Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(883 intermediate revisions by 13 users not shown)
Line 21: Line 21:
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
==March 14, 2024==
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
=== TAGC debrief ===
  
 +
==February 22, 2024==
  
 +
===NER with LLMs===
  
== May 7, 2020 ==
+
* 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%)
  
=== Alliance COVID Page ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
* Available on stage
 
* Textpresso for Coronavirus up for testing
 
  
=== SimpleMine at Alliance ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Still some confusion about what it is
 
* Will try to help clarify on PI meeting on Friday
 
  
=== Development environment for Alliance work ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* Raymond and Juancarlos have been working on
 
* Existing hardware is strained; set up virtual machine
 
* Still some technical issues
 
  
=== Open Publishing Festival ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Later this month
 
* Micropublications involved
 
* Organized by the Collaborative Knowledge Foundation
 
* Will involve publishers of books, journals, etc.
 
* Will have a MOD-focused event, would be good to have WB curators participate/attend
 
* Open to all
 
  
=== Genotype class ===
 
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
 
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
 
* There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
 
* Would be good to be clear/transparent about which components were automatically inferred
 
  
=== WS277/278 ===
 
* Pipelines are pushed back by about 14 days/2 weeks
 
  
 +
==February 15, 2024==
  
==May 13, 2020==
+
=== 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
  
=== SURF students ===
+
===== Manually validate paper - topic flags without curating =====
* Welcome Fernando!
+
*Facet for topic
* Will work on neuron function with respect to dauer formation
+
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
=== Progress Report ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* Review Google Doc from Paul to make sure you're latest updates are there
+
* Search ABC with paper identifier
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
+
* Migrate to Topic and Entity Editor
 +
* View all associated data
 +
* Manually validate flags, if needed
  
===Genotype class===
+
=== PDF Storage ===
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
+
* At the Alliance PDFs will be stored in Amazon s3
*Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
+
* We are not planning to formally store back-up copies elsewhere
*Disease OA annotations now converted to the newly created genotypes where needed
+
* Is this okay with everyone?
*Need to work on disease dumper changes next
 
  
=== What genes should be linked to genotypes? ===
+
==February 8, 2024==
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
+
* TAGC
* What should we consider a "relevant gene"?
+
** Prominent announcement on the Alliance home page?
* We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
 
* For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
 
* For rearrangements, consider relevant any genes "inside" the rearrangement?
 
* For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
 
* In the future, we may want to consider genes that have been specifically annotated as having some functional consequence and informs that the gene is of functional relevance to the genotype
 
  
=== Volunteer Community Curators ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
* Have had an additional 13 people volunteer
 
* Single one-on-one tutorial for someone in Hong Kong this past Monday
 
* Chris will hold a tutorial today and tomorrow for everyone else
 
* Have received many new community annotations from volunteers (and authors), validation still pending
 
  
=== Open Publishing Festival ===
+
==February 1, 2024==
* Ranjana will join as a panelist
+
* Paul will ask Natalia to take care of pending reimbursements
* Other MOD curators will also join
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
* Festival calendar: https://openpublishingfest.org/calendar.html
 
  
=== Move to Chen building ===
+
==January 25, 2024==
* Scheduled for late January 2021
 
  
=== First completely virtual GO meeting ===
+
=== Curator Info on Curation Forms ===
* Kimberly: went really well
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* Only met 4 hours per day, due to time zone differences
 
* Had breakout sessions for focus groups
 
  
=== Alliance Literature Acquisition working group ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
* Plan to come up with use cases for OntoMate and Textpresso
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
 
  
* Kimberly plans to draw up most common use cases for Textpresso
+
* 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.  
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
 
  
 +
* 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.
  
== May 21, 2020 ==
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
=== Volunteer curators ===
+
=== Update on NN Classification via the Alliance ===
* Received surge of annotations earlier this week
+
* Use of primary/not primary/not designated flag to filter papers
* All tutorials done for now; all but 3 recorded
+
* Secondary filter on papers with at least C. elegans as species
* Each tutorial is ~1 hour in length
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
  
=== AFP tutorial ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
* AFP group working on tutorial/webinar
+
* NNC html pages will show NNC values together with species.
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
+
* Show all C. elegans papers first and other species in a separate bin.
  
=== Open Publishing Festival ===
+
=== Travel Reimbursements ===
* Had micropublication session yesterday, went well
+
* Still waiting on October travel reimbursement (Kimberly)
* Had ~50 participants
+
* Still waiting on September and October travel reimbursements (Wen)
* Saved Zoom chats? Can get public ones, maybe not private ones
 
  
 +
=== 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.
  
== May 28, 2020 ==
+
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
=== Wormicloud ===
 
* Introducing a new tool for a graphical summary of queried papers, Please take a look and leave any comments on it. (http://textpressocentral.org:5010/)
 
  
=== Genes to Physical Map ===
+
==January 11, 2024==
* https://colab.research.google.com/drive/1e83jv94-eO_VQ7kKdJ36TgDDb4WRkFhM?usp=sharing
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
To run: Runtime->Run All. Change the list of gene names and run again.
+
** 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 18:18, 14 March 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


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