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]]
  
−
==2011 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_February_2011|February]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_March_2011|March]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_April_2011|April]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_May_2011|May]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_June_2011|June]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_July_2011|July]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_August_2011|August]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_September_2011|September]]
 
−
 
 
−
 
 
−
 
 
−
== October 6, 2011 ==
 
−
 
 
−
SVM
 
−
*SVM Manuscript in process of resubmission
 
−
*Messy procedures in place; needs to be cleaned up
 
−
*Yuling able to get pipeline running from beginning to the end
 
−
*May take longer than previously expected to get up and running
 
−
*FlyBase has code running for SVM
 
−
*Yuling should contact FlyBase to make sure they're OK, once he has WormBase SVM working
 
−
*SGD would like to incorporate SVM into they're database
 
−
*Yuri would work on SGD SVM, ultimately
 
−
 
 
−
 
 
−
Physical interaction model
 
−
*Close to done
 
−
*Once model approved, work on:
 
−
**Converting BioGRID file to the ACE model
 
−
**Convert existing YH data into new model
 
−
 
 
−
 
 
−
Image curation
 
−
*Need to establish legal process for acquiring images
 
−
*Contact Caltech Office of the General Counsel for approval
 
−
 
 
−
 
 
−
WORM Paper
 
−
*Karen working on it
 
−
*Need a clearer/new plan
 
−
 
 
−
 
 
−
Expression pattern display
 
−
* Showing composite images with the option to see greater detail
 
−
* Separate out detail images according to Qualifier tags (Certain, Uncertain, Partial)
 
−
* Render oblique angles of cells/tissues to show 3D features/morphology of anatomy objects and, possibly, animations
 
−
* "Real" images should always take precedence to "virtual" images
 
−
* May talk to John Murray or Bill Mohler for confocal images of embryos
 
−
 
 
  
−
Worm Method (Worm Book)
+
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
−
*Any new web pages for C. elegans researchers, send to Raymond
 
−
*URL-finder for neuroscience (Yuling)
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
−
Textpresso
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
−
*Working on Fly Textpresso site (and others)
 
−
*Rose Oughtred would like Wnt Textpresso tools
 
−
*PDF tools (URL extractor)
 
−
*SVM re-working
 
−
*Arun working on GSA editor
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
Grants
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
−
* Need to think about next grant in a couple of months (winter); due in October 2012? 30 pages, short?
 
−
* Focus on writing papers (anatomy function, WORM, virtual worm, etc.)
 
−
* Focus on human-relevance
 
−
* Need Gantt charts and quarterly statements of progress
 
−
* Stats
 
−
** Where are we with each data type
 
−
** Status of website
 
−
** Automation
 
−
** What is different in the field?
 
−
** How is data changing?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
== October 13, 2011 ==
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
WORM Publiction
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
*Looks good overall
 
−
*Change "library" of papers to "index"
 
−
*Putative deadline of November 15th
 
−
*Put in more details about the new website?
 
−
*Figures? Screenshots from new website? Gene page features?
 
−
*Save other (detailed) content for future papers
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
Paper pipeline
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
*Need to fix some PubMed IDs
 
−
*Over 900 articles in Postgres do not have a PubMed ID; Why? How to fix?
 
−
*Could some aspects of the pipeline be accomplished by a non-PhD?
 
−
*Supplemental hires? Students?
 
−
*What tasks would need to be done?
 
−
*Can these tasks be scripted/automated? Community input?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
SVM
+
==April 18th, 2024==
−
*Almost all scripts working
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
−
*Output of SVM slightly different from Ruihua's results
 
−
*Need to resolve the differences
 
−
*Data inconsistencies
 
−
*Need to spot check the papers to see what the major problems might be
 
−
*Yuling ~90% confident in his results
 
−
*Get feedback from relevant/interested curator(s)
 
−
*One-day CPU/computation time (~30 hours for 70 papers with 9 models)
 
  
 +
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
NAR Publication Accepted
+
==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==
  
−
Genetic Interaction Curation
+
=== TAGC debrief ===
−
*Sharing curated genetic interactions with BioGRID
 
−
*What tools will each database use and how will we share data?
 
−
**Both BioGRID and WormBase will use the IMS tool at BioGRID for physical interactions
 
−
**WormBase will use the Ontology Annotator for genetic interactions
 
−
**BioGRID may still use IMS for genetic interactions, but the format will have to be parsed to populate Postgres
 
−
*BioGRID-curated genetic interactions can be flagged as such for later review
 
  
 +
==February 22, 2024==
  
−
Physical Interaction model
+
===NER with LLMs===
−
*Kimberly and Paul Davis discussing
 
−
*XREF questions
 
−
**Paul would like to minimize the number of XREFs in the model
 
−
**Which XREFs can we remove?
 
  
−
Elsevier Linking
+
* 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%)
−
*Establishing pipeline for linking Science Direct papers to Wormbase and viceversa
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
== October 20, 2011 ==
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
Data Submission Working Group
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
*One representative from each site
 
−
*Raymond from Caltech, with Juancarlos
 
−
*Have a discussion for every type
 
−
**How are we doing?
 
−
**Are we up to date?
 
−
**Do we want unpublished data?
 
−
**Quality control
 
−
**Data type priority?
 
−
*Groups/people that have a lot of data of a particular type; acquire their data
 
−
**How can we facilitate data submission from these groups/individuals?
 
−
**Ultimately like to train these users/submitters to use curator tools
 
−
*Form-filling as part of publication process?
 
−
*What data types are we missing? Wiki Pages
 
−
**qPCR?
 
−
**Nanostring?
 
−
**Single molecule studies, absolute quantities?
 
−
**SAGE?
 
−
**3C (Chromosome Conformation Capture), 4C, 5C
 
−
**Metabalome?
 
−
**Pathways/Processes?
 
−
**Drug/disease interactions?
 
−
**Infections?
 
−
**Examples of C. elegans as a model?
 
−
*Expression data
 
−
**How do annotate a presence/absence call on expression of a given gene?
 
−
**rpkm cutoff?
 
−
**Number of molecules?
 
−
**Case-by-case thresholds
 
−
*Disease vs Process pages?
 
−
**100 diseases modeled in ''C. elegans''?
 
−
**Flat-file capture and display of disease-relevance information (as opposed to ontology-based)
 
−
*"Subject" vs. "Process" vs. "Disease"
 
−
**Examples of "Subject": Sewage treatment, Biofilm formation, etc.
 
−
**Examples of "Disease": Alzheimer's, Huntington's, Cancer, etc.
 
−
**Examples of "Process": Development, Innate immunity, Organ formation, etc.
 
−
**User experience?
 
−
*User-submitted data inconsistency/discrepancy flag?
 
  
  
−
WORM Paper
 
−
*Still requesting any major comments or content changes
 
−
*"Final" version available next week
 
  
 +
==February 15, 2024==
  
−
''C. elegans'' Research Resources Chapter (WormBook)
+
=== Literature Migration to the Alliance ABC ===
−
*Yahoo-like Yellow pages of useful URLs with brief descriptions of each site
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
*URLs being pulled from papers by Yuling
+
===== 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
  
−
== October 27, 2011 ==
+
=== 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?
  
−
NAR Proofs are in
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
*Karen will send around
 
−
*Going back out tomorrow; everyone check
 
−
*Add Arun as author
 
  
 +
==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.
  
−
Predicted Gene Interactions
+
==January 25, 2024==
−
*Wei wei contacted Paul
 
−
*Who is the contact person? Xiaodong can be point person
 
−
*Add URLs to Gene Orienteer and Interolog database on gene pages
 
−
*Issue is with syncing the databases and updating
 
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
SVM
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
*Yuling finsished running SVM pipeline; can make run every two weeks
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
*Need to learn how to best train the models; do we need to retrain?
 
−
*Gary Williams sent e-mail; incorrect paper IDs on some SVM results
 
−
**Gene structure correction papers have been incorrect
 
−
**May need to retrain the gene structure correction SVM
 
−
**Need someone at Caltech to work with Yuling to retrain the model
 
−
*Kimberly will look through e-mail archive about the issue
 
−
*We could really improve the training set, as original set may have been inadequate
 
−
*What data types do we retrain: Expression pattern? Phenotype?
 
−
*Improve training by including verified positive papers from last two years (since last training)
 
−
*In past, needed 400 papers to train; would be best to lower requirement
 
−
*Antibody and transgene SVM works well; maybe incorporate for Expression pattern SVM?
 
−
*Use pattern matching to correct SVM results or vice versa?
 
−
*Good to make progress on Gene Structure correction papers
 
−
*Keeping track of sentences/paragraphs; performing SVM on paragraphs (vs papers)?
 
  
 +
* 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.
  
−
Collecting URLs from papers (Raymond)
+
* 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.
−
*For interesting/relevant URLs for C. elegans
 
−
*Journal URLs are problematic
 
−
*Yuling runs scripts on Textpresso corpus to collect URLs
 
−
*PubMed XML of journals (Kimberly)
 
  
 +
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
−
WORM Publication
+
=== Update on NN Classification via the Alliance ===
−
*Final version available
+
* Use of primary/not primary/not designated flag to filter papers
−
*Review for corrections
+
* Secondary filter on papers with at least C. elegans as species
−
*To submit early next week (before Wednesday)
+
* 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)
  
−
== Novermber 3, 2011 ==
+
=== 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
  
−
Gene ID mapping problems (as discussed in site-wide call)
 
−
*Does CIT need to worry about consistency of gene IDs over database builds?
 
−
*Hyper-linking entities in papers could be an issue
 
−
*Acquire an ID for every gene for every new genome?
 
−
*When mark a paper, separate into two different types of genes :stable vs unstable
 
−
**Stable genes map to stable ID
 
−
**Unstable genes map with a version number
 
−
*WormBase communicate/work with DCC personnel for data wrangling during post-DCC era?
 
  
 +
==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.
  
−
Updating Predicted Gene Interactions
+
==January 4, 2024==
−
*Wei wei asking about how to update with WormBase
+
* ACKnowlegde pipeline help desk question:
−
*WormBase predicted interaction objects can be updated simply via link to Gene Orienteer
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*If we want a live interaction browser, we would need to pull the data into the build process
+
* Citace upload, current deadline: Tuesday January 9th
−
*Do we want a single object per pair of genes? One object per instance of evidence (per paper)?
+
** 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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