Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
Line 5: Line 7:
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
−
= January 10, 2013 =
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
Site-of-action pages
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
−
*No cell function pages exist
 
−
*Tried to display cell function info on anatomy pages
 
−
*Trying to display site-of-action data on relevant gene pages
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
Process pages
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
−
*Rudimentary process page up
 
−
*Has overview widget with all relevant entities
 
−
*Should be something by SAB
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
Intermine
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
*JD is working on; should have something ready by SAB
 
−
*Will replace WormMart entirely
 
−
*We should make an announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it
 
−
*We can perform queries for users in the meantime, if necessary
 
−
*Intermine interface isn't very intuitive; maybe we can improve it in time
 
−
*Can build queries with a query builder and perform complex queries
 
−
*Precanned queries could be made and proposed to users
 
−
*Curators can try YeastMine or FlyMine to try it out
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
Species expression data from Itai Yanai
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
*Importing pictures; potentially flagging each to a particular species
 
−
*Pictures typically linked to Expr_pattern objects
 
−
*Can images be linked to sequences, rather than gene objects?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
Documentation for Protein-2-GO tool
+
==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
  
−
Brugia database
+
==April 4th, 2024==
−
*Mark Blaxter offered to donate his Brugia database into WormBase
+
* Continued discussion on sustainability
−
*Papers from 1600s!!!
+
* 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==
  
−
Nematode Textpresso
+
=== TAGC debrief ===
−
*~10,000 new papers available (open access?)
 
  
 +
==February 22, 2024==
  
−
Species in Phenotype curation
+
===NER with LLMs===
−
*Species tag in phenotype
 
−
*Default dumping with species as C. elegans; some data was removed during the dump
 
−
*Do phenotypes need a species tag? We should add species tag to everything, to be safe
 
−
*Do we create a separate Citace for each species (potentially 100s)?
 
−
*Dump all data for all species in one file for testing, and individual files for upload?
 
−
*Should discuss with Kevin Howe
 
  
 +
* 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%)
  
−
Upload Stats
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
*Wen will process upload statistics as curators submit data
 
−
*Curators can check for discrepancies right away, rather than wait for the build and submission to notice errors
 
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
Legacy info complete!
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
Curation Status Form
 
−
*Will be live (on Tazendra) once some SVM reruns are done
 
  
  
−
INDI (Interesting, Not-yet-modeled Data Index)
+
==February 15, 2024==
−
*Wiki page generated to capture data types that do not fit cleanly into current data models
 
−
*http://wiki.wormbase.org/index.php/INDI
 
  
 +
=== 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
  
−
Community Annotation of Concise Descriptions, WikiPathways
+
===== Manually validate paper - topic flags without curating =====
−
*Concise Descriptions
+
*Facet for topic
−
**Ranjana wrote up a template; Kimberly and Ranjana were stress testing the form
+
*Facet for manual assertion
−
**Goal: Useful to WB curators, specific community members (experts) for trial curation, and finally general users
+
**professional biocurator assertion
−
**Scripting simple descriptions, manual annotation of complex descriptions
+
***ABC - no data
−
**Prioritizing genes that have no descriptions
 
−
**Form should allow a user comment box to indicate data that is missing from WormBase (must have reference or data to support)
 
−
*WikiPathways
 
−
**How do we engage the community in WikiPathways? Prepopulating pages with lists of genes?
 
−
**WormBase-approved models vs. community suggestions/ideas
 
−
*We could focus on specific data types (for this year, say) and really push a public agenda to get community annotation rolling
 
  
 +
===== 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
  
−
SAB Meeting
+
=== PDF Storage ===
−
*Few weeks away
+
* At the Alliance PDFs will be stored in Amazon s3
−
*What do we present?
+
* We are not planning to formally store back-up copies elsewhere
−
*We want to discuss our process: curation pipeline, Curation Status Tool
+
* Is this okay with everyone?
−
*Human disease relevance
 
−
*Generate consistent theme or topic flow; divy up to people to present
 
−
*How do we engage the community? What tools do we develop? How will they work? Educational outreach?
 
−
*Display
 
−
**How do we display transcription regulatory networks (TRNs)?
 
−
**How do we display/capture pathways?
 
−
*Topics: Multiple genomes, Natural variants, Transcriptomics, TRNs, Community Annotation, Pathways, Human relevance, Drugs/molecules
 
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
= January 17, 2013 =
+
==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==
  
−
Curation Status Form
+
=== Curator Info on Curation Forms ===
−
*Expression data
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
**Daniela going through and validating negative papers
 
−
**No record of truly negative papers during Andrei's first pass
 
−
**~2000 papers flagged positive for other_expr but not curated
 
−
**Papers up to year 2000 were carefully, manually scored for expression data
 
−
*We can present the form at SAB meeting
 
−
*Transgene, antibody, and disease are coming from Textpresso, not SVM; papers will be flagged through Curator First Pass form
 
−
*Microarray datatype to be added to form
 
−
**GEO data with no reference? Ignore
 
−
*Need to add a "Positive but not curatable" pre-canned comment
 
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
SAB Meeting agenda
+
* 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.
−
*Chris' will present flagging and curation pipeline overview
 
−
*Human relevance
 
−
**Diseases, disease ontology
 
−
*"Spontaneous" updates to DB/website? Mirrors?
 
−
*Processes and pathways
 
−
*Transcription Regulatory Networks
 
−
**Show Cytoscape view of regulatory interactions
 
−
**Show GBrowse with PWMs, for example
 
−
**Cytoscape cell lineage?
 
−
**BioTapestry
 
−
**Cytoscape network filters? (temporal, spatial, process)
 
−
*OICR and Hinxton will present first
 
−
*Kimberly can present on LEGO
 
−
*GO curation pipeline
 
−
*Future plans
 
−
*Community Annotation
 
−
*Meeting at Millikan boardroom
 
−
*SAB Monday night dinner @ Morgan Library
 
−
*Sunday meeting
 
−
**Discuss Cytoscape options with OICR team
 
  
 +
* 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.
  
−
Gene Disaese OA
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Ranjana and Juancarlos developed OA for gene/disease relationships
 
−
*Connections to Reactome via human genes
 
  
 +
=== 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
  
−
Cori Bargmann
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*Giving talk this Tuesday 4pm
+
* NNC html pages will show NNC values together with species.
−
*She'll meet WormBase Wednesday morning ~9am-10:30am
+
* 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)
  
−
Prioritization of Allele/Phenotype curation
+
=== UniProt ===
−
*Lack of data
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*Process-based curation
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*Top priority: phenotypes for genes that have no existing data
+
* Stavros escalates the issue on Hinxton Standup.
−
*Consider throughput of data sets (large scale may be less reliable/granular)
+
* 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
  
−
Community Concise Descriptions
 
−
*Focus on C. briggsae and Brugia malayi
 
  
 +
==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.
  
−
Dead genes
+
==January 4, 2024==
−
*Plan is to maintain record of original genes (dead or not) referred to by objects in Postgres (and other curation databases)
+
* ACKnowlegde pipeline help desk question:
−
*At dump, genes will be recognized as dead and replaced where applicable
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*ACEBD and website will display only updated genes but have a "Historical_gene" tag and a remark indicating original reference to a dead gene
+
* 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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