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]]
  
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
−
==2012 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
−
 
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_January_2012|January]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_February_2012|February]]
 
  
−
[[WormBase-Caltech_Weekly_Calls_March_2012|March]]
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_April_2012|April]]
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_May_2012|May]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
== June 7, 2012 ==
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
Midbuild
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
*Wen needs all .ace files ready to test the midbuild
 
−
*Chris will send modified WS232 models.wrm to Wen
 
−
**Chris will add all model changes proposed for WS233
 
−
**?Interaction model "Rearrangement" tag needs an XREF and ?Rearrangement model needs an "Interactor" tag
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
New Interaction OA
+
==April 18th, 2024==
−
*Curators should take a look at the new Interaction OA on the sandbox (mangolassi) and notify Juancarlos, Chris, and/or Xiaodong of any problems
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
−
*All interactions, including Yeast-Two-Hybrid and Yeast-One-Hybrid experiments, are in the new OA
 
  
 +
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
Paper pipeline for other species
+
==April 4th, 2024==
−
*Kimberly will update pipeline to include papers from other species
+
* Continued discussion on sustainability
−
*Papers can go through data tagging pipeline (SVM etc.)
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
*Images could be captured from cooperating journals
+
** Data is still going to SPELL and enrichment analysis
−
*Are PDFs available?
+
** 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.
−
*~1600 papers for Brugia malayi, for example
+
* Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
−
*Mapping to genomes will be an issue (e.g. RNAi)
+
* Michael's presentation on LLMs - Named Entity Recognition (NER)
−
*We would want an automated curation mechanism in place for non-core species
 
  
 +
==March 14, 2024==
  
 +
=== TAGC debrief ===
  
−
== June 14, 2012 ==
+
==February 22, 2024==
  
 +
===NER with LLMs===
  
−
Mock Upload
+
* 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%)
−
*Everything was OK
 
−
*Wen will leave files in the same directories, so curators will need to overwrite or replace if you want a new file
 
−
*Ghost objects? Allele-phenotype didn't have correct life stages; fixed
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
Anatomy terms
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*Juancarlos changed obsolete anatomy terms to red text in the Term Info section of the OA
 
−
*We will update the anatomy terms somewhat periodically
 
−
*Some terms get deprecated; if a term gets deleted, a replacement needs to be found
 
−
*Merges can be dealt with more automatically
 
−
*Raymond will periodically check for "floating" anatomy terms
 
−
*Update went smoothly
 
−
*Not many 'obsolete' terms being used
 
−
*Many subsumed terms
 
−
*Paper-anatomy term associations in Citace Minus; Raymond will take care of them
 
−
*Kimberly uses legacy data for anatomy term associations to papers
 
−
*Cell/Cell-Group issues
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
Interaction OA
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
*Interaction OA and dumper script essentially finished
 
−
*Curators should check the OA on the sandbox once more before we make it live
 
−
*Interaction summary vs. Remark
 
−
**Interaction summary is for biological info/summary
 
−
**Remark is more for technical details
 
−
**We will ask Juancarlos if Remark data from old Interaction objects can be transferred to Interaction_summary field/table
 
−
*Make Interaction type unique (single ontology field)
 
−
*Move the "Phenotype" field to the first TAB
 
−
*Error checks
 
−
**5 Fatal errors (Interaction does not get dumped) if the following are not satisfied
 
−
***1) There are at least two interactors
 
−
***2) There is a reference
 
−
***3) The Interactor types are compatible
 
−
***4) There is an Interaction ID
 
−
***5) There is an Interaction type
 
−
**1 Non-fatal error (Interaction gets dumped but error is reported in error file on dump)
 
−
***Interaction type and directionality of interactors
 
−
*Additional error check for Karen - duplicate interactions on multiple rows
 
−
*"Check Data" button, what is it doing now? Can it do all the same checks as the dumper?
 
  
  
  
−
== June 21, 2012 ==
+
==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
  
−
First Pass Forms
+
===== Manually validate paper - topic flags without curating =====
−
*We get e-mails when first pass forms are complete, even if PDF is not ready
+
*Facet for topic
−
*Can we set up the system to hold off on e-mailing curators until the PDF is ready?
+
*Facet for manual assertion
−
**Already for Author First Pass, not for Journal First Pass (GSA/DJS)
+
**professional biocurator assertion
−
**Right now:
+
***ABC - no data
−
***1) Paper gets accepted by GSA/DJS
 
−
***2) Journal sends Author First Pass form to authors on paper
 
−
***3) Journal submits XML of paper to us
 
−
***4) Linking script runs on XML
 
−
***5) Quality Control checks on linked XML performed
 
−
**Mary Ann would rather only get alerts after PDF is available
 
−
**We can add a note about whether or not the PDF is available to the First Pass list, so Mary Ann can sort on that parameter
 
−
*The form currently e-mails curators whenever data is changed; do we want updated alerts?
 
  
 +
===== 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
  
−
WormMart
+
=== PDF Storage ===
−
*WormMart wasn't accessible from EBI
+
* At the Alliance PDFs will be stored in Amazon s3
−
*Raymond removed software that affects firewalls; seems to have resolved the issue
+
* 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?
  
−
Upload deadline June 28th, 2012
+
* 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.
  
−
High School student volunteer
+
==January 25, 2024==
−
*Kristy (Yingjie) Ren from Diamond Bar High School
 
−
*Does she want lab experience only, or would she want to do some WormBase work?
 
−
*We should ask her
 
−
*Work study approach? We pay 20%, govt pays 80%; better situation?
 
  
 +
=== 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.
  
−
== June 28, 2012 ==
+
* 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.
  
−
Kristy Ren (summer high school student)
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Will come in tomorrow at 10am
 
−
*Ranjana, Raymond, Paul, Hillel, and Karen will speak to her
 
−
*Curation efforts may be better for college students (work study)
 
  
 +
=== 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
  
−
Itai Yanai paper
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*Daniela curating expression pattern data
+
* NNC html pages will show NNC values together with species.
−
*Temporal expression patterns across 5 species during development
+
* Show all C. elegans papers first and other species in a separate bin.
−
*Microarray data
 
−
*Itai wants to display his expression images in WormBase
 
−
*He should provide sequence names instead of gene names
 
−
*EBI will do mapping to genes
 
−
*Should original/raw data go into SPELL? Probably
 
−
*What do we do with images that Itai can submit?
 
−
*How do we capture/store/process original data, and what do we display/capture in database?
 
−
*If we get a spreadsheet of the data, place on FTP site
 
−
*Custom Agilent arrays
 
  
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
Upload tomorrow at 10am
+
=== UniProt ===
−
*New models (WS233) in CitaceMinus
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*Life_stage names have not been changed in yet
+
* 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
  
−
Yeast Two Hybrid Experiments
 
−
*Need to update ~11,000 experiments in OA to "High throughput"
 
−
**Can use OA batch form (or possibly script to query multiple PGIDs)
 
−
*Requested original data from 2004 Li et al Science paper from Vidal Group (Michael Calderwood)
 
−
*Many erroneous objects need to be fixed
 
−
**Some have only bait or only target
 
−
**Some interactions may be wrong
 
  
 +
==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.
  
−
Grant Application
+
==January 4, 2024==
−
*Paul will submit a grant application in 3 months
+
* ACKnowlegde pipeline help desk question:
−
*Paul will talk to PIs about big picture goals of the project
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*What is the 5 year plan?
+
* Citace upload, current deadline: Tuesday January 9th
−
*30 pages total (short)
+
** All processes (dumps, etc.) will happen on the cloud machine
−
*What will we need to think through?
+
** Curators need to deposit their files in the appropriate locations for Wen
−
**Curation approach/process
+
* Micropublication pipeline
−
**Gene expression
+
** Ticketing system confusion
−
***Generating images from digital expression data
+
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics
−
**Gene regulation/interaction
 
−
**Physical interactions (Protein-Protein, Protein-Nucleic Acid)
 
−
**Function/GO
 
−
**Pathways/Processes
 
−
***Work study student to curate pathways via WikiPathways (potential pilot)
 
−
***Develop process pages for the website?
 
−
**Anatomy
 
−
**Other species
 
−
**Outreach
 
−
**Life stages
 
−
**Data retrieval/mining; querying?
 
−
**Website/database
 
−
**What we want to display and how?
 
−
**Advanced Queries; Ontology Browsers; Data integration
 
−
**Tools
 
−
**Host/pathogen interaction (collaborate with pathogen curator groups?)
 
−
**Behavior? Process oriented?
 
−
**Disease/drug discovery
 
−
*Want to determine ASAP what we may need to pilot or experiment with
 
−
*Website
 
−
**Ontology browsers/searches
 
−
**Process pages
 
−
**Molecule pages
 

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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