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]]
  
−
==2012 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
−
 
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_January_2012|January]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_February_2012|February]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_March_2012|March]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_April_2012|April]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_May_2012|May]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_June_2012|June]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_July_2012|July]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_August_2012|August]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_September_2012|September]]
 
−
 
 
−
 
 
−
 
 
−
== October 4, 2012 ==
 
−
 
 
−
 
 
−
FlyBase SAB topics
 
−
*Genome Space - can integrate data in different formats
 
−
**Cloud-based data integration
 
−
**File conversion done automatically - no need to write scripts
 
−
*FlyBase talking about joining [http://www.genomespace.org/ Genome Space]?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
Protein-to-GO Tool
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
−
*Ranjana and Kimberly performing data checks for testing
 
−
*If file can get to Rachel and Tony, maybe can discuss this weekend (at GO meeting)
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
GO Annotator Tool
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
−
*Kimberly looking over
 
−
*James will make a couple slides to introduce tool and provide demo
 
−
**1-minute demo: can have file in XML/HTML format, can highlight, annotate a sentence, and save annotation as a link
 
−
***Demo: simpler = better
 
−
***Prepare for live feedback and discussion
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
Curation Status/Statistics Tool
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
*How many papers have given data types?
 
−
*How many papers have been curated, how many not?
 
−
*How many objects/connections do we have of a given type?
 
−
*How many objects per paper (average, distribution?)?
 
−
*Estimated number of objects/papers exist vs. how many we have curated?
 
−
*Do we care about types of flagging? Curator first pass, author first pass, etc? Yes
 
−
**All flagging types should be shown; combined and individual statistics would be useful
 
−
*Interactive form vs. static page showing curation/flagging statisitcs
 
−
*Tracking negatives (true vs false)
 
−
*Data types in OA vs not (microarray, Protein-to-GO output)
 
−
**Microarray data - Wen can write script to generate stats for microarray curation
 
−
*Curation stats per paper (Raymond): write comments in a remark field; traceable, transparent, available
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
Process pages
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
*GPML - may be able to automatically map Postgres data to GPML
 
−
*WikiPathways has color, formatting, labels, etc. so we can define types/views of different relationships (should follow standards)
 
−
*AWC-ON/AWC-OFF sample page: only single connection type; can be many different types, as we define it
 
−
*"Too many arrows" editorial?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
Physical interaction curation
+
==April 18th, 2024==
−
*On interaction OA (Tab2) physical interactions; 'Colocalizes', etc.
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
−
*Need to establish our data exchange with BioGRID; get BioGRID data in Postgres/OA (daily cronjob?)
 
−
*Interaction model was modeled to be compatible with BioGRID's data
 
−
*Revive curator first pass for physical interactions? To tag papers (in the meantime)
 
  
 +
==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)
  
−
== October 11, 2012 ==
+
==March 14, 2024==
  
 +
=== TAGC debrief ===
  
−
Molecules
+
==February 22, 2024==
−
*Changing to WBMolIDs
 
−
*OA dumpers need to be modified
 
  
 +
===NER with LLMs===
  
−
GO Meeting
+
* 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%)
−
*How to make GO more expressive/inclusive
 
−
*How can GO represent more of the biology
 
−
*GO Extensions: LEGO
 
−
*Deeper annotations can help develop the "big picture"
 
−
*Phenotype-2-GO mapping: What is the purpose? How does it work?
 
−
**Broad vs specific term mapping; how good is the mapping?
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
CSHace merge with CITace?
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*PCR_product info discrepancies
 
−
*CITace data was overwriting CSHace data, but changed
 
−
*8 classes of data in CSHace
 
−
*CSHace data had never been read into CITace minus
 
−
*Proposal: read CSHace data into ACEDB and then read in CITace minus data (which would overwrite CSHace data with CITace data where there is a conflict)
 
−
*Can we assume that all CITace data is better/newer/more-up-to-date than CSHace data?
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
Consensus Sequence tag in PWM model
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
*OK to add, but leave as 'Text' not '?Text'
 
−
*DNA_text field instead? Xiaodong will run by EBI
 
−
*This data is denormalized from a PWM if both are provided
 
−
*Should only be used if no PWM is provided
 
−
*Perhaps this should not be added
 
  
  
−
== October 25, 2012 ==
 
  
 +
==February 15, 2024==
  
−
Curation Stats Table
+
=== Literature Migration to the Alliance ABC ===
−
*Can be viewed (on sandbox) here: http://mangolassi.caltech.edu/~postgres/cgi-bin/curation_status.cgi
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
*Click on the button "Curation Statistics Page"
+
===== 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 =====
−
*Will show overall statistics per data type as well as per flagging method
+
*Facet for topic
−
*Working out details/aesthetics of display
+
*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
  
−
WS235 Upload next Thursday (Nov 1)
+
===== 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?
  
−
Microarrays
+
==February 8, 2024==
−
*24 new datasets
+
* TAGC
−
*Five new species
+
** Prominent announcement on the Alliance home page?
−
*We want to perform cluster analysis for end users (SPELL itself not capable)
 
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
PWM/PFM data
+
==February 1, 2024==
−
*~5000 PFM/PWM data objects in .ace files from Stormo data set
+
* Paul will ask Natalia to take care of pending reimbursements
−
*How the motif finder tool should work? (without using 1000s of GBrowse tracks?)
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
*Single GBrowse track that consolidates all PFMs/PWMs; one track with all 'binding sites' above threshold?
 
−
*Another tool to look for, for example, co-occurrence?
 
  
 +
==January 25, 2024==
  
−
Disease info
+
=== Curator Info on Curation Forms ===
−
*Adding 'Disease_relevant_info' tag in Gene model
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
*Human ortholog pulled from OMIM by Hinxton/EBI
 
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
Ranjana will do a blog item every Thursday
+
* 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.
−
*Doing series heading, e.g. "Developments to GO"
 
−
**Updates could fall under same headings to organize blog posts
 
  
 +
* 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.
  
−
New RNAi clones from Ahringer lab
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Working with Kevin Howe as to how the new PCR_product and Oligo objects should be created and stored
 
−
*Ultimately would like (for all RNAi clones) to have a one-to-one mapping of best RNAi clones for a gene
 
−
*Gene pages could then display "THE" RNAi clone for a gene per library (e.g. Vidal or Ahringer), along with resource address/location
 
−
*If multiple clones per gene, indicate which clone is unique to that gene
 
  
 +
=== 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
  
−
Protein-2-GO Tool
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*Gene-product-information file
+
* NNC html pages will show NNC values together with species.
−
*Working with other MODs
+
* 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)
  
−
Transgenes up to date
+
=== 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
  
−
Legacy phenotypes
 
−
*Still have ~800 legacy phenotypes to add through phenotype curation
 
  
 +
==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.
  
−
Process pages
+
==January 4, 2024==
−
*Karen writing summaries for processes
+
* ACKnowlegde pipeline help desk question:
−
*People can help cull the list and/or help write summaries
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*Look at Processes in the Process OA by querying for "Karen" as a curator
+
* Citace upload, current deadline: Tuesday January 9th
−
*Connecting to relevant papers (reviews, research articles, WormBook chapters/abstracts)
+
** All processes (dumps, etc.) will happen on the cloud machine
−
*Linking to WikiPathways, Reactome?
+
** Curators need to deposit their files in the appropriate locations for Wen
−
*What should be editable by users/broader community?
+
* 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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