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_March_2020|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
== April 2, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
 
 
=== Community phenotype requests ===
 
* March 9-28
 
* 2,548 emails went out; 89 bounced; 6 resent; 13 backup; 2,478 successful emails
 
* 361 annotations overall
 
* 48 papers requested received curation (2% response rate)
 
* 53 distinct papers overall (5 papers without request)
 
* 53 distinct persons overall
 
  
=== Community curation volunteers ===
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
* Tracking volunteers [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing here]
 
* 14 volunteers so far, all have been assigned a WBPerson ID
 
* Chris will set up a webinar tutorial in the coming week or two
 
  
=== AFP pipeline ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* Will resend email requests to authors that haven't already responded
 
* May also send out for older papers
 
* May work with people to help
 
* Does the old AFP form still work? It should
 
* If someone has a link to the old form, they won't get one for the new form
 
* Maybe could set up an automatic redirect from the old form to the new form
 
* Received many submissions recently (>20% response rate)
 
  
=== Ontology Annotator ===
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
* Need to work on Genotype OA dumper
 
* Turns out semicolons are problematic (currently in genotypes and transgenes) for object names (ontology fields)
 
* Ampersands (&) are also problematic for object names in the OA
 
** 20237  | Is[Pgcy-5::daf-2a::venus; Punc-122::mCherry]                          | 2014-10-08 10:32:45.874519-07
 
** 20239  | Ex[Pgcy-5::casy-1::venus; Pgcy-5::aman-2::mCherry; Punc-122::mCherry] | 2014-10-08 10:45:23.202362-07
 
** 20238  | Is[Pgcy-5::daf-2c::venus; Punc-122::mCherry]                          | 2014-10-08 10:38:19.859078-07
 
** 25249  | Ex[Prheb-1::rheb-1::GFP; unc-119(+]                                  | 2018-06-29 10:16:40.784295-07
 
** 16283  | [hlh-13::GFP;unc-119(+)]                                             | 2013-02-07 17:43:22.384819-08
 
** 26131  | Ex[pedc-3EDC-3::DsRed;pRF4]                                           | 2019-08-14 08:44:49.91063-07
 
  
=== Use Slack More ===
 
* Slack is a good tool for quick communication among team members; would be good for all curators to join Slack to enable efficient communication
 
  
 +
== September 3, 2020 ==
  
== April 9, 2020 ==
+
=== WS279 Citace upload ===
 +
* September 25
 +
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
  
=== Volunteer curators ===
+
=== New AFP datatype for curation status form (CSF)? ===
* Have sent out emails to schedule tutorials
+
* afp_othergenefunc (to capture gene function other than enzymatic activity)
* Chris had one tutorial with Michael Davies (Alyson Ashe's lab) yesterday
+
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
* One already scheduled for next Monday with Wilber and Stephanie from Paul's lab
 
* Two others already scheduled for next Tuesday with Lina Dahlberg and Colin Dolphin
 
  
===TAGC is virtual (4.22-25.2020)===
+
=== GO annotation for description ===
FYI in case you missed it
+
* Kimberly will look into 'male tail tip developement' terms for description
*You still have to register (it's free), if you hadn't before
 
https://genetics-gsa.org/tagc-2020/registration/
 
  
===summer students===
+
=== Migrate wobr1 server to AWS ===
* Caltech SURF students (and other summer students worldwide) now are looking for projects
+
* SOLR, WOBr, SObA, Enrichment analysis
* Maybe they could curate for WormBase
+
* Working with Sibyl on the process
* In addition to phenotype, they could curate:
+
* Will try migrating wobr1 first, as a test case
** Allele/lesion sequence curation (using Allele Sequence form); maybe Paul Davis could make a tutorial video?
+
* May eventually move, for example, Tazendra
** Anatomy function, looking for novel info; opportunity to program/code
+
** 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)
  
=== OA semicolon issue ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Juancarlos has fixed the issues on sandbox
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Curators should test on Mangolassi
+
* 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
  
=== Textmining/automation ===
 
* Daniela will discuss with Christina Zorn from Xenbase
 
* Will discuss SVM, AFP, Textpresso, etc.
 
  
=== Retracted WBPapers ===
+
== September 10, 2020 ==
* Jae & Kimberly put in GitHub ticket to make retractions clear on WormBase site
 
* https://github.com/WormBase/website/issues/7637
 
* Can we systematically detect retractions? Yes
 
* What about finding papers that cite retractions? Maybe, but likely tricky
 
  
 +
=== 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
  
== April 16, 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, ??
  
=== Community Phenotype Curation Tutorials ===
+
=== WormBase talk at Worcester Area Worm Meeting ===
* Chris has run 6 tutorials, recorded 4
+
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
* MPG files saved on DropBox; ask Chris for access
+
* 30 minute slot; complementary to BAWM talk?
* Plan to edit videos to make tutorial video to post on WB YouTube channel
+
* WormBase members can attend
  
=== Author First Pass ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* May run a webinar and use Zoom to record
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* May make a short tutorial video
+
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
* Jae: Is there documentation for terminology used in the form?
+
* WormBase members can attend; Zoom link will be sent next Monday
  
=== Zoom accounts ===
+
=== Worm Anatomy Ontology Fixes ===
* People can try to use Caltech Zoom account
+
* 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
  
== April 23, 2020 ==
+
=== WS279 Citace Upload ===
 +
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
  
=== Community Phenotype Curation Tutorials ===
 
* Chris has finished first round of tutorials; 8 tutorials, 6 video recordings
 
* There are ~8 new volunteers; will setup tutorials for them soon
 
  
=== ECO code implementation ===
+
== September 17, 2020 ==
* ?ECO_term to replace ?GO_code in ACEDB models
 
* GAF files with three-letter codes can still be generated by mapping
 
  
=== Simplemine for Alliance ===
+
=== Species errors in CITace ===
* Wen has presented proposal to Search group
+
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
* Plan is to have a link to the Alliance Simplemine prototype from the Alliance web page
 
  
=== Venn diagram tool ===
+
=== Webinars ===
* Conceived by Jae, implemented by Sibyl
+
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
* Currently used for interactions data
+
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
* Could use for other data types like phenotype (e.g. comparing RNAi vs. allele phenotype)
+
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
* Could also use for Expression data, e.g. comparing results from different methods
+
* Chris and Wen can discuss how to setup
* Could maybe use for disease data
+
* Should we have people register? Maybe
 +
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
  
=== AFP tutorial ===
+
=== Transcription factors and regulatory networks ===
* Daniela, Kimberly, Valerio will run through the AFP form with Nikita from Gupta lab tomorrow
+
* Had another question about TFs, asking for common TFs for a list of genes
* May record in the future to make a tutorial video
+
* An issue is that the TF binding data we have is in disparate forms, trying to reconcile
* Daniela may (re-)start curating markers for relevant expression patterns
+
* We have a ?Transcription_factor class; it would be good to update and integrate with other related data types
* Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
 
  
=== Expression markers ===
+
=== Alzheimer's disease portal ===
* SURF student projects: Identifying good expression markers? Maybe, but may require more curation experience
+
* Funding has been awarded for Alzheimer's research
* Wen looked at expression cluster data; hard to find good, very specific (i.e. neuron) markers
+
* Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
* Daniela may (re-)start curating markers for relevant expression patterns
+
* Paul S: Alliance SAB tomorrow; we'll see what the SAB says
* Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
+
* Can look at other resources like RGD disease portals and Reactome disease-related pathway models
* Already have an "Expression markers" widget on anatomy term pages
+
* Ruth Lovering is doing some work in this regard
* Could combinations of genes (e.g. cGal) act as markers?
 
  
== April 30, 2020 ==
+
=== 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
  
=== Adding ?ECO_term class for WS278 ===
+
=== New GAF 2.2 file ===
* Proposed[https://wiki.wormbase.org/index.php/Evidence_Code_Ontology#.3FECO_term_Model ?ECO_term model]
+
* Kimberly has reviewed and sent feedback to Michael P
** How are the Parent/Child and Ancestor/Descendant tags used in WB for ontology classes?  Do we still need them in .ace files?
+
* Valerio would like to stay in the loop to test the new files
*Confirm proposed changes to class models that will use this tag:
 
** ?GO_annotation
 
** ?Phenotype
 
** ?Disease_model_annotation
 
  
* Discuss using ?RO_term values in our WB ontology term models
+
=== Data mining tool comparison sheet ===
* Currently relations between ontology terms are captured with text that is sometimes inconsistent for the same concept, e.g. is_a
+
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
* Where possible, should be use ?RO_term to express the relations between ontology terms in our WB models?
+
* Needs an update
* Impact on web display?
+
* 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.

Revision as of 16:39, 17 September 2020

Previous Years

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2014 Meetings

2015 Meetings

2016 Meetings

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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