Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
= 2021 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
 
  
 +
==March 14, 2024==
  
== March 4, 2021 ==
+
=== TAGC debrief ===
  
=== Webinar Monday ===
+
==February 22, 2024==
* Juancarlos can send a reminder email; he just needs the text for the body of the email message
 
* Can we send the webinar reminder to WB staff? Cannot use staff@wormbase.org to register
 
* Raymond will try to remember to forward to staff
 
  
=== Neural Network (NN) evaluation ===
+
===NER with LLMs===
* Kimberly (and other curators) looking through NN results
 
* Had previously prevented LOW scoring SVMs(?) from being sent to authors
 
* We need an agreed upon protocol for evaluation
 
* To avoid bias, we should randomly sample papers; usually will find negatives; how do we represent high, medium and low-scoring papers in the set without making curators review >> 100 papers?
 
* Michael will come up with protocol and send around list of papers for each data type (in Google Doc)
 
* Perhaps evaluation should happen on non-curated, newer papers
 
  
 +
* 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%)
  
== March 11, 2021 ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
=== Spreadsheet for Data not in ACEDB ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Magdalena/Hinxton would like to know how much data at Caltech doesn't get into ACEDB
 
* Sheet here: https://docs.google.com/spreadsheets/d/1VcFykdyBcoMBvYliem8tnch5Q2VDMImL6EqlcEBCU-s/edit?usp=sharing
 
* We want to pull everything into the Alliance eventually, but maybe not everything needs to be harmonized
 
* We should evaluate existing forms and fields/tables for whether they need to be harmonized or can stay as is
 
  
=== CeNGEN To Dos ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* Daniela, Wen, Valerio, Eduardo, Raymond met with CeNGEN
 
* Want to add JBrowse track for promoters(?)
 
* Three things:
 
** CeNGEN will provide histograms that we can put on each gene page, similar to modENCODE plots (do they provide static images or data that we process and display as histograms?) Both are possible (Raymond)
 
** Their tool can assess "enriched" genes by cell type (enriched vs. neurons or vs. all cell types; not just housekeeping genes); these can be sent to WB -> SObA and enrichment analysis
 
** We will link to the CeNGEN homepage wherever appropriate
 
* All else will depend on Eduardo's tools for single cell expression data
 
* Raymond will be WB point person to communicate with CeNGEN
 
* Display solutions can be used for Alliance single-cell data in general
 
* May want to consider future use cases, e.g. mutant-vs-WT expression, chemical/drug-induced expression, etc.
 
  
=== Chen building access ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* You'll need an ID with RFID? (Yes, 20 year old IDs don't work)
 
* help.caltech.edu -> request type Card Office
 
* It will be ready and wait for you at the Reddoor cafe.
 
  
  
== March 18, 2021 ==
 
  
=== Caltech Alliance source? ===
+
==February 15, 2024==
* Could some data (like paper class/data) go to the Alliance directly from Caltech? Could be quicker and more efficient (and allow special characters that are lost at the acedb layer)
 
* Data would no longer be coming from the "Single Source of Truth" for WB data (i.e. ACEDB/Datomic)
 
* WB paper data would be ahead of the ACEDB paper data
 
* Kimberly will reach out to Magdalena et al. to propose
 
  
=== CITAce upload ===
+
=== Literature Migration to the Alliance ABC ===
* Upload to Hinxton on April 19 (? Friday April 16th ?)
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* Upload to CITace for Wen on Friday before (April 9th) by end of the day
+
===== 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
  
=== Alliance biological working groups priority ===
+
===== Manually validate paper - topic flags without curating =====
* Keep working on harmonization and LinkML models for data types
+
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
=== LinkML data visualization ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* Is there a way to visualize data coming from LinkML models? Like in .ACE files?
+
* Search ABC with paper identifier
* There may be some software that can render that kind of visualization, but we need to see
+
* Migrate to Topic and Entity Editor
* Curators want a way to make sure the model and the data are correct before officially submitting
+
* View all associated data
* Adam plans to demonstrate a visualization of literature data next Tuesday at literature acquisition working group (this was in the context of having a UI for seeing what's stored in the persistent database without waiting for elastic search processing to pass it to the regular UI, currently Literature is not modeled off of the LinkML yet)
+
* Manually validate flags, if needed
  
=== QC analysis for steps in Alliance ingest pipeline ===
+
=== PDF Storage ===
* Curators can get access to the FMS to look at uploaded files, processed files; need to know how to process JSON files
+
* At the Alliance PDFs will be stored in Amazon s3
* Curators can also access Neo, but need to know how to query
+
* We are not planning to formally store back-up copies elsewhere
* Would be good to have readable reports to provide numbers for overall data sets
+
* Is this okay with everyone?
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
== March 25, 2021 ==
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
=== How to access data at the Alliance ===
+
==February 1, 2024==
* Google doc summary here: https://docs.google.com/document/d/1FvrsFHZ5ga5KzPtQCFJixSdulkOXJfAEjW-qJ4N34Gc/edit?usp=sharing
+
* Paul will ask Natalia to take care of pending reimbursements
* Alliance data pipeline (simple): DQMs and Ferret pipelines --> FMS API --> FMS --> Loader --> Neo4J --> Java API --> Web Interface & Download Files
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
* FMS Swagger UI: https://fms.alliancegenome.org/swagger-ui/index.html
+
 
* Peruse all data types: https://fms.alliancegenome.org/api/datatype/all
+
==January 25, 2024==
* Neo4J web browser (via CalTech VPN):
+
 
** Stage: http://stage.alliancegenome.org:7474/browser/
+
=== Curator Info on Curation Forms ===
** Production: http://www.alliancegenome.org:7474/browser/
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* Alliance (Java) API Swagger UI: https://www.alliancegenome.org/api/swagger-ui/
+
 
* AGR Schemas repo: https://github.com/alliance-genome/agr_schemas
+
=== 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
 +
** 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