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]]
  
−
[[WormBase-Caltech_Weekly_Calls_June_2016|June]]
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
[[WormBase-Caltech_Weekly_Calls_July_2016|July]]
+
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
[[WormBase-Caltech_Weekly_Calls_August_2016|August]]
+
==April 4th, 2024==
 +
* Continued discussion on sustainability
 +
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
 +
** Data is still going to SPELL and enrichment analysis
 +
** Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
 +
* Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
 +
* Michael's presentation on LLMs - Named Entity Recognition (NER)
  
−
[[WormBase-Caltech_Weekly_Calls_September_2016|September]]
+
==March 14, 2024==
  
 +
=== TAGC debrief ===
  
−
== October 6, 2016 ==
+
==February 22, 2024==
  
−
=== Citace upload ===
+
===NER with LLMs===
−
* Tuesday, October 25th, 2016
 
  
−
=== Automated descriptions ===
+
* 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%)
−
* Ranjana working with Juancarlos to run and update automated descriptions pipeline
 
  
−
=== Intellectual lineage ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* First draft up on WormBase development site
 
  
−
=== Noctua ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Raymond trying to annotate axioms for anatomy function
 
−
* How to connect cell types in different organisms to those in C. elegans anatomy ontology?
 
−
* Maybe best way is to connect based on biological function, e.g. regulate osmolarity (kidney, excretory cell)
 
−
* Raymond attempting to use Noctua to draw relationships between anatomy terms and function
 
−
* There's a distinction between annotating to an instance vs. to a class
 
−
* Raymond worked on modeling a statement on excretory cell function from WormAtlas
 
−
* Question: how much redundancy might we end up with if we annotate to higher level (cell/anatomy function) and lower level (individual gene product function)? There may be, but all of this information is valuable
 
  
−
=== Expr_pattern model change ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Daniela proposed a CRISPR-Cas9 tag for the expression pattern class as an experiment type
 
−
* Would be inline with "Reporter gene", "In situ", "Antibody", etc.
 
−
* Probably want "Genome editing" instead of "CRISPR-Cas9" so as to be more generic
 
−
* Would a GFP knock-in via genome editing be distinct from "Reporter gene"?
 
−
* Could have a super tag "Genome_editing" and sub-tags "CRISPR-Cas9", "Zinc_fingers", "TALEN"
 
−
* Maybe we'll just stick with a "Genome_editing" tag
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
== October 13, 2016 ==
 
  
−
=== Strain requests ===
 
−
* Ranjana sending strain requests to Mary Ann
 
−
* Mary Ann processing published strains requested by Ranjana
 
  
−
=== GO meeting ===
+
==February 15, 2024==
−
* Registration is now setup
 
−
* Sarah (Torres) could register all WB CIT participants
 
−
* Kimberly is helping organize
 
  
−
=== AGR Portal Use Case working group update ===
+
=== Literature Migration to the Alliance ABC ===
−
* Working on first use case, basic text search for genes, GO terms, diseases, and orthology groups
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Data is being collected into a "Portal Data" Google drive: https://drive.google.com/drive/u/1/folders/0B9qQtJIEUDEhRnJKWF9NTTVMVGs
+
===== 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 =====
−
* Some MODs providing more data than requested; That's OK, we just want to keep it simple for the first implementation
+
*Facet for topic
−
* We only want, for the first pass, to retrieve genes, GO terms (no GO-gene annotations), diseases (no disease-gene annotations), and orthology groups
+
*Facet for automatic assertion
−
* We likely already have enough data for a first pass implementation; not comprehensive data, but that is fine for now
+
**neural network method
−
* Disease data dumped from ACEDB, based on Disease Ontology; not comprehensive for OMIM disease list
+
*Facet for confidence level
−
* We'll eventually want to pull data directly from OMIM and GO
+
**High
 +
*Facet for manual assertion
 +
**author assertion
 +
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
−
=== Extending SPELL virtual machine ===
+
===== Manually validate paper - topic flags without curating =====
−
* Has a lot of data; may be contributing to SPELL downtime
+
*Facet for topic
−
* Could possibly move to the cloud, but we would need a machine in the cloud
+
*Facet for manual assertion
−
* Can only install SPELL on Ubuntu 8; SGD uses RedHat; we can ask them what they're using, how it's working
+
**professional biocurator assertion
−
* Possibly SGD could run a worm instance on their machine(s)
+
***ABC - no data
  
−
=== Transgenome ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* Junacarlos finished parsing the transgenome data with Daniela
+
* Search ABC with paper identifier
−
* Checking parse output numbers with the Transgenome group
+
* Migrate to Topic and Entity Editor
−
* Will the expression data be dumped out in the expression GAF? Yes, should be
+
* View all associated data
−
* Data from Transgenome are not necessarily peer-reviewed; need to make that clear in display
+
* Manually validate flags, if needed
−
* Some Expr_pattern objects can be linked to WBPerson, if not a WBPaper
 
−
* Data in GAF will point to the 2012 Cell paper as a reference for the Transgenome project
 
−
* Raymond suspects issues with it; what if users cannot trace data back to source (by looking up the paper)?
 
−
* Would be best to link directly to the respective Transgenome database page when displaying their data
 
−
* Notes can be added to release notes that the Transgenome data has been added to the database
 
  
−
=== Micropublications ===
+
=== PDF Storage ===
−
* Trial with uploading Nemametrix data; aiming in putting data for the next upload (2-4 micro)
+
* At the Alliance PDFs will be stored in Amazon s3
−
* Added micropublication type in the ?Paper class
+
* We are not planning to formally store back-up copies elsewhere
−
* Micropublications will acquire WBPaper IDs
+
* Is this okay with everyone?
−
* Previous micropublications were only ?Expr_pattern objects; now will be ?Paper objects
 
−
* Ideally micropubs. will be indexed by PubMed and enter the WB pipeline through the normal paper route
 
−
* Question: create WBPaper objects as soon as accepted? That is plan for now
 
−
* Micropubs. will first be hosted by WormBase, but may move to an independent repository (Micropublication: biology)
 
−
* Will we display images/figures from micropubs. only or for all papers? We'll need to wait and see
 
−
* Could we accommodate any digital data to associate with the micropub.? E.g. data points, plasmid maps, etc.
 
−
* Micropubs. text will be marked up as much as possible; what about making all sentences OWL statements?
 
−
* Would this be changing the way that authors write papers? Maybe, but should be independent of core micropublication pipeline
 
−
* Each micropublication/data/result could be combined as modules to create a larger, more comprehensive narrative
 
−
* There is a notion of a "millipublication" that could be a larger narrative from collected micropublications
 
−
* One original idea was that micropublications would capture data that people would not otherwise want to publish
 
−
* Data submitted as micropublication will not be able to be submitted as another publication later but will be cited as data point
 
−
* Micropubs. will be considered primary research article, not just an abstract (equivalent to meeting abstract)
 
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
== October 20, 2016 ==
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
=== AGR search prototype ===
+
==February 1, 2024==
−
* URL: http://search.alliancegenome.org/
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Searching "WNT4", then choosing category "Gene Ontology" provides facets for species
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* Question is: how are these species associated to the GO terms?
 
−
* Associated genes could have a species prefix or indicator
 
  
−
=== AGR gene page ===
+
==January 25, 2024==
−
* There was resistance to creating AGR gene pages
 
−
* Some see it as redundant with what is already available elsewhere
 
−
* Although we may want to build a foundation gene page and develop from there
 
−
* Maybe MODs could develop their respective gene pages to look more like an AGR standard
 
−
* One main reason to create AGR is to have a consolidated, consistent, standard view for data, including genes
 
−
* Would be good to assemble a user group (or intended audience) to receive feedback from
 
−
* Use Case working group has put together some ideas for a gene comparison page, keyed off of orthology group:
 
−
** https://docs.google.com/presentation/d/1frMMh3xfepesJq5iqSXAwwLOrb45cuqe3LValEOd4bM/edit#slide=id.p
 
  
−
=== Citace upload ===
+
=== Curator Info on Curation Forms ===
−
* Next Tuesday, October 25th 10am
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
=== Curator call next week ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* Topic: curation styles
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
* Curation by paper, by topic, etc.
 
−
* Curation inter-dependencies
 
−
* Daniela will present for WormBase
 
−
* Send ideas to Daniela for her to cover
 
−
* Send older slides with relevant information to Daniela
 
  
 +
* 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.
  
−
== October 27, 2016 ==
+
* I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  
−
=== AGR Portal Use Case working group ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
* Working group had call yesterday with Paul Thomas and Judy Blake
 
−
* Decision was made to abandon the idea of displaying "orthology groups"/"homology groups"
 
−
* Instead we will display a gene-centric page with comparisons of focus gene data with data from all orthologs and paralogs
 
−
* Paul Thomas' group had built a prototype for pulling out orthologs with GO info: http://umodtest.usc.edu/
 
−
* This prototype returns closest orthologs of a focus/query gene and then displays a table of all GO annotations for all genes
 
−
* We would want to display orthologs for a focus gene as well as paralogs
 
−
* This display is very similar to the gene comparison page mockup the use case working group had been envisioning, except now the focus will be a single gene, not a PANTHER subfamily
 
  
−
=== Disease-Strain curation ===
+
=== Update on NN Classification via the Alliance ===
−
* Ranjana working on disease-strain associations for WormBase
+
* Use of primary/not primary/not designated flag to filter papers
−
* Disease group working on the DAF (disease association file) format
+
* Secondary filter on papers with at least C. elegans as species
−
* Ranjana will discuss the strain curation pipeline with Mary Ann and Karen
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
−
* Will want a unique ID for each strain, especially for when we merge strain data with other MODs
+
* Next NN clasification scheduled for ~March
−
** One solution is to just prefix the strain name with "WBStrain:" to indicate it came from WormBase
 
  
−
=== Kimberly visiting CA ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
* Kimberly will be at CIT next Wednesday
+
* NNC html pages will show NNC values together with species.
−
* Noctua developers will be around to discuss integration with Textpresso
+
* Show all C. elegans papers first and other species in a separate bin.
−
* Kimberly can send around schedule for the GO meeting
 
−
* Would be good for curators to setup a Noctua account before the Noctua workshop (on Nov 7)
 
−
* Kimberly will also be at CIT on Tuesday Nov 8th
 
  
−
=== Paper editor CGI ===
+
=== Travel Reimbursements ===
−
* Michael had some issues with the paper editor
+
* Still waiting on October travel reimbursement (Kimberly)
−
* Seems to be working now
+
* Still waiting on September and October travel reimbursements (Wen)
  
−
== November 2, 2016 ==
+
=== UniProt ===
 +
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
 +
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
 +
 
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
 +
 
 +
 
 +
==January 11, 2024==
 +
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
 +
** Curators should make sure that, when pasting special characters, the duplicate function works
 +
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
 +
 
 +
==January 4, 2024==
 +
* ACKnowlegde pipeline help desk question:
 +
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 +
* Citace upload, current deadline: Tuesday January 9th
 +
** All processes (dumps, etc.) will happen on the cloud machine
 +
** Curators need to deposit their files in the appropriate locations for Wen
 +
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 16:04, 18 April 2024

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

2023 Meetings

April 18th, 2024

  • NNC pipeline being switched off locally and moving into the Alliance ABC.

April 11th, 2024

  • Caltech WS293 ace files ready for the upload

April 4th, 2024

  • Continued discussion on sustainability
  • CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
    • Data is still going to SPELL and enrichment analysis
    • Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
  • Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
  • Michael's presentation on LLMs - Named Entity Recognition (NER)

March 14, 2024

TAGC debrief

February 22, 2024

NER with LLMs

  • Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
  • Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  • There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.


February 15, 2024

Literature Migration to the Alliance ABC

Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)?

Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic
  • Facet for topic
  • Facet for automatic assertion
    • neural network method
  • Facet for confidence level
    • High
  • Facet for manual assertion
    • author assertion
      • ACKnowledge method
    • professional biocurator assertion
      • curation tools method - NULL
Manually validate paper - topic flags without curating
  • Facet for topic
  • Facet for manual assertion
    • professional biocurator assertion
      • ABC - no data
View all topic and entity flags for a given paper and validate, if needed
  • Search ABC with paper identifier
  • Migrate to Topic and Entity Editor
  • View all associated data
  • Manually validate flags, if needed

PDF Storage

  • At the Alliance PDFs will be stored in Amazon s3
  • We are not planning to formally store back-up copies elsewhere
  • Is this okay with everyone?

February 8, 2024

  • TAGC
    • Prominent announcement on the Alliance home page?
  • Fixed login on dockerized system (dev). Can everybody test their forms?

February 1, 2024

  • Paul will ask Natalia to take care of pending reimbursements
  • Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.

January 25, 2024

Curator Info on Curation Forms

  • Saving curator info using cookies in dockerized forms. Can we deploy to prod?

ACKnowledge Author Request - WBPaper00066091

  • I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  • The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
  • I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  • Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.

Update on NN Classification via the Alliance

  • Use of primary/not primary/not designated flag to filter papers
  • Secondary filter on papers with at least C. elegans as species
  • Finalize sources (i.e. evidence) for entity and topic tags on papers
  • Next NN clasification scheduled for ~March
  • We decided to process all papers (even non-elegans species) and have filters on species after processing.
  • NNC html pages will show NNC values together with species.
  • Show all C. elegans papers first and other species in a separate bin.

Travel Reimbursements

  • Still waiting on October travel reimbursement (Kimberly)
  • Still waiting on September and October travel reimbursements (Wen)

UniProt

  • Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
  • Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
  • Stavros escalates the issue on Hinxton Standup.
  • Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.

January 18, 2024

  • OA showing different names highlighted when logging in the OA, now fixed on staging


January 11, 2024

  • Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
    • Curators should make sure that, when pasting special characters, the duplicate function works
  • OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
    • If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
  • Chris tested on staging and production the phenotype form and the data are still going to tazendra
    • Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
    • Raymond: simply set up forwarding at our end?
  • AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
  • Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
  • Valerio would like to use an alliancegenome.org email address for the openAI account
  • New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
  • Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
  • Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
  • Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
  • It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
  • Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.

January 4, 2024

  • ACKnowlegde pipeline help desk question:
    • Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
  • Citace upload, current deadline: Tuesday January 9th
    • All processes (dumps, etc.) will happen on the cloud machine
    • Curators need to deposit their files in the appropriate locations for Wen
  • Micropublication pipeline
    • Ticketing system confusion
    • Karen and Kimberly paper ID pipeline; may need sorting out of logistics
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