Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 13: Line 13:
 
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
= 2016 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2016|January]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2016|February]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2016|March]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_April_2016|April]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
== May 5, 2015 ==
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
=== Tissue enrichment tool ===
+
==April 11th, 2024==
−
* Some slight modifications have been made
+
*Caltech WS293 ace files ready for the upload
−
* Raymond/Juancarlos request testing
 
−
* Made adjustments to gene name handling
 
−
* Tool could go live for the next release
 
−
* Data will remain frozen at WS252
 
  
−
=== Gene summaries ===
+
==April 4th, 2024==
−
* Paul asked Norbert about gene descriptions
+
* Continued discussion on sustainability
−
* FB has been getting good community response for contributing gene descriptions
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
* Automation still sounds like the right way to go
+
** Data is still going to SPELL and enrichment analysis
−
* Ranjana will look at summaries at other MOD sites
+
** 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)
  
−
=== Phenotype display ===
+
==March 14, 2024==
−
* MGI/MGD had a graph display of phenotype ontology (Paul S.)
 
−
* Made phenotype ontology slim for the summary heatmaps
 
−
* How do all of the MODs display phenotypes?
 
  
−
=== Progress reports ===
+
=== TAGC debrief ===
−
* Curators can write a paragraph on innovation
 
−
** Community curation (report numbers)
 
−
** WOBr
 
−
** SObA
 
−
** Automated descriptions
 
−
** Micropublications
 
  
−
=== Curation pipeline comparisons ===
+
==February 22, 2024==
−
* Would be nice to compare how MODs prioritize curation, triage papers, etc.
 
−
* How many MODs curate paper-by-paper (for all datatypes at once) vs. our method, by datatype?
 
−
** WB & MGI curate by datatype, most others by paper (for all datatypes)
 
−
* How are all MODs doing in terms of paper coverage?
 
−
** Do we need more manual effort, more automation? How much, given cost of each?
 
  
−
=== SPELL ===
+
===NER with LLMs===
−
* SGD uses SPELL but does not develop
 
  
 +
* 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%)
  
−
== May 12, 2016 ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
===Communication tools for umod teams===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*Mike Cherry set up Stanford umod-project- email lists for the different umod groups, PIs, software developers, and curators
 
−
**umod-project-curation@lists.stanford.edu
 
−
**https://mailman.stanford.edu/mailman/listinfo/umod-project-curation
 
−
**note: if you signup for a digest, you will receive e-mails from the list on a different time scale than people who didn't choose 'digest'
 
−
*Slack is back, download the app and look umod-project. You can also visit https://umod-project.slack.com/.  
 
−
**Browse the channels and join the ones that you want.
 
−
**Create any new channel, it seems there is no limit to the channels that can be created.
 
−
*Suzi Lewis will be setting up a github account for project tracking and wiki pages
 
  
−
=== Human Disease working group meeting ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Next Monday and Tuesday, in Kerckhoff 024
 
−
* Curators will review data models for human disease at each site
 
−
* Brainstorming session for future plans
 
−
* Possibility of molecule-disease interactions ("exacerbated by", "ameliorated by")
 
  
−
=== Metabolomics ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Wen came across metabolic profiling papers while looking for proteomics papers
 
−
* Wen will send to Karen, who is managing metabolites as part of molecule class
 
−
* BIGG database, a new metabolite database (http://bigg.ucsd.edu/)
 
  
−
=== Progress Report ===
 
−
* Send Paul progress report blurbs in next week (by Thursday)
 
  
−
=== Cross MOD call ===
 
−
* Reviewed FlyBase and Rat Genome Database this week
 
−
* Will review SGD and MGI next week
 
−
* Suzi Lewis asking about Intermine instances; what can Mine do that the Base cannot, and vice versa?
 
−
* Other MODs have more fully functional and fully populated InterMine instances
 
−
* Agenda and Minutes: http://bit.ly/1NXuBVD
 
−
* Schedule and Topic signup: http://bit.ly/243UNL2
 
  
−
=== FraqMine/SimpleMine ===
+
==February 15, 2024==
−
* http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/fraqmine.cgi
 
−
* We want to make the tool available to users, maybe under Tools menu
 
−
* Will need to discuss with Todd (Paul sending email)
 
  
−
=== Micropublications ===
+
=== Literature Migration to the Alliance ABC ===
−
*BioCADDIE developers are currently working on indexing datasets requested by the NIH for inclusion in a June 30 Prototype test. After then they will reach out to us to look into the WormData (micropublication) indexing.
+
==== 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
  
−
== May 19, 2016 ==
+
===== 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
  
−
=== Dead genes in FraqMine? ===
+
=== PDF Storage ===
−
* User asked for gene IDs for dead genes from list of sequence IDs
+
* At the Alliance PDFs will be stored in Amazon s3
−
* FraqMine/SimpleMine does not currently accept/return dead genes
+
* We are not planning to formally store back-up copies elsewhere
−
* Juancarlos will make changes to script to add an additional column indicating that a gene is dead, after Wen changes the source files to include the data
+
* Is this okay with everyone?
  
−
=== Community curation request delay ===
+
==February 8, 2024==
−
* Currently we wait 3 months before sending additonal community curation requests to authors
+
* TAGC
−
* Considering making delay only 1 month or less; opinions?
+
** Prominent announcement on the Alliance home page?
−
* Most annotations come within a week of a request
 
−
* One month is probably good
 
−
* Should we send list of alleles to lab heads with annotated phenotypes?
 
−
* Show community curated alleles/annotations on WB homepage?
 
−
* Show top 20 community curators on WB homepages?
 
−
* Make use of the "Activity" widget on homepage? Replace random page with community contributions?
 
  
−
=== Citace upload ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* June 28th, 10am
 
  
−
=== uMOD Phenotype call ===
+
==February 1, 2024==
−
* Today 11am Pacific
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Join BlueJeans call: https://bluejeans.com/626771895
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* To be discussed at NHGRI meeting next Monday & Tuesday
 
  
−
=== Distinctions between Human Disease curation and Phenotype curation? ===
+
==January 25, 2024==
−
* WB and other MODs have been curating phenotype and human disease separately
 
−
* Some consider phenotypes and disease as the same (Monarch perspective)
 
−
* We should consider the extent to which these overlap and are distinct
 
  
−
=== Human Disease meeting ===
+
=== Curator Info on Curation Forms ===
−
* People are looking for commonalities
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* Disease Ontology is a good starting point of commonality
 
−
* Agreement to curate experimental models
 
−
* UMOD Disease portal: search for a gene and get links to each individual MOD
 
−
* DBs should serve a disease data file
 
−
** WB has gene-disease association file
 
−
* Sources of disease files: OMIM, Medic(?), etc.
 
−
* MIM-to-gene file
 
−
* Query tools: what should they look like? What kind of results?
 
−
** Simple table views as results
 
−
* UMOD disease detail report page ideas
 
−
* Want to consider relations to molecules/chemicals ("modifiers")
 
−
** Exacerbates, ameliorates, is a therapeutic for
 
−
* Drug-induced models
 
−
* Disease strains/genotypes, how to handle
 
−
* Should disease curation expand to capturing alleles/genotypes/strains?
 
−
** We can, going forward
 
  
−
=== Objectifying Genotypes ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* Increasingly, we are encountering needs to objectify genotypes
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
* We have strain objects, although strains are not always specified in papers
+
 
−
* We could potentially create strain objects that are named according to a paper ID
+
* 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.
−
* This would enable us to capture certain phenotype and genetic interaction annotations
+
 
−
* We need to consider a strain's phenotype in relation to a control strain
+
* 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.
−
* We already annotate phenotypes to transgenes while specifying the gene (in the transgene) that causes the phenotype
+
 
−
* It will be good for WB cuartors to hear from other MODs about how they handle this
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
* We can reconvene after today's phenotype call and focus on this discussion for future cross-MOD calls
+
 
 +
=== Update on NN Classification via the Alliance ===
 +
* Use of primary/not primary/not designated flag to filter papers
 +
* Secondary filter on papers with at least C. elegans as species
 +
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
 +
 
 +
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
 +
* NNC html pages will show NNC values together with species.
 +
* Show all C. elegans papers first and other species in a separate bin.
 +
 
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
 +
 
 +
=== UniProt ===
 +
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
 +
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
 +
 
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
 +
 
 +
 
 +
==January 11, 2024==
 +
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
 +
** Curators should make sure that, when pasting special characters, the duplicate function works
 +
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
 +
 
 +
==January 4, 2024==
 +
* ACKnowlegde pipeline help desk question:
 +
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 +
* Citace upload, current deadline: Tuesday January 9th
 +
** All processes (dumps, etc.) will happen on the cloud machine
 +
** Curators need to deposit their files in the appropriate locations for Wen
 +
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 16:04, 18 April 2024

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

2023 Meetings

April 18th, 2024

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

April 11th, 2024

  • Caltech WS293 ace files ready for the upload

April 4th, 2024

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

March 14, 2024

TAGC debrief

February 22, 2024

NER with LLMs

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


February 15, 2024

Literature Migration to the Alliance ABC

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

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

PDF Storage

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

February 8, 2024

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

February 1, 2024

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

January 25, 2024

Curator Info on Curation Forms

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

ACKnowledge Author Request - WBPaper00066091

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

Update on NN Classification via the Alliance

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

Travel Reimbursements

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

UniProt

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

January 18, 2024

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


January 11, 2024

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

January 4, 2024

  • ACKnowlegde pipeline help desk question:
    • Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
  • Citace upload, current deadline: Tuesday January 9th
    • All processes (dumps, etc.) will happen on the cloud machine
    • Curators need to deposit their files in the appropriate locations for Wen
  • Micropublication pipeline
    • Ticketing system confusion
    • Karen and Kimberly paper ID pipeline; may need sorting out of logistics
Retrieved from "https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls&oldid=38418"