Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 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]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
 +
 +
[[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.
 +
 +
==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)
  
−
==2012 Meetings==
+
==March 14, 2024==
  
 +
=== TAGC debrief ===
  
−
[[WormBase-Caltech_Weekly_Calls_January_2012|January]]
+
==February 22, 2024==
  
−
[[WormBase-Caltech_Weekly_Calls_February_2012|February]]
+
===NER with LLMs===
  
−
[[WormBase-Caltech_Weekly_Calls_March_2012|March]]
+
* 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%)
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
== April 12, 2012 ==
 
  
−
RNAi OA
 
−
*OA almost ready to go live
 
−
*Testing now with test curation
 
−
*Should go live next week for official curation
 
  
 +
==February 15, 2024==
  
−
New Website
+
=== Literature Migration to the Alliance ABC ===
−
*Most problems are being fixed in a timely manner
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
*Curators can now edit links and add custom widgets
+
===== 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 =====
−
*Issues (tracked on GitHub) being dealt with quickly
+
*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
  
−
BioCurator Meeting
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
*Good meeting, bigger than before
+
* Search ABC with paper identifier
−
*Common themes: data standards, how to educate users of database materials and how to use it (and think critically)
+
* Migrate to Topic and Entity Editor
−
*How can MODs work better with journals and PubMed to solve the 'triage' problem?
+
* View all associated data
−
**Streamlining the paper acquisition/curation process
+
* Manually validate flags, if needed
−
**MODs should ask NLM to take the burden of retrieving PDFs
 
−
**Get lawyers involved to make available?
 
−
**Publishers tend to be lax on text mining rules, maybe will evolve into an easier process
 
−
*Maybe write a grant for research project as a proof-of-principle that triage can be done in an effective/efficient manner
 
−
*May ask ISB (Int Society Biocurators) for help with this
 
−
*Sequence and protein curation: tools, databases (topic-specific; pathways, cancer, etc.)
 
−
*GeneWiki for human gene annotation
 
−
**One page for each gene; already have ~10,000 articles
 
−
**~Dozen editors, credibility of authors checked (?)
 
−
**Reasonably satisfied with coverage of human disease genes
 
−
*Whole-genome sequencing of individuals
 
−
**Newly identified genetic disorder
 
−
**VAST instead of BLAST
 
−
*Tool to identify primers from papers and map them to the genome automatically
 
−
*Intermine discussed
 
−
**Comparable to WormMart
 
−
**Object-oriented database
 
−
**Performs similar to WormBase
 
−
**Many pre-canned queries
 
−
**Advanced search Query-builder available
 
−
**MODs switched over to Intermine from BioMart
 
−
**WormMart - Will Spooner tried to provide queries that are more natural
 
−
**We can work to build an interface on top of Intermine, etc.
 
−
**Todd has made progress with getting Intermine for WormBase
 
−
*Lot's of specialized talks, reduced the productivity (compared to BioCreative meeting)
 
−
*Curators explaining their curation pipeline
 
−
*Textpresso still popular ;)
 
−
**Six out of seven MODs using Textpresso
 
−
**Discussed text mining in particular applications (eg. CCC)
 
−
**Textpresso only tool using full-text for mining
 
−
**Pete from FlyBase: SVM results are deteriorating (similar to WormBase)
 
−
***Start training from scratch; hopefully get better recall/precision numbers
 
−
*Natural language processing on figure legends/captions
 
−
**Tries to find text in the body that relates to figure
 
−
**Possible collaboration with Texpresso
 
−
*NLP research group in Germany
 
−
**'Actor', 'agent' etc. and relationships (RDF triplets)
 
−
*Doug Howe (ZFIN), zebrafish corpus small enough, doesn't need Textpresso
 
−
*Julio Collado-Vides, Textpresso for E. coli fell apart, but trying to get back together
 
  
 +
=== 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?
  
−
Paul will meet someone from Elsevier
+
==February 8, 2024==
−
*Image curation/ rights issues
+
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
Genetic Interaction ontology
+
==February 1, 2024==
−
*SGD on board with ontology so far; performing trial curation
+
* Paul will ask Natalia to take care of pending reimbursements
−
*FlyBase interested in using as well; will meet with Chris and Rose in May to discuss
+
* 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?
  
−
== April 19, 2012 ==
+
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
Interaction object displays on WormBase website
+
* 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.
−
*Chris and Maher will sort out on GitHub
 
−
*Chris will map data from old tags to new tags and suggest display changes for new data types where necessary
 
−
*One issue to deal with is the complex objects with multiple Interaction_types (and intended to be separate objects)
 
  
 +
* 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.
  
−
Interaction model and intragenic suppression
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*We need to make some modifications to the new Interaction model if we want to accommodate intragenic suppression (or other intragenic) events
 
−
*Proposed change is to:
 
−
#Make each allele a separate object
 
−
#Move the Variation (and Transgene) tag out of the Interactor_info hash and into the main Interaction model under the Interactor tag
 
−
#Add a Cis_intragenic_suppression and a Trans_intragenic_suppression tag under the Interaction_type tag (perhaps also intragenic_enhancement?)
 
−
*With these changes:
 
−
**Each variation (and transgene) can be listed as an interactor with Interactor_info indicating Affected, Effector, or Non_directional
 
−
**Genes associated with intragenic, interacting variations will display (in Cytoscape view) as interacting with themselves via a Genetic Interaction
 
−
**Mary Ann can then indicate/curate the flanking sequences for each allele
 
  
 +
=== 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
  
−
Life_stage objects still dump as names, not IDs
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*This is because ACEDB only handles names, not IDs
+
* NNC html pages will show NNC values together with species.
−
*Daniela is in charge of this class; we can discuss with her when she's back
+
* Show all C. elegans papers first and other species in a separate bin.
−
*We likely want to change to a system where we use only IDs in .ACE objects
 
  
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
URL Constructors for GSA markup
+
=== UniProt ===
−
*Todd has taken care of much of the issue of URL construction for GSA marked-up papers
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*Karen will send Todd examples of Anatomy_term/Anatomy_name links that need to be checked
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*GSA papers will need to be rechecked to ensure that all links are working
+
* 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
  
−
Network outages
 
−
*Various office network ports are non-functional as of yesterday
 
−
*IMSS/Network admins aware of issue and working on it
 
  
 +
==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.
  
−
Interaction and Gene_regulation objects for next upload
+
==January 4, 2024==
−
*Conversion scripts will need to be run again to convert objects to new model format
+
* ACKnowlegde pipeline help desk question:
−
*Chris will look into whether or not the mapping files (needed to update Gene_regulation objects) will need to be updated for the newest data
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*Xiaodong will dump Gene_regulation objects out of the OA using the old dumping script
+
* 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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