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_May_2017|May]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_June_2017|June]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_July_2017|July]]
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
[[WormBase-Caltech_Weekly_Calls_August_2017|August]]
+
==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)
  
−
== September 14, 2017 ==
+
==March 14, 2024==
  
−
=== WB Grant ===
+
=== TAGC debrief ===
−
* Want to focus on community outreach
 
−
** site visits, training, etc.
 
−
* Need to work on pathway models & diagrams
 
−
* Transcriptional regulatory network models need work
 
−
* Will look at regularly occurring quarterly milestones
 
−
** Chris will look at curation goals, want ambitious but realistic
 
−
* Metabolomics? Maybe leave out since we need other funding to accomplish
 
−
* Would be good to generate lists of TF target genes and have available as a gene set/list for enrichment analyses and/or a WormMine list
 
−
* People can look over and make sure that we’re addressing important, exciting issues
 
−
* Put in blurb on “MicroReviews”
 
−
* Concise descriptions: people can contribute manually written descriptions, but would be best if people/labs took ownership for maintaining them
 
−
* How many papers did we get into the database in the past 5 years?
 
  
−
=== NAR Paper ===
+
==February 22, 2024==
−
* Punted until the end of the month
 
−
* Raymond fixing up to send around first draft
 
  
−
=== Author First Pass ===
+
===NER with LLMs===
−
* Proposing sending emails to authors AFTER SVM flagging, asking them to validate our automated flagging pipeline flags
 
−
* May want to incorporate other flagging methods like string matching
 
−
* We will want a mechanism such that each datatype flag requires action by the author, in order to get an official AFP flag, positive or negative, otherwise the paper does not get an AFP flag for that paper
 
−
* Maybe shouldn’t include data types in AFP form that are not actively being curated
 
−
* Want to strike a balance between too many and too few data types
 
  
−
=== Incentives for community curation ===
+
* 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%)
−
* Could consider not putting journal article (primary) papers on WB website until it has curation (by WB or community)
 
−
* We would like to collect a list of all regional worm meetings to reach out to
 
−
* How do we attribute annotations to community curators? Already a mechanism in place for concise descriptions and phenotype, but would need changes for other data types
 
−
* Have table of top community curators; will also work on having top contributors for past 2 or 3 months (Chris will discuss with Sibyl)
 
  
−
=== Leaving remark about corrections ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* When authors make a typo about, e.g. a construct or transgene, can leave remark in the object in the OA
 
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
== September 21, 2017 ==
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
=== Grant ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Please review grant and send comments or revisions to Paul
 
  
−
=== Citace upload ===
 
−
* Check upload numbers from Wen; report any problems to her
 
  
−
=== Gene Ontology ===
 
−
* Number of complex terms being propagated to root terms
 
−
* There is a ticket to resolve this issue; Seth Carbon commented on it recently
 
−
* ~9000 terms ending up as direct descendants of root term "biological process"
 
−
* Same problem in AMIGO
 
−
* May be due to logical definitions
 
  
−
=== Reatcome/GO-CAM collaboration ===
+
==February 15, 2024==
−
* Kimberly will meet Monday with Reactome and GO-CAM folks to work together
 
  
−
=== Site visits ===
+
=== Literature Migration to the Alliance ABC ===
−
* We can start a Google spreadsheet of local meetings
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Curators can sign up for particular meetings
+
===== 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 =====
−
* We should gather the schedules and organize trips (chain of meetings to present)
+
*Facet for topic
−
* Each presentation could include all major topics of interest at WormBase (community curation, micropublications, Textpresso, etc.)
+
*Facet for automatic assertion
−
* Can include specific topics relevant to presenter, but should also be somewhat standardized
+
**neural network method
−
* Can include tutorials
+
*Facet for confidence level
−
* Also should include joining or presenting at individual lab meetings
+
**High
−
* Daniela near some Texas meetings/labs
+
*Facet for manual assertion
−
* Chris near Baltimore meeting and North Carolina triangle area meeting (Raleigh, Durham, Chapel Hill)
+
**author assertion
−
* Chris and Wen will present in Baltimore on March 16, 2018
+
***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
  
−
== September 28, 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
  
−
=== Updating the Phenotype Form ===
+
=== PDF Storage ===
−
* http://www.wormbase.org/submissions/phenotype.cgi
+
* At the Alliance PDFs will be stored in Amazon s3
−
* Current form allows users to submit multiple genetic perturbations simultaneously
+
* We are not planning to formally store back-up copies elsewhere
−
* This was originally intended to make it easier for users to submit multiple experimental results
+
* Is this okay with everyone?
−
* Now we are finding that users want to submit double mutant phenotypes, but we need a way to distinguish multiple alleles in a complex genotype (single experiment) from multiple alleles, each observed individually for phenotypes (multiple experiments)
 
−
* Some are confusing the "Allele" field for the genetic background of an RNAi experiment
 
−
* Also, optional details like inheritance pattern, mutation effect, and temperature sensitivity cannot be unambiguously assigned to one allele if multiple are submitted
 
−
* Some solutions:
 
−
** Make it clear that each submission represents a single experiment; then, multiple perturbations would represent complex genotypes
 
−
** If we make it single experiment at a time, we could offer a way to keep the same fields populated for next submission (for easier editing/filling out)
 
−
** Get rid of inheritance pattern, mutation effect, and temperature sensitivity fields
 
−
** Allow multiple experiments to be submitted simultaneously, but create distinct submission blocks for each experiment
 
−
** Add a checkbox that indicates multiple perturbations are all part of the same complex genotype
 
−
** Have separate forms for single perturbation phenotypes and complex genotype phenotypes
 
−
** Have a CANTO-style submission process with multiple steps with a decision tree
 
  
−
=== Mary Ann's transition ===
+
==February 8, 2024==
−
* Paul, Mary Ann will talk to Tim about transition of responsibilities
+
* TAGC
−
* Will consider who will take over different curation tasks
+
** Prominent announcement on the Alliance home page?
−
* Congrats to Mary Ann and best of luck!!
 
  
−
=== NAR Paper ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Raymond would like to wrap up today or tomorrow
 
−
* Please review and send comments:
 
−
* https://docs.google.com/document/d/1CEeGMHpzS7SE8v40QALJINmHgF9i63tjGiXTatQDti0/edit
 
  
−
=== Jae's experience so far ===
+
==February 1, 2024==
−
* Jae is trying out phenotype curation
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Working with the OA and curation status form
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* Learning GO-CAM/Noctua with Kimberly
+
 
−
* Million mutation project alleles not all necessarily in the OA
+
==January 25, 2024==
−
** Will need to request alleles to be loaded into the OA, unless we load all of them, but will slow the OA
+
 
−
** Could include only those mentioned in literature according to Textpresso
+
=== Curator Info on Curation Forms ===
−
** Variations now coming from Geneace; having already(?) filtered out most gk* alleles
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* Protein-protein, genetic interactions; will discuss with Chris & Kimberly
+
 
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
 +
 
 +
* The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
 +
 
 +
* I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
 +
 
 +
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
 +
 
 +
=== Update on NN Classification via the Alliance ===
 +
* Use of primary/not primary/not designated flag to filter papers
 +
* Secondary filter on papers with at least C. elegans as species
 +
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
 +
 
 +
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
 +
* NNC html pages will show NNC values together with species.
 +
* Show all C. elegans papers first and other species in a separate bin.
 +
 
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
 +
 
 +
=== UniProt ===
 +
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
 +
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
 +
 
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
 +
 
 +
 
 +
==January 11, 2024==
 +
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
 +
** Curators should make sure that, when pasting special characters, the duplicate function works
 +
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
 +
 
 +
==January 4, 2024==
 +
* ACKnowlegde pipeline help desk question:
 +
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 +
* Citace upload, current deadline: Tuesday January 9th
 +
** All processes (dumps, etc.) will happen on the cloud machine
 +
** Curators need to deposit their files in the appropriate locations for Wen
 +
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 16:04, 18 April 2024

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

2023 Meetings

April 18th, 2024

  • NNC pipeline being switched off locally and moving into the Alliance ABC.

April 11th, 2024

  • Caltech WS293 ace files ready for the upload

April 4th, 2024

  • Continued discussion on sustainability
  • CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
    • Data is still going to SPELL and enrichment analysis
    • Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
  • Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
  • Michael's presentation on LLMs - Named Entity Recognition (NER)

March 14, 2024

TAGC debrief

February 22, 2024

NER with LLMs

  • Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
  • Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  • There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.


February 15, 2024

Literature Migration to the Alliance ABC

Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)?

Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic
  • Facet for topic
  • Facet for automatic assertion
    • neural network method
  • Facet for confidence level
    • High
  • Facet for manual assertion
    • author assertion
      • ACKnowledge method
    • professional biocurator assertion
      • curation tools method - NULL
Manually validate paper - topic flags without curating
  • Facet for topic
  • Facet for manual assertion
    • professional biocurator assertion
      • ABC - no data
View all topic and entity flags for a given paper and validate, if needed
  • Search ABC with paper identifier
  • Migrate to Topic and Entity Editor
  • View all associated data
  • Manually validate flags, if needed

PDF Storage

  • At the Alliance PDFs will be stored in Amazon s3
  • We are not planning to formally store back-up copies elsewhere
  • Is this okay with everyone?

February 8, 2024

  • TAGC
    • Prominent announcement on the Alliance home page?
  • Fixed login on dockerized system (dev). Can everybody test their forms?

February 1, 2024

  • Paul will ask Natalia to take care of pending reimbursements
  • Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.

January 25, 2024

Curator Info on Curation Forms

  • Saving curator info using cookies in dockerized forms. Can we deploy to prod?

ACKnowledge Author Request - WBPaper00066091

  • I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  • The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
  • I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  • Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.

Update on NN Classification via the Alliance

  • Use of primary/not primary/not designated flag to filter papers
  • Secondary filter on papers with at least C. elegans as species
  • Finalize sources (i.e. evidence) for entity and topic tags on papers
  • Next NN clasification scheduled for ~March
  • We decided to process all papers (even non-elegans species) and have filters on species after processing.
  • NNC html pages will show NNC values together with species.
  • Show all C. elegans papers first and other species in a separate bin.

Travel Reimbursements

  • Still waiting on October travel reimbursement (Kimberly)
  • Still waiting on September and October travel reimbursements (Wen)

UniProt

  • Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
  • Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
  • Stavros escalates the issue on Hinxton Standup.
  • Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.

January 18, 2024

  • OA showing different names highlighted when logging in the OA, now fixed on staging


January 11, 2024

  • Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
    • Curators should make sure that, when pasting special characters, the duplicate function works
  • OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
    • If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
  • Chris tested on staging and production the phenotype form and the data are still going to tazendra
    • Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
    • Raymond: simply set up forwarding at our end?
  • AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
  • Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
  • Valerio would like to use an alliancegenome.org email address for the openAI account
  • New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
  • Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
  • Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
  • Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
  • It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
  • Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.

January 4, 2024

  • ACKnowlegde pipeline help desk question:
    • Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
  • Citace upload, current deadline: Tuesday January 9th
    • All processes (dumps, etc.) will happen on the cloud machine
    • Curators need to deposit their files in the appropriate locations for Wen
  • Micropublication pipeline
    • Ticketing system confusion
    • Karen and Kimberly paper ID pipeline; may need sorting out of logistics
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