Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2017|February]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_March_2017|March]]
 
  
  
== April 6, 2017 ==
 
  
=== AGR time spent ===
+
= 2020 Meetings =
* Paul S asking about %time spent on AGR project
 
* Time spent on working groups, conference calls, AGR development
 
* Send estimates to Paul
 
  
=== SimpleMine ===
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
* Two tables added to SimpleMine for human orthology
 
* Now SimpleMine output has many columns (30+)
 
* We may want to give users the option to specify which output they want
 
* Users could specify groups of data (with checkboxes): gene IDs/names, phenotypes, orthology, etc.
 
* All checkboxes can be checked by default
 
  
=== Enrichment tools ===
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
* Raymond working on display for paper
 
  
=== Gene Ontology SObA graph ===
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
* Raymond, Juancarlos working on
 
* Working on paper
 
  
=== WormMine updates ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* WS258 adding gene class
 
* WS259 adding more info (almost all meta data) on variations, laboratory and strains, RNAi phenotypes (hopefully)
 
* Expression data in WormMine is problematic
 
* Many genes being annotated to the same ~6 tissues or so
 
* Resulting in erroneous data for some genes
 
* Chris will send GitHub ticket to Todd
 
* Todd will discuss with Paulo today
 
  
=== Gene Ontology ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* Some very complex terms becoming immediate children of root terms (e.g. "biological process")
 
* May be result of attempt to create logical definitions/equivalence axioms
 
* Raymond will discuss with Kimberly
 
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
== April 13, 2017 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
=== Methods in Molecular Biology chapter ===
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
* Chapter draft sent out Monday night
 
* Will send to Martin at MiMB by late next week
 
* Please take a look and send comments
 
* Authors check their sections and send figure legends to Chris
 
  
=== Progress report ===
 
* If someone finds the 2016 report, send around to group
 
* May 1st deadline (need to verify)
 
  
=== 2017 IWM ===
+
== September 3, 2020 ==
* Early registration Deadline May 18th
 
  
=== Models for citace ===
+
=== WS279 Citace upload ===
* Wen will fit models to local citace, should be ready by tomorrow
+
* September 25
 +
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
  
=== Citace Upload ===
+
=== New AFP datatype for curation status form (CSF)? ===
* Tuesday, April 25th, 10am
+
* 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
  
=== Enrichment tool ===
+
=== GO annotation for description ===
* Now available for gene ontology and phenotype on live site
+
* Kimberly will look into 'male tail tip developement' terms for description
* Paper being submitted soon
 
* Need to change "Tissue Enrichment Analysis" link title under WormBase Tools menu
 
  
=== SObA for Gene Ontology ===
+
=== Migrate wobr1 server to AWS ===
* Data source was server on Berkeley BOP; thought it was public but were discouraged to use
+
* SOLR, WOBr, SObA, Enrichment analysis
* Seth Carbon said we could use it but might not always be working; now it seems to be down or dysfunctional
+
* Working with Sibyl on the process
* SObA for GO will be broken until we install our own local server (Raymond working on)
+
* 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)
  
=== Dumping data for upload, taking over for Karen ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Karen will take care of dumping and uploading the data for this upload
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Karen will review the molecule curation with other curators at the IWM
+
* 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
  
=== Datomic meeting ===
 
* Matt, Sibyl, Adam, Todd, Juancarlos, Raymond sat in
 
* Raymond: thought Datomic would take over from ACEDB completely, but it seems we will still use ACEDB for some time for e.g. FMap
 
* Seems there should be an executive meeting about Datomic to make clear what it will be used for and what it won't be used for
 
* Several web pages and widgets are now being served by Datomic
 
* There's a question about how we now handle model changes going forward
 
* Juancarlos will send around link for newest Datomic querying tool; may require access for specific IP addresses
 
  
 +
== September 10, 2020 ==
  
== April 20, 2017 ==
+
=== 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
  
=== Gene Ontology data for SObA ===
+
===Disease files on FTP===
* Use of GO server; hasn't been reliable
+
*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)
* Raymond working on establishing our own server to host all GO data
+
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
* Raymond and Juancarlos will keep working on SObA representation of GO annotations
 
  
=== Progress Report ===
+
=== WormBase talk at Worcester Area Worm Meeting ===
* WS259 can be used as the current reference
+
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
* Paul will send around last year's progress report
+
* 30 minute slot; complementary to BAWM talk?
* What was the last release that we referenced in last year's progress report? We'll say WS254
+
* WormBase members can attend
* Wen will generate numbers for WS254 (resurrect WS254 ACEDB)
 
* Opportunity to specify/narrow scope of project
 
* Want to push community/automated curation, with curators laying foundation of data models, forms
 
* Promote LEGO curation; need to learn what needs to be said about plan going forward/what we want to accomplish
 
  
=== LEGO curation ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Phenotype curation in LEGO? Need to review phenotype-to-GO pipeline
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Want/need a mapping of phenotype terms to GO process terms; may require context-dependent mapping (e.g. "dumpy" phenotype)
+
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
* We don't make direct associations of phenotypes to LEGO models, although we do have "inferred from mutant phenotype" evidence code
+
* WormBase members can attend; Zoom link will be sent next Monday
* Want a mechanism to automate conversion of WB annotations into LEGO models
 
* Want a display mechanism that is user friendly, convert hairball into pathway
 
* We could focus on a particular topic/disease and collectively contribute
 
* Do we want to write a proposal to take existing, granular annotations (e.g. at level of mutation details) and map to LEGO model?
 
* Can we integrate the micropublication pipeline into LEGO model generation?
 
* How to assess the confidence of assertions?
 
  
=== Follow up on transgene question from user ===
+
=== Worm Anatomy Ontology Fixes ===
* Karen will contact authors of paper
+
* 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
  
=== Citace upload ===
+
=== Dead Variations in Postgres ===
* Tuesday, Apr 25th, 10am
+
* 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 ===
 +
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
 +
* Needs an update
 +
* Could we make this available to users? A link in the Tools menu?
 +
* Is this useful to users? Would they understand it? Maybe be better as a curator resource
 +
* Could this be micropublished?
 +
** Possible; may want to consider a series of publications with videos of webinars, etc.

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