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]]
  
−
2013 Meetings
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
−
 
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_January_2013|January]]
 
−
 
 
−
 
 
−
= February 7, 2013 =
 
−
 
 
−
Person Cytoscape
 
−
*Person-person network viewing on website
 
−
*Use person lineages
 
−
*Will discuss with web team
 
−
 
 
−
 
 
−
WormBook History
 
−
*Paul editing a person history section, starting with John White
 
−
*Can use history info to link people
 
−
 
 
−
 
 
−
Binary vs. Non-binary interaction display
 
−
*Cytoscape and interaction table are only displaying interactions as binary interactions, regardless of number of interactors
 
−
*We need to assess how many interactions we have that have more than 2 interactors
 
−
*Once we have assessed that, we should discuss with web team about how to display these cases
 
−
 
 
−
 
 
−
Curation Statistics
 
−
*Wen can generate numbers for Citace AND the complete build (rather than Hinxton)?
 
−
*Will let Hinxton build the queries
 
−
*End-of-build summary for curators (with more database technical numbers) separate from the Release Notes for public (with more biologically interesting numbers)
 
−
*Will separate Wiki page into two sections to reflect this
 
−
*Public info will continue to be displayed in Release Notes
 
−
*Internal info - where should that be displayed?
 
−
 
 
−
 
 
−
Postgres info table (on [[OA_forms,_tables,_scripts,_etc|Wiki page]])
 
−
*Curators will continue to add info to Wiki on scripts, dependencies, ontologies, etc. for each Ontology Annotator
 
−
 
 
−
 
 
−
Intermine
 
−
*JD gave short demo yesterday
 
−
*Will give another tutorial next week (Thursday, Feb 14, 2013 - 8:30am PST)
 
−
*Curators can/should test
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
Nick Brown visit
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
−
*PI of FlyBase Cambridge
 
−
*Will be here tomorrow around 11am
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
= February 21, 2013 =
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
WS237 Upload March 1, 2013
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
*Citace upload on February 28
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
WS236 will go live on April 5, 2013
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
*One week later than previously planned (March 29th)
 
  
 +
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
New genome assemblies and gene names across species
+
==April 11th, 2024==
−
*How do we handle independent, conflicting genome assemblies and gene models?
+
*Caltech WS293 ace files ready for the upload
−
*Can we collect all gene models, for example, without any bias and display any info we have?
 
−
*How might we display conflicting models, etc.?
 
−
*Should we prioritize easier-to-handle, "more important" genomes?
 
−
*Can we establish automated (minimal manual effort) pipeline to handle these issues?
 
  
 +
==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)
  
−
Expression graphs
+
==March 14, 2024==
−
*Wen and Daniela have been generating expression graphs
 
−
*Yanai probes need to be mapped
 
−
*Multiple probes mapped to the same gene will be averaged
 
−
*SPELL construction has changed; all data sets exist as separate flat files
 
  
 +
=== TAGC debrief ===
  
−
Expression table
+
==February 22, 2024==
−
*Table of expression data to display all details of an expression pattern object
 
−
*Place in separate widgets on the gene page
 
−
*Perhaps, separate large-scale from small-scale studies
 
  
 +
===NER with LLMs===
  
−
Phenotype Ontology
+
* 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%)
−
*How stable/complete is the current phenotype ontology?
 
−
*Good, but we may consider a reconstruction/re-ordering of existing terms
 
−
*Group phenotypes by e.g. anatomy term, life stage, etc.?
 
−
*Link anatomy terms, life stages to relevant phenotypes (at .ACE level or website level)
 
−
*Perhaps use cross-products of various ontologies to get the same effect?
 
−
*May want to consider using .OWL format as opposed to .OBO
 
−
*Need a sustainable, long-term approach to maintaining the ontologies
 
−
*AMIGO 2 only consumes .OWL format, not .OBO
 
−
*Should we consider switching to Protege, as a local ontology browser/editor (as opposed to OBO-Edit)?
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
LEGO Call
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*How to use annotation extensions for LEGO model?
 
−
*Consistent use?
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
Intermine
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
*Target for first release, minimal functionality for sequence-based queries
 
−
*JD working on importing sequence-based data
 
−
*How much can we get into Intermine by the first freeze/release (in April)?
 
−
*How should we prioritize?
 
−
*Can we build a "worm-version" of FlyMine (existing classes, e.g.)?
 
−
**Probably not a good approach for first release in April, but maybe useful for long-term
 
−
*Production server (unstable) vs live/testing server (more stable)
 
−
*Major testing will start in April
 
  
  
−
Staging tests
 
−
*WS236 Staging site now available
 
−
*Everyone should test rigorously
 
  
 +
==February 15, 2024==
  
−
[http://www.celegans.org/2013/ 2013 International Worm Meeting]
+
=== Literature Migration to the Alliance ABC ===
−
*WormBase workshop
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
*What do we need to consider/prepare for, for the meeting?
+
===== 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 =====
−
*Someone should be in touch with organizers?
+
*Facet for topic
−
*Who are the organizers?
+
*Facet for automatic assertion
−
**Monica Colaiacovo and Ralf J. Sommer
+
**neural network method
−
*WormBase souvenirs?
+
*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
  
−
Dead genes
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
*Going to add "Historical_gene" tag to relevant class models (e.g. ?Interaction, ?Expr_pattern, ?Transgene, etc.)
+
* Search ABC with paper identifier
−
*Will modify OA dumping scripts with Juancarlos to automate recognition of dead genes and replace them (if merged)
+
* Migrate to Topic and Entity Editor
−
*Dumper will add remark about existence of dead gene in original object
+
* View all associated data
−
*Will consider adding original gene reference through #Evidence hash under "Published_as" tag, as Other_name (gene synonym), as possibly as a separate free-text tag in the models that captures the verbatim reference to the original gene
+
* Manually validate flags, if needed
−
*Will not try to re-annotate old objects WRT the gene synonyms/verbatim references, but can consider doing this going forward only
 
  
 +
=== 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?
  
−
Transgenes
+
==February 8, 2024==
−
*CGC transgenes have been completed/unified with existing WBTransgene objects
+
* TAGC
−
*Updating new CGC strains will become a monthly task
+
** Prominent announcement on the Alliance home page?
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
GO task
+
==February 1, 2024==
−
*Can we link two or more genes based on ,e.g., process for enrichment analysis?
+
* Paul will ask Natalia to take care of pending reimbursements
−
*What should we be getting out of enrichment analyses that we aren't currently?
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
*Link all genes as part of "FGF signaling", "DAF-2 signaling", "PAR genes", etc.
 
−
*Gene sets based on pathway, process, etc.
 
−
*Intermine should be able to filter by these means (eventually)
 
  
 +
==January 25, 2024==
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
= February 28, 2013 =
+
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
WS237 Upload
+
* 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.
−
*Upload happening today
 
−
*May be some delay due to script issues (being fixed)
 
−
*Transgene and Life Stage
 
  
 +
* 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.
  
−
BioCurator meeting coming up
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Karen, Kimberly, Michael, and Daniela going
 
−
*Topics: entity recognition, curation pipelines
 
  
 +
=== 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
  
−
Kimberly attended NESCENT summit
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*Meeting: Resource Coordination for NESCENT group, Text mining for annotations
+
* NNC html pages will show NNC values together with species.
−
*Kimberly spoke about Textpresso
+
* Show all C. elegans papers first and other species in a separate bin.
−
*Setting up Textpresso for butterfly?
 
−
*Amer Soc Plant Bio attended, wanted to know more about Genetics/G3 markup pipeline
 
  
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
Galaxy workshop next Tuesday, March 5, 2013
+
=== UniProt ===
−
*Biologists workshop 11am - 2pm, in Braun 151
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*Lunch provided
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*Web-based platform for sequence analysis
+
* Stavros escalates the issue on Hinxton Standup.
−
*Protein trees, alignments, RNA-seq data
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
−
*Run remotely or locally as a server
 
  
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
−
Bioinformatics Club
 
−
*Could start a LinkedIn group (Caltech BioInformatics "huddle" group?)
 
−
*Main goal: find out who's on campus and what they do
 
−
*What are most people interested in?
 
−
*Create forum and wiki page?
 
−
*Mitch Gutman coming this summer, maybe give intro talk?
 
−
*Georgi Marinov in Wold lab
 
  
 +
==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.
  
−
Xiaodong visited two labs in Bejing
+
==January 4, 2024==
−
*Gave WormBase tutorials
+
* ACKnowlegde pipeline help desk question:
−
*Lab is still using legacy site
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*Said they had trouble finding things on new site
+
* Citace upload, current deadline: Tuesday January 9th
−
*Xiaodong showed SPELL and modENCODE data
+
** All processes (dumps, etc.) will happen on the cloud machine
−
*WormMart demo and some queries
+
** Curators need to deposit their files in the appropriate locations for Wen
−
*~30 C. elegans labs in China, and growing?
+
* Micropublication pipeline
−
*Xiaodong encouraged them to send questions to WormBase Help
+
** Ticketing system confusion
−
*Someone (WB person) should go to the Asia WormBase meeting (every 2 years)
+
** 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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