Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 17: Line 17:
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
= 2018 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
== February 1, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
=== Automated gene descriptions - orthology ===
+
==April 18th, 2024==
−
* Some genes have human orthology mentioned in automated descriptions, even though the orthology call has not been called in DIOPT
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
−
* WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT)
 
−
* Orthology synchrony is a challenge; WormBase and FlyBase may need to pay special attention to orthology calls and discrepancies
 
−
* DIOPT is purely automated, does not consider other information about orthology evidence
 
−
* We should be clear about how the orthology calls are made
 
  
−
=== Next upload ===
+
==April 11th, 2024==
−
* Unclear of exact date
+
*Caltech WS293 ace files ready for the upload
−
* Probably end of March
 
  
−
=== SimpleMine issue ===
+
==April 4th, 2024==
−
* Redundant genes in input list are merged
+
* Continued discussion on sustainability
−
* Should SimpleMine provide an option to keep redundancies?
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
** Give option up front? Provide submission step to point out redundancies? Ask for choice?
+
** Data is still going to SPELL and enrichment analysis
−
* We can default to show row-by-row correspondence, and display the number of redundant entries
+
** 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.
−
* Conclusion: Make an option for users to indicate if they want row-by-row correspondence or a merged list
+
* 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)
  
−
=== Cell type expression ===
+
==March 14, 2024==
−
* Waterston paper
 
−
* 40,000 random cells, clusters sequenced individually to a depth of 20,000 reads; ~1000 genes per cell; cluster data; make judgement call as to what cell types they likely are
 
−
* For now, we can do a simple annotation: significantly expressed genes for each cell type
 
−
* Supplemental table S5 for neurons
 
−
* Maybe just ignore the hybrid calls like AQM/PVM, etc.
 
−
* It may be good to isolate the single cell data from other expression data
 
−
* We should annotate/capture the expression clusters
 
−
* Would be good to be able to do enrichment analysis on the clusters; compare data sets
 
−
* Data has not been placed in SPELL yet, Gary considered the data a work in progress
 
−
* We can communicate with Waterston group; are they collecting more data?
 
−
* Wen will take another look at the data
 
−
* Gary W. concerned about the reported/assumed/inferred identity of the cells in the paper
 
−
* Probably cannot curate to individual cells, but we can annotate to a higher level term
 
−
* We want to annotate and display expression enrichment as well as presence/absence calls
 
  
 +
=== TAGC debrief ===
  
−
== February 8, 2018 ==
+
==February 22, 2024==
  
−
=== Release schedule ===
+
===NER with LLMs===
−
* Wen will ask Hinxton to update the published release schedule (for next data upload)
 
  
−
=== New York Worm Meeting ===
+
* 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%)
−
* Wen and Kimberly will present a WormBase tutorial on March 24
 
−
* Wen communicated to Oliver Hobert; suggested topics:
 
−
** Multi-gene (batch) search tools
 
−
** How literature info gets into WormBase? Curation process?
 
−
** Should we discuss completeness?
 
  
−
=== GO curation ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* New simple input form for Noctua, being developed at USC
 
−
* Not very much GO curation happening at WB right now
 
−
* Protein-2-GO pipeline
 
−
* Do we have a good Phenotype-2-GO(Process) mapping pipeline? We have our old mappings; not very reliable; would need to spend more time expanding the worm phenotype ontology and GO to improve
 
−
* Cellular component curation will come in from WB expression curation
 
−
* Don't have pipeline for Interactions-2-GO
 
−
* Textpresso Molecular Functions pipeline?
 
−
* geneprod and catalyticact data types for molecular function pipeline
 
−
* Textpresso can send molecular function annotations to Noctua
 
−
* For high-level pathway curation; we should probably read WormBook chapters (or other reviews) and develop pathways (using non-experimental evidence codes)
 
−
* We could potentially seed Noctua models from Reactome
 
−
* We would like to have complete curation for major pathways for gene enrichment analysis
 
−
* Roles of small molecules in Noctua models still being worked out
 
  
−
=== Phenotype curation ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Chris has had community curation pipeline on back burner while updating Wiki and dealing with AGR, WormMine, etc.
 
−
* Will get back to soon; will resend email requests for newer papers sent over a year ago
 
  
−
=== Expression curation ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Daniela getting back to expression curation after Micropublication stuff has quieted down
 
  
−
=== Gene regulation curation ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* April came across dataset involving regulation of siRNAs that don't seem to have gene objects in WB
 
−
* May need to instantiate genes for these?
 
  
−
=== Physical interaction curation ===
 
−
* SVM classification; do we flag a paper as negative that has protein interactions but no interactions for C. elegans
 
−
* Can we generate a good SVM that only identifies WB-curatable papers?
 
  
−
=== Disease curation ===
 
−
* Now curating the specific genetic entities involved in a disease model
 
−
* Will also capture environmental conditions, treatments (e.g. ameliorates, exacerbates)
 
−
* Curation in-line with AGR standards
 
−
* Evidence code needed for assertions that an animal is a model of disease in which the assertion is based on background knowledge and experimental evidence, together
 
−
* Evidence Code Ontology (ECO) is developing a new term to accommodate
 
−
* Disease curators can use new evidence code as well as any existing codes
 
−
* Is there a definition of a "disease model"?
 
−
* What are the minimal criteria for considering something a disease model?
 
−
* WB and FB curators focus on cellular phenotype and relation to the disease
 
  
−
=== Expression cluster curation ===
+
==February 15, 2024==
−
* 27 papers in pipeline
 
−
* Will then work on "single-cell" RNAseq
 
−
** Wen, Raymond, and David should discuss
 
  
−
=== April and May Worm Meetings ===
+
=== Literature Migration to the Alliance ABC ===
−
* Midwest and Colorado meetings
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Wen submitting abstracts
+
===== 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 =====
−
* Wen and Kimberly can write up abstract template for New York meeting and send around to be modified for future meetings
+
*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
  
−
=== WormBook ===
+
===== Manually validate paper - topic flags without curating =====
−
* Published last version for legacy site
+
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
=== Papers ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* Daniel requested 13 (older) papers from Caltech library through inter-library process
+
* Search ABC with paper identifier
−
* Received more than half as images; would need optical character recognition (OCR) for Textpresso purposes
+
* Migrate to Topic and Entity Editor
−
* What is the state of the art of OCR now? How good is it? Can we ask Caltech library for the service?
+
* View all associated data
−
* Are these high priority papers? Need to check to see if worth processing
+
* Manually validate flags, if needed
  
−
=== AGR ===
+
=== PDF Storage ===
−
* Disease working group setting up a face-to-face meeting
+
* At the Alliance PDFs will be stored in Amazon s3
−
* Variant working group may need a face-to-face meeting as well
+
* We are not planning to formally store back-up copies elsewhere
−
* Expression working group working out initial AGR site data display mockups
+
* Is this okay with everyone?
−
* Interaction working group; we will want to incorporate miRNA/target interactions (RNA-RNA interactions); will look at miRBase
 
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
== February 15, 2018 ==
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
=== Model changes ===
+
==February 1, 2024==
−
* Models freeze March 2nd
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Will need to get model changes proposed and tested by then
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
  
−
=== Sys admin of Tazendra/Mangolassi ===
+
==January 25, 2024==
−
* Raymond will discuss with Juancarlos to centralize
+
 
−
* Need good documentation for forms, tools, etc.
+
=== Curator Info on Curation Forms ===
−
* Will be a push to put all code for tools and forms on GitHub
+
* 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
 +
** 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
Retrieved from "https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls&oldid=38418"