Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
Line 5: Line 7:
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
2013 Meetings
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2013|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2013|February]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2013|March]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_April_2013|April]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_May_2013|May]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_June_2013|June]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
 +
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
= July 11, 2013 =
+
==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)
  
−
Geneace daily dump
+
==March 14, 2024==
−
*EBI is moving nameserver location
 
−
*Getting real-time updates of gene list for genes in OA
 
−
*Michael Paulini set up nightly geneace dumps to FTP site
 
−
*We have gene file from nameserver: cgc name, public names, sequence name, live/dead status, gene IDs
 
−
*What data do we want additionally? Synonyms?
 
  
 +
=== TAGC debrief ===
  
−
Spica has officially been moved to new machine
+
==February 22, 2024==
−
*Let Raymond know of any problems
 
−
*Would be good to track all accounts on Spica (and any other machine)
 
−
**Can use log of all user logins
 
  
 +
===NER with LLMs===
  
−
AMIGO 2 still moving forward
+
* 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%)
−
*AMIGO 2 might go live July 17th
 
−
*We should be able to start configuring for WormBase at that point
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
Process Pages/WikiPathways
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*iFrame window doesn't work/load on Firefox; they are working on it
 
−
*iFrame window interactive display somewhat problematic
 
−
*Discussing Cytoscape as alternative?
 
−
*Using Cytoscape to display pathways would require significant development
 
−
*Some app available to load GPML from WikiPathways into Cytoscape, but JD couldn't get it working (yet)
 
−
*Having all process-related interactions in an Interactions widget on Process Pages
 
−
**Users need a clearer legend explaining what the different edges mean
 
−
**We need to modify some edges (e.g. flat ends do not mean repression; maybe they should)
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
Author First Pass Forms
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
*Currently we collect data from authors that we may not have intention of curating (at least right away)
 
−
*We can provide a disclaimer on the letter to authors explaining that some data may not be curated immediately
 
−
*All data is catalogued
 
  
  
−
Sequence Feature curation
 
−
*Xiaodong met with Gary Williams and Mary Ann Tuli at IWM
 
−
*Enhancer curation?
 
−
*Significant backlog on sequence feature curation
 
−
*Margie Ho asking about curated enhancers, regulatory regions
 
−
*Margie has 30 papers with highly annotated regulatory regions
 
−
*Gary W. is prioritizing curation of these now
 
−
*Gary will propose appropriate model changes (e.g. Add "silencer" and "enhancer" to method for GBrowse display)
 
  
 +
==February 15, 2024==
  
−
User use case: All G-protein coupled receptors expressed in AWC neurons
+
=== Literature Migration to the Alliance ABC ===
−
*Quantitative expression data is not effectively linked to anatomy terms
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
*Wen will propose model fix to accommodate this association
+
===== 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 =====
−
*Genes expressed above some pre-defined threshold will be associated with a cell
+
*Facet for topic
−
*For example, Ping (in Paul's lab) will be performing AWC single cell profling
+
*Facet for automatic assertion
−
*AWA and BAG neurons has been profiled by tiling arrays
+
**neural network method
−
*Male linker cell by RNA-Seq (Erich and Mihoko)
+
*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
  
−
Curation strategies
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
*Change our paper-by-paper curation
+
* Search ABC with paper identifier
−
*We may be able to make use of a Textpresso categorization program to tag papers
+
* Migrate to Topic and Entity Editor
−
*Caltech curators can then prioritize their curation based on a particular category or topic
+
* View all associated data
−
*We can look at the [http://www.biomedcentral.com/1471-2105/7/370 Textpresso paper] and reconvene next week to discuss
+
* 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?
  
−
= July 18, 2013 =
+
* 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.
  
−
Textpresso Paper categorization
+
==January 25, 2024==
−
*Prioritization of papers based on: 1) SVM-Textpresso script categorization, and 2) Ideal prioritization scheme according to curation status
 
−
*How does this tie into our grant quarterly progress report?
 
−
*Can we create a putative milestone to achieve for the WS240 upload?
 
−
*How do we consider backlog size wrt priorities and categorization?
 
−
*Even if a data-type backlog is small, it would be worth going back to older curation to check for accuracy and consistency
 
−
*Will this pipeline be more efficient? We should define metrics to measure curation effectiveness/efficiency
 
−
**Compare curation statistics of new pipeline to last year or two of curation statistics
 
−
*Yuling can run existing SVM pipeline on corpus (supervised learning); unsupervised learning will require more human effort
 
−
*We can provide lists of keywords to improve the categorization
 
−
*There are 1750 papers with author first pass responses, Juancarlos emailed the paperIDs with timestamp of response
 
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
Upload
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
*Next upload (WS240) deadline will be last Friday in September (Sept 27th, 2013)
+
* 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.
  
−
ACEDB, Citace Minus
+
* 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 will remove write-access from citace, moving personal files to citpub for write-access
 
−
*Wen will send out a summary e-mail
 
−
*Raymond can/will create individual user accounts (for those who want it) with access to personal versions of CitaceMinus and WS
 
−
**Personal versions of CitaceMinus and WS will be write-accessible
 
−
**Write e-mail to Raymond to request an account on Spica
 
  
 +
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
−
Nightly GeneAce dumps
+
=== Update on NN Classification via the Alliance ===
−
*What data from nameserver do we want to pull nightly?
+
* Use of primary/not primary/not designated flag to filter papers
−
*We need schema and existing data from Michael Paulini
+
* Secondary filter on papers with at least C. elegans as species
−
*Until curators (Kimberly ?) tell Juancarlos what we want to extract, we're keeping the scripts that get data from the nameserver.
+
* 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.
  
−
= July 25, 2013 =
+
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
Ontology Browsers
+
=== UniProt ===
−
* We are currently testing and developing AMIGO2 for integration into WormBase
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
** most recent version at http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/amigo.cgi
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
* Example Browsers:
+
* Stavros escalates the issue on Hinxton Standup.
−
** [http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service (OLS)] from EBI
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
−
** [http://www.sequenceontology.org/browser/obob.cgi MISO] (Sequence Ontology Browser from www.sequenceontology.org)
 
−
** OBO-Edit
 
−
** Protege
 
−
* We are trying to decide on what would be an optimal ontology browsing experience
 
−
* Browser experience features to consider:
 
−
** Directed Acyclic Graph (DAG) view
 
−
*** Good for visualizing "Path to Root" relationships of an ontology term
 
−
** Viewing children, parents, and/or siblings
 
−
*** Interactive expanding/collapsing of terms
 
−
*** Static tree or table views
 
−
*** "Inferred Tree View" - a compressed path to root tree view (in text format)
 
−
** Clicking to open a new web page versus interactive browsing without reloads
 
−
* Consensus is that interactive expandable and collapsible nodes would be ideal
 
−
* We will use the Gene Ontology as a pilot ontology to first introduce/integrate into the WormBase site; other ontologies can come later
 
−
* We will provide link outs to AMIGO and related sites/services to take advantage of their data and tools
 
  
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
−
Sequence features related to expression patterns and gene regulation interactions
 
−
* Add a "Transcription factor binding" tag to Expr_pattern model? Not necessary?
 
−
* Already captured in gene regulation interactions?
 
−
* We need to discuss (site-wide) what model changes (if any) would be required to adequately capture this information
 
−
* Gary Williams working on curating sequence features to link appropriately to Expr_pattern, Interaction (regulatory), and (maybe) Transgenes
 
  
 +
==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.
  
−
Author First Pass paper word frequency analysis
+
==January 4, 2024==
−
* Yuling performed word frequency analysis of whole papers and now sections
+
* ACKnowlegde pipeline help desk question:
−
* Karen took the "Titles" analysis, filtered out words with less than 10 hits, highlighted potential keywords
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
* How should we go about choosing a topic?
+
* Citace upload, current deadline: Tuesday January 9th
−
* We will choose AFP papers with "stress" in the title and assess curation status of each paper for our individual data types
+
** 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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