Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
−
==2012 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
−
 
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_January_2012|January]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_February_2012|February]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_March_2012|March]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_April_2012|April]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_May_2012|May]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_June_2012|June]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_July_2012|July]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_August_2012|August]]
 
−
 
 
−
 
 
−
 
 
−
== September 6, 2012 ==
 
−
 
 
−
Canopus
 
−
*Will become a server (heavy outside access)
 
−
*Raymond will take precautions to restore properly; should take a week or less
 
−
*Used for:
 
−
**Picture curation
 
−
**Virtual worm web page & FTP
 
−
 
 
−
 
 
−
Grant Writing
 
−
*Approach & future plans - do we need to discuss and add more to proposal?
 
−
*Virtual worm access to data
 
−
*Browsing data
 
−
**Browse genes/proteins by class/GO annotation
 
−
*Intermine queries
 
−
**Queries can be saved and used again later (available to other users)
 
−
**Results can be stored and displayed on web pages
 
−
*Displaying large scale expression (microarray) data (from SPELL)
 
−
**SPELL data currently stored in relational (MySQL?) form
 
−
**We could extend the WormBase web app to interact with SPELL data
 
−
**RESTful-compliant data serving would be best
 
−
 
 
−
 
 
−
Migration away from ACEDB?
 
−
*Scalability - ACEDB does not scale to genome-scale studies
 
−
*We (EBI & OICR) spend a lot of time building ACEDB database
 
−
*ACEDB not actually used so much
 
−
*Makes more sense to adopt a more central database
 
−
*Migration would take place over entire grant cycle
 
−
*We should continue extending models as we see fit, in the meantime
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
Massmails
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
−
*Discuss again with Paul about Worm Breeder's Gazette and WormBook.
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
== September 13, 2012 ==
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
Grant
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
*Two things to work on:
 
−
**1) Metrics and quality control
 
−
***Metrics: Transparent about our coverage (e.g. "We estimate XXX many RNAi experiments/papers and we have ~62% coverage")
 
−
****SVM form (in development) vs Curation Status form (needs work/update); can generate numbers for coverage to display on the web?
 
−
****What is the vision of a new Curation Status form? (Daniela will write something)
 
−
****Stats with new SVM results on pre-2000 papers: state them in grant as pre-2000 corpus
 
−
***Quality Control: How do we demonstrate that our curation is correct/accurate?
 
−
****Sampling First-pass curation (false negative estimates)
 
−
****WormBase person would check on case-by-case basis the accuracy of data (e.g. expression pattern, RNAi experiment, etc.); what percent do you need to check to ensure good quality control? Blind/independent re-curation? Collection of facts to use for metrics
 
−
****Contact senior author on a paper to check the quality of data from a paper; experts for a process; prioritize based on who responds to author-first-pass
 
−
****Data-type specific issues
 
−
****Internal consistency checks
 
−
****Ontology based curation checks (granularity; branch-consistency)
 
−
**2) Training and user interaction
 
−
***Screencasts and FAQs list (Chris will write some sentences)
 
−
***User guide status? Currently needs major revamp and new information (old Wiki User Guide is now obsolete)
 
−
***Online chat: has been broken for months; should it only be allowed for logged-in users?
 
−
*Daily updates with low-connectivity data (not relying on sequence mapping) from PostgreSQL database?
 
−
**Have different CGI forms to populate the data on the website?
 
−
*Are we committed to migrating away from ACEDB? Who then is responsible for managing data models?
 
−
**Migrate to Chado? Do we need detailed plan for this?
 
−
**FlyBase has migrated; they like Chado, but the migration was painful
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
Worm Breeder's Gazette & WormBook outreach
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
*Mass mailings should be an Opt-in system, as opposed to blanket mass mailings
 
−
*One mass mail for each to ask about Opting-in to e-mail alerts?
 
−
*Regional & International worm meetings; don't hand all e-mails over to meeting organizers.
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
Itai Yanai expression datasets
+
==April 18th, 2024==
−
*Including images from microarray expression data directly from paper for now
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
−
*Plan is to generate time-course expression data 'on-the-fly' later on so that other data sources can be compared and included in the same graph, given that they are the same type of data
 
−
*Eventually, the paper images will be superceded by the new, calculated 'on-the-fly' images
 
  
 +
==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)
  
−
Phenotype Images
+
==March 14, 2024==
−
*We were asked if we wanted to join a consortium that is collecting images portraying different phenotypes
 
−
*We may in the future, but not right now; we would need to develop a method for collecting and curating such images
 
  
 +
=== TAGC debrief ===
  
−
== September 20, 2012 ==
+
==February 22, 2024==
  
 +
===NER with LLMs===
  
−
Canopus back online
+
* 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%)
−
*Cron job for pulling pictures; need to make sure it still works
 
−
*Raymond lifted Todd's directories over to new hard drive
 
−
*/usr/local gone; Raymond did not restore
 
−
*Todd was pulling from somewhere in /usr/local (/usr/local/wormbase/image ?)
 
−
*Pictures in OICR directory
 
−
*Raymond will send directory to Todd
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
Molecule curation
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*"Drug" vs. "Molecule"
 
−
*Synthetic vs Non-Synthetic?
 
−
*Endogenous vs. Exogenous?
 
−
*Focus of study
 
−
*Textpresso categories including some molecules (e.g. 'glucose') throw off predictions for papers having 'drugs'
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
Remote backup storage
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
*Juancarlos suggesting storing some data/files remotely
 
−
*Amazon will back up 1 GB data 12.5 cents/month; Essentially free to upload; Pay for download (12 cents/GB)
 
−
*Data to store: Postgres data (for example)
 
−
*Data could be encrypted, if we are concerned
 
  
  
−
Curation Prioritization
 
−
*Curating papers by process or topic
 
−
**Reinstate some Textpresso categorization of papers by topic/process
 
−
**Tied to pathway curation (LEGO and WikiPathways)
 
−
*Prioritization of curation for genes that currently have no annotations
 
  
 +
==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
  
−
== September 27, 2012 ==
+
===== 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
  
−
Microarrays from other species
+
=== PDF Storage ===
−
*Storing data?
+
* At the Alliance PDFs will be stored in Amazon s3
−
*Will keep in a separate database (separate from C. elegans)
+
* We are not planning to formally store back-up copies elsewhere
−
*Curating Itai Yanai's paper (5 species)
+
* Is this okay with everyone?
−
*Only found 4 microarray data sets from C. briggsae (from GO search) including Yanai paper; very few from other species so far
 
−
*There may be more microarray data on non-Caenorhabditis species (parasites, etc.)
 
−
*No way, currently, to inter-compare data sets (across species)
 
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
Yanai data set
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
*Everything in sandbox (images and data)
 
  
 +
==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.
  
−
Process Pages
+
==January 25, 2024==
−
*Marc Perry is working on generating the pages
 
−
*Newer data not available on website yet
 
−
*WikiPathway for male mating (Karen made); Marc made mock page and put it up
 
−
*Interactive pages; can click on entities
 
−
*Process search not up and running yet
 
−
*Can we get WormBase data into WikiPathways programatically? Not yet
 
−
*Can use GenMAPP files
 
−
*Wikipathways has node/edge hyperlinks
 
−
*Figure out a way to pull data (programatically) from WormBase process
 
−
**Create and place GPML objects spaced evenly on a page
 
−
*Process pages have lists of: genes, cells, molecules, microarray expression clusters
 
−
*Process pages are a good home for expression clusters
 
−
*Process page: Summary, WikiPathways widget, lists
 
−
*Phenotype to Process mapping of objects
 
−
*Big-picture mapping of pathways (top down approach)
 
−
*LEGO will become the bottom up approah
 
−
*Would be good to capture pathway connections/structure in the ACEDB data model
 
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
GO Meeting @ Caltech
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
*[http://wiki.geneontology.org/index.php/Consortium_Meetings GO Wiki] has details
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
*October 7-9
 
  
 +
* 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.
  
−
PWM data
+
* 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.
−
*Gary Stormo paper coming out with lots of new PWM data (5000 binding sites)
 
−
*Genome wide conserved elements (some experimentally verified)
 
  
 +
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
−
Transcription Factor -to- Target Gene Associations
+
=== Update on NN Classification via the Alliance ===
−
*We need better data display methods/tools
+
* Use of primary/not primary/not designated flag to filter papers
−
*ModENCODE ChIP-seq data really would benefit from conversion to digital/discrete objects/associations
+
* 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.
  
−
Curating with respect to topic
+
=== Travel Reimbursements ===
−
*Karen already doing this to some extent for processes
+
* Still waiting on October travel reimbursement (Kimberly)
−
*Clustering (papers) based on GO Biological Process terms
+
* 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
  
−
== October 4, 2012 ==
 
  
 +
==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.
  
−
FlyBase SAB topics
+
==January 4, 2024==
−
*Genome Space - can integrate data in different formats
+
* ACKnowlegde pipeline help desk question:
−
*FlyBase talking about joining [http://www.genomespace.org/ Genome Space]?
+
** 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
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