Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 13: Line 13:
 
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
= 2016 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2016|January]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2016|February]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2016|March]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_April_2016|April]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_May_2016|May]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_June_2016|June]]
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
[[WormBase-Caltech_Weekly_Calls_July_2016|July]]
+
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
[[WormBase-Caltech_Weekly_Calls_August_2016|August]]
+
==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==
  
−
== September 1, 2016 ==
+
=== TAGC debrief ===
  
−
=== Working group discussions ===
+
==February 22, 2024==
−
* More clear about issues surrounding orthology sets
 
−
* ZFIN has protein curation that may be becoming a bit out of date
 
  
−
=== Single-cell RNA profiling ===
+
===NER with LLMs===
−
* We've been curating some data, but not clear how to display the data
 
−
* Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue
 
−
* Genes that are detected at convincing levels (present call) in cell/tissue
 
−
* Should we display expression data that we do not (or cannot) update differently from other data
 
−
* Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not
 
−
* Could capture quantitative assessments; transcripts per million, etc.
 
−
* Should we provide an analysis of raw data to users to perform their own comparative analyses
 
−
* Bob Goldstein's group prepared software tools in their paper; could we make use of them?
 
−
* Big question: how do we handle divergent (expression) data?
 
−
* David (Angeles) working on an expression data analysis pipeline
 
−
* Single-cell RNA-Seq data: should it be merged with expression pattern data? Ideally, yes
 
−
* There's difficulty in reconciling small and large datasets (or different data types)
 
−
* Would we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
 
−
* In general for expression, it would be great to consolidate data to directly connect genes to anatomy/life stage
 
  
 +
* 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%)
  
−
== September 8, 2016 ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
=== TransgeneOme import (Daniela) ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* adding a Community_curator tag or Curator tag in the Expression model to acknowledge the community curators that annotated/will annotate the data.
 
−
* for the records- documentation on the import here: http://wiki.wormbase.org/index.php/TransgeneOme_import
 
−
* Daniela and Juancarlos worked on parsing large JSON import
 
−
* Data is dynamic: people can add images and annotations; will be updated every WormBase release
 
−
* Do we want to import the person that created the annotation via the TransgeneOme project?
 
−
** Maybe, but should be free text instead of a modeled tag for WBPersons (Raymond)
 
−
** It is likely sufficient to point WB users to the TransgeneOme annotation, without explicitly referencing the contributor
 
  
−
=== Phenotype assay model proposal (Chris) ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Trying to create a model that can accommodate complex genotypes and make querying phenotype experimental data easier
 
−
* Want to co-opt an existing, unused model ?Phenotype_assay to encapsulate details of an experiment
 
−
* Proposal is to pull several tags from ?RNAi and #Phenotype_info into the ?Phenotype_assay class
 
−
* Remaining tags in ?RNAi could be used to hold RNAi mapping information
 
−
* Remaining rags in #Phenotype_info can be used to describe the nature of an allele in the context of a phenotype, or nature of phenotype (Ease of scoring)
 
−
* Maybe should keep penetrance, quality and EQ annotations in #Phenotype_info so as to provide detail for each phenotype when multiple phenotypes are used
 
−
* It is currently difficult to recreate a phenotype annotation made by a curator using the OA, as so much experimental detail is captured exclusively in the hash
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
== September 15, 2016 ==
 
  
−
=== Strain curation with disease ===
 
−
* People create transgenic strains for modeling human disease
 
−
* We currently only curate strains in CGC (where we get our strain list)
 
−
* Other strains have been added via direct communication with Mary Ann
 
−
* Ranjana would like to capture strains affecting human disease from the literature
 
−
* Many strains not available in WormBase
 
−
* Is it worth curating these other strains? Yes; one concern that we would be diluting the quality of existing strains
 
−
* Big concern is whether or not the strain(s) are available
 
−
* (Raymond) Two aspects of strain curation: 1) strains that are available (e.g. from CGC) 2) carrier of genotype to use for other curation (like disease)
 
−
* (Raymond) We could just capture genotype as free text
 
−
* Would be best to curate the strains, regardless of availability
 
−
* Ranjana will send some example papers/strains to Mary Ann and they will discuss
 
−
* We could create links from strains in WB to the CGC (or state that people should write directly to the source lab; might be problematic).
 
  
−
=== WormBase header changes ===
+
==February 15, 2024==
−
* Miyuki has been working on new WormBase header; requests feedback
 
−
* Available on staging
 
  
−
=== Tissue enrichment analysis ===
+
=== Literature Migration to the Alliance ABC ===
−
* Tool is live and ready to use
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Raymond has added a link to the tool on the Tools page
+
===== 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 =====
−
* Raymond will submit a ticket to put on the main Tools dropdown
+
*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
  
−
== September 22, 2016 ==
+
===== 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
  
−
=== GOC meeting at USC, November 4-6, Noctua Workshop, November 7 ===
+
=== PDF Storage ===
−
*Next GO Consortium meeting is in early November at USC
+
* At the Alliance PDFs will be stored in Amazon s3
−
*The consortium meeting will run from Friday, 11/4 - Sunday, 11/6
+
* We are not planning to formally store back-up copies elsewhere
−
*Noctua/LEGO workshop will be on Monday, 11/7 (9am - 3pm)
+
* Is this okay with everyone?
−
*[http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Logistics Meeting Logistics Page]
 
−
**We will need to add all WB curators to the attendees table
 
−
*[http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda Meeting Agenda - in progress]
 
−
* People interested in going to the consortium meeting or the workshop should register or let Kimberly know
 
−
* Kimberly can setup accounts for people to try Noctua trial curation
 
  
−
=== Display of top community curators ===
+
==February 8, 2024==
−
* Sibyl has setup a widget for the homepage and submit data page displaying top 20 community curators
+
* TAGC
−
* Chris has compiled numbers from phenotype community annotations
+
** Prominent announcement on the Alliance home page?
−
* We want to gather community annotations from other forms as well (historically and from newer forms)
 
  
−
=== Intellectual Lineage ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Will display on person page
 
−
* There exist "unknown" relationships; can we update those to known relationships?
 
−
* We can email both parties of each unknown relationship asking about the nature of the relationship
 
  
−
=== Gene Ontology development ===
+
==February 1, 2024==
−
* There may be a need for an additional ontology developer/editor
+
* Paul will ask Natalia to take care of pending reimbursements
−
* There's an accumulation of GitHub tickets requesting new terms/edits
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* It's not clear how the ontology will evolve in light of LEGO curation
 
  
−
=== Tables in PDF ===
+
==January 25, 2024==
−
* Some tables have been converted from Excel to PDF
 
−
* PDF tables are difficult to parse
 
−
* We can/should ask authors for original Excel spreadhseet
 
  
−
=== Metabolomics efforts ===
+
=== Curator Info on Curation Forms ===
−
* PIs working on grants to study metabolomics in accumulated mutation lines
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* Want to contribute data to WormCyc
 
−
* BioCyc doesn't use same standard vocabularies that WormBase does (e.g. ChEBI)
 
  
−
=== AGR Portal use cases ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* Working group had started working on a gene page, but have made a new use case for general search
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
* The draft use case would describe searching with general text to find matches to genes, diseases, GO terms, and orthology groups
 
−
* Next will try to work out a use case for arriving at a gene comparison page, e.g. starting with a human gene
 
−
* Would probably be good to break into smaller groups of 2-3 people to independently work on different use cases
 
−
* Starting simple is good, even if the added value isn't immediately clear
 
  
 +
* 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.
  
−
== September 29, 2016 ==
+
* 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.
  
−
=== AGR Portal Use Case update ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
* Use case working group now working on a gene/gene-product comparison page for all genes in an orthology group/PANTHER family or subfamily
 
−
* Plan is to display information for genes side-by-side for each data type
 
−
* First data types would include gene descriptions, gene ontology annotations, and disease associations
 
−
* For GO terms many would like to see the "ribbon" display with GO slim terms or context-specific terms
 
−
* Would be good if ribbon content was dynamically generated (rather than a predetermined set of terms), to reflect the nature of genes in an orthology group
 
−
* Could be useful to use SObA logic in selecting terms to show in ribbon
 
−
* Would be nice to display the genes according to species or listed by their relationships within a phylogenetic tree, for each data type
 
−
* Highlighting commonalities between genes in the group would be nice
 
  
−
=== Intellectual lineage display ===
+
=== Update on NN Classification via the Alliance ===
−
* Juancarlos working on display of the lineage on WBPerson pages in a widget
+
* Use of primary/not primary/not designated flag to filter papers
−
* Data will be pulled from ACEDB and used to generate display
+
* Secondary filter on papers with at least C. elegans as species
−
* Performing necessary calculations was crashing the machine
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
−
* Want to scale the display based on number of connections
+
* Next NN clasification scheduled for ~March
  
−
=== Changes to Disease Term OA ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.  
−
* This OA will be used when information about the disease model cannot be curated to a C. elegans gene, e.g. when a human gene was put into the worm.
+
* NNC html pages will show NNC values together with species.  
−
* Changes incorporate information for strains, genotypes, treatments like drugs etc.
+
* Show all C. elegans papers first and other species in a separate bin.
−
* There's still a question about how to encapsulate the information from a single annotation
 
−
* Separate annotations will be made if a second paper uses the same disease model (described in the paper being curated) and adds a treatment to it to show amelioration or exacerbation of disease; separate annotation means a different row with a different PGID in the OA.
 
−
* Modeling can be done once more trial curation is done, some AGR modeling decisions to be made
 
−
* Could curate and store data in OA for now, holding it until we have an appropriate data model and display pipeline
 
−
* Want to capture strain, drug treatment, conditions, etc.
 
−
* How do we connect disease-relevant genetic interactions to the disease or disease models?
 
−
* Disease group working out standards for disease model curation
 
−
* Ranjana will email interaction curators when she needs to, in these cases
 
  
−
=== Noctua/LEGO ===
+
=== Travel Reimbursements ===
−
* Can we annotate details of experiment in Noctua? It's not clear
+
* Still waiting on October travel reimbursement (Kimberly)
−
* Noctua has predominantly been used in the context of GO annotations
+
* Still waiting on September and October travel reimbursements (Wen)
−
* Kimberly happy to demo Noctua in group meeting or individual Skype session
+
 
 +
=== 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
 +
** 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.
 +
 
 +
==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

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"