Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 15: Line 15:
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2017|February]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2017|March]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_April_2017|April]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_May_2017|May]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_June_2017|June]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_July_2017|July]]
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
[[WormBase-Caltech_Weekly_Calls_August_2017|August]]
+
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
[[WormBase-Caltech_Weekly_Calls_September_2017|September]]
+
==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)
  
−
[[WormBase-Caltech_Weekly_Calls_October_2017|October]]
+
==March 14, 2024==
  
 +
=== TAGC debrief ===
  
−
== November 2, 2017 ==
+
==February 22, 2024==
  
−
=== Site visits ===
+
===NER with LLMs===
−
* Invited to give 25+5 minute talk at Worcester Area Worm Meeting on November 14th
 
−
* Had particular interest in micropublications
 
−
* 25-30 minutes probably insufficient to present everything that we want
 
−
* Also, fairly short notice
 
−
* Travel budget?
 
−
* Would be good to meet with individual labs and lab members to discuss WormBase
 
−
* Will probably decline this offer and wait until a longer talk next year
 
−
* Will point them to micropublication.org to find out more info
 
−
* Maybe Karen/Daniela could do a webinar during the Nov 14 slot
 
  
−
=== GO annotation for Expression cluster ===
+
* 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%)
−
* Wen asking about some GO annotation details for expression clusters
 
−
* Want to annotate a particular data set with a GO term
 
−
* Wen will discuss with Kimberly
 
  
−
=== Tazendra issue ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* Had a problem Sunday-Monday
 
−
* We should consider moving curation database to a new machine/location and/or creating a backup system
 
−
* Move to the cloud? Would reduce maintenance time but will add cost
 
−
* Install on different local server?
 
−
* What are the requirements? Disk space? Computation?
 
  
−
=== Marker help desk question ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Someone looking for promoter sequences of pan-neuronal genes; neuronal marker
 
−
* Can go to "neuron" anatomy page and search expression patterns table for the term "marker"; not optimal
 
−
* Can also (reverse) sort the "Expression Pattern" column of table to pull up "Marker" annotations
 
−
* Create a "Markers" widget? "Tissue Marker" or "Expression Marker"? Daniela will create ticket
 
−
* Existing markers in Associations widget will remain there
 
−
* Are markers still being curated?
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
== November 9, 2017 ==
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
=== Citace upload ===
 
−
* Upload files to Spica for Wen by 6pm next Friday (17th)
 
  
−
=== New models file for WS263 ===
 
−
* Changes snuck up on some CIT curators
 
−
* Anatomy function model: Proposal to make Remark entry unique; Raymond asking to remove the UNIQUE in the model
 
−
* Still want to have multiple remarks (each on a separate, new line)
 
−
* May request a rollback of Anatomy function model change
 
−
* Are curators tracking model changes on GitHub?
 
  
−
=== Data migration call ===
+
==February 15, 2024==
−
* At noon PST today, if people want to join and ask questions
 
  
−
=== Caltech library ===
+
=== Literature Migration to the Alliance ABC ===
−
* Wen asked about getting articles that we can't get from Caltech library
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Was told each person can get 10 articles per year through inter-library loan
+
===== 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 =====
−
* We need about 500 articles per year that aren't in Caltech library
+
*Facet for topic
−
* Can get articles within an hour
+
*Facet for automatic assertion
−
* Maybe we can talk to library to make an agreement to get more articles
+
**neural network method
−
* If we get preprints, will it be additional cost to get official final version?
+
*Facet for confidence level
 +
**High
 +
*Facet for manual assertion
 +
**author assertion
 +
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
−
=== Micropublications ===
+
===== Manually validate paper - topic flags without curating =====
−
* Currently, curation is performed manually
+
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
=== AGR disease working group update ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* Next focus, for AGR 1.3 release in March 2018, is to pull allele objects with basic info into AGR
+
* Search ABC with paper identifier
−
* First we will only pull in alleles that have disease data and that only have associations to a single gene
+
* Migrate to Topic and Entity Editor
−
* Basic allele information will be provided on respective AGR gene pages in an Alleles table, along with associated disease data (?)
+
* View all associated data
−
* Alleles may also be referenced within a gene page disease table
+
* Manually validate flags, if needed
−
* Disease pages will show Association tables with alleles in addition to genes
 
−
* In both contexts, alleles will link to the MOD allele page (until AGR develops an allele page)
 
−
* Alleles will be added to the disease association file (DAF) and respective JSON files
 
−
* Dedicated AGR allele pages will come at a later release, probably as a work product of the AGR Variants working group
 
−
* We will want to work closely with the AGR Variants working group
 
−
* Alleles will be stepping stone to other genotype components and then complex genotypes, as well as treatments/conditions/chemicals etc.
 
−
* Also discussed the possibility of a Disease ribbon, showing diseases in AGR orthologs
 
−
* If we show disease associations inferred by orthology, we need to be explicit about evidence codes and data provenance; maybe different tables for experimental versus inferred associations?
 
  
−
=== AGR orthology ===
+
=== PDF Storage ===
−
* AGR orthology based exclusively on sequence similarity
+
* At the Alliance PDFs will be stored in Amazon s3
−
* Some "orthologs" are actually just homologs
+
* We are not planning to formally store back-up copies elsewhere
−
* Jae sent email to info@alliancegenome.org last week (Wed Nov 1) but hasn't heard back from anyone
+
* Is this okay with everyone?
−
* How do we explicitly define "ortholog"? Sequence similarity? Synteny? Functional complementation?
 
−
* How do we accommodate both manual and automated assertions of orthology?
 
  
−
=== Help Desk question: finding all alcohol dehydrogenase genes ===
+
==February 8, 2024==
−
* There is no single root "alcohol dehydrogenase" term in the GO MF branch, but many more specific terms that exist in different branches
+
* TAGC
−
* This means that one has to search for terms that explicitly have "alcohol dehydrogenase" in the name of the term and cannot take advantage of the Ontology Browser to see all gene associations, direct and inferred
+
** Prominent announcement on the Alliance home page?
−
* This approach also will miss terms like "methanol dehydrogenase" or other logical descendant terms
 
−
* Also, can search for protein domains/motifs that explicitly have "alcohol dehydrogenase" in the name of the motif, but domains are not (as far as I'm aware, in InterPro or PFAM at least) organized into an ontology
 
−
* Note: GO tries to classify MFs according to the [http://www.enzyme-database.org/class.php?c=1&sc=1&ssc=*&sh=1 Enzyme Classification] system.  In this classification, the alcohol dehydrogenase (NAD) activity is a sibling of methanol dehydrogenase activity.
 
−
*There is a comment associated with the alcohol dehydrogenase entry, E.C. 1.1.1.1, that says:
 
−
    Comments: A zinc protein. Acts on primary or secondary alcohols or hemi-acetals with very broad specificity; however the enzyme oxidizes methanol much more
 
−
    poorly than ethanol. The animal, but not the yeast, enzyme acts also on cyclic secondary alcohols.
 
−
*This may explain why methanol dehydrogenase is a sibling and not a child of alcohol dehydrogenase in this classification.
 
  
−
=== Alliance/AGR interactions working group ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Now formed, first meeting tomorrow (Friday Nov 10th) at 1pm PST/4pm EST
 
−
* Can find folder and related documents in the Alliance "Working Groups" Google folder
 
  
−
=== AGR gene expression data working group ===
+
==February 1, 2024==
−
* Starting up now; awaiting first meeting
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Talk to Wen and/or Daniela if you want to join
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
  
−
=== Site visits ===
+
==January 25, 2024==
−
* Daniela and Karen might be able to join Bay Area worm meeting
 
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
== November 16, 2017 ==
+
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
=== Inter-library loan ===
+
* 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.
−
* Getting papers (otherwise unavailable) through inter-library loan
 
−
* Have to fill out request forms for (each?) paper that we request
 
−
* No charge unless it is a rush request
 
  
−
=== Social media ===
+
* 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.
−
* Wen attended social media training at Caltech
 
−
* How to use social media to promote their work
 
−
* Sean Carroll has > 1 million Twitter followers
 
−
* Facebook Caltech posts; target students and faculty, as well as donors
 
−
* Social media strategies: videos useful, schedule posts
 
−
* Interviews
 
−
* Videos: viewers lose interest after ~1 minute
 
−
* Would be good to make blog post announcements on FaceBook
 
−
* Use Twitter, FaceBook, WB blog to announce next WB tutorial
 
−
* Can post several times per month, rather than once per ~3 months
 
−
* Wen can work with Ranjana and Todd, to make blog posts available on FB and Twitter
 
−
* Helpful to have fun posts; photos, videos, interviews
 
−
* Wen connected with Andy Golden about Baltimore worm meeting on FB
 
−
* WB needs to follow other members of the community, PIs, etc.
 
−
* Can make posts about interesting papers
 
−
* Can post top community curator for the month
 
−
* Would be good to have a social media point person, Wen and Ranjana? Involve Todd
 
−
* One post per week?
 
−
* Good to have specific posts about papers and researchers
 
−
* Reward labs with most community curation, highlight their research
 
  
−
=== Juancarlos' vacation ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
* May want contingency plan while he is away (Dec 19 - Feb 15)
 
−
* Next upload Jan 19
 
−
* Will need to consider required changes to models/dumpers before he leaves
 
  
 +
=== 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
  
−
== November 30, 2017 ==
+
* 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.
  
−
=== ISB Meeting, April 2018 ===
+
=== Travel Reimbursements ===
−
*https://www.biocuration.org/biocuration-2018-call-for-abstracts/
+
* Still waiting on October travel reimbursement (Kimberly)
−
*This year abstracts are invited for the following topic areas:
+
* Still waiting on September and October travel reimbursements (Wen)
−
**Precision Medicine
 
−
**Phenotypes, genotypes, and variants
 
−
**Data Standards and Ontologies
 
−
**Text Mining
 
−
**Functional Annotation
 
−
**Community Annotation
 
−
**Data Integration and Visualization
 
−
**Deep Learning in curation process
 
−
**Softwares, Applications and Systems in biocuration
 
−
**Curation Standards and Best Practice; inference from evidence; data and annotation quality
 
−
* What does WormBase need to take away from the meeting? What does WB have to present? Important projects
 
−
* Micropublication group/member will go
 
−
* Could send people on behalf of AGR or AGR projects/working group
 
  
−
=== Expression Cluster -> WOBr ===
+
=== 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.
  
−
It looks like we have a data annotation issue where the data is about {AFD and/or AWB} but WormBase annotation usage is meant as {AFD} and {AWB}.
+
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
−
The data source publication is <http://www.wormbase.org/tools/tree/run?name=WBPaper00024671;class=Paper;expand=Refers_to#Refers_to>, and the dataset is  Expression cluster » WBPaper00024671:AFD_AWB_vs_unsorted_upregulated <http://www.wormbase.org/species/c_elegans/expression_cluster/WBPaper00024671:AFD_AWB_vs_unsorted_upregulated#013--10>.
 
  
−
Given that {AFD and/or AWB} is not a natural anatomy group (that is, there is no specific functional meaning nor is it a frequently used grouping), I don't think the solution is to invent an anatomy ontology term just for this dataset.
+
==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
 +
** 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.
  
−
Instead, I propose that we remove the {AFD and/or AWB} datasets from associating with AFD and AWB respectively, so that the associations don't get interpreted incorrectly. This 'rule' should be applied to all ambiguous datasets.
+
==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]
−
=== AGR Gene Descriptions working group ===
+
* Citace upload, current deadline: Tuesday January 9th
−
* Met yesterday for first time
+
** All processes (dumps, etc.) will happen on the cloud machine
−
* Reviewed how each group does gene descriptions
+
** Curators need to deposit their files in the appropriate locations for Wen
−
* Yeast mostly manual; SGD gold standard descriptions
+
* Micropublication pipeline
−
* Many are automated (worm, rat, fly)
+
** Ticketing system confusion
−
* Group will meet twice a month, for now
+
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics
−
* Want to standardize the structure/construction of descriptions
 

Latest revision as of 16:04, 18 April 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

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
Retrieved from "https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls&oldid=38418"