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_2015|2015 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2012|February]]
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2012|March]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_April_2012|April]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_May_2012|May]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_June_2012|June]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_July_2012|July]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_August_2012|August]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_September_2012|September]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_October_2012|October]]
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
[[WormBase-Caltech_Weekly_Calls_November_2012|November]]
+
==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==
  
−
= December 6, 2012 =
+
=== TAGC debrief ===
  
 +
==February 22, 2024==
  
−
Concise descriptions
+
===NER with LLMs===
−
*Concise descriptions tool as a pilot for community annotation
 
−
*How can concise descriptions be generated on an automated basis?
 
−
*Prioritize with genes with little to no known information
 
−
*Focus on genes in other species
 
−
*GBrowse-visible description (30 character limit)
 
−
*Complex gene information will still be best handled manually
 
−
*''Brugia malayi'' good starting point; Also, ''Pristionchus'' and ''C. briggsae''
 
−
*Ralf Sommer would help generate concise descriptions
 
−
*Working with ''Brugia'' community already
 
−
*Could we select what type of GBrowse description is visible (potential drug targets, molecular function (GO term?), secreted proteases, resistance locus, etc.)? Using radio buttons, for example?
 
−
*Use GO annotations in automated fashion?
 
−
*Parasitic worm vs. Free-living worm descriptions (host, drugs, species-specific genes, etc.)
 
−
*30-character controlled vocabulary for genes?
 
−
*Annotate (and then display) based on drug sensitivity, resistance, no effect? Show "potential" drug interactions?
 
−
*Icons on genes indicating drug interaction, for example
 
  
 +
* 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%)
  
−
PAINT meeting
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
*Ranjana going to next week
 
−
*PAINT: Panther tree-based transfer of GO annotations across species
 
−
*Orthologs/paralogs adopt annotations
 
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
AMIGO update
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
*Can display our ontologies now
 
−
*User interface may take some time
 
−
*Would be best if Raymond could work with a programmer (Juancarlos?)
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
Remark field display issues
 
−
*Todd commented that he would like the "Remark" and "Summary" fields to display similar type of info across all pages/objects/data-types
 
−
*Transgene curation (and others?) may need adjustment to what goes in the "Summary" and "Remark" field
 
−
*May create new tag to accommodate info?
 
  
  
−
Upload
+
==February 15, 2024==
−
*Data upload will be Dec 20th
 
−
*Database build will happen second week of Janurary
 
  
 +
=== 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
  
−
= December 13, 2012 =
+
===== Manually validate paper - topic flags without curating =====
 +
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
PAINT Meeting
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
*Looking at whole tree of all genes across all species
+
* Search ABC with paper identifier
−
*Applying gene (GO) annotations across all species
+
* Migrate to Topic and Entity Editor
−
*Broad perspective
+
* View all associated data
−
*Annotations help PAINT, PAINT helps annotations
+
* Manually validate flags, if needed
−
*"Viewing the tree"
 
−
*GO annotations can be applied/dragged onto most recent common ancestor, and PAINT fills the annotation in to all genes in between
 
−
*Feature requests discussed
 
−
*Subfamilies/subclades color-coded for easier viewing
 
−
*Annotation matrix to view along with tree
 
−
*Molecular functions most readily conserved; processes less so (cell component intermediate)
 
−
*Reliability/prioritization of annotations: molecular function -> cell component -> biological process
 
−
*How much is rule-based? How is Quality Control handled/established?
 
−
*Liberal vs Conservative annotations; try to back up with literature
 
−
*"Triangulation" tools
 
−
*Good rules could replace manual annotation with automated annotation
 
−
*Automatic quality-control e-mailing
 
−
*Sample annotating of gene families
 
−
**Nitric oxide synthase
 
−
**Some transcription factors
 
−
**Some enzymes
 
−
*Panther trees describe relationships between genes, but really use proteins to make associations
 
−
*Duplications? How to annotate? Tricky; requires some literature searching
 
−
*Key annotations: species-specific genes/proteins for (relatively) sparsely annotated species; identifying unknowns, high value annotations
 
  
 +
=== 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?
  
−
WormBase GO progress report
+
==February 8, 2024==
−
*Kimberly working on; will send out to relevant people
+
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
Common GO Annotation Tool
+
==February 1, 2024==
−
*Uniprot tool: Protein-2-GO?
+
* Paul will ask Natalia to take care of pending reimbursements
−
*Adopt aspects of the WormBase Ontology Annotator
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
*Some MODs are heavily embedded in an in-house tool
 
−
*Good to have a general common tool for all data types
 
  
 +
==January 25, 2024==
  
−
AMIGO 2 Ontology Browser
+
=== Curator Info on Curation Forms ===
−
*Would like to develop feedback cycle of use/development
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
*Versioning issues
 
−
*Branching off of current AMIGO 2
 
−
*Seth wouldn't want anatomy or phenotype terms showing up in his ontologies
 
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
= December 20, 2012 =
+
* 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.
  
−
SPELL
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Athena updated to Ubuntu 4, not compatible with old Ruby
 
−
*SPELL still runs on older Ruby/Rails
 
−
*Difficulty updating code to accommodate OS change
 
−
*Currently building database on Athena and migrating to other machine
 
−
*Will continue running the older Ubuntu OS for now
 
−
*Front end is Ruby, back end is Java; maybe somehow ditch Ruby layer
 
−
*Proficient Ruby programmer could (maybe) upgrade the SPELL code appropriately
 
−
*What are other MODs (SGD?) doing? How can we emulate that?
 
−
*Also: there are some queries we would like to be able to perform that SPELL doesn't currently provide
 
−
**Develop another interface/query functionality?
 
−
**Use intermine? Intermine does not have good microarray data module
 
−
**Integration with other data types
 
−
**Query example: Find genes that have similar expression profile and physical interaction?
 
−
*Will try to contact Matthew Hibbs for update
 
−
*Do Matt et al have description of the API that we could look at, use?
 
  
 +
=== 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
  
−
AMIGO 2
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*Juancarlos and Raymond still working on
+
* NNC html pages will show NNC values together with species.
−
*Juancarlos communicating with Seth
+
* Show all C. elegans papers first and other species in a separate bin.
−
*Need to work out smooth architectural design so Juancarlos can work on code at our end, we can test locally
 
−
*AMIGO/Seth wants to move to Git version system
 
−
*Next, get at annotation info/files so that annotation data can be attached/linked to the ontology terms
 
−
*Seth said in ~month transitioning to new/stable version of software
 
  
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
Process Pages
+
=== UniProt ===
−
*Karen and JD working on
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*Karen explained what should be displayed, where and how on the page
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*Mark Perry had worked on/developed display stuff for Molecules
+
* Stavros escalates the issue on Hinxton Standup.
−
*Should be complete for SAB meeting
+
* 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
  
−
Images on Staging
 
−
*Images are not displaying on the staging site
 
−
*Daniela will generate a GitHub ticket
 
  
 +
==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.
  
−
Disease Ontology
+
==January 4, 2024==
−
*DO terms going to citace/ACEDB for upload
+
* ACKnowlegde pipeline help desk question:
−
*Upgrading OBO files as well?
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*Now we make the OBO files generally available to community
+
* Citace upload, current deadline: Tuesday January 9th
−
*Curation will produce association files (connecting terms to genes)
+
** All processes (dumps, etc.) will happen on the cloud machine
−
*Association files in GAF format? (AMIGO-useable format)
+
** 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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