Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
= 2015 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2015|January]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2015|February]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_March_2015|March]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_April_2015|April]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_May_2015|May]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_June_2015|June]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_July_2015|July]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_August_2015|August]]
 
  
[[WormBase-Caltech_Weekly_Calls_September_2015|September]]
+
==March 14, 2024==
  
 +
=== TAGC debrief ===
  
== October 1, 2015 ==
+
==February 22, 2024==
  
=== Micropublications ===
+
===NER with LLMs===
* General discussion on DOI handling for micropublications and using the ?Paper model
 
* Project started with expression pattern submissions
 
* Micropublications were displayed on ?Expr_pattern pages on WormBase/WormBook
 
* We do currently assign a DOI to these URLs/pages
 
* If we put the micro publications in Wormbook shall we request a different DOI? May be enough to request a DOI for WormBook, with just a link to the respective WormBase page
 
* Daniela has requested changes to ?Expr_pattern model to accommodate micropublication
 
** So many of the tags were shared (or could be shared) with the ?Paper class
 
* If micropublications will be indexed by MEDLINE, we could use our standard paper pipeline to capture paper data
 
** Any lag in indexing is likely negligible (~1 day)
 
* Daniela & Paul asked NLM to change the title of WormBook from "WormBook: An online review of C. elegans biology" to just "WormBook" to accommodate a broader scope; haven't heard back yet
 
  
=== Community Curation paper ===
+
* 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%)
* Due at end of October
 
* Daniela communicating with Mary Ann; should micropublications be mentioned?
 
* Database issue that is published concurrently with the BioCurator meeting
 
* Hopefully we have some feedback by the time we need to make revisions (end of January)
 
* E-mails to authors for concise description and allele-phenotype will go out today/soon
 
  
=== WS251 citace upload tomorrow ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
=== Community editing of concise descriptions ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Would like community to edit manually-written and automated gene descriptions
 
* Would be nice to have a link to the concise description form from gene overview/existing description
 
* Same for allele-phenotype form
 
  
=== Traveling to labs ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* Soliciting community contributions AND providing user help/guidance
 
* Need to emphasize the importance of MODs and why they need support
 
* We should cater our discussions to what the labs specifically work on
 
* Could start with 2-4 days of trial; half-day at campuses
 
* Needs to be short talk/seminar (not an hour, much shorter)
 
* Should we go to local/area meetings
 
* Will likely be effective to have one-on-one discussions with PIs, lab members
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
== October 8, 2015 ==
 
  
=== Soliciting community curation ===
 
* Juancarlos, Ranjana and Chris working on a pipeline to e-mail authors
 
* Will try to automate as much as possible
 
* Will avoid e-mailing authors that have already been AFP e-mailed in the last 3 months
 
* Juancarlos writing scripts to generate list of valid papers with relevant e-mail information
 
* Would be good to parse corresponding author and first author from paper XMLs, but publishers are not uniform in their format
 
  
=== SObA in Cytoscape ===
+
==February 15, 2024==
* Juancarlos working on adapting SObA to Cytoscape
 
* Would allow zooming in for details, zooming out to hide details
 
  
=== Help Desk query ===
+
=== Literature Migration to the Alliance ABC ===
* Looking for all mutations in a Million Mutation strain
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* Currently, large queries on website point users to FTP site, but without direction
+
===== 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 =====
* Would be good to provide more clear directions to users (point to specific file)
+
*Facet for topic
* We used to have a mechanism for users to download a flat file for large datasets, but missing now
+
*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
  
=== Community Curation paper ===
+
===== Manually validate paper - topic flags without curating =====
* Will wait for the right time to write, after feedback, etc.
+
*Facet for topic
* Biocurator meeting is in April, by which time we will hopefully have good results to present (talk/poster/workshop).
+
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
=== Cell Ontology project ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* Didn't get funding on first round application
+
* Search ABC with paper identifier
* However, may get funded through GO
+
* Migrate to Topic and Entity Editor
* Species agnostic, but tries to draw connections between human and C. elegans cell types
+
* View all associated data
* Example, human epithelial cells using FGF/Wnt etc. connected to C. elegans epithelial cells using FGF/Wnt etc.
+
* Manually validate flags, if needed
  
=== Micropublications ===
+
=== PDF Storage ===
* WormBook gets indexed by NCBI/PubMed
+
* At the Alliance PDFs will be stored in Amazon s3
* We want micropublications to be indexed
+
* We are not planning to formally store back-up copies elsewhere
* Marie-Anne Felix asked about species descriptions
+
* Is this okay with everyone?
* We have a micropublication form for expression data; can we build for other data types?
 
* Data in form does not, currently, read into Postgres
 
* Would be good to automatically generate a PDF
 
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
== October 15, 2015 ==
+
==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.
  
=== VPC annotations ===
+
==January 25, 2024==
* Expression pattern data will be incorporated into concise descriptions.
 
* The annotations done to vulval precursor cells are currently done to the generic (sex-agnostic) term Pn.p (e.g. P5.p, P6.p, etc..).
 
* This applies to Gene expression, Gene regulation, Phenotype classes -possibly others.
 
* All curators that have annotations to sex-agnostic VPC terms should change their annotations, e.g. P5.p -> P5.p hermaphrodite (going back to the papers)
 
* Ranjana will open a ticket about it.
 
* Wen will be notified and will help pulling out all the annotations that have been made to those terms (Wen- I can brief you on this)
 
  
===Obsolete terms===
+
=== Curator Info on Curation Forms ===
* For ontology terms that become obsolete we should implement a system to notify curators, in the same fashion as GO operates:
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* e-mail curators when a term becomes obsolete
+
 
* have a check in place: when curators submit their files a script would alert them in case they contain obsolete terms
+
=== 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