Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
= 2016 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
== January 7, 2016 ==
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
=== SAB 2016 ===
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
* Schedule for Caltech talks:
 
−
** SAB wiki: http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks
 
−
** Mary Ann, Chris, and Ranjana will discuss how to condense and streamline a presentation on community curation
 
−
** We should have a talk about LEGO curation and pathways; Kimberly happy to present
 
−
*** LEGO adoption can be made cross-MOD and encourage collaboration
 
−
** Maybe move micropublication talk to the end of the day; it will generate a lot of discussion; will try earlier in the day, 5 min talk, 5 min discussion before longer discussion
 
−
** Maybe include discussion of expression summary description in Gary Williams talk about large scale expression data and visualization
 
  
−
=== Expression summaries ===
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
* We want to consolidate large-scale expression data into a human-readable summary
 
−
* Would be good to consolidate large-scale and small-scale expression data
 
−
* We will adapt anatomical expression data for the SObA graph in future
 
  
−
=== Phenotype form ===
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
* Now on sandbox, allows for RNAi transgene data
 
−
* Will finish up, write documentation and make live
 
−
* Will continue to send out e-mail requests
 
  
−
=== E-Merge Tech outsourcing ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
* Company called Chris asking if we would want them to curate for us
 
−
* Website: http://www.e-mergeglobal.com/
 
−
* Will send them some phenotype curation for some papers and ask them to curate new papers, as a pilot
 
−
* They will give us a cost estimate after a free pilot
 
−
* Will see if it is cost-effective; good to know what they charge
 
  
−
== January 14, 2016 ==
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
===LEGO===
+
==April 11th, 2024==
−
*Sent out slides for an overview talk of LEGO and the Noctua curation tool. (Kimberly)
+
*Caltech WS293 ace files ready for the upload
  
−
=== Collecting info for SAB ===
+
==April 4th, 2024==
−
* Chris would like to collect summaries of curation progress over last year in a Google Doc
+
* Continued discussion on sustainability
−
* Google doc: https://docs.google.com/document/d/1S8EjL20owW07RH9kIi8HbnTAtP5JierliBuyOo2oDVc/edit
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
* Would be good to include progress on various projects or curation efforts (or curation changes)
+
** Data is still going to SPELL and enrichment analysis
−
* Next week at group meeting we can review and decide what should be presented as the overview for curation to the SAB
+
** 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==
  
−
== January 21, 2016 ==
+
=== TAGC debrief ===
  
−
=== SAB ===
+
==February 22, 2024==
−
* Agenda items for literature curation overview
 
−
* Todd will discuss outreach; Chris will talk to Todd about Caltech plans for outreach
 
−
* Cataloging web usage on WB site, SPELL, etc.
 
−
* We can discuss hosting all WB services and tools under the same web domain
 
  
−
=== Phenotype form ===
+
===NER with LLMs===
−
* New phenotype form is live: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/allele_phenotype.cgi
 
−
* We should point out response rate and paper coverage for community curation
 
−
* How long can we expect to complete curation for phenotype with current pipelines
 
−
* Can request PIs to check coverage of their allele phenotypes
 
−
* We want this to lead to development of pathways
 
  
−
=== The Allied Genetics Conference, Orlando, July 2016 ===
+
* 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%)
−
* WB needs to decide who will go
 
−
* Intermine project will have their own room
 
−
* MODs will present together
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
== January 28, 2016 ==
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
=== SAB talks ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Literature curation overview
+
 
−
** General publication trends for C. elegans and data types
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
** Our coverage, backlogs, outreach and curation efforts
+
 
−
* Automated paper flagging and data identification (Karen)
+
 
−
** SVM pipeline, keyword/string matching, data extraction
+
 
−
* Automated gene descriptions (Ranjana)
+
==February 15, 2024==
−
** Manual writing doesn't scale (currently ~5000 descriptions)
+
 
−
** Amenable to automation (pulling together primary data for descriptions)
+
=== Literature Migration to the Alliance ABC ===
−
** Mention gene description form
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Community annnotation numbers (Mary Ann & Chris)
+
===== 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 =====
−
** Other MODs efforts
+
*Facet for topic
−
** WB submission forms and pilot response rates
+
*Facet for automatic assertion
−
* Micropublications
+
**neural network method
−
** Incentivizing community contributions
+
*Facet for confidence level
−
** Micropublication form
+
**High
−
** How data is displayed on WormBase
+
*Facet for manual assertion
−
* LEGO
+
**author assertion
−
** What it is, how it's different, why it's important
+
***ACKnowledge method
−
** Priorities for LEGO models: signaling pathways, development, human disease biology (signal transduction, cilia pathology, etc.)
+
**professional biocurator assertion
−
* SObA
+
***curation tools method - NULL
−
** WB uses ontologies extensively, many annotations
+
 
−
** Need an easy-to-consume data display
+
===== Manually validate paper - topic flags without curating =====
−
** Have WOBr
+
*Facet for topic
−
** Convention is to provide list format of data display, e.g. mouse expression summary
+
*Facet for manual assertion
−
** SObA: intuitive summary view of ontology annotations from gene perspective
+
**professional biocurator assertion
−
** Ontology trimmed to display only relevant ontology terms
+
***ABC - no data
−
* What do we not have a talk about:
+
 
−
** Human disease curation
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
** SPELL/modSeek
+
* Search ABC with paper identifier
−
** Metabolite curation
+
* Migrate to Topic and Entity Editor
−
* Google Doc: https://docs.google.com/document/d/1uvSIIecWTmVjhUPA8f4FHIECSTJhloy8Z2ocujx96Uw/edit
+
* 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
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
 +
 
 +
==January 4, 2024==
 +
* ACKnowlegde pipeline help desk question:
 +
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 +
* Citace upload, current deadline: Tuesday January 9th
 +
** All processes (dumps, etc.) will happen on the cloud machine
 +
** Curators need to deposit their files in the appropriate locations for Wen
 +
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 16:04, 18 April 2024

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

2023 Meetings

April 18th, 2024

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

April 11th, 2024

  • Caltech WS293 ace files ready for the upload

April 4th, 2024

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

March 14, 2024

TAGC debrief

February 22, 2024

NER with LLMs

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


February 15, 2024

Literature Migration to the Alliance ABC

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

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

PDF Storage

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

February 8, 2024

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

February 1, 2024

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

January 25, 2024

Curator Info on Curation Forms

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

ACKnowledge Author Request - WBPaper00066091

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

Update on NN Classification via the Alliance

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

Travel Reimbursements

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

UniProt

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

January 18, 2024

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


January 11, 2024

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

January 4, 2024

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