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]]
  
−
==2011 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_February_2011|February]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_March_2011|March]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_April_2011|April]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_May_2011|May]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_June_2011|June]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_July_2011|July]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_August_2011|August]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_September_2011|September]]
 
  
−
[[WormBase-Caltech_Weekly_Calls_October_2011|October]]
+
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_November_2011|November]]
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
== December 1, 2011 ==
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
WORM paper
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
−
*Sorted out at conference call
 
−
*EBI will take lead on rewrite
 
−
*We want a paper on the new website to go to a broader audience
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
Interaction model
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
*Almost sorted out and working
 
−
*Chris & Kimberly will discuss
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
Elsevier linking (images)
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
*Caltech attorney's want the agreement with Elsevier to be under US law
 
−
*Usage data relating to Elsevier content access must be deleted within 3 months(???)
 
−
*Should not be an issue?
 
  
 +
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
Local AQL queries
+
==April 11th, 2024==
−
*Running on Caltech mirror? Currently getting an error: "Connection closed by remote server"
+
*Caltech WS293 ace files ready for the upload
−
*Can run AQL from xace on spica
 
  
 +
==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==
  
−
== December 8, 2011 ==
+
=== TAGC debrief ===
  
 +
==February 22, 2024==
  
−
Bio Curator Meeting
+
===NER with LLMs===
−
* In Washington DC next April
 
−
* Wen will send an abstract on SPELL
 
−
* Kimberly, Arun and Michael will be there as well
 
−
* Abstracts to submit: 3 in total (Kimberly, Arun, Wen)
 
  
 +
* 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%)
  
−
WomrBase curator ad officially posted
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
WormBase meeting announcement
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* What is our policy? Should we send info to everyone?
 
−
* We can send to PIs only
 
−
* Meeting announcements are an appropriate use of the list (if a bonafide ''C. elegans'' meeting)
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
Beta site Protein Page review
 
−
* Common protein name e.g. 'UNC-26' or 'Synaptojanin'
 
−
* Use GO curation, PAINT/PANTHER tool to assign name?
 
−
* What's the best method (automated, if possible) to assign a useful name?
 
−
* Refer to Uniprot for names; can EBI pull names directly from Uniprot?
 
−
* GO: Molecular Function and Cell Component are annotated to gene, in some cases an isoform is attributed
 
−
* Want to enable curation to isoforms when info is available
 
  
  
−
Interactions
+
==February 15, 2024==
−
* Interaction model still being tweaked
 
−
* Will try to 'swallow up' Gene Regulation objects and tags into main Interaction model
 
−
* #Interaction_info and #Interacor_info may be removed
 
  
 +
=== 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
  
−
Anatomy nomenclature discrepancies
+
===== Manually validate paper - topic flags without curating =====
−
* Oliver Hobert raised issue of consistency of names
+
*Facet for topic
−
* For example, sometimes "DA neurons" refers to dopamine neurons as opposed to the anatomical 'DA' neuron
+
*Facet for manual assertion
−
* DA neurons are actually cholinergic
+
**professional biocurator assertion
−
* Maybe post on the blog
+
***ABC - no data
−
* Make synonym for dopaminergic neuron as 'DA neuron'?
 
  
 +
===== 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
  
−
Citace upload date (WS230)?
+
=== PDF Storage ===
−
* Monday, December 19th
+
* At the Alliance PDFs will be stored in Amazon s3
−
* Scripts to be run manually
+
* 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?
  
−
GSA Markup at FlyBase
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Flybase's role in markup and QC?
 
−
* 3 month notice to stop curator QC at FB
 
−
* FB curators do not want to QC, even with the 'QCFast' tool
 
−
* How to make the tool user-friendly for authors?
 
  
 +
==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.
  
−
== December 15, 2011 ==
+
==January 25, 2024==
  
−
Interactions display on Beta
+
=== Curator Info on Curation Forms ===
−
*Under 'Phenotype' reads "Interaction_Phenotype" e.g. let-60
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
*On interaction page, no reference
 
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
Dead genes in interaction objects
+
* 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.
−
*In citace minus, dead genes hidden in hashes
 
−
*Some data stored as .ace files, others (large-scale) in flat files; flat files easier to manage
 
−
*We don't want large-scale data in the OA; take up too much space? (Megabytes of data, ~quarter million objects?)
 
−
*Interaction objects have to be edited one-by-one to clean up dead genes, very tedious
 
−
*Keep data in flat files? Who will manage the flat file? Xiaodong
 
−
*Juancarlos has script to screen all objects for dead genes
 
−
*Still need to upload the data (from OA and flat file) for every release/upload/build
 
−
*Old interaction objects still in Citace Minus (never removed); Wen will erase
 
−
*Keep dead genes in large-scale interactions for now, script their removal later
 
−
*Suppress entire objects from loading to ACEDB if has dead genes? No, still dump, but add cautionary remark?
 
−
*RNAi interaction objects likely have dead gene assigments (need to check)
 
−
*'Dead genes' 29128, totally 'dead' vs. 'merged' genes?
 
−
*Juancarlos will generate list of 'killed' genes (not 'merged')
 
−
*Move 'killed' genes to flat files?
 
−
*OA will throw error in interaction has only one gene if dumped
 
−
*Need to reconcile the fact that the Interaction objects require a GeneID for Interactor tag
 
−
*Need to deal with RNAi-to-gene mapping for interactions
 
  
 +
* 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.
  
−
Preparation for Arun's departure
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Arun will check all code into SVM repository
 
−
*Repository has taken in a bunch of unnecessary data (PDF files, etc.); will avoid from now on
 
−
*Daniela will meet with Arun and Yuling, to extract images from PDFs, and marking positive/negative figure legends
 
−
*SGD QCFast editor finished (although may not be able to test extensively before Arun leaves)
 
−
*Arun will discuss maintenance of QCFast with Michael
 
−
*Arun will prepare documentation
 
−
*How much work will it take to generate FlyBase editor?
 
−
**Providing capacity/functionality to delete as well as add links in paper
 
  
 +
=== 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
  
−
IAIC (International Arabidopsis Information Consortium)
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*Imagine 10+ years from now; what data does Arabidopsis researcher have access to?
+
* NNC html pages will show NNC values together with species.  
−
*People listed features wish-list
+
* Show all C. elegans papers first and other species in a separate bin.
−
*What specifications required to achieve wish-list? APIs, user documentation, code, etc.
 
−
*Ideas fall to the side based on difficulties
 
−
*Optimistic vs pessimistic approach
 
−
*People then start writing specifications in grant format
 
−
*At end, 38 page document capturing all ideas/thoughts
 
−
*Divide into 4 groups, to pick up all ideas that fell through the cracks
 
−
*NSF, MRC, German, Austrian groups
 
−
*Community annotation focus
 
−
*Core references developed upon consistent, repeated user-generated annotations
 
−
*Wikipedia-type monitoring and annotation (minimal staff)
 
−
*Moving from single gene queries to multi-gene/process queries
 
−
*Looking for appropriate PIs to take charge
 
−
*Publicly available document (Jan 2012?)
 
−
*NSF has spent $1B on Arabidopsis research, cannot let data just wither
 
  
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
BioCreative group conference
+
=== UniProt ===
−
*BioCreative is text mining research/development group
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*After BioCurator meeting in April
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*Requires submission of 2-page document describing curation workflow
+
* Stavros escalates the issue on Hinxton Standup.
−
*Kimberly has written a draft and would like feedback (will send out)
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
−
*Track II section of BioCreative
 
−
*Document = Description of biocurative workflow (for a text miner audience)
 
  
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
−
Communicating Script function and maintenance pipeline
 
−
*How to best document script generation, development, updating, and maintenance
 
  
 +
==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.
  
−
Ian Hope's New Expression data set
+
==January 4, 2024==
−
*Daniela handling importing of data
+
* ACKnowlegde pipeline help desk question:
−
*Ian will update us when data is available
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*Method paper is out
+
* 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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