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]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
= 2018 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
 +
==May 23rd, 2024==
 +
*Publication bias workshop NINDS
 +
** Registered report -> the protocol is sent before publication
 +
** How many negative curated data? Do we want to pull this out?
 +
** Two billion dollars worth of research not published each year
 +
**Octopus.ac publishing platform
  
 +
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
== March 1, 2018 ==
+
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
=== Elsevier paper-linking through Scholix ===
+
==April 4th, 2024==
−
* Bidirectional linking in place with ScienceDirect, Elsevier
+
* Continued discussion on sustainability
−
** We link to their papers via DOI
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
** They link papers to WB
+
** Data is still going to SPELL and enrichment analysis
−
* Scholix
+
** Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
−
** http://www.scholix.org
+
* Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
−
** Scholix becoming a standard platform for linking to DB websites
+
* Michael's presentation on LLMs - Named Entity Recognition (NER)
−
** WB would need to establish Scholix integration?
 
−
** Daniela to check in with the Alliance to see what the other groups are doing
 
−
** Would Caltech library need to establish a pipeline or would WB do it?
 
−
* Would be good to revisit the paper page display for what is referenced in the paper
 
−
** GO terms are not showing currently
 
−
** Would be good to assess what else is not showing currently
 
  
−
=== Upstate NY Worm Meeting ===
+
==March 14, 2024==
−
* Confirmation from organizers?
 
−
* Kimberly and Wen reached out to organizers about WB presentation
 
−
* 20-30 minute time slot for talk
 
−
** What are most important topics to bring up?
 
−
** Ask authors to submit sequence for sequence features, etc.
 
−
** Micropublications
 
−
*** Would be good to have answers to common questions about micropublications (how we get reviewers, etc.)
 
−
** Alliance of Genome Resources
 
−
** Help Desk/ Online chat service
 
−
* Organizers want WB to have table at meeting
 
−
* Meeting in Syracuse
 
  
−
=== Midwest Worm Meeting ===
+
=== TAGC debrief ===
−
* Organizers asked for $50-$100 sponsorship
 
  
−
We can pay for registration but we are not a company to sponsor events.
+
==February 22, 2024==
  
−
=== Metrics ===
+
===NER with LLMs===
−
* How do DBs help research?
 
−
* How much time do MODs/Alliance etc. databases save researchers?
 
  
 +
* Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
  
−
== March 8, 2018 ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
=== SimpleMine interactions ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Wen considering adding interaction data to SimpleMine
 
−
** Should we add a single column listing interacting genes with types in parentheses
 
−
** Wouldn't want to add too many columns
 
−
** Want to indicate, for a query gene, genes for which multiple interaction types have been observed
 
−
* Once interaction data is in WormMine, we can omit it from SimpleMine
 
−
* SimpleMine is not too difficult to develop or maintain as long as data models don't change
 
  
−
=== SimpleMine preserving input list ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Adding functionality to WormMine that preserves original gene list
 
−
* Some input genes return multiple hits/rows
 
−
* We need to recognize these entries and deposit extra rows separately
 
  
−
=== Alliance working group project plans ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Interactions
 
−
** What are prioritized deliverables?
 
−
** Predicted (physical) interactions: Interologs, Inter-species extrapolations
 
−
* (Automated) gene descriptions
 
−
** Ranjana and Ceri have added content to project plan
 
−
** Add phenotype data to description for information-poor genes (currently last on priority list)
 
−
* Disease/phenotypes
 
−
** Cindy et al. producing project plan documents for disease and phenotype separately
 
  
  
−
== March 15, 2018 ==
 
  
−
=== HTTP vs HTTPS ===
+
==February 15, 2024==
−
* Plan to move to https site-wide as a standard
 
−
* Google site ranking includes metric for https security
 
−
* All pieces in place on main site; just a few small things at Caltech to resolve
 
−
* What services are having problems?
 
−
* Raymond: Don't know the SSL details; has made Caltech machines using SSL layer
 
−
* Todd: Not needed; should be handled by proxy
 
−
* Todd needs to just know what are problematic URLs; should all be handled by main URL www.wormbase.org
 
−
* Ontology Browser broke, Juancarlos went to fix then had problem with https
 
−
* Todd: haven't setup https for all development sites yet, but will do that
 
−
* Gene Set Enrichment Tool: redirects to local/Caltech site that serves the page
 
−
** Todd & Sibyl looking at; one possible solution is to get the recent code on staging and replace it (tool breaks on staging)
 
−
* Juancarlos, Raymond, Sibyl, and Todd will discuss later (Slack channel?)
 
  
−
=== Disease model annotation class display ===
+
=== Literature Migration to the Alliance ABC ===
−
* Ranjana has two GitHub tickets open
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
** https://github.com/WormBase/website/issues/6044
+
===== Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic =====
−
** https://github.com/WormBase/website/issues/6241
+
*Facet for topic
−
* Data has gone into ACEDB, but no display is configured yet
+
*Facet for automatic assertion
−
* Ranjana would like to Skype with Sibyl to explain
+
**neural network method
−
* Bypass ACEDB altogether? Go right into Datomic? Need to check, but will probably pull into ACEDB and do the conversion to Datomic at the same time?
+
*Facet for confidence level
 +
**High
 +
*Facet for manual assertion
 +
**author assertion
 +
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
−
=== Baltimore Area Worm Meeting ===
+
===== Manually validate paper - topic flags without curating =====
−
* Chris presenting tomorrow at the meeting
+
*Facet for topic
−
* Will cover data mining tools, new data and displays
+
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
=== Alliance ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* Paul S: Work on Alliance plans; important
+
* Search ABC with paper identifier
 +
* Migrate to Topic and Entity Editor
 +
* View all associated data
 +
* Manually validate flags, if needed
  
−
=== Citace upload ===
+
=== PDF Storage ===
−
* Next Tuesday (March 20th) at 10am Pacific
+
* At the Alliance PDFs will be stored in Amazon s3
 +
* We are not planning to formally store back-up copies elsewhere
 +
* Is this okay with everyone?
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
== March 22, 2018 ==
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
=== WB grant critique ===
+
==February 1, 2024==
−
* Great comments
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Skeptical that community curation will take off (or that it will get all curation done)
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* Positive reviews of Alliance interactions with WB
 
  
−
=== New York worm meeting ===
+
==January 25, 2024==
−
* Kimberly and Wen will head to local worm meeting to present on WB
 
  
−
=== Human Genetics meeting ===
+
=== Curator Info on Curation Forms ===
−
* Meeting in October
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* Will have Alliance presence there
 
  
−
=== Alliance ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* How important is it to have the MOD?
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
* What is the added value of the Alliance portal?
 
−
* What are the use cases that can be uniquely handled by the Alliance website/portal? MOD site?
 
−
* Something to think about; send thoughts and ideas to Paul S.
 
−
* Parallel development pipelines?
 
−
** Valerio discussing with AGR developers tomorrow
 
−
** So far, AGR development has been centralized; may need to allow parallel development for efficiency/efficacy
 
−
** Example: development of automated gene descriptions
 
−
** JBrowse and GO Ribbon currently developed independently
 
  
−
=== Person curation ===
+
* The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
−
* Cecilia had looked at how other MODs/groups curate authors/persons? Interact with community?
 
−
* How can the Alliance do the same (union of all approaches)?
 
−
* ZFIN has person page
 
  
−
=== Variant graphical viewer ===
+
* I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
−
* As requested by Andy Golden and others
 
−
* Hope to have a mockup by April
 
−
* Use synteny viewer/browser? Long evolutionary distances (human-worm) may be tricky
 
  
−
=== Baltimore Area Worm Meeting ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
* [https://docs.google.com/presentation/d/1i_LEZsolKXy1NrEqua0u4apgWHiQbkQhifgtMTbz2H4/edit?usp=sharing| Chris' slides]
 
−
* Enthusiasm for Micropublications
 
−
* Enthusiasm for the Alliance of Genome Resources
 
−
* Questions:
 
−
** How to download RNASeq data values from gene page?
 
−
** What does "WS" mean?
 
−
** WormBase provides protein-coding gene exon expression evidence, what about small, non-coding RNAs?
 
−
** How are micropublication reviewers selected?
 
−
*** Authors suggest reviewers; uP team suggest reviewers
 
−
*** PIs, post-docs and senior grad students (vetted; already have published papers)
 
−
** Are phenotypes included in Ontology Browser also from genetic interactions? Answer: "No", response: "Good"
 
−
** Are we going to lose WormBase and functionality?
 
−
* Comments:
 
−
** FTP README docs need work, updating
 
−
** WormMine is not intuitive
 
−
** It's hard to know what each data mining tool is good/best for
 
−
*** Would be good to have a simple document that outlines the best uses of each tool
 
−
*** How would we best provide such a document? Location? Versioning? Micropublication?
 
−
*** Create a one page PDF to print out and give out at meetings?
 
−
*** Update blogs (describing nature of updates to each tool)?
 
−
*** Existing FAQ Wiki?
 
−
*** Important to have a single place for documentation (to avoid denormalization)
 
−
* Requests:
 
−
** Create simple Galaxy import of WB genome sequence
 
−
** Display prevalence of splice junctions
 
−
** Add README docs to FTP site (and/or update them)
 
−
** Separate RNAi and allele based phenotypes
 
−
*** Probably worth considering; have heard from users before
 
−
*** Could also provide functionality in Phenotype Graph
 
−
** Include BioRxiv papers in gene page References widget
 
−
*** Could provide links to BioRxiv (with relevant search results)?
 
−
*** Is there a way to link BioRxiv papers to the eventually published paper?
 
−
*** Are full texts indexed?
 
  
 +
=== Update on NN Classification via the Alliance ===
 +
* Use of primary/not primary/not designated flag to filter papers
 +
* Secondary filter on papers with at least C. elegans as species
 +
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
  
−
== March 29, 2018 ==
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
 +
* NNC html pages will show NNC values together with species.
 +
* Show all C. elegans papers first and other species in a separate bin.
  
−
=== Gene Set Enrichment Analysis: duplicate entries ===
+
=== Travel Reimbursements ===
−
* Although duplicate genes in an input list are not counted more than once, the output lists the valid gene list that includes duplicates
+
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
=== Interactions Venn Diagram ===
+
=== UniProt ===
−
* Jae generated mockups for displaying a Venn diagram of gene pairs represented by interactions on a gene page
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
* Mockups here: https://drive.google.com/file/d/1z15GwvLT1dUH9VkYCz-NoQ2oFzi_3ds3/view?usp=sharing
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.  
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
  
−
=== GO term and spatiotemporal expression comparison ===
+
==January 18, 2024==
−
* Jae generated mockups for representing a GO term and spatiotemporal expression comparison for interacting gene pairs
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
−
* The data display would/could use the ribbon-style annotation display
 
−
* Mockups here: https://drive.google.com/file/d/1z15GwvLT1dUH9VkYCz-NoQ2oFzi_3ds3/view?usp=sharing
 
  
−
=== GO enrichment analysis for interacting genes ===
 
−
* Jae generated mockups for displaying the results of GO term enrichment analysis on the list of genes that interact with a focus gene
 
−
* Mockups here: https://drive.google.com/file/d/1rwy8iuuaXJgu6TnQrGvvfVOXgA5wvtyt/view?usp=sharing
 
  
−
=== Inclusion of negative GO annotations in Alliance GO ribbon ===
+
==January 11, 2024==
−
* See cpx-1 gene page: http://www.alliancegenome.org/gene/WB:WBGene00022271
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
−
* In the GO ribbon, the term "nucleus" is highlighted, yet this is only because of two negative annotations coming from mouse and rat
+
** Curators should make sure that, when pasting special characters, the duplicate function works
−
* Do we want negative GO annotations included in the display by default? Shouldn't we alert users to this if we are going to do this?
+
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
−
* Thoughts?
+
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
  
−
=== Upstate NY C elegans Meeting ===
+
==January 4, 2024==
−
*Wen and Kimberly presented at the UNYCEM in Syracuse last Saturday (3/24)
+
* ACKnowlegde pipeline help desk question:
−
*Feedback:
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
**WormMine is hard to learn (but performing operations on lists of genes is something people really want/need to do)
+
* Citace upload, current deadline: Tuesday January 9th
−
**Video tutorials would be very helpful, especially for teaching students different WB functionality
+
** All processes (dumps, etc.) will happen on the cloud machine
−
**Micropublications were well received
+
** Curators need to deposit their files in the appropriate locations for Wen
−
***People were specifically interested in publishing negative results; maybe make that point even more prominent on the FAQs?
+
* Micropublication pipeline
−
**Downloading sequences that include coding and non-coding, it would be really helpful to have visual cues for coding vs non-coding
+
** Ticketing system confusion
−
**Should the C. elegans community consider moving towards more mammalian-centric gene names, even if that means changing current gene names?
+
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics
−
**A better mobile app would be great; people want to look up C. elegans info on their phones and the current view is cumbersome
 
−
* Denise (organizes neuro topic meeting); suggested that WB present at Neuro meeting
 
−
** Meeting in Madison, WI June 25-28
 

Latest revision as of 18:09, 23 May 2024

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

2023 Meetings

May 23rd, 2024

  • Publication bias workshop NINDS
    • Registered report -> the protocol is sent before publication
    • How many negative curated data? Do we want to pull this out?
    • Two billion dollars worth of research not published each year
    • Octopus.ac publishing platform

April 18th, 2024

  • NNC pipeline being switched off locally and moving into the Alliance ABC.

April 11th, 2024

  • Caltech WS293 ace files ready for the upload

April 4th, 2024

  • Continued discussion on sustainability
  • CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
    • Data is still going to SPELL and enrichment analysis
    • Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
  • Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
  • Michael's presentation on LLMs - Named Entity Recognition (NER)

March 14, 2024

TAGC debrief

February 22, 2024

NER with LLMs

  • Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
  • Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  • There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.


February 15, 2024

Literature Migration to the Alliance ABC

Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)?

Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic
  • Facet for topic
  • Facet for automatic assertion
    • neural network method
  • Facet for confidence level
    • High
  • Facet for manual assertion
    • author assertion
      • ACKnowledge method
    • professional biocurator assertion
      • curation tools method - NULL
Manually validate paper - topic flags without curating
  • Facet for topic
  • Facet for manual assertion
    • professional biocurator assertion
      • ABC - no data
View all topic and entity flags for a given paper and validate, if needed
  • Search ABC with paper identifier
  • Migrate to Topic and Entity Editor
  • View all associated data
  • Manually validate flags, if needed

PDF Storage

  • At the Alliance PDFs will be stored in Amazon s3
  • We are not planning to formally store back-up copies elsewhere
  • Is this okay with everyone?

February 8, 2024

  • TAGC
    • Prominent announcement on the Alliance home page?
  • Fixed login on dockerized system (dev). Can everybody test their forms?

February 1, 2024

  • Paul will ask Natalia to take care of pending reimbursements
  • Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.

January 25, 2024

Curator Info on Curation Forms

  • Saving curator info using cookies in dockerized forms. Can we deploy to prod?

ACKnowledge Author Request - WBPaper00066091

  • I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  • The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
  • I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  • Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.

Update on NN Classification via the Alliance

  • Use of primary/not primary/not designated flag to filter papers
  • Secondary filter on papers with at least C. elegans as species
  • Finalize sources (i.e. evidence) for entity and topic tags on papers
  • Next NN clasification scheduled for ~March
  • We decided to process all papers (even non-elegans species) and have filters on species after processing.
  • NNC html pages will show NNC values together with species.
  • Show all C. elegans papers first and other species in a separate bin.

Travel Reimbursements

  • Still waiting on October travel reimbursement (Kimberly)
  • Still waiting on September and October travel reimbursements (Wen)

UniProt

  • Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
  • Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
  • Stavros escalates the issue on Hinxton Standup.
  • Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.

January 18, 2024

  • OA showing different names highlighted when logging in the OA, now fixed on staging


January 11, 2024

  • Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
    • Curators should make sure that, when pasting special characters, the duplicate function works
  • OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
    • If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
  • Chris tested on staging and production the phenotype form and the data are still going to tazendra
    • Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
    • Raymond: simply set up forwarding at our end?
  • AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
  • Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
  • Valerio would like to use an alliancegenome.org email address for the openAI account
  • New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
  • Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
  • Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
  • Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
  • It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
  • Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.

January 4, 2024

  • ACKnowlegde pipeline help desk question:
    • Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
  • Citace upload, current deadline: Tuesday January 9th
    • All processes (dumps, etc.) will happen on the cloud machine
    • Curators need to deposit their files in the appropriate locations for Wen
  • Micropublication pipeline
    • Ticketing system confusion
    • Karen and Kimberly paper ID pipeline; may need sorting out of logistics
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