Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
 
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
 +
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
==July 9th, 2020==
 
===Gene names issue in SimpleMine and other mining tools===
 
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
 
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
 
*Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
 
*Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
 
*Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
 
**single public name is assigned to multiple WBgene ID, Wen has a list of these genes
 
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
 
**overlapped or dicistronic, but has a single sequence name, examples:
 
    exos-4.1 and tin-9.2 (B0564.1)
 
    eat-18 and lev-10 (Y105E8A.7)
 
    cha-1 and unc-17 (ZC416.8)
 
  
**simple confusion from authors, ex. mdh-1 and mdh-2
+
== September 3, 2020 ==
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
 
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
 
*Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools.  They will also write a microPub explaining this issue to the community.
 
  
===Wormicloud===
+
=== WS279 Citace upload ===
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
+
* September 25
*Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
+
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
*Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.
 
  
===Noctua 2.0 form ready to use===
+
=== New AFP datatype for curation status form (CSF)? ===
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
+
* 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
  
===Nightly names service updates to postgres===
+
=== GO annotation for description ===
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.
+
* 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)
  
==July 16th, 2020==
+
=== WormBase talk at Boston Area Worm Meeting ===
===Citing ontologies and their versions===
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
*Came up in the context of the Alliance: It would be best practice to provide users with the list of ontologies used and their versions/date.
+
* Meeting will be virtual on Zoom
*If WB ontology developers could make sure their ontology file headers (WB anatomy ontology, WB life stage, etc.) conformed to obo file header specifications, then it would be easy to pull in version and date information into the Alliance.
+
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
*Some useful links
+
* Send topic requests to Chris for the talk
**http://www.obofoundry.org/principles/fp-004-versioning.html
+
* Current topics:
**http://obo-dashboard-test.ontodev.com/ (you can see that wbbt, wbls version metadata attribute is generating a warning).
+
** Micropublications
**Note: OBO-foundry may not have been updated, but good practice to check your headers, anyway.
+
** Author First Pass
* Chris worked with Nico yesterday to update the ODK version for WBbt and WBls; versioning should be fine now (once the OBO dashboard runs again (hasn't run since February))
+
** Automated Gene Descriptions
* Important point: the GitHub release version date tag (e.g. "v2020-06-30") needs to match the ODK release date (as stored in the OBO and OWL file headers)
+
** Community Curation
** There are some existing mismatches, Chris is cataloging them now
+
** 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
  
=== Gene Name Sanitizer ===
 
* Would be good to always (when possible) make users aware of name ambiguities
 
* Wen will keep the "Multiple Output" section at the bottom of SimpleMine output
 
* The gene name sanitizer will be built as a stand alone tool
 
* Important to include history of gene names
 
  
=== Tools linking to SimpleMine ===
+
== September 10, 2020 ==
* Vennter and other tools link to SimpleMine with hard coded field/column names; we should have more dynamic/robust linking without relying on hard coded field names
 
  
 +
=== 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
  
== July 23rd, 2020 ==
+
===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, ??
  
=== Alliance pathway working group ===
+
=== WormBase talk at Worcester Area Worm Meeting ===
* Integrating pathways from GO-CAM, Reactome, Meta-cyc
+
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
* Raymond, Chris interested
+
* 30 minute slot; complementary to BAWM talk?
* Laurent-Philippe wants to work on user-friendly displays of GO-CAM models
+
* WormBase members can attend
  
=== Working on Alliance paralogs ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* In the works
+
* 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
  
=== Summer project ===
+
=== Worm Anatomy Ontology Fixes ===
* Neuronal regulation of dauer formation
+
* Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
* Fernando has been collecting literature
+
* Assessing the best way to address them
* Will work on GO-CAMs and build a relevant model(s)
+
* 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
  
=== Disk failures ===
+
=== Dead Variations in Postgres ===
* Brought down wobr1, wobr2, spica
+
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
* Raymond has upgraded OS from 8-year old OS, beefed up hardware
+
* Noticed that many transgene names were being included, which can result in false positives for the categories
* wobr1 and wobr2 are back to full function
+
* Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
* Having trouble bringing back spica on the network
+
* 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
  
=== WormMine updates ===
+
=== WS279 Citace Upload ===
* Paulo working on importing new classes: SO_term, disease_model_annotation, transgene, construct, molecule, wbprocess, interaction
+
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
* Chris is working with Paulo to move them in; talk to Paulo and/or Chris if interested in discussing
 
* Spreadsheet to map ACEDB/XML attributes to ACEDB attributes: https://docs.google.com/spreadsheets/d/1-fpzVU3rblN3Rp38wQjd3121z3rVkxmR9_i5T0EIPNo/edit?usp=sharing
 
* Still have some loader headaches
 
* Do we know the usage stats of WormMine?
 
* BlueGenes
 
** New interface coming; in the works, not sure when it will be fully functional
 
** Lacks some useful features in the current Intermine (Intermine devs are aware and working on it)
 
** Does BlueGenes have better loading? Don't know
 
  
=== WB move to Chen building ===
 
* Need to sort out what will get moved over; will be more limited space
 
* How late can move happen? If all is OK, move will happen 2nd week of January 2021
 
  
=== Caltech BBE retreat ===
+
== September 17, 2020 ==
* Will be online; may be more accessible
 
* Wen will submit a request to present on the Alliance
 
  
=== WormBase Webinars ===
+
=== Species errors in CITace ===
* Could run a WormMine webinar in September
+
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
** 30-45 minute webinar with 15 minutes of questions and discussion
 
** Would be good have people register
 
* Chris has slot at Worcester Area Worm Meeting and Boston Area Worm Meeting coming up (late in 2020); these will likely be virtual
 
  
=== Gene Name Sanitizer ===
+
=== Webinars ===
* Juancarlos and Wen are working on tool prototype
+
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
* Prototype recognizes ambiguous gene names/IDs and returns them to the user
+
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
* Will return HTML or single download file with a status/classification column
+
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
* Four types:
+
* Chris and Wen can discuss how to setup
** good/valid (unambiguous match to a live gene)
+
* Should we have people register? Maybe
** ambiguous (matches multiple genes)
+
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
** invalid (unambiguous match to dead or suppressed gene)
 
** not found (no match)
 
  
 +
=== 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
  
== July 30, 2020 ==
+
=== 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
  
=== Gene Name Sanitizer ===
+
=== 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
  
=== Help Desk ===
+
=== 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
  
* https://github.com/WormBase/website/issues/7803
+
=== Data mining tool comparison sheet ===
 
+
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
* Hi, I was wondering if there is a way to search for maternally versus zygotically enriched splice variants of a gene. I was looking through the RNAseq data and am not sure how to pull that out. I'm specifically looking at afd-1, but any help on that would be great!
+
* 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

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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