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_February_2017|February]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_March_2017|March]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_April_2017|April]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
== May 4, 2017 ==
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
=== Strategies for GO-CAM (Noctua) curation ===
 
* GO-CAM (Gene Ontology - Causal Activity Model(ing))
 
* Proposal for curation report page (Kimberly)
 
* Paper-by-paper approach vs. big-picture approach
 
* Kimberly presented proposal for curation tool:
 
** Given a list of genes and keywords, tool could pull up all relevant annotations to help start with GO CAM model building
 
** Tool could return GO annotations, expression patterns, phenotypes, interaction-based phenotypes, etc.
 
* Could have a table to fill out that could then be imported into Noctua
 
* Can we use SObA to visualize relevant annotations for a set of genes? Help visualize common vs. distinct annotations?
 
* Process could highlight the need for micropublications
 
  
=== GO SObA ===
 
* Raymond & Juancarlos have been working on autocomplete tool for search bar; not trivial
 
  
 +
==March 14, 2024==
  
==May 11, 2017==
+
=== TAGC debrief ===
  
===Phenotype Strain curation (ky)===
+
==February 22, 2024==
* Changing Strain tag in the Phenotype class, which is used as a primary object for annotating a phenotype to, to clarify its purpose.
 
* A Strain tag also exists in phenotype assay, which is meant to capture the parent strain in which a mutant or other primary object (transgene or rearrangement) is part of. 
 
* These two tags have been causing confusion for curators and it causes errors upon the dump, in addition strains entered into the Control_strain field of the phenotype form are throwing errors during the dump as they are being recognized as "Strains".
 
* The dumper does not allow more than one primary phenotype affected object, it can be Variation OR Strain. 
 
* Control_strain data from the phenotype form are being dumped as "Strain", not Control_strain. Chris will work with Juancarlos to fix
 
  
===Metabolic curation (ky)===
+
===NER with LLMs===
* Michael Witting has hired a student to curate elegans metabolic data.
 
* I will be talking to him to see what we can provide to help them share these curated data with WB. This might be as minimal as an spreadsheet although if they are submitting their own data, I will aim for a micropublication template. If there is another curator that wants to sit in on a call with Michael and me, that would be appreciated.
 
* Mary Ann will join the call
 
  
===CGC login===
+
* 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%)
* CGC site now has a login. While we will be able to access all the info without logging in (the log in is required for placing an order or viewing an order history), do we need want a login?
 
* Aric talked with people at wormbase a while ago about the changes, was there any decision about if there will be a wormbase group login. I asked if they will be using logins to track activity on the site, he said no.
 
* We do not need to do anything, we have the access we need.
 
  
=== Methods in Molecular Biology ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
* Received comments back from editor, Chris going through them now
 
* Chris is working through the comments; will send around to staff
 
  
=== SObA Gene Ontology interface ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Raymond and Juancarlos have resolved most suggestions
 
* Have settled on a search scheme
 
* Haven't yet implemented highlighting GO Slim nodes; will work on
 
** Maybe allow user to request "highlighting" of GO Slim nodes
 
** Button "Show GO Slim terms"? Default highlighting of GO Slim nodes?
 
* URL should still be active
 
  
=== Progress report ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* There is a WormBase progress report and an AGR progress report
 
* Send WB reports to Paul
 
  
=== Phenotype display ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Putting phenotype remarks in their own column; in-line evidence
 
* Adam & Sibyl are working on phenotype display from Datomic
 
* We can wait until they ask us to review to make comments about phenotype display
 
* What about changes to phenotype model? Will make changes to phenotype model soon, but display shouldn't wait
 
  
=== Database migration ===
 
* 3 year vision request; where do we want to be in 3 years?
 
* ACEDB to Datomic? AGR dependent activities? May need to consider both
 
  
  
==May 11, 2017==
+
==February 15, 2024==
  
=== GO SObA update ===
+
=== Literature Migration to the Alliance ABC ===
* Auto complete [http://131.215.12.204/~raymond/cgi-bin/soba_biggo.cgi complete]?
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* GO slim nodes highlighted, [http://131.215.12.204/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&autocompleteValue=TP53BP1%20(Homo%20sapiens,%20UniProtKB:Q12888,%20Tumor%20suppressor%20p53-binding%20protein%201,%20TP53B_HUMAN)%3Cbr%3E example].
+
===== 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 18, 2017==
+
===== 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
  
===Texas Women University visit report===
+
=== PDF Storage ===
* Tissue enrichment tool
+
* At the Alliance PDFs will be stored in Amazon s3
* Cytoscape
+
* We are not planning to formally store back-up copies elsewhere
* WormMine and Simplemine
+
* Is this okay with everyone?
* User's traffic
+
 
* Micropubs
+
==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 18:18, 14 March 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


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