Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 1: Line 1:
 +
= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
  
−
==2011 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_February_2011|February]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_March_2011|March]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_April_2011|April]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_May_2011|May]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_June_2011|June]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_July_2011|July]]
 
  
−
[[WormBase-Caltech_Weekly_Calls_August_2011|August]]
+
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_September_2011|September]]
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_October_2011|October]]
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
== November 3, 2011 ==
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
Gene ID mapping problems (as discussed in site-wide call)
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
*Does CIT need to worry about consistency of gene IDs over database builds?
 
−
*Hyper-linking entities in papers could be an issue
 
−
*Acquire an ID for every gene for every new genome?
 
−
*When mark a paper, separate into two different types of genes :stable vs unstable
 
−
**Stable genes map to stable ID
 
−
**Unstable genes map with a version number
 
−
*WormBase communicate/work with DCC personnel for data wrangling during post-DCC era?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
Updating Predicted Gene Interactions
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
*Wei wei asking about how to update with WormBase
 
−
*WormBase predicted interaction objects can be updated simply via link to Gene Orienteer
 
−
*If we want a live interaction browser, we would need to pull the data into the build process
 
−
*Do we want a single object per pair of genes? One object per instance of evidence (per paper)?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
 +
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
== November 10, 2011 ==
+
==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)
  
−
Worm Publication is under review
+
==March 14, 2024==
  
 +
=== TAGC debrief ===
  
−
NAR paper is published - has DOI
+
==February 22, 2024==
−
*Williams et al has to be added to bibliography
 
  
 +
===NER with LLMs===
  
−
Citace, Development Release
+
* 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%)
−
*Cron-jobs/scrips used to update the database, but now requires manual manipulation
 
−
*Manual versus automated updating of database
 
−
*Need a plan for the future
 
−
*Migration to EBI affecting the process; will things change again
 
−
*Where will WS release files exist
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
SVM
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*Collecting feedback from curators
 
−
*Curators need to review results
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
Motifs in WormBase
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
*Xiaodong working on it
 
  
  
−
Interaction Model
 
−
*Discuss with Todd the integrated model of 4 types (physical, genetic, predicted, regulatory)
 
−
*Change WBID names (WBInteraction versus WBPhysicalInteraction, WBGeneticInteraction, WBRegulatoryInteraction, WBPredictedInteraction)
 
−
*Put together series of example data objects; send to Todd/Paul to test out
 
−
*Need Interaction_type tag to distinguish the 4 basic types
 
−
*Types will need to be parsed/extracted after the build for FTP download etc.
 
  
 +
==February 15, 2024==
  
−
Human Disease Relevance Descriptions
+
=== Literature Migration to the Alliance ABC ===
−
*Started going in from last build
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
*Ranjana will discuss with Web Team
+
===== 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 =====
−
*Disease-paper connections
+
*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
  
−
== November, 17, 2011 ==
+
=== 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?
  
−
Handling 50-100+ genomes
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
*Annotation, gene finding, storage, handling
 
−
*~1 week to build all genome browsers and BLAT/BLAST servers
 
−
*Homology run takes longer; from Compara pipeline
 
−
*Species-by-species build processes?
 
−
*Lookup if genome in ACEDB; if not, look up gene models in GFF databases
 
  
 +
==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==
  
−
Beta site
+
=== Curator Info on Curation Forms ===
−
*What is needed:
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
**Need eyes to look at current pages
 
−
**Suggestions as to what is needed on individual pages
 
−
*Currently not adding a lot of new features
 
−
*Data models browsable/searchable?
 
−
*If we provide AQL, need to provide data models
 
−
*Intermine will eventually make AQL obsolete(?)
 
−
*Run AQL queries from a local ACEDB instance for better performance (and fewer time outs)
 
−
*Time out limits currently set to 2 minutes on AQL queries
 
  
 +
=== 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.
  
−
Expression pattern curation
+
* 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.
−
*Confidence flags
 
−
*Ex: expressed in HSNs, in HSNL
 
−
*Annotate to parent term unless explicitly (and confidently) stated observed in child term/object
 
−
*Consistency of curation?
 
−
*Discussion between Raymond, Wen, Daniela, etc.
 
−
*Want list of ALL genes expressed in a cell (with some cutoff)
 
−
*Also want list of genes expressed ONLY in that cell and not others
 
−
*New technology generating paradigm shift; how to best represent data
 
−
*Categorize data sets (based on methods)
 
−
*Use evidence codes (text?) to categorize (ECO?)
 
  
 +
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
−
ncRNA transcripts
+
=== Update on NN Classification via the Alliance ===
−
*To pull out ncRNA genes and GO terms (Sarah Burge)
+
* Use of primary/not primary/not designated flag to filter papers
−
*Need to exclude protein-coding genes from query
+
* 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)
  
−
GO Meeting (Kimberly)
+
=== UniProt ===
−
*A lot of changes to be put in place
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*Infrastructure, annotation changes - we'll need to sort out what this means for WormBase
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*Annotation: "Annotation extension" column to add additional info
+
* Stavros escalates the issue on Hinxton Standup.
−
*Make explicit annotations for gene products
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
−
*Next meeting in February at Stanford (focused annotation meeting)
 
−
**Workout specifications for common annotation framework
 
  
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
−
WormMart status
 
−
*Are we switching over to BioMart-run WormMart?
 
−
*OICR crew working on new data-loading tool
 
−
*Update still pending...
 
−
*Check modmine (http://intermine.modencode.org/)
 
  
 +
==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.
  
−
Reviews in on SVM paper
+
==January 4, 2024==
−
*Maybe done in 3 weeks
+
* ACKnowlegde pipeline help desk question:
−
*Reviewer wanted more metrics
+
** 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"