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]]
  
−
==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]]
 
−
 
 
−
 
 
−
== May 5, 2011 ==
 
−
 
 
−
Citace upload
 
−
*Using current citace release (WS226) for Progress Report
 
−
 
 
−
 
 
−
Pictures
 
−
*Daniela did not actually curate ~7000 pictures this month ;)
 
−
*Script to fetch pictures automatically
 
−
 
 
−
 
 
−
Snehal starts next week
 
−
*working on phenotype curation
 
−
**90 genes >= 10 publications
 
−
**Of these 90, 54 with no annotated phenotype
 
−
**20,000 genes with RNAi data
 
−
*Concise Descriptions? May be appropriate
 
−
**Prioritize by genes that currently have no description but have new papers
 
−
*Picture curation?
 
−
*Learning an ontology may be difficult, but she can stick to familiar material
 
−
 
 
−
 
 
−
Aldrin
 
−
*Karen, Raymond, Chris will talk to Todd
 
−
*Lineage browser for ontologies?
 
−
*Cell lineage browser? Capture multi-parentage issues
 
−
 
 
−
 
 
−
Ranjana - Preplanning WormBase side meetings at IWM?
 
−
 
 
−
 
 
−
Periodically sending someone to different sites
 
−
*E.g. Someone from Caltech goes to Hinxton, etc.
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
−
Practice Talks before International Worm Meeting
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
−
*on Monday before meeting
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
== May 12, 2011 ==
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
Example of Bandana for International Worm Meeting
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
−
*Looks good!
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
GO Consortium meeting next week
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
*Paul, Michael, Ranjana, and Kimberly going
 
−
*Discussion about tools (Juancarlos?)
 
−
*Section in meeting agenda to discuss curation
 
−
**Textpresso-based curation
 
−
**Ontology Annotator
 
−
**Demo by Kimberly or Ranjana?
 
−
**Relatively trivial (depending on situation) to setup new OA for a new site (Juancarlos)
 
−
**Discuss what's been proposed in the grant
 
−
**What does the consortium want? Brainstorming/Fantasizing
 
−
**People are likely partial to their own tools
 
−
**Make use of the best parts of everyone's tools
 
−
**Are others using flat/text files or web-based/java-based tools? Mostly web-based
 
−
**Phenote? Funding? Bio-Portal e-mail?
 
−
**PAINT tool (Phylogenetic Annotation and INference Tool) (http://wiki.geneontology.org/index.php/PAINT)
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
Progress Report
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
*Paul has received some reports, but not all, yet
 
  
 +
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
Picture curation
+
==April 4th, 2024==
−
*Started receiving permission from Elsevier!!
+
* Continued discussion on sustainability
−
*Blanket-permission for 11 journals
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
*Publicly display list of cooperating journals online
+
** 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==
  
−
Talks at the Int Worm Meeting
+
=== TAGC debrief ===
−
*Paul S listed for a Plenary talk during Workshop
 
−
*Two Wormbase Plenary talks
 
  
 +
==February 22, 2024==
  
−
Snehal
+
===NER with LLMs===
−
*Concise descriptions
 
−
*Kimberly helping
 
−
*Will get into phenotypes soon
 
  
 +
* 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%)
  
−
Juancarlos waiting to hear back from some people about OA
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
*People need more time to test
 
−
*Karen has encountered some issues; needs to reproduce
 
−
*Ranjana - loads slowly?
 
−
*Mangolassi issues?
 
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
Genetic Interactions
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
*Group met on Tuesday
 
−
*Made headway on genetic interaction organization
 
−
*Add "Additive" type term and "No Apparent Interaction", etc.
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
Paper pipeline
 
−
*Kimberly & Juancarlos working on
 
−
*Documented on Wiki
 
−
*CGI's still being used?
 
−
*Remove outdated or unused CGI's?
 
  
  
−
Rewriting script from Jack Chen
+
==February 15, 2024==
−
*Neuron connection search
 
−
*Inroad to working on more web-interface topics
 
  
 +
=== 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
  
−
Adding interaction datasets into WormMart (Xiaodong and Ruihua)
+
===== 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
  
−
Gene interaction dumping script (Raymond/Todd)
+
=== 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?
  
−
Strain Display
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
*Karen doing queries at CGC
 
−
*How many genes represented in CGC strain list?
 
−
*Protein-coding genes with alleles in strains?
 
−
*12,000 genes that are NOT represented in CGC
 
−
*Discrepancy wrt alleles; negative in AQL query, but present on site
 
−
*Strains with LOTS of alleles; how to handle?
 
−
*Polymorphisms vs. alleles
 
  
 +
==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.
  
−
Aldrin Montana working over the summer
+
==January 25, 2024==
−
*We invited him to visit
 
−
*We'll come up with projects
 
−
*Web team fully involved in web site
 
−
*Help with minor GO issues (Ranjana)
 
−
**Requires knowledge of Perl
 
−
**Non-C.elegans species
 
−
**InterPro-to-GO mapping
 
−
**Export pipelines for other species?
 
−
**Maybe small project; requires more communication than coding?
 
−
*Raymond could help provide projects
 
−
*Would be nice to use PAINT across the nematodes for annotation
 
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
New Web site (Todd)
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
*Web team wrapping up various projects
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
*Polishing user interface
 
−
*Abby working on user interface
 
−
*Todd working on production environment
 
−
*Norie working on code that interfaces with database
 
−
*Release beta version at International Worm Meeting
 
−
*Working with Kevin Howe to standardize formats of files used during build
 
−
*Can now host new data for new species
 
  
 +
* 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.
  
−
== May 19, 2011 ==
+
* 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
  
−
Login System for people to submit and modify (WBPerson) personal information
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*How to validate that someone registering for the site is the actual person?
+
* NNC html pages will show NNC values together with species.
−
**Use e-mail address, although some people don't have e-mail addresses; snail mail?
+
* 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)
  
−
Poster Session Help Desk for International Worm Meeting
+
=== UniProt ===
−
*Wen- yes, all set
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*People will bring their own laptops
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*Wen will make a Wiki page for people to sign up for sessions
+
* 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
  
−
Aldrin visiting
 
−
*June 16th/17th OK for people
 
−
*We could start making a list of possible topics for Aldrin to work on
 
  
 +
==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.
  
−
Clone Model Update
+
==January 4, 2024==
−
*Working with current clone model to test adding plasmid objects
+
* ACKnowlegde pipeline help desk question:
−
**Works OK, but will probably want a couple of new tags
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
**One idea is to have a tag that links nematode-specific sequence in the plasmid to genomic regions and GBrowse viewer
+
* Citace upload, current deadline: Tuesday January 9th
−
*Test plasmid objects and ideas for genome alignment sent to Paul Davis, waiting to hear back
+
** 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

Revision as of 18:05, 11 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 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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