Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
= 2018 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
==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)
  
−
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
==March 14, 2024==
  
−
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
=== TAGC debrief ===
  
−
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
+
==February 22, 2024==
  
−
[[WormBase-Caltech_Weekly_Calls_September_2018|September]]
+
===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%)
  
−
== October 4, 2018 ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
=== SimpleMine ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Automated descriptions will be removed from Postgres/OA
 
−
* SimpleMine needed to update where it pulls the automated descriptions from
 
−
* Will add expression cluster and automated description columns output (in addition to concise description)
 
−
* Added RNAseq FPKM download function for 9 species: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/fpkmmine.cgi
 
−
* Added SimpleMine-like topic search: http://tazendra.caltech.edu/%7Eazurebrd/cgi-bin/forms/spellmine.cgi
 
−
* Should put the new tools under the WormBase Tools menu
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
== October 11, 2018 ==
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
=== Ready for new round of phenotype requests ===
 
−
* Some users are getting confused about the name & email prepopulation based on IP address
 
−
** May want to stop autopopulating name and email or autopopulate based on email recipient only (encode in URL sent in email)
 
−
** Could we use cookies? Possibly, but may only help if a computer is shared but the browser isn't
 
−
* Current autocomplete expects exact match to person primary name; e.g. "Scott Emmons" will not match the official name "Scott Wilson Emmons"
 
−
** Maybe we could improve search matching; algorithm from Cecilia/Juancarlos? Elastic search by Valerio?
 
−
** Can we capture incomplete sessions? We may be able to learn from them. May be flooded by robot visits? Is it worth going through all the logs/sessions? Info is there if we want to look at it.
 
−
* Will go ahead and send emails for only new set of papers (won't resend requests for papers that had emails sent in June/July)
 
−
* Maybe go back to papers that already had a request sent at the 6 month time point
 
−
* Include other papers in need of curation at bottom of email; possibly, would it turn off users?
 
  
−
=== Worm Phenotype Ontology ===
 
−
* WPO has a new home on GitHub
 
−
** https://github.com/obophenotype/c-elegans-phenotype-ontology
 
−
* Edits should only be made to the edit file
 
−
** https://github.com/obophenotype/c-elegans-phenotype-ontology/blob/master/src/ontology/wbphenotype-edit.owl
 
−
* Anyone interested in contributing to the WPO should contact Chris for update pipeline info
 
−
* Need to make sure that all users of the WPO have the updated link information
 
  
−
=== Provide provenance in query tools ===
+
==February 15, 2024==
−
* Prompted by user question/request
 
−
* Specifically in WOBr, Anatomy pages
 
−
* WOBr provides genes annotated to term; should provide provenance of each gene and its annotations
 
−
* Expression pattern and expression cluster gene lists (in context of Anatomy WOBr); want to provide provenance for this data
 
−
* Provenance = an object ID, like "Expr1234" or "WBPaper00032062:age_regulated_genes" with link to relevant page
 
  
−
=== WOBr disease associations ===
+
=== Literature Migration to the Alliance ABC ===
−
* Ranjana wondering if WOBr is using updated disease-gene associations
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Gene association file (for disease) being generated by script; likely need to update where the data is coming from
+
===== 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 =====
−
* Ranjana will discuss with Raymond and Kevin
+
*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
  
−
=== New WormMine superuser ===
+
===== Manually validate paper - topic flags without curating =====
−
* Now all template queries are owned by a new superuser
+
*Facet for topic
−
* If people are interested in adding or editing templates talk to Chris or Paulo for superuser access
+
*Facet for manual assertion
−
* We were running into login, template ownership, and consistency issues
+
**professional biocurator assertion
 +
***ABC - no data
  
−
=== Next upload Nov 16 ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* WS269 citace upload Tuesday, November 13
+
* Search ABC with paper identifier
−
* Can we add upload dates to Google calendar for WormBase?
+
* 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?
  
−
== October 18, 2018 ==
+
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
=== Upload for WS269===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* To Hinxton Nov 16
 
−
* Citace upload to Wen Nov 13
 
  
−
=== Data provenance in WOBr tools ===
+
==February 1, 2024==
−
* Juancarlos and Raymond have been working on
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Awaiting pull request
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* Can test: juancarlos.wormbase.org
 
−
** Go to WOBr and test anatomy ontology
 
−
** Now WOBr gene count results show data objects from which the associations come (Expr_pattern and Expression_cluster objects)
 
  
−
=== New SPELL server ===
+
==January 25, 2024==
−
* New server on Amazon (modifying server SGD uses)
 
−
* Raymond, Wen, and Todd working on
 
−
* Currently only have an SGD mirror running
 
−
* Wen will swap the data later today
 
−
* WormBase header link (to WormBase) or only link to Alliance site? We want a unified site for Alliance
 
−
* Each MOD would still support their own server for their data (MOD-specific grants support each server, for now)
 
  
−
=== Alliance expression data ===
+
=== Curator Info on Curation Forms ===
−
* Anatomy-LifeStage pair required for Alliance expression annotations
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* Since many expression pattern annotations don't have both, the missing entity would default to ontology root term
 
−
* Need to link anatomy root term to Uberon for ribbon display; root term annotations fall under the "Other" category in the ribbon slim
 
−
* Create "Anatomical_part" term to serve as the default "Other"/root term?
 
−
* All life-stage-only annotations will fall into anatomy "Other" and flood the list; should these be filtered out?
 
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
== October 25, 2018 ==
+
* 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.
  
−
=== WormBase SPELL on Amazon Web Service ===
+
* 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.
−
* http://34.224.93.60/ is running WormBase SPELL on WS267, based on the SPELL code supported by SGD. It is more stable and faster than the current Caltech server
 
−
* Waiting for Todd to respond if we can use this site as the official server for WormBase SPELL.
 
−
* Also need to get an instance (preferably also from WormBase AWS as a development site of WormBase SPELL.
 
−
* Caltech will focus on generating new data instead of SPELL code development.
 
  
−
=== Linking annotation evidence to Anatomy Ontology Browser ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
Each gene expression annotation shown on WOBr is linked to the object so that users can more easily examine the evidence.
+
 
−
[https://juancarlos.wormbase.org/tools/ontology_browser/show_genes?focusTermName=neuron&focusTermId=WBbt:0003681 Example]
+
=== Update on NN Classification via the Alliance ===
 +
* Use of primary/not primary/not designated flag to filter papers
 +
* Secondary filter on papers with at least C. elegans as species
 +
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
 +
 
 +
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
 +
* NNC html pages will show NNC values together with species.
 +
* Show all C. elegans papers first and other species in a separate bin.
 +
 
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
 +
 
 +
=== UniProt ===
 +
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
 +
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
 +
 
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
 +
 
 +
 
 +
==January 11, 2024==
 +
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
 +
** Curators should make sure that, when pasting special characters, the duplicate function works
 +
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
 +
 
 +
==January 4, 2024==
 +
* ACKnowlegde pipeline help desk question:
 +
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 +
* Citace upload, current deadline: Tuesday January 9th
 +
** All processes (dumps, etc.) will happen on the cloud machine
 +
** Curators need to deposit their files in the appropriate locations for Wen
 +
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 16:04, 18 April 2024

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

2023 Meetings

April 18th, 2024

  • NNC pipeline being switched off locally and moving into the Alliance ABC.

April 11th, 2024

  • Caltech WS293 ace files ready for the upload

April 4th, 2024

  • Continued discussion on sustainability
  • CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
    • Data is still going to SPELL and enrichment analysis
    • Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
  • Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
  • Michael's presentation on LLMs - Named Entity Recognition (NER)

March 14, 2024

TAGC debrief

February 22, 2024

NER with LLMs

  • Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
  • Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  • There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.


February 15, 2024

Literature Migration to the Alliance ABC

Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)?

Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic
  • Facet for topic
  • Facet for automatic assertion
    • neural network method
  • Facet for confidence level
    • High
  • Facet for manual assertion
    • author assertion
      • ACKnowledge method
    • professional biocurator assertion
      • curation tools method - NULL
Manually validate paper - topic flags without curating
  • Facet for topic
  • Facet for manual assertion
    • professional biocurator assertion
      • ABC - no data
View all topic and entity flags for a given paper and validate, if needed
  • Search ABC with paper identifier
  • Migrate to Topic and Entity Editor
  • View all associated data
  • Manually validate flags, if needed

PDF Storage

  • At the Alliance PDFs will be stored in Amazon s3
  • We are not planning to formally store back-up copies elsewhere
  • Is this okay with everyone?

February 8, 2024

  • TAGC
    • Prominent announcement on the Alliance home page?
  • Fixed login on dockerized system (dev). Can everybody test their forms?

February 1, 2024

  • Paul will ask Natalia to take care of pending reimbursements
  • Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.

January 25, 2024

Curator Info on Curation Forms

  • Saving curator info using cookies in dockerized forms. Can we deploy to prod?

ACKnowledge Author Request - WBPaper00066091

  • I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  • The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
  • I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  • Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.

Update on NN Classification via the Alliance

  • Use of primary/not primary/not designated flag to filter papers
  • Secondary filter on papers with at least C. elegans as species
  • Finalize sources (i.e. evidence) for entity and topic tags on papers
  • Next NN clasification scheduled for ~March
  • We decided to process all papers (even non-elegans species) and have filters on species after processing.
  • NNC html pages will show NNC values together with species.
  • Show all C. elegans papers first and other species in a separate bin.

Travel Reimbursements

  • Still waiting on October travel reimbursement (Kimberly)
  • Still waiting on September and October travel reimbursements (Wen)

UniProt

  • Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
  • Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
  • Stavros escalates the issue on Hinxton Standup.
  • Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.

January 18, 2024

  • OA showing different names highlighted when logging in the OA, now fixed on staging


January 11, 2024

  • Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
    • Curators should make sure that, when pasting special characters, the duplicate function works
  • OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
    • If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
  • Chris tested on staging and production the phenotype form and the data are still going to tazendra
    • Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
    • Raymond: simply set up forwarding at our end?
  • AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
  • Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
  • Valerio would like to use an alliancegenome.org email address for the openAI account
  • New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
  • Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
  • Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
  • Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
  • It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
  • Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.

January 4, 2024

  • ACKnowlegde pipeline help desk question:
    • Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
  • Citace upload, current deadline: Tuesday January 9th
    • All processes (dumps, etc.) will happen on the cloud machine
    • Curators need to deposit their files in the appropriate locations for Wen
  • Micropublication pipeline
    • Ticketing system confusion
    • Karen and Kimberly paper ID pipeline; may need sorting out of logistics
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