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]]
  
= 2018 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
== January 4, 2018 ==
 
  
=== WS264 Upload ===
 
* Citace upload to Wen, Tuesday January 16th, by 10am PST
 
* Upload to Hinxton on Jan 19th
 
  
=== Strain data import to AGR for disease ===
 
* Will begin to consider pulling in strains into AGR
 
* Will need to think about how genotypes are built and stored at other MODs
 
* We should encourage authors to include strain IDs
 
* Diseases are annotated to genes, alleles, and strains within WB
 
  
=== Curating phenotypes and diseases to strains or genotypes ===
+
= 2020 Meetings =
* Should we generate a ?Genotype class to capture genotypes without a known strain name? Or to capture relevant/relative genotypes thought to be responsible for a phenotype or disease?
 
* We could create un-named strain objects, that use a new unique identifier as a primary identifier and represent the entire genotype of a strain used
 
** Introduction of a new ?Strain class attribute of a unique serial identifier (like WBStrain00001) would be very costly to implement; would need to consider how crucial this is before implementing
 
** We can, instead, use new strain (public) names like "WBPaper00012345_Strain1", etc. instead of creating new unique ID attribute for un-named strains
 
* When curating phenotypes to strains, we will want to specify what is the relevant/relative genotype that is causative/correlated with the disease or phenotype observation
 
** Would be best if the specification of the relevant genotype used controlled vocabularies (when possible) and free text (when needed); would need to work out the logistics/mechanics of such curation
 
** Transgene-phenotype curation currently specifies causative gene, but would be more complicated for strains
 
* Alternatively, we could create the ?Genotype class to represent the abstract "relative"/"relevant" genotype thought to be responsible for the phenotype or disease, and annotate directly to that ?Genotype object
 
* ?Strain approach:
 
** Use strain if named (but important to know if the control strain is not simply N2)
 
*** If control strain is simply N2, causative genotype (and respective components) can be inferred from strain genotype
 
*** If control strain is not N2, causative genotype and components would need to be specified at the moment of phenotype/disease curation (by mechanism to be worked out)
 
** If no strain name provided, create "un-named" strain that contains the entire genotype provided by authors
 
*** Control strain issues above would still need to be addressed
 
* ?Genotype approach:
 
** ?Genotype class could represent individual instances of relevant/relative genotypes that are suggested to be causative for a disease or phenotype
 
** ?Genotype objects would be created with formal construction, with DB associations to each component object (e.g. alleles, transgenes, etc.) as well as free text descriptions (for components with no corresponding DB object)
 
** Such ?Genotype objects could be used repeatedly throughout a paper when applicable, but would likely not be used in any other papers (we would likely accumulate redundant objects in the DB)
 
* We may want to consider strains with same public name that have diverged
 
** Apply new strain names with prefixes/suffixes? Create new strain objects? Keep original?
 
* Need to determine how each AGR member DB curates phenotypes or diseases to genotypes: is each "genotype" a relative or absolute genotype?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
== January 11, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
=== IWM swag ===
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
* Eppendorf tube openers with WormBase logo?
 
  
=== Update on AFP Form ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
*[https://docs.google.com/presentation/d/1anFOFRK9Ida1UEvrXWf2OBAJ9F4xyU4lWJGy-qr6wRU/edit#slide=id.p3 In-progress mock-up of new form]
 
*[https://docs.google.com/spreadsheets/d/1sS_uAjBJ2r5H90Lam62Ai0HunjwvfjnklkFNrDoNXeU/edit#gid=1929595460 Data type spreadsheet]
 
*[http://wiki.wormbase.org/index.php/First-pass_flagging_pipelines#Author_first-pass_form_revisions Curation forms info]
 
  
*Idea is to move from author flagging to author validation of text mining and data submission wherever possible
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
*Goal is to flag all data types in a paper and either curate at WB or share with a group that does curate that data
 
*SVM flags and author flags can/will be used as filters in TPC
 
*Provide examples of what we want for each type of data to help avoid confusion
 
* Recognize entities automatically and show list to author
 
** Species, strains, genes, alleles, transgenes, etc.
 
** Ask to verify or add unrecognized
 
** Could show known/existing objects with checkboxes
 
** Possibly include unrecognized pattern matching objects? Ask author to verify if these are real?
 
** For strains:
 
*** Show recorded genotype for verification; maybe ask to update/modify if needed?
 
** For transgenes:
 
*** When author submits new transgene, send them to a transgene form, or send them an email asking for details?
 
*** Form could be for both strain and transgene
 
* Mapping data: still ask for? Maybe for balancers, but no one is reporting that. Could still ask if there's interest
 
* Maybe provide option for author to save their progress and return to the form later
 
* Phenotypes
 
** Ask for allele, RNAi and overexpression phenotypes with links to Phenotype form
 
** Also ask for drug/chemical and environmental perturbations (call treatment?); store as free text for now, accommodate with new data model when available
 
* Gene site- and time-of-action, mosaic
 
** Appears to be confusion from authors about mosaics. Should we keep this?
 
** Will keep gene site-of-action and time-of-action; leave unchecked (no SVM, yet) but allow users to indicate
 
* Cell and anatomy data
 
** Cell function ("Cell ablation (laser/genetic) data, optogenetics")
 
** Ultrastructural analysis
 
* Interaction data
 
** Genetic interactions
 
** Physical interactions
 
** Functional complementation
 
* Comparative genomics
 
* Gene expression & regulation
 
  
  
 +
== June 4, 2020 ==
  
== January 18, 2018 ==
+
=== Citace (tentative) upload ===
 +
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 +
* Citace upload to Hinxton on Friday, July 10th
  
=== WormBase Tutorials ===
+
=== Caltech reopening ===
* May be good to get (possibly anonymous) written questions or suggestions after presenting
+
* Paul looking to get plan approved
* Wen will have Skype call with Yishi Jin
+
* People that want to come to campus need to watch training video
* Micropublications
+
* Masks available in Paul's lab
** how do we peer-review single experiment? No supporting information to corroborate a larger story
+
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
** Is the greater benefit of peer-review that the whole story is assessed by reviewers
+
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
** Do MPs help or hurt reproducibility?
+
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
** Larger papers may have lots of poor experiments that don't get much attention but still pass peer review
+
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
** Dedicated peer review on single experiment may be more rigorous
+
* Also, need to submit who you were in contact with for contact tracing
** What are the criteria/minimal requirements to micropublish?
+
* Form is used all week, and hold on to it until asked to be submitted
* Concise descriptions
+
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
** SimpleMine has multiple descriptions output; people asked about the different types
 
** Yishi Jin suggested that we remind users to update manually written descriptions
 
** Showing last-updated date is important
 
** Automated descriptions relies on primary data; will rely on forms and community submissions
 
** Microreviews? Would want to guide authors what data we want; provide a template?
 
* Public/community education issues
 
** Users shouldn't assume that WormBase is comprehensively up to date
 
* Wen will also present at MidWest meeting (Ann Arbor, MI) in April and Boulder, Colorado in May
 
** Will assess topic interest ahead of time
 
  
=== New Cytoscape display for interactions ===
+
=== Nameserver ===
* Sibyl developed a new Cytoscape display for interactions, now live with WS262 release
+
* Nameserver was down
* Simplified colors and subtypes
+
* CIT curators would still like to have a single form to interact with
* Redraw button to clean up the graph based on what you want to see
+
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
* Play around and let Sibyl and/or Chris know about issues
+
* 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
  
== January 25, 2018 ==
 
  
=== UCSF visit report ===
+
== June 11, 2020 ==
  
Questions from the audience
+
=== Name Service ===
*Is there a way in WB to pull out verified CRISPR guides?
+
* Testing site now up; linked to Mangolassi
*Single cell RNAseq from Waterson lab in WB? Paper is in WB, person-paper connections might be on staging, Kimberly verifying this. Gary W will put data in WS264. Comments from Gary on this paper:
+
* CGI from Juancarlos not accepting all characters, including double quotes like "
‘The main problem is that the authors can sort the cells into groups (corresponding to tissues, I think) and sometimes sort them into single cells, but it is hard to identify the tissues or cells. I think they found 29 groups, of which about 20 appear to be single cells.
+
* Example submission that fails via CGI
I think they have a website where they invite other researchers to make suggestions about how to identify cells in their data.
+
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
Currently I regard this data set as still undergoing analysis and I'm waiting to see if they improve the deconvolution and identification of the cells.
+
* Juancarlos will look into and try to fix
The RNASeq data from this paper will be going into the current Build (WS264) but I will not be adding it to SPELL this Build because displaying it probably requires more thought.
 
I'm not sure that tools for displaying single-cell data have been developed very much yet. There is potentially a lot of information if eventually all 959 or 1031 somatic cells are displayed!
 
  
*List of fem-3 alleles excluding natural variants in WormMine, how to do that? The template should be fixed (checkbox)
+
=== Alliance Literature group ===
*Is the increase of published paper due to an increased number of labs? Expansion of the field? Is there a correlation between the increased number of publications and increased number of labs
+
* Textpresso vs. OntoMate vs. PubMed
*One user found powerful to be able to use the Galaxy server to do analysis after exporting data from WormMine
+
* Still some confusion about what the different tasks can be performed in each tool
*Can you do protein domain analysis with WormMine? Is the protein->motif precanned query the best option?
+
* Working on collecting different use cases on spreadsheet
*Enrichment: how to see which genes are expressed in a tissue or cell -> pointed user to the ontology browser
+
* 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?
  
=== Skype call with Yishi Jin and Sreekanth Chalasani ===
+
=== Alliance priorities? ===
Participants: Daniela, Karen, Wen, Jin, Shrek
+
* 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.
  
*Not all images available due to publisher agreement -> not clear to users, we should put a disclaimer somewhere
+
=== Sandbox visual cues ===
*Shrek: thinks gene expression display should improve => hard to figure out all expression patterns
+
* 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)
**Shrek and Jin feel the most important info is the reagent, and that should be displayed on the gene page/expression widget other than the Expression page
+
* AFP and Micropub dev sites have indicators
*Images are identical -> example on the eat-4 expression page. This is normal since one image depicts multiple neurons and the association Anatomy neuron applies.
+
* Could play with changing the background color? Maybe too hard to look at?
http://www.wormbase.org/species/c_elegans/gene/WBGene00001135#1860--10
+
* Change the color of the title of the form, e.g. the OA?
**On the eat-4 expression page the problem is amplified as one picture shows 70+ neurons
+
* Will add red text "Development Site" at top of the OA form
**We should remove the image column and have links to images only on the panel above (as currently displayed)
+
 
**The image column should be replaced with reagent and description, if possible. Will need to talk to Sibyl and see what is duable.
+
=== Evidence Code Ontology ===
*Shrek pointed out that the eat-4 concise description is out of date, we explained that in the near future the manual descriptions will be superseded by automatic descriptions
+
* Kimberly and Juancarlos have worked on a parser
*Neuron connectivity: missing neuron connectivity pages, there is a new reconstruction of neuroanatomy from david hall, would be great to integrate
+
* 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
 +
** 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)
 +
 
 +
=== 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)

Latest revision as of 19:13, 25 June 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)