Difference between revisions of "WormBase-Caltech Weekly Calls"

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GoToMeeting link: https://www.gotomeet.me/wormbase1
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= 2020 Meetings =
 
= 2020 Meetings =
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
== March 5, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
=== WormBase curation ===
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
* Tim Schedl: WB needs to do more curation for phenotype and variation
 
* Doing community curation, but not fast enough
 
* Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
 
  
=== Alaksa ===
 
* Joesph may be able to meet with Raymond
 
* How can the tool be maintained? If it can't it needs to be pulled
 
  
=== Single cell expression tool ===
+
== September 3, 2020 ==
* Tool is here: http://de.wormcells.com/
 
* What do we need to consider for pulling into WormBase?
 
* Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
 
** Would want it to be in sync with WormBase releases
 
** May not need to reprocess with every release with current (small-ish) data set
 
* Fully integrated tool versus an embedded tool?
 
  
=== Name service updates ===
+
=== WS279 Citace upload ===
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
+
* September 25
* Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
+
* 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
  
== March 12, 2020 ==
+
=== GO annotation for description ===
 +
* Kimberly will look into 'male tail tip developement' terms for description
  
=== Cancelled meetings ===
+
=== Migrate wobr1 server to AWS ===
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
+
* SOLR, WOBr, SObA, Enrichment analysis
* We should start doing online advertisement for micropublications with webinars
+
* 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)
  
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Valerio would like to add these to Postgres to keep a more central repository of them
+
* Meeting will be virtual on Zoom
* Chris would still like to be able to readily update/edit the content of those lists
+
* 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
  
* Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres
 
  
=== Updates on Alaska ===
+
== September 10, 2020 ==
  
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
+
=== GO GAF Files ===
The future plan is to move the platform to Google colab to reduce maintainance work.
+
* 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
  
==Nameservice discussion==
+
===Disease files on FTP===
*Getting a token has worked for Chris and Ranjana
+
*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)
*Karen and Daniela need to get tokens
+
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
  
==Noctua GO-CAM updates==
+
=== WormBase talk at Worcester Area Worm Meeting ===
*Noctua is a production tool available for annotations right now
+
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
*Create as many interconnected models and make available for curators is the ongoing goal
+
* 30 minute slot; complementary to BAWM talk?
*Reactome models are in the process of being imported
+
* WormBase members can attend
*Real time validation messages as curation is being done, is being worked on
 
*Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
 
  
 +
=== 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
  
== March 19, 2020 ==
+
=== 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
  
=== Citace Upload ===
+
=== Dead Variations in Postgres ===
* Tuesday, March 31st
+
* 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
  
=== Latest ACEDB ===
+
=== WS279 Citace Upload ===
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
+
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
  
=== Storing email addresses/persons to omit from requests ===
 
* Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
 
  
=== Mailing lists ===
+
== September 17, 2020 ==
* Let Todd know if you want to keep your caltech.edu account on the mailing lists
 
  
 +
=== Species errors in CITace ===
 +
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
  
==March 26th==
+
=== Webinars ===
===Community curation===
+
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
*Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
+
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
* Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
+
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
* Blog about phenotype form to make people generally aware
+
* Chris and Wen can discuss how to setup
* Could the phenotype form be adapted for other species? Possibly but depends on:
+
* Should we have people register? Maybe
** Whether genotypes could be loaded and recognized
+
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
  
=== AFP for older papers ===
+
=== Transcription factors and regulatory networks ===
* Discussed recently
+
* Had another question about TFs, asking for common TFs for a list of genes
* Many (all?) Old papers have already gone through the old AFP pipeline
+
* An issue is that the TF binding data we have is in disparate forms, trying to reconcile
* Need to check what has already been curated
+
* We have a ?Transcription_factor class; it would be good to update and integrate with other related data types
  
=== Omit form ===
+
=== Alzheimer's disease portal ===
* http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi
+
* Funding has been awarded for Alzheimer's research
* Can view, add, or edit persons, email addresses, and IP addresses to omit from email requests (and IP addresses to block)
+
* 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
  
=== Problems accessing Textpresso Central ===
+
=== GO meeting ===
* Ranjana had noticed that the server was acting slow
+
* All are welcome to attend
* Unknown problem; hard to pin down
+
* Will discuss GAF format changes, etc.
* Definitely a Caltech network system
+
* Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
* Issue for past couple of weeks
+
** Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss
* May be able to ask Caltech IMSS for a diagnostic analysis
 
* Bad switch? Maybe; there is an unused switch that could be used to test
 
** Maybe should dedicate an ethernet socket to the server(s) (avoiding switch altogether)
 
* Tazendra is good, mangolassi seems to have had some trouble recently as well
 
* All on subnet 52; Raymond has been monitoring and seems to be working well; could suggest a local (e.g. computer-specific, switch-specific) issue
 
  
=== Automated concise pathway descriptions? ===
+
=== New GAF 2.2 file ===
* Could we generate pathway descriptions based on, for example, GO-CAM models?
+
* Kimberly has reviewed and sent feedback to Michael P
* Might be straightforward if clear guidelines can be documented (important players/genes, important/central functions/processes)
+
* Valerio would like to stay in the loop to test the new files
  
=== Genotype OA on Sandbox ===
+
=== Data mining tool comparison sheet ===
* http://mangolassi.caltech.edu/~postgres/cgi-bin/oa/ontology_annotator.cgi
+
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
* Take a look and send feedback to Juancarlos and Chris
+
* 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