Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
== February 2, 2017 ==
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
=== Methods in Molecular Biology chapter ===
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
* Chris and Mary Ann will be in touch with individuals about section writing
 
−
* Karen: FlyBase chapter has small sections rather than long articles about their pages; should we keep our sections small; a few paragraphs each?
 
−
** As long as we stick to the "how to" focus, we can write as much as needed
 
−
* Raymond: We should try to write so that the content remains pertinent for a while
 
  
−
=== Pharyngeal phenotype terms ===
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
* Karen has made pharyngeal pumping phenotype terms for NemaMetrix micropublications
 
−
* It is common for many groups to involve serotonin-induced pharyngeal pumping to analyze strains; we do have a serotonin-induced pharyngeal pumping variant term- should I use this for all pumping phenotypes? In addition we have an EPG variant term and again, people tend to use EPGs to record pumping activity - should all reported pharyngeal pumping phenotypes that were measured  by EPGs be annotated with this term?  These questions highlight a need to revisit the pharyngeal phenotype branch and clarify how we should be focused on annotating these reported annotations.
 
−
* Karen asked Raymond/Gary and any other person interested in the group to help with pharyngeal phenotype term organization
 
−
* Raymond: Not very familiar with the existing usage of the terms and phenotype ontology structure wrt pharyngeal terms
 
−
* Authors submit phenotype data as part of the micropublication process
 
−
* Proposal for phenotype ontology going forward: create terms with logical definitions (OWL statements)
 
−
* We will start exploring more usage of logical definitions for phenotypes
 
−
* Will start meeting Thursday afternoons, starting next week (Feb 9), 1:30pm Pacific
 
−
* Karen will prepare the terms to be looked through.....
 
  
−
=== SObA graph for GO ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
* Juancarlos & Raymond making progress
 
−
* Added toggling for different roots of GO
 
−
* Difficult to navigate graph when lots of terms (e.g. tax-4)
 
−
* What can be done to improve the display?
 
−
* Filtering out IEA annotations; currently only for phenotype annotations; will expand to all IEA annotations
 
−
* Kimberly generating GO slim, 15-20 terms for each branch of GO, possible to use in ribbon display
 
−
* Could we distinguish between is_a, part_of, and regulates relationships?
 
−
* To simplify graph, could we further minimize the display of higher level/indirect nodes?
 
−
* Would we want parallel paths to root to be trimmed?
 
  
 +
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
== February 9, 2017 ==
+
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
=== AGR Disease working group ===
+
==April 4th, 2024==
−
* disease association file (DAF) pretty much worked out; data quartermasters are creating DAF files for each DB
+
* Continued discussion on sustainability
−
* Have a simple mockup for the display of disease data on a gene report page: https://docs.google.com/presentation/d/1YuD4_-mPS2AhIfaX41M8IIhiS63iiSy9ebcOQEZxoJQ/edit#slide=id.p4
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
* We should remove underscores from "is_model_of" and translate to "is a model of"
+
** Data is still going to SPELL and enrichment analysis
−
* Should spell out evidence codes
+
** 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.
−
* Kevin, WB data quartermaster, working on developing the disease association file (DAF) from the WormBase build
+
* Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
−
* Ranjana working on a new ?Disease_model_annotation class and model
+
* Michael's presentation on LLMs - Named Entity Recognition (NER)
−
* Disease working group has handed off mockup to AGR UI working group to start development
 
  
−
=== C3 working group ===
+
==March 14, 2024==
−
* Proposing ontology working group to handle ontology data and display
 
  
−
=== Datomic ===
+
=== TAGC debrief ===
−
* Juancarlos discussing with Adam, Sibyl, Matt, Kevin
 
−
* People are working on URL widgets: person widgets updated and ready for production, except for lineage widget.
 
−
* Some other URL widgets have also been completed
 
  
−
=== ACEDB dependencies ===
+
==February 22, 2024==
−
* Raymond was asked to collect all CIT curator uses of ACEDB, e.g. programmatic access via ACE Perl
 
−
* Send Raymond list of any CIT ACEDB-dependent processes
 
−
* Going forward, how are model changes made/proposed?
 
−
* Are we still proposing models in ACEDB and having them be converted? Not sure
 
−
* We need to establish a models migration plan
 
−
* Curators should review cronjobs that may need access to ACEDB
 
−
* Juancarlos can collect list of cronjobs using ACEDB; will send email of list
 
−
* Karen: WB Wiki page for OA forms, tables, scripts, etc. : http://wiki.wormbase.org/index.php/OA_forms,_tables,_scripts,_etc
 
  
−
=== Upload ===
+
===NER with LLMs===
−
* CIT upload February 28th? Need to check with Hinxton
 
  
−
=== Nemametrix ===
+
* 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%)
−
* Sent two micropublications
 
−
* In review and given DOI's
 
  
−
=== Methods in Molecular Biology chapter ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* Submission deadline April 1
 
−
* Mary Ann and Chris are organizing, will contact authors of older WormBook chapters
 
−
* We want to co-opt text from WormBook chapters that are specifically how-to guide with troubleshooting tips
 
−
* Everyone that has contributed this type of text, now or in this process, will be given authorship
 
−
* In future, could have small methods descriptions as micropublications; e.g. how to navigate the phenotype widget
 
−
* Content in older WormBook chapters that doesn't make it into the MIMB chapter could be micropublished
 
−
* We can review help desk inquiries to inform us as to what content should be included
 
  
 +
* 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 16, 2017 ==
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
=== SObA graph for GO annotations ===
 
−
* May be able to download a single image that can be browsed offline
 
−
* Phantom.js screenshot?
 
−
* Maybe download an SVG?
 
−
* May need to use the unweighted view for downloadable images
 
−
* Will want to create SObA graphs for expression soon
 
  
−
=== Phenotype and GO enrichment tools ===
 
−
* David (Angeles) has built the tools
 
−
* Raymond will send around links to the tools when ready
 
−
* Something to consider for GO enrichment: consider three branches separately or together?
 
  
−
=== Biocuration abstract deadline ===
+
==February 15, 2024==
−
* Tomorrow (Feb 17) deadline for poster abstracts
 
−
* AGR Disease working group submitted an abstract
 
  
−
=== LEGO curation call ===
+
=== Literature Migration to the Alliance ABC ===
−
* Regular Monday calls
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Lots of good discussion; much about using proper relations
+
===== 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 =====
−
* GO group this week discussed possibly establishing standards or recommendations
+
*Facet for topic
−
* May be good to divide up biological topics among curators
+
*Facet for automatic assertion
−
* Concern about over-proliferation of relations
+
**neural network method
 +
*Facet for confidence level
 +
**High
 +
*Facet for manual assertion
 +
**author assertion
 +
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
−
== February 23, 2017 ==
+
===== Manually validate paper - topic flags without curating =====
 +
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
=== SObA graph for GO annotations ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* Added the ability to download a single image that can be browsed offline
+
* Search ABC with paper identifier
−
Go to a graph for say, [http://tazendra.caltech.edu/~azurebrd/cgi-bin/testing/amigo/soba_go.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00002335&fakeRootFlag=1&filterLongestFlag=1 let-60]
+
* Migrate to Topic and Entity Editor
−
Zoom in to a level where labels are visible for all the nodes you want to show (Don' worry if they are off canvas).
+
* View all associated data
−
  Click "export png", right mouse button to "Save Image As"
+
* Manually validate flags, if needed
−
Saved image is 8000 dpi wide, sufficient to show all text clearly.
+
 
 +
=== 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
 +
** 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
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