Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[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]]
  
 +
==May 30th, 2024==
 +
===Entity association with references - Alliance ABC (Kimberly)===
 +
* Need to make sure we have the right classes in the ATP ontology for what WB wants to associate wrt transgenes
 +
** Variation
 +
** Construct
 +
** Transgene
 +
** Rearrangement
 +
* Suggestion: create a new child of allele: transgenic allele and use that for WB transgenes
 +
* Question: should affected genomic model be a child of entity?
  
−
== June 2, 2016 ==
+
===AWS costs===
  
−
=== SimpleMine ===
+
==May 23rd, 2024==
−
* Wen will create ticket to create wormbase.org URL
+
*Publication bias workshop NINDS
−
* Will go under Tools menu
+
** Registered report -> the protocol is sent before publication
−
* Ranjana will make blog post once it is live
+
** 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
  
−
=== Postgres Timestamps ===
+
==April 18th, 2024==
−
* Wen, Chris, and Juancarlos have been working on updating older timestamps for OA entries in Postgres
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
−
* For OA entries generated upon creation of some OA's, the Postgres timestamp is the data of OA creation, not the original data of the object
 
−
* Chris identified all objects from various OAs that had the same initial import timestamp, Wen determined the original ACEDB timestamps for those objects, and Juancarlos is updating the OA entries (curator timestamps) to reflect the object's original timestamp
 
−
* This will be good for consistency going forward and for tracking history of object generation over time
 
  
−
=== Transgenome project ===
+
==April 11th, 2024==
−
* Daniela spoke to developer on project
+
*Caltech WS293 ace files ready for the upload
−
* They're fixing/cleaning up data on their end
 
−
* Working on mapping fosmids to latest release of WormBase
 
−
* Probably will import data in a month
 
  
−
=== UMOD phenotype call yesterday ===
+
==April 4th, 2024==
−
* Discussed phenotype data associations
+
* Continued discussion on sustainability
−
* Many MODs curate phenotypes to genotype; cannot always make direct, unambiguous associations to a single gene
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
* SGD curate to gene, using controlled vocabulary
+
** Data is still going to SPELL and enrichment analysis
−
* Monarch phenotype data exchange format; can include many levels of detail
+
** 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.
−
* Common challenge: identifying the single causative agent/mutation
+
* 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)
  
−
== June 9, 2016 ==
+
==March 14, 2024==
  
−
=== SimpleMine ===
+
=== TAGC debrief ===
−
* Wen will make it work off current (live) release of WormBase
 
−
* Do we want to make it more versatile? Add features to specify information to retrieve (specify columns)?
 
−
* Maybe later, but is sufficient for now
 
−
* WormBase official [URL| <http://www.wormbase.org/tools/mine/simplemine.cgi>]
 
−
* Is there a gene # limit? Will test
 
−
* Wen wants to add WormPep ID column; needs to retrieve all WormPep IDs for a gene
 
  
−
=== Flagging papers for species ===
+
==February 22, 2024==
−
* Going forward, Kimberly, Jane, and Michael will manually flag papers for species
 
−
* Retroactively, papers will be flagged by scripts
 
−
* ~1000 papers not flagged as C. elegans, but likely mentioned in body of paper; Kimberly reviewing
 
−
* These papers often don't have curatable data
 
  
−
=== Associating genotypes to phenotypes ===
+
===NER with LLMs===
−
* There is increasing need to annotate phenotypes to complex genotypes (not just single alleles/genes, etc.)
 
−
* MGI captures genotype-to-phenotype connections, but can't always attribute a single causative gene
 
−
* We can capture complex genotype phenotypes in interaction objects, but it may be vague to end users
 
−
* Chris will draw up use cases and generate a data model proposal to accommodate
 
  
−
=== Topic for next curator call ===
+
* 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%)
−
* Still being voted on via Slack poll
 
−
* Should Doug and Karen decide topic?
 
−
* We need to define/narrow the topic to cover in one hour
 
−
* What are common/different annotations captured by DBs? What data model/infrastructure changes would be required to come to common ground?
 
−
* Paul S. will discuss with Karen and Doug about topics
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
== June 16, 2016 ==
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
=== SimpleMine on WB frontpage? ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Wen has asked to put it under the Tools menu
 
  
−
=== Curating phenotypes to complex genotypes ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Should we objectify phenotype experiments, much like ?RNAi objects
 
−
* This would allow encapsulation of genotype elements and phenotype info
 
−
* Curators could explicitly state causative gene in a transgene, but keep automated mapping for RNAi, alleles, and rearrangements
 
−
* Chris will work on data model
 
−
* This may mean we want to eventually merge the Phenotype OA and the RNAi OA
 
  
−
=== Datomic queries ===
 
−
* Variation not currently connected to phenotype
 
−
* Matt R. is working on it
 
  
−
== June 23, 2016 ==
 
−
===TAGC===
 
−
NOTE: this meeting is the C. elegans Development, Cell Biology and Gene Expression Topic meeting.
 
−
*we will be at a shared booth with Flybase and SGD
 
−
====poster====
 
−
* Room for one poster at SGD/FB/WB booth
 
−
** Large scale gene expression (SPELL) + Pathways
 
−
OR
 
−
** Community annotation + Micropublication
 
−
** Projector in the shared booth - can bring a slide deck
 
−
** Need to come up with the AGR unified poster
 
  
−
* One poster for MOD Demo room - will be a table, easel for displaying poster (2nd poster)
+
==February 15, 2024==
−
*Paul, will you be presenting a poster during the normal poster session? Can bring it to the Demo room for further display and demo textmining
 
  
 +
=== 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
  
−
====swag====
+
===== Manually validate paper - topic flags without curating =====
−
*bags from past IWM - how many, how would we get them to Orlando - Sarah ships them?
+
*Facet for topic
−
*SGD will have bottle openers
+
*Facet for manual assertion
−
*tattoos?
+
**professional biocurator assertion
−
*special gifts? SGD will have hats (50); do we have any fly swatters left? If so, how many?
+
***ABC - no data
  
−
*coloring book publishing
+
===== 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
  
−
=== Automated descriptions ===
+
=== PDF Storage ===
−
* Michael and Ranjana fixed the pipeline for orthology (was missing many orthology statements)
+
* 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?
  
−
=== Citace upload ===
+
==February 8, 2024==
−
* Next Tuesday (June 28) 10am
+
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
=== Disease annotations ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Most disease info currently captured as gene-to-disease connections
 
−
* Ranjana may want to create disease annotation objects in the database
 
−
* Could be modeled similarly to GO annotation objects
 
−
* Will help to encapsulate the data into one object per experiment in a paper, for example
 
  
−
=== Phenotype report objects ===
+
==February 1, 2024==
−
* Want to capture complex genotypes, zygosity, RNAi with multiple targets, etc.
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Chris proposing a potential new "phenotype report" class to subsume RNAi objects and allele- or transgene- phenotypes
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* Would require many changes to mapping and build pipeline adn data display, so need to discuss issues with Hinxton and OICR
 
  
−
=== Evidence Code Ontology (ECO) ===
+
==January 25, 2024==
−
* Would be worth considering adopting ECO or similar evidence code system
 
−
* Kimberly: there is an experimental factor ontology, and OBI (ontology of biomedical investigations)
 
−
* Raymond: XCO, experimental condition ontology
 
  
−
=== Community petition for MOD support ===
+
=== Curator Info on Curation Forms ===
−
* GSA and fly board put together a letter to NIH with signatures
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* Would be good to link to the letter from WB homepage
 
−
* Ranjana will create blog post
 
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
== June 30, 2016 ==
+
* 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.
  
−
=== Virtual Worm images on anatomy pages ===
+
* 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.
−
* Daniela, Raymond, Chris working on importing existing cell and anatomy object images into WB anatomy pages
 
−
* There are currently no images of tissues/cells on each page
 
−
* We have links to WormAtlas but not their images
 
−
* Virtual Worm cells and cell groups have already been rendered
 
  
−
=== Citpub on Spica ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
* Testing instance of citpub ACEDB, single instance to be shared (cannot be used by multiple users simultaneously)
 
−
* People can create their own instance for ACEDB testing
 
−
* If someone else is already running citpub ACEDB, people can read but not write (when reading in .ace files for testing)
 
  
−
=== Proteomic paper data ===
+
=== Update on NN Classification via the Alliance ===
−
* Wen has been looking at proteomics papers
+
* Use of primary/not primary/not designated flag to filter papers
−
* She's been looking for "proteome" in titles and journal names, "SILAC" technique in whole text
+
* Secondary filter on papers with at least C. elegans as species
−
* Already curated 31 expression cluster proteomics papers
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
−
* 39% precision, 61% recall (183 new papers)
+
* Next NN clasification scheduled for ~March
−
* Tried "LC-MS" but was too non-specific
 
−
* Wen has worked with Gary Williams to identify mass-spec papers
 
−
* Will ask Yuling about any paper flagging pipelines
 
  
−
=== Phenotype curation interface call yesterday ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
* ZFIN curates via the ZFIN site (after logging in) and data goes live immediately
+
* NNC html pages will show NNC values together with species.
−
* ZFIN uses spatial ontology to specify regions of anatomy or cell affected by phenotype
+
* Show all C. elegans papers first and other species in a separate bin.
−
* ZFIN and RGD build phenotype annotations by selecting terms and sending them to a phenotype "bucket"
 
−
* RGD includes disease annotations in parallel to phenotype annotations (connecting rat, mouse, and human)
 
−
* RGD captures detailed numbers
 
  
−
=== Phenotype report objects ===
+
=== Travel Reimbursements ===
−
* Chris considering a change to phenotype data model to capture phenotype report objects
+
* Still waiting on October travel reimbursement (Kimberly)
−
* We will surely want to capture differential phenotypes and differential genotypes
+
* Still waiting on September and October travel reimbursements (Wen)
−
* We will need to consider if we want to (and how to) capture absolute phenotype measurements
 
−
* Objectifying phenotype annotations may be similar to the Monarch phenopacket model
 
−
* Karen has communicated with Chris Mungall about including anatomy, molecule, lifestage information in the phenotype association file that he can use to map Worm Phenotypes to Human phenotypes.
 
  
−
=== RGD paper lookup ===
+
=== UniProt ===
−
* RGD curators lookup phenotype and related terms and lookup papers with that information
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
* Looks similar to Textpresso Central lookup; not sure if they have access to full text or just abstract
+
* 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 18:12, 30 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 30th, 2024

Entity association with references - Alliance ABC (Kimberly)

  • Need to make sure we have the right classes in the ATP ontology for what WB wants to associate wrt transgenes
    • Variation
    • Construct
    • Transgene
    • Rearrangement
  • Suggestion: create a new child of allele: transgenic allele and use that for WB transgenes
  • Question: should affected genomic model be a child of entity?

AWS costs

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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