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_February_2015|February]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2015|March]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_April_2015|April]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_May_2015|May]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_June_2015|June]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_July_2015|July]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_August_2015|August]]
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
[[WormBase-Caltech_Weekly_Calls_September_2015|September]]
+
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
[[WormBase-Caltech_Weekly_Calls_October_2015|October]]
+
==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==
  
−
== November 5, 2015 ==
+
=== TAGC debrief ===
  
−
=== IEA GO Annotations informating descriptions for non-elegans ===
+
==February 22, 2024==
−
* Some non-elegans genes have confident-sounding descriptions, about localization for example; likely not manual
 
−
* Will make sure automated descriptions handle IEA's appropriately
 
  
−
=== Wen using Textpresso machine to build SPELL ===
+
===NER with LLMs===
−
* Athena was taking 48 hours to build SPELL (4GB max memory allotted)
 
−
* Textpresso machine took 24 hours (8GB memory allotted)
 
−
* Maybe we can use Textpresso machine for future builds
 
−
* SPELL java program running on Athena (alloted 4GB out of 6GB)
 
−
* Can monitor Athena memory usage; check for any memory leaks
 
  
−
=== Community Curation Tracker CGI ===
+
* 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%)
−
* Purpose: To automate many steps of the e-mailing process to authors requesting community curation and to track those papers for which we've sent e-mails
 
−
* There is a "Ready" form and a "Tracker" form; "Ready" for generating list of papers to e-mail about, "Tracker" to track the status of papers that have already been e-mailed about
 
−
* Wiki documentation at: http://wiki.wormbase.org/index.php/Contacting_the_Community#Community_Contact_.26_Curation_Tracker_CGI
 
−
* Sandbox CGI located at: http://mangolassi.caltech.edu/~postgres/cgi-bin/community_curation_tracker.cgi
 
−
* EMAIL FUNCTIONALITY IS LIVE: please note!
 
−
* Allele-phentoype("New mutant" datatype) CGI is live on Tazendra
 
−
* Concise description version will be cloned from the New Mutant CGI and modified as needed
 
  
−
=== SObA Graphs for phenotype ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* Juancarlos will transfer code tomorrow, if there are no change requests before then
 
−
* Existing feature requests will be added to future releases of SObA
 
  
−
=== Micropublications ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Daniela spoke with Daniel about having web pages in WormBook style to house micropublications
 
  
−
=== Status of WormBase User Survey? ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Paul sent around paper this morning: http://www.nature.com/nature/journal/v527/n7576_supp/full/527S16a.html
 
−
* What aspects of databases really get used by users?
 
−
* How can we be more efficient with existing curation pipelines?
 
−
* Question of the month on WormBase?
 
−
* We could get user feedback when visiting labs
 
  
−
=== Sending author updates ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Would be nice to have a mechanism to update authors on what has been curated for their paper
 
−
* Could give paper data summaries as well as recent updates to curation for a paper
 
  
−
=== Objectifying/Itemizing annotations from Postgres ===
 
−
* What if we objectified itemized Postgres entries for easier display of all annotations per paper, for example?
 
−
* May require addition of a text field tag to the ?Paper class, for example, that would capture each annotation item for a paper
 
−
* This would be ''in lieu'' of actually objectifying all annotations
 
  
  
−
== November 12, 2015 ==
+
==February 15, 2024==
  
−
=== Citace upload Dec 1st ===
+
=== 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
  
−
=== SAB set for Feb 4-5, 2016 ===
+
===== Manually validate paper - topic flags without curating =====
 +
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
=== Concise description form ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* URL for listing genes mentioned in a paper
+
* Search ABC with paper identifier
−
* Ranjana will send to Kimberly
+
* Migrate to Topic and Entity Editor
 +
* View all associated data
 +
* Manually validate flags, if needed
  
−
=== Community curation CGI ===
+
=== PDF Storage ===
−
* Almost ready for prime time
+
* At the Alliance PDFs will be stored in Amazon s3
−
* ~155 e-mails sent out for allele-phenotype; ~25-30 responses
+
* We are not planning to formally store back-up copies elsewhere
 +
* Is this okay with everyone?
  
−
=== Scripts for community description form ===
+
==February 8, 2024==
−
* James wrote scripts that will need to inform community CGI
+
* TAGC
−
* Ranjana will work with Juancarlos
+
** Prominent announcement on the Alliance home page?
  
−
=== FlyBase text mining ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Text mining for Fly corpus, entity recognition and extraction, esp. for transgenes
 
−
* Need to improve SVM on transgene and allele recognition
 
−
* Textpresso working on tools for FlyBase
 
  
−
=== Phenotype SObA graph ===
+
==February 1, 2024==
−
* Making progress towards making the graph a widget on the gene page
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Still issues to iron out; working with Sibyl
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* Some conflicts with Cytoscape for interactions vs. SObA
 
  
−
=== Data Visualization program opportunity ===
+
==January 25, 2024==
−
* Will have to write a grant
 
−
* Would pay for one person, get two with grant
 
−
* Anyone with ideas should consider a proposal
 
−
* Dec 15th deadline
 
  
−
=== WormBook ===
+
=== Curator Info on Curation Forms ===
−
* Daniel prepared mockup for new web page
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
=== Biocuration meeting ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* Mary Ann working out plans for community curation workshop
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
* Does PomBase track their community curation?
 
  
−
=== HT115 vs HT115(DE3) E.coli strains ===
+
* 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.  
−
* Redundant, should probably merge HT115 into HT115(DE3), as the RNAi-host E.coli strain
 
  
−
=== Visualization plans ===
+
* 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.
−
* Karen e-mailed around older proposal for work with Santiago Lombeyda
 
−
* Original project was to upgrade visualization of pathways and virtual worm in WB page
 
  
 +
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
−
== November 19, 2015 ==
+
=== 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
  
−
=== Community curation ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
* Community e-mailing for allele-phenotype: 315 e-mails sent, 49 papers curated, 260 community annotations in the Phenotype OA
+
* NNC html pages will show NNC values together with species.
−
* Chris gave Paul list of all sy* alleles and phenotypes
+
* Show all C. elegans papers first and other species in a separate bin.
−
* Paul going through table to add phenotypes not already in WB
 
−
* Paul using Textpresso and an allele-phenotype worksheet
 
−
* Do we want to create more elaborate forms or parallel forms? Probably parallel forms (in future)
 
−
* How can we assess completeness of curation? Very difficult to automate, currently
 
−
** Check figures and tables
 
−
** Ask authors about completeness
 
−
* Publication templates/worksheets? Streamline data submission concurrent with publication
 
−
* Can discuss at SAB in Feb
 
−
* We can send PI's/authors lists of alleles and what phenotypes WB has
 
  
−
=== Working with NCBI ===
+
=== Travel Reimbursements ===
−
* Interested in Textpresso text-mining and SVM categorizing
+
* Still waiting on October travel reimbursement (Kimberly)
−
* How might we work with NCBI & PubMed Central to curate? They are willing to run SVM on PMC corpus
+
* Still waiting on September and October travel reimbursements (Wen)
  
−
=== Minimum information requirements ===
+
=== UniProt ===
−
* RNAi MI seemed bulky and not complete
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
* Asks authors for genes targeted, not dsRNA sequence
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
* We could write up a paragraph outlining the complaints about the proposed RNAi MI
+
* Stavros escalates the issue on Hinxton Standup.
−
* Maybe micropublish the paragraph
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
  
−
=== Micropublications ===
+
==January 18, 2024==
−
* Should go into PubMed Central
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
−
=== Allele descriptions ===
 
−
* Karen wants to adapt Ranjana and James' automated gene descriptions for alleles
 
−
* Start working on in January
 
  
−
=== SObA ===
+
==January 11, 2024==
−
* Juancarlos making progress on integrating into the WB site
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
−
* There are difficulties getting SObA into it's own widget on the gene page
+
** Curators should make sure that, when pasting special characters, the duplicate function works
−
** Conflicts with other settings (javascript / cytoscape) on same page, e.g. Interactions widget (w/Cytoscape viewer)
+
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
−
** Updated cytoscape.min.js version on Interactions viewer
+
** 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.
  
−
=== Corresponding author curation ===
+
==January 4, 2024==
−
* Juancarlos and Cecilia have worked out a pipeline to capture corresponding authors for each paper
+
* ACKnowlegde pipeline help desk question:
−
* Once paper editor changes are decided, can go live
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
 
+
* Citace upload, current deadline: Tuesday January 9th
−
=== WormBook chapters for WormBase ===
+
** All processes (dumps, etc.) will happen on the cloud machine
−
* Each chapter written for users, but we likely want to avoid too much technical jargon
+
** Curators need to deposit their files in the appropriate locations for Wen
−
* We do want transparency
+
* Micropublication pipeline
−
* We can separate the chapters into less-technical and more-technical, for easier reading
+
** 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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