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_2018|2018 Meetings]]
  
−
= February 2015 =
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
== February 5, 2015 ==
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
=== Community Annotation ===
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
* Mary Ann discussed with Paul S.
 
−
* Mary Ann would like to develop a prototype curation form (for variations/molecular lesions) for the international meeting
 
−
** Test version in 6 weeks?
 
−
** Juancarlos would need a list of required fields, field types, data connections, etc.
 
−
** Could take advantage of existing forms
 
−
* Ranjana and Juancarlos working on the concise description form
 
  
−
=== Changing GAF format ===
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
* What implications does this have for the WormBase Ontology Browser?
 
−
* What testing of generation of the GAF could be done (and sent to Raymond)?
 
−
* Kimberly will discuss with Kevin
 
  
−
=== Automated descriptions with updated release schedule ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
* WS247 database will not be ready with enough time for Ranjana and James to incorporate into the automated description generation
 
−
* They can make do with older files
 
  
−
=== Citace upload for WS248 ===
+
==April 18th, 2024==
−
* Tuesday March 3rd
+
*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)
  
−
== February 12, 2015 ==
+
==March 14, 2024==
  
−
=== Physical Interaction Curation ===
+
=== TAGC debrief ===
−
* We have begun physical interaction in Interaction OA
 
−
* We are establishing a pipeline to share all physical and genetic interactions with BioGRID
 
−
* It would be good to clarify which curators can/will curate physical interactions
 
−
* Would be good if phenotype curators could curate genetic AND physical interactions in the same paper
 
−
* Something that John DeModena could do?
 
−
* Xiaodong capturing protein-DNA interactions
 
−
* We still need to decide what level of detail we would like to capture
 
−
* We could try to capture specific protein sequences used in experiments
 
−
* We don't have individual protein/peptide sequence objects, maybe we want them? IDs for domain instances?
 
−
* We have an SVM pipeline "geneprodgo"
 
−
* A lot of GO protein interaction data to extract; might use ?Analysis objects to track attribution of curation
 
  
−
=== BioGRID interaction sharing ===
+
==February 22, 2024==
−
* Provenance and attribution issues
 
−
* ?Analysis object can be created for BioGRID attribution
 
−
* WormBase has imported all worm (C. elegans) physical (protein-protein) interactions from BioGRID
 
−
* Working on importing BioGRID genetic interactions, or at least resolving overlap
 
−
* WormBase will send physical and genetic interaction data to BioGRID at every upload
 
−
* Rose et al are considering regulatory interaction data, currently discussing
 
  
−
=== WormBook WormBase Chapter ===
+
===NER with LLMs===
−
* Feb 28 deadline coming up
 
−
* Can be about 3 pages per chapter
 
−
* Sections can be written as stand alone and merged as necessary
 
−
* Putatively 8 - 10 chapters being written
 
  
−
=== User submitted Phenotype (RNAi) data ===
+
* 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%)
−
* A user recently requested addition of RNAi data for a handful of papers
 
−
* I (Chris) directed them to our trial [https://docs.google.com/a/wormbase.org/spreadsheets/d/1lLxMZ016g81EpR11eKILm3H17DbcrsUuwq5lqmIIKWk/edit#gid=0 RNAi data submission table]
 
−
* Would be good to embed community annotation forms into WormBase website so that users could log in and add data without having to re-enter personal information
 
−
* Can we map user login info to WBPerson ID? Is that already the case? Would be good.
 
  
−
=== Clone Mapper Software ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* We will adopt Clone Mapper for RNAi clone mapping
 
−
* Chris and Kevin working with Jonathan Ewbank
 
−
* Important issue remains: what cutoff for the Clone Mapper tool do we choose?
 
−
* We are working on creating RNAi reagent objects in WormBase to capture targets (and off targets) independently of any RNAi experiments
 
  
−
=== WormBase PI meeting for database migration ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Next week to discuss current new database considerations
 
−
* Datomic, MongoDB, etc. front runners
 
  
−
=== Virtual Fly Brain ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Paul S will talk to group
 
−
* 8:30am meeting next Monday
 
−
* Coordination with fly and fish groups
 
−
* Working out applicable ontologies
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
== February 19, 2015 ==
 
  
−
=== Citace Upload ===
 
−
* 10am March 3rd
 
  
−
=== International Meeting Workshop ===
+
==February 15, 2024==
−
* Raymond will cover WormBase Ontology Browser
 
−
* Ranjana will cover concise description submission/correction
 
−
* Paul S. will present at plenary session to make a call for community annotation
 
−
* Kevin will present Parasite and sequence repositories/submission
 
  
−
=== Int. Mtg. Booth and Posters? ===
+
=== Literature Migration to the Alliance ABC ===
−
* Would be good to have a projector at booth like last time; show people how to get data, etc.
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Keep the poster for advertisement/outreach and displaying the most current WB poster (Xiaodong's SeqFeat)
+
===== 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 =====
−
* Could have prepared presentation/slides displayed on projector at booth by default as a background; change to live demo as needed
+
*Facet for topic
−
* Could demonstrate community annotation?
+
*Facet for automatic assertion
−
* Advertisement & Outreach
+
**neural network method
−
* Community annotation poster?
+
*Facet for confidence level
 +
**High
 +
*Facet for manual assertion
 +
**author assertion
 +
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
−
=== WS247 WormBase Ontology Browser built ===
+
===== Manually validate paper - topic flags without curating =====
−
* Number of genes with Gene Ontology annotations dropped
+
*Facet for topic
−
* May be explained by lack of Phenotype-to-GO annotations
+
*Facet for manual assertion
−
* Raymond can send numbers to Kimberly
+
**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
  
−
== February 26, 2015 ==
+
=== 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?
  
−
=== WormBook chapter(s) ===
+
==February 8, 2024==
−
* We'll do a round of reviews and edits on Google Docs
+
* TAGC
−
* Eventually we'll transition to Word Docs
+
** Prominent announcement on the Alliance home page?
−
* We can hand in next week sometime
 
−
* WRT community annotation, we can discuss what we already have
 
  
−
=== 2015 International C. elegans meeting ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Posters
 
−
** Could submit abstracts for 1-2 posters
 
−
** Could project slides/posters projected at Help Desk booth
 
−
** Self explanatory slides projected?
 
−
* Workshop
 
−
** Volunteers:
 
−
*** Raymond : WOBr
 
−
*** Mary Ann : Community annotation (for variation)
 
−
*** Ranjana : Concise descriptions
 
−
*** Kevin : Parasite, sequence repositories & submission
 
−
*** Chris : WormMine
 
−
*** Kimberly : Finding and using GO annotations
 
−
*** Scott Cain : JBrowse
 
−
* WormBase staff could have distinctive outfits (shirts or hats)
 
−
** Paul S could wear it at opening plenary talk
 
−
* Maybe Kevin Howe could request a booth for ParaSite?
 
  
−
=== Model change errors for WS248 upload ===
+
==February 1, 2024==
−
* Historical_gene tag accidentally removed from ?Construct model
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Would be good for all curators to see an explicit diff output to confirm all changes made
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* Before testing the models, would be good for Paul Davis to send a formal diff of all changes made to confirm
 
  
−
=== Automated concise descriptions ===
+
==January 25, 2024==
−
* Orthology pipeline needed to be reworked
 
−
* Find best match by multiple orthology searching methods
 
−
* 120,000+ total automated descriptions
 
−
** 5 Caenorhabditis species
 
−
** Pristionchus pacificus
 
−
** Brugia malayi
 
−
** Onchocerca volvulus
 
−
* One-to-many orthologies start to become unwieldy
 
−
* Because of upload time crunches, we may want to fall back on older files if necessary
 
  
−
=== Database infrastructure ===
+
=== Curator Info on Curation Forms ===
−
* Narrowed down to Datomic and MongoDB
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* Thomas, Lincoln thought Datomic was better
 
−
* Datomic *could* possibly be bought out
 
−
** Could still be changed over; would require work, but would have technology in place, worth it
 
−
* Will have timestamps
 
−
* Still planning to have a single all-encompassing database
 
  
−
=== BioGRID data sharing pipeline ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* Juancarlos developed a BioGRID TAB2 dump file from the Interaction OA
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
* Eventually will send all worm genetic and physical interactions to BioGRID
 
−
* Will omit genetic no_interactions
 
−
* Will omit interactions with no PubMed ID: reviews or person evidence only
 
−
* Will omit interactions with uncloned genes (no Entrez ID)
 
−
* As of Feb 25, 2015, we have ~8220 total novel* genetic interactions to submit to BioGRID (*novel to BioGRID)
 
  
−
=== Species for genes in Postgres ===
+
* 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.
−
* We will talk to Michael Paulini about getting species info for genes
+
 
−
* Need to get from GeneACE or some place else
+
* 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.
−
* Added after meeting - yes, all Species are in Geneace. (Mary Ann)
+
 
 +
* 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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