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]]
  
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2011|January]]
+
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
−
 
 
−
 
 
−
==2012 Meetings==
 
−
 
 
−
 
 
−
==January 5, 2012==
 
−
 
 
−
Interactions patch
 
−
*One large scale paper omitted from upload
 
−
*Patch sent in; all OK
 
−
 
 
−
 
 
−
Integration of 3rd party data
 
−
*BioGRID, Gene Orienteer, Interolog database, etc.
 
−
*Gene Orienteer
 
−
**May only want interactions above a threshold
 
−
*Interolog database
 
−
**Get gene pages linked to their database
 
−
**Display data on gene pages, but keep display distinct?
 
−
*FlyBase links out to BioGRID, Interolog
 
−
*modEncode Transcription Regulatory Network display/diagrams?
 
−
 
 
−
 
 
−
New site release with WS230?
 
−
*About 2 months
 
−
 
 
−
 
 
−
Textpresso Interaction Sentences
 
−
*Now have sentences associated with interactions
 
−
*Need to discuss what sentences should be kept as adequate evidence of interaction and placed in remarks
 
−
*See if Textpresso can pull out paragraphs (or +/- 4 sentences?) for each sentence to see context
 
−
*Can we devise some automation to handle interaction updates?
 
−
 
 
−
 
 
−
 
 
−
== January 12, 2012 ==
 
−
 
 
−
SVM
 
−
*Genetic Interaction SVM
 
−
*How well does it work?
 
−
*Do we have sentences?
 
−
*Kimberly will follow up with Xiaodong
 
−
*For HIV papers?
 
−
 
 
  
−
Human Diseases Connections
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
−
*Should be on new gene pages
 
−
*Browse function not yet fully functional
 
−
*Search with autocomplete available
 
−
*Table from 2000 Review, human/C. elegans orthologs and diseases - put on website?
 
−
*Indexed ACEDB data used for searches; create table from indexed data?
 
−
*Textpresso pipeline flags relevant disease papers; can info be added to database?
 
−
*?Human_disease model vs tag in ?Gene model?
 
−
*Similar discussion to ?Process model discussion
 
−
*Let's propose a ?Human_disease model; see what objections/suggestions anyone has (EBI?)
 
−
*Will follow the OBO/NCBI human disease ontology
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
Gloworm links
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
−
*Raymond made links from Anatomy pages to Gloworm site
 
−
*Can view movie relevant to Anatomy object at Gloworm
 
−
*Gloworm seems to only work on Macs (firewalled on Windows, doesn't work at all on Linux)
 
−
*Can we add an Apple symbol/logo next to Gloworm links on new site?
 
−
**Logo difficult, but we could add a text caveat
 
−
**New window opens with links; users should see error and be able to send Bill Mohler a message
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
Ontology Searches
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
−
*Status?
 
−
*Gary and Karen talking about fixing/cleaning up Phenotype Ontology
 
−
*Would be useful to have a filter on ontology searches
 
−
*Phenotype search available now, but no filters
 
−
*New search features not likely to be made in near future
 
−
*Intermine may be better tool for this
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
Genetic Interactions
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
*Rose discussed genetic interaction ontology with BioGRID et al in December
 
−
*BioGRID will stick with older terms (at least for now) as SGD and Entrez Gene need to also be on board
 
−
*Chris will review older 'Genetic' interactions with new terms as a proof of concept
 
−
*Can send results to BioGRID, SGD, and Entrez Gene
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
GSA markup
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
*Flybase wants authors to take care of all markup QC
 
−
*Pipeline: Author QC -> DJS -> Flybase check
 
−
*Flybase has minimal QC Fast service
 
−
*Michael added an 'UNDO' button for QC Fast
 
−
*Remove author ability to add links?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
SVM Computers in Church 63
+
==April 18th, 2024==
−
*SVM papers still in review (long process)
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
−
*Need to wait until SVM paper accepted before moving those computers
 
  
 +
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
== January 19, 2012 ==
+
==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==
  
−
Parsing Legacy data into database
+
=== TAGC debrief ===
−
*Need some model changes to get the data in
 
−
*Model changes would be to:
 
−
** Add an Ease_of_scoring (ES) tag to #Phenotype_info, and
 
−
** Add a Mating_efficiency tag under ?Variation
 
  
 +
==February 22, 2024==
  
−
Rescue_by_transgene tag
+
===NER with LLMs===
−
*If a transgene rescues an allele, it is placed under Rescue_by_transgene tag in the ?Variation class
 
−
*Move Rescue_by_transgene tag to #Phenotype_info in context of an Allele/Variation
 
−
*Can we display the transgene summary (i.e. genotype) in the Variation page? Yes
 
  
 +
* 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%)
  
−
Changing author names in abstracts
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
*Changing the text/authors of an abstract was decided to be not allowed
 
−
*Is this a work issue or just a policy issue?
 
−
*Both, but most importantly a policy issue
 
−
*We get asked to make many changes to abstracts (sometimes content)
 
−
*It was decided (for fairness) that we wouldn't make any changes
 
−
*Polls were already taken at International meeting; consensus is that no changes will be made
 
−
*Formalize an 'Erratum' remark; Author(s) can submit?
 
−
*Authors need to login, verify their identity and authorship before being able to make an Erratum comment
 
−
*Occasionally we may need to verify/resolve issues; that's OK
 
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
SPELL download
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
*Users can download all (gene-centric, WormBase-parsed) SPELL data
 
−
*Wen wants to place the entire SPELL download on the FTP site
 
−
*Wen can send it to Todd
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
RNAi probe mappings
 
−
*EBI will eventually take over RNAi probe mappings to genome
 
−
*EBI already maps genomic coordinates to genes
 
−
*If EBI can take over the first step of mapping, we can develop an RNAi OA
 
−
*Ideally, curators could submit: PCR product names (e.g. sjj_W02C12.3), raw DNA sequence, primers
 
−
*Maybe EBI only wants DNA text? Need to check with them
 
  
  
−
ePCR
+
==February 15, 2024==
−
*Old script
 
−
*Any newer scripts available? Substitution?
 
  
 +
=== 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
  
−
SVM paper accepted
+
===== Manually validate paper - topic flags without curating =====
−
*Computers in Church 63 may be able to be moved
+
*Facet for topic
−
*Michael and Yuling need to check the data on them
+
*Facet for manual assertion
−
*Need to touch base with Ruihua to ensure the computers can be moved
+
**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?
  
−
== January 26, 2012 ==
+
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
Luke Hutchison talking
+
* 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.
  
−
SPELL server hanging on Amazon
+
==January 25, 2024==
−
*Raymond working on fixing
 
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
Interaction Model
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
*New ?Interaction model proposal consolidates current ?YH, ?Gene_regulation, and ?Interaction classes
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
*Various changes will be made to current version
 
  
 +
* 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.
  
−
SVM paper done
+
* 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
  
−
== February 2, 2012 ==
+
* 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)
  
−
EPIC data into WormBase
+
=== UniProt ===
−
*Daniela spoke to John Murray
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*Need to modify model and display for data
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*3D movies as ?Movie objects
+
* 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
  
−
Endrov
 
−
*Tom Burglin and student Johan developed Endrov.net
 
−
*May be able to incorporate Endrov visualizations of Blender model and cell lineage into WormBase website?
 
−
*Need to talk to Todd and Web team
 
  
 +
==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.
  
−
Elsevier legal issues
+
==January 4, 2024==
−
*Science-direct website links to-and-from WormBase website
+
* ACKnowlegde pipeline help desk question:
−
*Daniela still working with contacts at MGI (Mouse Genomics Institute/Jackson Labs) & Elsevier
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*MGI already has established links with Elsevier
+
* 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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