Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
= 2018 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
  
== August 2, 2018 ==
+
== June 4, 2020 ==
  
=== AFP ===
+
=== Citace (tentative) upload ===
 +
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 +
* Citace upload to Hinxton on Friday, July 10th
  
* The AFP pipeline is currently emailing authors from karen's e-mail address
+
=== Caltech reopening ===
* Use same e-mail account Chris is using for phenotype community curation requests or create a new account for AFP (gmail)
+
* Paul looking to get plan approved
* Can use outreach@wormbase.org for consistency
+
* People that want to come to campus need to watch training video
* May use the PMID in the subject line so e-mails will not be all in the same thread
+
* Masks available in Paul's lab
* Todd and Chris have email credentials
+
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
** Chris will send to Valerio, Juancarlos, Daniela, and Kimberly
+
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
* Let Valerio and Juancarlos know what pipelines use AFP before they modify
+
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
* Do curators still want to receive emails when authors flag their data type?
+
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
** We will leave the alert emails as is for now
+
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
 +
=== Nameserver ===
 +
* Nameserver was down
 +
* CIT curators would still like to have a single form to interact with
 +
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 +
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 +
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 +
* Hinxton is pulling in CGC strains, how often?
 +
* Caltech could possibly get a block of IDs
  
== August 9, 2018 ==
+
=== Alliance SimpleMine ===
 +
* Any updates? 3.1 feature freeze is tomorrow
 +
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
  
=== AFP ===
 
* Mei Zhen, SAB member suggested that we include disease models in the AFP form.
 
* The AFP group will work with Ranjana to incorporate it. Ranjana will prepare a mock by next week.
 
* We will then decide about using the existing afp_humdis tables or creating new ones.
 
  
=== Tazendra ===
+
== June 11, 2020 ==
  
* Shall we move tazendra.caltech.edu to the cloud? Either WormBase cloud or Caltech cloud?
+
=== Name Service ===
 +
* Testing site now up; linked to Mangolassi
 +
* CGI from Juancarlos not accepting all characters, including double quotes like "
 +
* Example submission that fails via CGI
 +
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
 +
* Juancarlos will look into and try to fix
  
 +
=== Alliance Literature group ===
 +
* Textpresso vs. OntoMate vs. PubMed
 +
* Still some confusion about what the different tasks can be performed in each tool
 +
* Working on collecting different use cases on spreadsheet
 +
* Sentence-based search is big strength of Textpresso
 +
* At latest meeting performed some large searches for OntoMate and Textpresso
 +
* Literature acquisition: still needs work
 +
** Using SVM vs. Textpresso search to find relevant papers
 +
** Species based SVM? Currently use string matching to derive different corpora
 +
** Finding genes and determining which species those genes belong to?
  
 +
=== Alliance priorities? ===
 +
* Transcription regulatory networks
 +
* Interactions can focus on network viewer eventually
 +
** May want different versions/flavors of interaction viewers
 +
** May also want to work closely with GO and GO-CAMs
 +
* Gene descriptions can focus on information poor genes, protein domains, etc.
  
== August 16, 2018 ==
+
=== Sandbox visual cues ===
 +
* Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
 +
* AFP and Micropub dev sites have indicators
 +
* Could play with changing the background color? Maybe too hard to look at?
 +
* Change the color of the title of the form, e.g. the OA?
 +
* Will add red text "Development Site" at top of the OA form
  
=== Tazendra ===
+
=== Evidence Code Ontology ===
* Moving to cloud? To avoid local hardware issues?
+
* Kimberly and Juancarlos have worked on a parser
* Need to discuss with Juancarlos and Paul S.
+
* Will load into ACEDB soon
* Need to consider logistics; put all of Tazendra functionality on cloud? Keep some things local?
 
** Postgres in cloud; forms local? Paper pipeline?
 
** Will consult with Textpresso
 
  
=== ICBO 2018 recap ===
 
* POTATO workshop (Phenotype Ontologies Traversing All The Organisms)
 
** Will work towards generating standardized logical definitions using Dead Simple OWL Design Patterns (DOSDP)
 
*** <Quality> and inheres_in some <Entity> (and has_modifier some <Mod>)
 
*** Exercise: Reconciling logical definitions for apparently equivalent phenotype terms across ontologies (e.g. MP vs. HP)
 
** Can use Protege to edit the OWL ontology and ROBOT for automating generation of many terms and logical definitions in parallel
 
** Will try to align WPO to UPheno as best as we can; will depend (at least in part) heavily on alignment with Uberon for anatomy
 
** Some Uberon alignment challenges: e.g. Fruit fly "tibia" and human "tibia"; human "tibia" parent is "bone" but fly "tibia" is not a bone
 
** Will participate in Phenotype Ontology Developer's call, every 2 weeks on Tuesdays (9am Pacific, 12pm East coast, 5pm UK)
 
*** Next meeting September 4, 2018
 
** Crash course in Protege, ROBOT, Ontology Development Kit, using GitHub to help develop OWL ontologies
 
** PATO needs work
 
** Questions that arose:
 
*** What should the scope of an ontology term be? Context? Life stage? Conditions? Treatment?
 
*** Being weary of ontology term count explosion; what's the right balance?
 
*** When defining phenotype terms, should the cause be included or only the observation? Maybe causes as a subclass (and assuming the observation includes assessment of cause)
 
** Some distinction between human phenotype terms and model organism terms: phenotype of individual vs. population
 
* Xenbase is trying to develop a phenotype ontology (spoke with Troy Pell, developer)
 
** Asked about WPO and how we curate
 
* Lots of plant talks
 
* Many talks on performing quality checks on ontology development and ontology re-use
 
* Domain Informational Vocabulary Extraction (DIVE) tool
 
** Entity recognition/extraction
 
** Working with two plant journals
 
** Tries to identify co-occurrence patterns of words
 
** Web interface and curation tool
 
* Semantic similarity tools and evaluation of them
 
  
=== WormBase Phenotype Ontology working group ===
+
== June 18, 2020 ==
* Chris will send around Doodle poll
 
* Goal is to discuss creation of logical definitions and alignment of phenotypes for Alliance
 
  
 +
=== Undergrad phenotype submissions ===
 +
* Chris gave presentation to Lina Dahlberg's class about community phenotype curation
 +
* Class took survey about experience with presentation and experience trying to curate worm phenotypes
 +
** Survey results: https://www.dropbox.com/s/00cit5aitv8yu27/Dahlberg_class_survey_results.xlsx?dl=0
 +
** Some students didn't benefit, but most did; nice feedback!
 +
** Lina intends to publish/micropublish the survey results so please don't share
 +
* Since April 24, the class has submitted 171 annotations from 23 papers (some redundant and some still under review)
  
== August 23, 2018 ==
+
=== Special characters in OA/Postgres ===
 +
* There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
 +
* In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
 +
* It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
 +
* Juancarlos wrote Perl script on Mangolassi at:
 +
** /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters/get_summary_characters.pl
 +
** Will find bad characters and their pgids for a given Postgres table
 +
** Will find bad data and their pgids for the same table
 +
** People can query their data tables for these characters
 +
* Chris & Wen will work on compiling a list of bad characters that tend to come up
  
=== Alliance tables ===
+
=== Citace upload ===
* Filtering/sorting priorities
+
* July 10th citace-to-Hinxton upload
* Open question about which tables on the Alliance website should be prioritized for acquiring sorting and filtering functionality
+
* July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th
  
=== Worm Phenotype Ontology working group ===
 
* Gary S., Karen, Kimberly, and Chris have responded to [https://doodle.com/poll/xzkxet8sb57enver#table Doodle poll]
 
* Looks like 12pm Pacific (3pm Eastern) on Thursdays is the time that works for everyone
 
** May start late on days when WB CIT meeting goes past 12pm Pacific
 
** May want to start a bit past 12pm to allow west coasters to get lunch, etc.?
 
* Goals:
 
** Work on logical definitions for WPO terms
 
** Consider any restructuring of WPO that would facilitate ontology alignment with other MODs and UPheno
 
** Could we eventually create a phenotype annotation tool (and term requester) that allows modular expressions of a phenotype observation to lookup existing terms or create new terms with logical definitions based on those modular elements?
 
  
=== Alliance anatomy ===
+
== June 25, 2020 ==
* Data quartermasters and expression working group are looking to get updated anatomy-Uberon mappings
 
* How frequent are data updates at the Alliance? Seems to be every ~2 months
 
* Anatomy-Uberon mappings will affect phenotype ontology alignments
 
  
=== Automated Gene Descriptions ===
+
=== Caltech Summer Student ===
*Ranjana and Valerio working to finish the new pipeline for automated descriptions for WB, will aim to finish them for the next upload, WS268.
+
* Paul has new summer student
* Working on one of the last data types--tissue expression; will use the anatomy ontology to perform logical trimming for the annotation set of cell/anatomy types (for each gene) including neurons (as opposed to using a file for neuronal term groupings taken from Oliver Hobert paper in the old pipeline)
+
** Molecular lesion curation, maybe
* Currently playing around with thresholds to see how the sentences look, will feedback any ontology related issues to Raymond
+
** Are early stops more or less likely to be null mutations?
* Working on incorporating feedback from users for information-poor genes (defined as genes with no human orthology and no GO annotations). Will include other types of information suggested by Users such as human ortholog function and protein domains, etc.
+
** Alleles are flagged as null in WB in the context of phenotypes
* When no other data is available, will include expression cluster data.  Users have complained that they don't find this data useful as it's non-specific and from large scale studies, so will give it the lowest priority for inclusion.
+
** Would be good to query Postgres for null alleles and work from there
*Suggestion to exclude the writing and storing of the thousands of automated descriptions to the Postgres database; there is really no advantage in them being in Postgres. 
+
* Fernando
* At the time of generation of the automated descriptions the related .ace files can also be generated; though will need to include the 6000+ manual descriptions that live in Postgres.  So will need to rethink this part a bit, though skipping Postgres will reduce the number of manual steps in the pipleline and Postgres will have less data that needs to be uploaded and downloaded from future cloud storage.
+
** Anatomy function
 +
** GO curation? Curating transcription factors?
 +
*** Checking for consistent curation
  
== August 30, 2018 ==
+
=== Worm Community Diversity Meeting ===
 +
* Organized by Ahna Skop and Dana Miller
 +
* Invite posted on Facebook "C. elegans Researchers" group
 +
* Two meetings held: one Thursday (June 18th), one Friday (June 19th)
 +
* Chris attended last Friday (June 19th)
 +
* Worm Board looking to take input and ideas from this meeting and incorporate into meetings and events
 +
* One idea was to document and track outreach efforts and what people have learned from them and organize them in a central location, maybe WormBase or Worm Community Forum
 +
* Also, there was a suggestion to have a tool that could inform potential students of worm labs in their respective local area
 +
** Ask Todd; he used to have a map of researchers; Todd had asked Cecilia to curate lab location and institution
 +
* Person and Laboratory addresses in ACEDB have a different format, so looking to reconcile
 +
* Do we know how many labs are still viable? Check for a paper verified in the last 5 years, or requested strains from the CGC recently
 +
** Most labs were real
  
=== EPIC dataset in the Alliance import ===
+
=== C_elegans Slack group ===
 +
* Called "C_elegans"
 +
* Chris made a "WormBase" channel for people to post questions, comments
 +
* Chris will look into inviting everyone and possibly integrating with help@wormbase.org email list
  
* the EPIC dataset has fine-grained anatomy-life stage annotations (e.g. single cell per minute)
+
=== WormBase Outreach Webinars ===
* This generates thousands of annotations per gene (up to 30,000) for the 127 genes analyzed in the study
+
* While travel is still restricted, we should consider WormBase webinars
* How to deal with this. In WB we do not display anatomy/life stage pairings but we display one list for anatomy terms and one for life stage. Also, we display the EPIC study in a separate panel on the gene page so that it does not ‘dilute’ small scale annotations (concerned raised by Oliver H at the time of the import).
+
* Scott working on a JBrowse webinar
 +
* Could have a different topic each month
 +
* Should collect topics to cover and assign speakers (maybe multiple speakers per topic; keep it lively)
 +
* Should set up a schedule
 +
* How should we advertise? Can post on blog, twitter, etc.
  
https://www.wormbase.org/species/c_elegans/gene/WBGene00015143#1--10
+
=== New transcripts expanding gene range ===
 +
* Will bring up at next week's site-wide call
 +
* Possibly due to incorporation of newer nanopore reads
 +
* Many genes coming in WS277 have expanded well beyond the gene limits as seen in WS276
 +
** Example genes: pes-2.2, pck-2, herc-1, atic-1
 +
* Has several repercussions:
 +
** WormBase does not submit alleles affecting more than one gene; with these gene expansions suddenly alleles once only affecting a single gene are now affecting two genes, and so are now omitted from loading into the Alliance (including any phenotype and/or disease annotations)
 +
** Some expanded genes are now being attributed with thousands of alleles/variants
  
*Possible solution:
+
=== Citace upload ===
** throw away the pairing information. e.g. for WBGene00020093, there are paired 10713 annotations from expression pattern Expr10421. On WormBase, we have a panel for Expr10421 (on the page for WBGene00020093) that shows 413 life-stage associations and 112 anatomy associations, with no pairing information. 
+
* Upload files to Spica/Wen by Tuesday (June 30th) 10am
***This approach will still give big tables (annotation in the hundreds) for the analyzed genes and the dilution problem will still be there. On the other hand, when the Alliance tables could be sorted/filtered this can be less of an issue
+
* Wen will clean up folders in Spica (older files from WS277 not cleared out for some reason)
 +
 
 +
==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
 +
*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===
 +
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
 +
*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.
 +
*Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.
 +
 
 +
===Noctua 2.0 form ready to use===
 +
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
 +
 
 +
===Nightly names service updates to postgres===
 +
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.

Latest revision as of 22:11, 9 July 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 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call


June 11, 2020

Name Service

  • Testing site now up; linked to Mangolassi
  • CGI from Juancarlos not accepting all characters, including double quotes like "
  • Example submission that fails via CGI
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | α β Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “   ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
  • Juancarlos will look into and try to fix

Alliance Literature group

  • Textpresso vs. OntoMate vs. PubMed
  • Still some confusion about what the different tasks can be performed in each tool
  • Working on collecting different use cases on spreadsheet
  • Sentence-based search is big strength of Textpresso
  • At latest meeting performed some large searches for OntoMate and Textpresso
  • Literature acquisition: still needs work
    • Using SVM vs. Textpresso search to find relevant papers
    • Species based SVM? Currently use string matching to derive different corpora
    • Finding genes and determining which species those genes belong to?

Alliance priorities?

  • Transcription regulatory networks
  • Interactions can focus on network viewer eventually
    • May want different versions/flavors of interaction viewers
    • May also want to work closely with GO and GO-CAMs
  • Gene descriptions can focus on information poor genes, protein domains, etc.

Sandbox visual cues

  • Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
  • AFP and Micropub dev sites have indicators
  • Could play with changing the background color? Maybe too hard to look at?
  • Change the color of the title of the form, e.g. the OA?
  • Will add red text "Development Site" at top of the OA form

Evidence Code Ontology

  • Kimberly and Juancarlos have worked on a parser
  • Will load into ACEDB soon


June 18, 2020

Undergrad phenotype submissions

  • Chris gave presentation to Lina Dahlberg's class about community phenotype curation
  • Class took survey about experience with presentation and experience trying to curate worm phenotypes
  • Since April 24, the class has submitted 171 annotations from 23 papers (some redundant and some still under review)

Special characters in OA/Postgres

  • There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
  • In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
  • It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
  • Juancarlos wrote Perl script on Mangolassi at:
    • /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters/get_summary_characters.pl
    • Will find bad characters and their pgids for a given Postgres table
    • Will find bad data and their pgids for the same table
    • People can query their data tables for these characters
  • Chris & Wen will work on compiling a list of bad characters that tend to come up

Citace upload

  • July 10th citace-to-Hinxton upload
  • July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th


June 25, 2020

Caltech Summer Student

  • Paul has new summer student
    • Molecular lesion curation, maybe
    • Are early stops more or less likely to be null mutations?
    • Alleles are flagged as null in WB in the context of phenotypes
    • Would be good to query Postgres for null alleles and work from there
  • Fernando
    • Anatomy function
    • GO curation? Curating transcription factors?
      • Checking for consistent curation

Worm Community Diversity Meeting

  • Organized by Ahna Skop and Dana Miller
  • Invite posted on Facebook "C. elegans Researchers" group
  • Two meetings held: one Thursday (June 18th), one Friday (June 19th)
  • Chris attended last Friday (June 19th)
  • Worm Board looking to take input and ideas from this meeting and incorporate into meetings and events
  • One idea was to document and track outreach efforts and what people have learned from them and organize them in a central location, maybe WormBase or Worm Community Forum
  • Also, there was a suggestion to have a tool that could inform potential students of worm labs in their respective local area
    • Ask Todd; he used to have a map of researchers; Todd had asked Cecilia to curate lab location and institution
  • Person and Laboratory addresses in ACEDB have a different format, so looking to reconcile
  • Do we know how many labs are still viable? Check for a paper verified in the last 5 years, or requested strains from the CGC recently
    • Most labs were real

C_elegans Slack group

  • Called "C_elegans"
  • Chris made a "WormBase" channel for people to post questions, comments
  • Chris will look into inviting everyone and possibly integrating with help@wormbase.org email list

WormBase Outreach Webinars

  • While travel is still restricted, we should consider WormBase webinars
  • Scott working on a JBrowse webinar
  • Could have a different topic each month
  • Should collect topics to cover and assign speakers (maybe multiple speakers per topic; keep it lively)
  • Should set up a schedule
  • How should we advertise? Can post on blog, twitter, etc.

New transcripts expanding gene range

  • Will bring up at next week's site-wide call
  • Possibly due to incorporation of newer nanopore reads
  • Many genes coming in WS277 have expanded well beyond the gene limits as seen in WS276
    • Example genes: pes-2.2, pck-2, herc-1, atic-1
  • Has several repercussions:
    • WormBase does not submit alleles affecting more than one gene; with these gene expansions suddenly alleles once only affecting a single gene are now affecting two genes, and so are now omitted from loading into the Alliance (including any phenotype and/or disease annotations)
    • Some expanded genes are now being attributed with thousands of alleles/variants

Citace upload

  • Upload files to Spica/Wen by Tuesday (June 30th) 10am
  • Wen will clean up folders in Spica (older files from WS277 not cleared out for some reason)

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
  • 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

  • Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
  • 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.
  • Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.

Noctua 2.0 form ready to use

  • Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways

Nightly names service updates to postgres

  • Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.