes expressed in ANY amphid process regardless of which cell
+
** Possible; may want to consider a series of publications with videos of webinars, etc.
** Propose to change to: "amphid process" part_of "amphid neuron" only
 

Latest revision as of 16:39, 17 September 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July

August


September 3, 2020

WS279 Citace upload

  • September 25
  • Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific

New AFP datatype for curation status form (CSF)?

  • afp_othergenefunc (to capture gene function other than enzymatic activity)
  • Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later

GO annotation for description

  • Kimberly will look into 'male tail tip developement' terms for description

Migrate wobr1 server to AWS

  • SOLR, WOBr, SObA, Enrichment analysis
  • Working with Sibyl on the process
  • Will try migrating wobr1 first, as a test case
  • May eventually move, for example, Tazendra
    • Will there be drawbacks to doing this?
    • Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
  • Don't yet know the details of the costs, but we can try and keep track
  • We should move into WB or Alliance AWS instances (or Stanford)

WormBase talk at Boston Area Worm Meeting

  • https://www.umassmed.edu/ambroslab/meetings/bawm/
  • Meeting will be virtual on Zoom
  • Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
  • Send topic requests to Chris for the talk
  • Current topics:
    • Micropublications
    • Author First Pass
    • Automated Gene Descriptions
    • Community Curation
    • WB Query Tools
  • Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
  • If the organizers record the talk, we can post it on the blog and WB YouTube channel


September 10, 2020

GO GAF Files

  • WS278 GO GAF is using the new 2.2 file format
  • Specifications
  • GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
  • Implications for gene descriptions, but what about other tools, applications at WB?
  • Some errors in the current WS278 GAF, but will get fixed soon
    • Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed

Disease files on FTP

  • No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
  • Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??

WormBase talk at Worcester Area Worm Meeting

  • Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
  • 30 minute slot; complementary to BAWM talk?
  • WormBase members can attend

WormBase talk at Boston Area Worm Meeting

Worm Anatomy Ontology Fixes

  • Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
  • Assessing the best way to address them
  • Would be good to be able to automate some edits; options:
    • Use OWL API (need someone proficient in coding with OWL API)
    • Convert to OBO, programmatically edit, convert back to OWL?
    • Use Cellfie plugin for Protege?
    • Should discuss with Nico once we have a sense as to what changes need to be made

Dead Variations in Postgres

  • Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
  • Noticed that many transgene names were being included, which can result in false positives for the categories
  • Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
  • Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
  • May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
  • We could use pattern matching to filter out transgene names
  • Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories

WS279 Citace Upload

  • Local Caltech upload to Spica, Tuesday September 22, 10am Pacific


September 17, 2020

Species errors in CITace

  • Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction

Webinars

  • We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
  • Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
  • Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
  • Chris and Wen can discuss how to setup
  • Should we have people register? Maybe
  • AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?

Transcription factors and regulatory networks

  • Had another question about TFs, asking for common TFs for a list of genes
  • An issue is that the TF binding data we have is in disparate forms, trying to reconcile
  • We have a ?Transcription_factor class; it would be good to update and integrate with other related data types

Alzheimer's disease portal

  • Funding has been awarded for Alzheimer's research
  • Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
  • Paul S: Alliance SAB tomorrow; we'll see what the SAB says
  • Can look at other resources like RGD disease portals and Reactome disease-related pathway models
  • Ruth Lovering is doing some work in this regard

GO meeting

  • All are welcome to attend
  • Will discuss GAF format changes, etc.
  • Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
    • Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss

New GAF 2.2 file

  • Kimberly has reviewed and sent feedback to Michael P
  • Valerio would like to stay in the loop to test the new files

Data mining tool comparison sheet