Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
−
= 2013 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2013|January]]
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2013|February]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2013|March]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_April_2013|April]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_May_2013|May]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_June_2013|June]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_July_2013|July]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_August_2013|August]]
+
[[WormBase-Caltech_Weekly_Calls_2023|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
  
−
== September 5, 2013 ==
+
==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==
  
−
=== SPELL ===
+
=== TAGC debrief ===
−
*Wen contacted Matt Hibbs
 
−
*Matt will not maintain SPELL in near future
 
−
*Undergrad at Caltech to maintain/upgrade (Ruby 2 -> Ruby 3)?
 
−
*Connect Matt with undergrad (work study?)
 
−
*Cynthia(?) at Caltech may know Ruby (needed for interface)
 
−
*Communicate with Mike Cherry / SGD as they use SPELL as well
 
−
*Does SGD have a SPELL developer?
 
−
*Java experience needed to maintain backend
 
  
 +
==February 22, 2024==
  
−
=== Expression Clusters ===
+
===NER with LLMs===
−
*Wen found that many authors don't publish lists of clustered genes
 
−
*We could take in the data
 
  
 +
* 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%)
  
−
=== Gene ACE Dumps ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
*Kimberly took a look at what Michael sent us
 
−
*Looked at gene objects specifically
 
−
*More in the full Gene ACE that we could make use of than what was included in the 'nightly' dump from Michael
 
−
*Could other curators take a look at what could be used/requested from GeneACE?
 
−
*Karen and Juancarlos will discuss for variations today
 
−
*Examples: CDS to Pseudogene changes, gene-to-variation mappings/pairings
 
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
=== Discussions on Value of Manual Curation ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
*What would WormBase look like without any manually curated data?
 
−
*Can concise descriptions be automated in any way? "This gene encodes ... It is involved in [GO process]..." etc.
 
−
*How are the concise description forms working? In progress...
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
=== Enhancer curation ===
 
−
*Gold-standard enhancers from Margie's list of papers
 
−
*Xiaodong will upload for WS240
 
  
  
−
=== Interaction changes ===
+
==February 15, 2024==
−
*Interaction model changed to update genetic interaction terms
 
−
*Also, "Electrophoretic Mobility Shift Assay" has been added as a 'Physical Interaction Detection Method'
 
−
*Interaction OA and dumper has been updated and is working properly
 
  
 +
=== 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
  
−
=== Historical Genes ===
+
===== Manually validate paper - topic flags without curating =====
−
*Abby has setup display of historical genes in Overview widgets of relevant objects (Interaction, Expr_pattern, Antibody, Transgene, Process)
+
*Facet for topic
−
*Looks good on staging
+
*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
  
−
=== Upgrading transgene curation ===
+
=== PDF Storage ===
−
*Capturing related sequences or sequence features and displaying on GBrowse
+
* At the Alliance PDFs will be stored in Amazon s3
−
*Single molecule FISH data: Use case
+
* We are not planning to formally store back-up copies elsewhere
−
**Look in GBrowse to see probe sequence vs transgene sequence; find discrepancy in expression patterns
+
* Is this okay with everyone?
−
*Tim Schedl would like to see what transgenes have been used for in vitro (purified from worms) experiments (e.g. physical interactions)
 
−
**Would like to capture epitope tags like FLAG, MYC, HIS, etc.
 
−
*Capturing what does or does not rescue a mutation
 
−
**Association with site-of-action data?
 
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
=== In silico phylogenetic tree data ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
*No current appropriate home for it in WormBase
 
−
*Wen and Karen working on how to house the data
 
−
*Data should go on Process pages
 
  
 +
==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 curation and associations ===
+
==January 25, 2024==
−
*Can we automatically infer associations to a process by, for example, a gene's mutant phenotype?
 
−
*What automatic connections can be made to processes?
 
−
*Do we 'hardcode' phenotype-to-process connections?
 
−
*Interaction widget with Cytoscape now functional on Process pages (on staging)
 
  
 +
=== 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.
  
−
== September 12, 2013 ==
+
* 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.
  
−
=== RNAi movies ===
+
=== Update on NN Classification via the Alliance ===
−
* RNAi.org movies need referencing
+
* Use of primary/not primary/not designated flag to filter papers
−
* May require adding a Database tag to the ?Movie model
+
* Secondary filter on papers with at least C. elegans as species
−
* We may be able to add the RNAi.org movie URL to the Movie object Remark field
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
−
* Chris will work it out with Todd
+
* 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)
  
−
=== Crispr-CAS9 Genome Editing methods ===
+
=== UniProt ===
−
* Will add to the Reagents page (will be under the Resources menu, not there on live site currently)
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
* URL is:  http://www.wormbase.org/resources/reagents
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.  
−
** Curators can edit or create new widgets if logged in
+
* Stavros escalates the issue on Hinxton Standup.
−
** Ranjana will add two new widgets: "Third Party Tools", "Methods"
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
−
** Will add Ortholist to the Third Party Tools
 
−
** Will add Crispr-CAS9 links to Methods
 
  
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
  
−
=== GeneACE Nightly Dump ===
+
==January 11, 2024==
−
* What data do we want to get from Hinxton (in general) on a daily/nightly basis?
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
−
* We will wait for Kimberly to settle on what we want
+
** 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:
−
=== AMIGO 2 ===
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
* Raymond establishing a WormBase development environment that Juancarlos can use
+
* Citace upload, current deadline: Tuesday January 9th
−
* Troubleshooting installation of Perl libraries
+
** All processes (dumps, etc.) will happen on the cloud machine
−
* Also, working to Establish a development environment for the WormBase Ontology Browser server
+
** Curators need to deposit their files in the appropriate locations for Wen
−
** With our own server we can supply WormBase-specific ontologies
+
* Micropublication pipeline
−
 
+
** Ticketing system confusion
−
 
+
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics
−
 
 
−
=== WormMine Data ===
 
−
* When can we/should we request new data for WormMine?
 
−
* JD is working on getting new data in; there is a Wiki page for requesting new data; we can add new data there
 
−
** http://wiki.wormbase.org/index.php/WormMine#New_data_wishlist
 
−
 
 
−
 
 
−
 
 
−
=== Cytoscape plugin update ===
 
−
* New viewer, has a different feel
 
−
* Need to click and hold to pan and scroll to zoom
 
−
* Hopefully adding back visible tools soon
 
−
* Implementing on Process pages and for Cell lineage browsing
 
−
* Cell lineage browsing
 
−
** First tried whole (embryonic) lineage but was too slow because too many nodes
 
−
** Now have a subtree rendering with 4 levels of the tree (great-grandparents, grandparents, parents, and children)
 
−
** May like to have full lineage at high resolution to zoom into for browsing a static image
 
−
* Process pages
 
−
** Cytoscape view of Process pages has all interactions related to the process
 
−
** Phenotypes for genetic interactions now listed in the legend
 
−
 
 
−
 
 
−
 
 
−
=== ORCID IDs for WormBase Persons ===
 
−
* We should incorporate ORCID IDs
 
−
* Can we do a reciprocal exchange of persons? Opt-in exchange?
 
−
* Should we ask WormBase users for their ORCID IDs?
 
−
* Came up while discussing Reuter's indexing (of gene name authors)
 
−
* We will add a request for ORCID IDs on the WormBase form for creating or editing WBPerson info
 
−
 
 
−
 
 
−
 
 
−
== September 19, 2013 ==
 
−
 
 
−
=== Caltech Development Environment ===
 
−
* Issues with running a local mirror
 
−
# Less tenable option; build and staging environments are distributed; Nothing sitting on a single machine
 
−
# Data size: amount of storage required; amount of time required for the build
 
−
* Build process lengthy; need to distribute the task or wait a week
 
−
* Todd can give an AMI (?) ID , letting Raymond create an instance
 
−
* Raymond wouldn't need to build the GFF database
 
−
* EC2 cost? Depends on how
 
−
* Storage is biggest cost; can minimize (use our MySQL hosts), still need to run ACE
 
−
* Run local storage off of femoral(?)
 
−
* EC2 instance:
 
−
** Running 24 hours a day? Use 25%?
 
−
** Let's say 24 hour EC2 instance, large size, heavy utilization, upfront cost of 1 year (with purchased reserved instance): ~$1166
 
−
** Plus bandwidth and storage costs
 
−
** Total cost : ~$1500 per year
 
−
* Environments change name to update: Development --> Staging --> Production
 
−
* 3rd option: setting Raymond up on development service (?)
 
−
** May be easiest approach
 
−
** Todd opts for this approach
 
−
** Raymond and Juancarlos can have their own logins
 
−
 
 
−
 
 
−
=== NAR Paper ===
 
−
* Todd is drafting the NAR manuscript
 
−
* Opting for the short format (2-3 pages); not many people read it; geared towards database people
 
−
* Todd wants to describe new WormBase approach in a different paper
 
−
* What are the big impact changes on the curatorial side?
 
−
** Curators could collect points and send them to Todd
 
−
* Deadline is the 1st week in October
 
−
* Curation section about 1 page; Focus on direction: processes, pathways, topic-based curation
 
−
 
 
−
 
 
−
=== Topic-based curation ===
 
−
* Curators can focus on building off of a 'standard' pathway diagram from a review article, for example
 
−
* Can start with a review, WormBook chapter
 
−
* What coverage are we shooting for? 90%?
 
−
* Start a WikiPathway; curators can build off of that
 
−
* Need to improve:
 
−
# How do we choose a topic?
 
−
# How do we find the papers?
 
−
# What do we capture? How do we converge our efforts?
 
−
* Karen made a process for each type of stress response
 
−
* We can start with Misfolded (Unfolded) Protein Response (related terms: "proteotoxicity", "ER stress")
 

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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