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]]
+
==May 23rd, 2024==
 +
*Publication bias workshop NINDS
 +
** Registered report -> the protocol is sent before publication
 +
** How many negative curated data? Do we want to pull this out?
 +
** Two billion dollars worth of research not published each year
 +
**Octopus.ac publishing platform
  
−
[[WormBase-Caltech_Weekly_Calls_September_2015|September]]
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
[[WormBase-Caltech_Weekly_Calls_October_2015|October]]
+
==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)
  
−
== November 5, 2015 ==
+
==March 14, 2024==
  
−
=== IEA GO Annotations informating descriptions for non-elegans ===
+
=== TAGC debrief ===
−
* 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 ===
+
==February 22, 2024==
−
* 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 ===
+
===NER with LLMs===
−
* 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 ===
+
* 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%)
−
* 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 ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* Daniela spoke with Daniel about having web pages in WormBook style to house micropublications
 
  
−
=== Status of WormBase User Survey? ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* 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 ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* 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 ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* 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 ==
 
  
−
=== Citace upload Dec 1st ===
+
==February 15, 2024==
  
−
=== SAB set for Feb 4-5, 2016 ===
+
=== 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
  
−
=== Concise description form ===
+
===== Manually validate paper - topic flags without curating =====
−
* URL for listing genes mentioned in a paper
+
*Facet for topic
−
* Ranjana will send to Kimberly
+
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
=== Community curation CGI ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* Almost ready for prime time
+
* Search ABC with paper identifier
−
* ~155 e-mails sent out for allele-phenotype; ~25-30 responses
+
* Migrate to Topic and Entity Editor
 +
* View all associated data
 +
* Manually validate flags, if needed
  
−
=== Scripts for community description form ===
+
=== PDF Storage ===
−
* James wrote scripts that will need to inform community CGI
+
* At the Alliance PDFs will be stored in Amazon s3
−
* Ranjana will work with Juancarlos
+
* We are not planning to formally store back-up copies elsewhere
 +
* Is this okay with everyone?
  
−
=== FlyBase text mining ===
+
==February 8, 2024==
−
* Text mining for Fly corpus, entity recognition and extraction, esp. for transgenes
+
* TAGC
−
* Need to improve SVM on transgene and allele recognition
+
** Prominent announcement on the Alliance home page?
−
* Textpresso working on tools for FlyBase
 
  
−
=== Phenotype SObA graph ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Making progress towards making the graph a widget on the gene page
 
−
* Still issues to iron out; working with Sibyl
 
−
* Some conflicts with Cytoscape for interactions vs. SObA
 
  
−
=== Data Visualization program opportunity ===
+
==February 1, 2024==
−
* Will have to write a grant
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Would pay for one person, get two with grant
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* Anyone with ideas should consider a proposal
 
−
* Dec 15th deadline
 
  
−
=== WormBook ===
+
==January 25, 2024==
−
* Daniel prepared mockup for new web page
 
  
−
=== Biocuration meeting ===
+
=== Curator Info on Curation Forms ===
−
* Mary Ann working out plans for community curation workshop
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* Does PomBase track their community curation?
 
  
−
=== HT115 vs HT115(DE3) E.coli strains ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* Redundant, should probably merge HT115 into HT115(DE3), as the RNAi-host E.coli strain
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
=== Visualization plans ===
+
* 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.
−
* 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
 
  
 +
* 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.
  
−
== November 19, 2015 ==
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
−
=== Community curation ===
+
=== Update on NN Classification via the Alliance ===
−
* Community e-mailing for allele-phenotype: 315 e-mails sent, 49 papers curated, 260 community annotations in the Phenotype OA
+
* Use of primary/not primary/not designated flag to filter papers
−
* Chris gave Paul list of all sy* alleles and phenotypes
+
* Secondary filter on papers with at least C. elegans as species
−
* Paul going through table to add phenotypes not already in WB
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
−
* Paul using Textpresso and an allele-phenotype worksheet
+
* Next NN clasification scheduled for ~March
−
* 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 ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
* Interested in Textpresso text-mining and SVM categorizing
+
* NNC html pages will show NNC values together with species.
−
* How might we work with NCBI & PubMed Central to curate? They are willing to run SVM on PMC corpus
+
* Show all C. elegans papers first and other species in a separate bin.
  
−
=== Minimum information requirements ===
+
=== Travel Reimbursements ===
−
* RNAi MI seemed bulky and not complete
+
* Still waiting on October travel reimbursement (Kimberly)
−
* Asks authors for genes targeted, not dsRNA sequence
+
* Still waiting on September and October travel reimbursements (Wen)
−
* We could write up a paragraph outlining the complaints about the proposed RNAi MI
 
−
* Maybe micropublish the paragraph
 
  
−
=== Micropublications ===
+
=== UniProt ===
−
* Should go into PubMed Central
+
* 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.
  
−
=== Allele descriptions ===
+
==January 18, 2024==
−
* Karen wants to adapt Ranjana and James' automated gene descriptions for alleles
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
−
* Start working on in January
 
  
−
=== SObA ===
 
−
* Juancarlos making progress on integrating into the WB site
 
−
* There are difficulties getting SObA into it's own widget on the gene page
 
−
** Conflicts with other settings (esp. with Cytoscape) on same page, e.g. Interactions widget (w/Cytoscape viewer)
 
−
** Updated javascript version on Interactions viewer
 
  
−
=== Corresponding author curation ===
+
==January 11, 2024==
−
* Juancarlos and Cecilia have worked out a pipeline to capture corresponding authors for each paper
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
−
* Once paper editor changes are decided, can go live
+
** 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.
  
−
=== WormBook chapters for WormBase ===
+
==January 4, 2024==
−
* Each chapter written for users, but we likely want to avoid too much technical jargon
+
* ACKnowlegde pipeline help desk question:
−
* We do want transparency
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
* We can separate the chapters into less-technical and more-technical, for easier reading
+
* 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 18:09, 23 May 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

May 23rd, 2024

  • Publication bias workshop NINDS
    • Registered report -> the protocol is sent before publication
    • How many negative curated data? Do we want to pull this out?
    • Two billion dollars worth of research not published each year
    • Octopus.ac publishing platform

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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