Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
Line 5: Line 7:
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
2013 Meetings
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2013|January]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2013|February]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
 +
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
= March 7, 2013 =
+
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
 +
==April 4th, 2024==
 +
* Continued discussion on sustainability
 +
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
 +
** Data is still going to SPELL and enrichment analysis
 +
** Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
 +
* Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
 +
* Michael's presentation on LLMs - Named Entity Recognition (NER)
  
−
Grant
+
==March 14, 2024==
−
*Grant gets reviewed next week
 
−
*Should hear results in ~two weeks
 
  
 +
=== TAGC debrief ===
  
−
Gene Concise Description form
+
==February 22, 2024==
−
*Ranjana, Kimberly working on form layout
 
−
*Easy to use form, simple drop down menus to select, e.g., Species
 
−
*Can users follow references for info?
 
−
*Citing references in concise descriptions has, in the past, greatly increased workload/time to write
 
−
*Prepopulated, precanned Textpresso info?
 
−
*Send out to targeted members of the community, get feedback; Who should we ask for other species?
 
−
*Curators could each try using form to make at least one concise descriptions, give feedback
 
−
*Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..."
 
−
*Can promote form at the International meeting
 
  
 +
===NER with LLMs===
  
−
Galaxy Workshop
+
* 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%)
−
*Screencast videos capturing use of Galaxy available
 
−
*Chris will send around
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
Genetic Interaction Ontology
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*Perhaps add "what is expected" info during curation?
 
−
*Good to have a comparison of curation with core set of common papers
 
−
**Cross check for consistency of curation (at least terms should lay in same lineage, if not at same depth)
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
= March 14, 2013 =
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
  
−
Cleaning up Citace Minus
 
−
*Stemming from Paul Davis' GitHub ticket pointing out small-scale data problems
 
−
*Bogus molecule objects (Chris will take care of)
 
−
*Homol_data from RNAi (and the housing RNAi objects) can be removed
 
−
*Ghost Expr_pattern objects, Wen taking care of (Xiaodong will remove from the Gene_regulation OA)
 
−
*Will need to create a better (more robust) pipeline (with SOPs) for converting, for example, object names to WBID#'s
 
−
**Once a conversion has been made, we need to check Postgres and Citace (& Citace Minus) for consistency
 
−
**Need to minimize the burden on Wen to perform quality and consistency checks
 
−
**Curators need to clean up/fix their data before a big change
 
−
**Scenarios to foramlize:
 
−
***Whole-class name changing
 
−
***Model changes
 
−
*Is there a list of classes (and objects?) that are held in Citace Minus?
 
−
**Cross-references create complexity
 
−
*We will suggest shifting the phase of the model proposal cycle: Propose to freeze all models one month before upload
 
  
 +
==February 15, 2024==
  
−
Queries
+
=== Literature Migration to the Alliance ABC ===
−
*AQL vs WQL vs AcePerl
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
*We may consider working out more formal pipelines for submitting queries (maybe to Wen?)
+
===== 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 =====
−
*AQL and WQL convenient but not necessarily efficient
+
*Facet for topic
−
*AcePerl efficient, but has a learning curve
+
*Facet for automatic assertion
−
*Todd highly recommends learning AcePerl as it has many advantages:
+
**neural network method
−
**Learning AcePerl will provide skills to handle other generic queries
+
*Facet for confidence level
−
**Whereas AQL and WQL will be obsolete when we leave ACeDB, AcePerl will still be useful (even if the details need updating)
+
**High
−
**Curators have GitHub access to all the AcePerl scripts, including those that generate FTP files
+
*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
  
−
Under Testing
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
*The "Under Testing" tag on GitHub issues is applied when something needs to be tested
+
* Search ABC with paper identifier
−
*Curators can filter for "Under Testing" issues and close them as they determine they are resolved
+
* 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?
  
−
= March 21, 2013 =
+
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
Protein browsing
+
==February 1, 2024==
−
*KOGs vs eggNOG; eggNOG may be the most current
+
* Paul will ask Natalia to take care of pending reimbursements
−
*Would be nice to be able to (for each species or all species in WormBase) browse protein sets as orthologous groups by functional classification
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
*Need to investigate
 
  
 +
==January 25, 2024==
  
−
Microarray data
+
=== Curator Info on Curation Forms ===
−
*Data that were not provided (no changes observed in an experiment) leaves gaps in data
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
*SPELL requires data for each experiment/probe (regardless of observation of change)
 
−
*FTP site for downloads of data (independent from, but related to, SPELL); Wen needs regular access to
 
−
**Can be hosted at Caltech FTP site (Todd can mirror over to main FTP site)
 
−
*Add explanatory page to SPELL site
 
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
Dead genes
+
* 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.
−
*Historical_gene tag will be added to several class models: ?Interaction, ?Transgene, ?Antibody, etc.
 
−
*How to handle GO annotations? GO will have mapping from proteins to GO terms, no need for new tag
 
−
*Chris will send around model proposal to add the tag to relevant models
 
−
*Curators will need to coordinate with Juancarlos how their respective OA dumpers should work
 
  
 +
* 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.
  
−
Beyond PDF conference
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Karen attended
 
−
*Peer-review process after open-access?
 
−
*Provenance of data issues
 
−
*[http://orcid.org/ ORCID] collaboration
 
−
*WormBase should coordinate WBPerson IDs with ORCID
 
−
*Reproducibility of research: cataloging raw data and making it available
 
−
*[https://www.authorea.com/ Authorea]: data published as a GitHub repository
 
−
*Discussions on contributing negative data
 
−
*[http://www.rubriq.com/ Rubriq]: Peer review system
 
  
 +
=== 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.
  
−
= March 28, 2013 =
+
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
IWM Meeting
+
=== UniProt ===
−
*Workshops and talks topics
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*2 Workshops (Kevin made Google Doc [https://docs.google.com/a/wormbase.org/document/d/1zdxmfJtVc4Eyc9ia5RHDwS-agyC-VO3G_eY7JCyGdd0/edit#heading=h.pd1qsrtkxi8g here] (requires login):
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*Two workshop time slots: Thursday 1 hour (1:30 - 2:30pm), Saturday 1.5 hours (1:30 - 3pm)
+
* Stavros escalates the issue on Hinxton Standup.
−
**Overview Workshop 1 (Thursday slot)
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
−
***Sequence perspective (Hinxton/EBI member)
 
−
**Data mining workshop (Thursday & Saturday slots)
 
−
***Modmine with extra half-hour on Saturday
 
−
**Overview Workshop 2 (Saturday slot)
 
−
***Biology perspective (Caltech: Chris Grove)
 
−
****Interactions, regulation
 
−
****WikiPathways
 
−
****Concise description forms
 
−
****Expression Data in WormBase
 
−
*Spreading the word:
 
−
**Catch people during poster sessions (booth with ~4 posters)
 
−
***Posters on: Wikipathways/Interactions, Species, Gene Expression & Regulation, Textpresso, Phenotypes & Diseases
 
−
***Have projector displaying screen demos
 
−
***We could create a template with a standard layout
 
−
***Create posters with Illustrator or [http://www.scribus.net/canvas/Scribus Scribus]
 
−
**WormBase events flyer to hand out or have placed in meeting program
 
−
*WormBase give away ideas:
 
−
**Mugs, aprons, gummy worms, LED light keychains, etc., etc.
 
  
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
−
Populating OA with variations for variation fields
 
−
*Huge number of variations (>1,000,000!)
 
−
*How to limit to relevant variations?
 
−
*Can we split into "useful" vs. "generated" mutations/variations?
 
−
*Splitting now on "Allele" tag
 
−
*Add a new tag to the variation model?
 
−
*Ask Hinxton to provide a file of all variations with a phenotype for FTP site
 
−
*Also get full list of variations from Hinxton for our internal processing
 
  
 +
==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.
  
−
Meeting
+
==January 4, 2024==
−
*Who's driving the whole peer-review process?
+
* ACKnowlegde pipeline help desk question:
−
*World-wide open access data meeting
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*How to make all data freely available?
+
* Citace upload, current deadline: Tuesday January 9th
−
*Data repositories, publishers, researchers involved
+
** All processes (dumps, etc.) will happen on the cloud machine
−
*Publishers will need to ensure that published data is made publicly available
+
** Curators need to deposit their files in the appropriate locations for Wen
−
*Data sharing plans
+
* 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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