Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2017|February]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2017|March]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_April_2017|April]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_May_2017|May]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_June_2017|June]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
== July 6, 2017 ==
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
=== Noctua ===
+
==April 11th, 2024==
−
* Use for all literature curation in future?
+
*Caltech WS293 ace files ready for the upload
−
* We would need to see how it could be used for all data types
 
−
* We would also want a full-time developer working on Noctua; maybe bring Juancarlos into the project
 
  
−
=== SPELL ===
+
==April 4th, 2024==
−
* SPELL related data - how to deal with?
+
* Continued discussion on sustainability
−
** Data: recalculated, mapping, results dependent on SPELL
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
** Analysis (clustering tool): clunky, freezes w/limited resources
+
** Data is still going to SPELL and enrichment analysis
−
* Wen will work with Juancarlos to generate a SimpleMine-like tool for downloading data sets
+
** 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.
−
* Wen has to remove log files to make space on machine
+
* Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
−
* ~360 data sets
+
* Michael's presentation on LLMs - Named Entity Recognition (NER)
−
* Current virtual machine has 10G memory; is becoming limiting
 
−
* SPELL has lots of dependencies; difficult to account for them all when building SPELL
 
−
* Would be good if we could setup a new (larger) virtual machine to run SPELL; how much time/resources do we want to spend on it?
 
  
−
=== Micropublications ===
+
==March 14, 2024==
−
* Poster at Zebrafish meeting pointing to micropublications
 
−
* Microarray micropublications? Unpublished results
 
−
* Can make links to GEO submissions
 
−
* Daniela and Karen can draw up a mock publication to look at as a template
 
  
−
=== Community Curation ===
+
=== TAGC debrief ===
−
* Considering sending requests to only one person, first author when have info
 
−
* This should allow for more emails to be sent out per week, and more submissions, even if we maintain the 16% response rate
 
−
* Chris will work with Juancarlos once he's back from vacation
 
−
* What's next data type? Interactions? Site of action? Anatomy?
 
−
* What's required for site of action? Phenotype, gene, cell/tissue where gene is introduced or removed
 
−
* Can send requests to lab heads to fill in phenotype info for alleles from their lab
 
  
−
=== Linking ===
+
==February 22, 2024==
−
* Will human genes link to AGR human gene pages? Gene Cards? HGNC?
 
  
 +
===NER with LLMs===
  
−
== July 13, 2017 ==
+
* 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%)
  
−
=== Allele attribute assignment ===
+
* Is this similar to the FlyBase system? Recording of presentation https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* Some attributes of alleles are currently only assigned in the context of a phenotype annotation
 
−
* Many times these attributes are reported independently of a phenotype experiment
 
−
* It would be good to have a mechanism to curate these attributes to alleles independent of phenotype curation
 
−
* As far as modeling goes I (Chris) had intended to do dump these attributes directly into the ?Variation object like this:
 
−
?Variation 
 
−
Null  ?Phenotype_experiment
 
−
* This would allow us to always point to a ?Phenotype_experiment object as a container of evidence, but if we don't always have a ?Phenotype_experiment object to point to then maybe a better approach is just to reference the paper like this:
 
−
?Variation 
 
−
Null  ?Paper
 
−
* This would require a separate curation pipeline from phenotype to capture these attributes; will discuss more with Mary Ann when she's back from vacation
 
−
* We discussed and came up with a couple of potential solutions:
 
−
* First:
 
−
?Variation
 
−
Variation_effect  Null ?Text  #Evidence
 
−
* Second:
 
−
?Variation
 
−
Variation_effect  Null  ?Paper  #Evidence
 
−
* The first solution allows to put in a free text remark, potentially referencing a phenotype or some detail, with the #Evidence hash allowing reference to a paper or a person_evidence
 
−
* The second solution requires reference to a ?Paper object, which would require a reworking of all person evidence/personal communication to become ?Paper objects, with an #Evidence hash to capture remarks
 
  
−
=== Phenotype form submission requests ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Originally we sent email requests independently of Author First Pass pipeline emails
 
−
* Now a link to phenotype form is being included in Author First Pass emails, and we're putting a hold on all new email requests to corresponding author for one month
 
−
* I (Chris) am considering returning to original approach of sending requests independently of AFP (and focusing on first authors), to see if we can get response rate up at all
 
  
−
=== New WormBase Caltech server ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* We're getting a new server, to consolidate different computers and their services
 
−
* Let Raymond know if you have an idea for another (extra) use of the server
 
−
* Will likely re-use altair.caltech.edu
 
−
* 96 GB memory, ~6 TB hard drive
 
  
−
=== SPELL ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* SPELL could go on new server
 
−
* Moved from current virtual machine to KVM
 
−
* Could expand memory and CPU
 
  
  
−
== July 20, 2017 ==
 
  
−
=== Variation effect assignment ===
+
==February 15, 2024==
−
* We had discussed last week having either of two models in the ?Variation class
 
−
* First:
 
−
?Variation  Variation_effect  Null  ?Text  #Evidence
 
−
* Second:
 
−
?Variation  Variation_effect  Null  ?Paper  #Evidence
 
−
* The first option can keep things as they are and can allow a remark in the ?Text entry, with paper or person evidence coming from the #Evidence hash
 
−
* The second option likely requires that we consider person evidence/communication as ?Paper objects
 
−
* Many entries in the Phenotype OA coming from Jonathan Hodgkin are from the C. elegans I and II books
 
−
** Would be good to create ?Paper objects for C. elegans I and II and reference them accordingly
 
−
*** Already exist:
 
−
**** C. elegans II WBPaper00004071
 
−
**** C. elegans I  WBPaper00004052
 
−
* Probably best to go with
 
−
?Variation  Variation_effect  Null  ?Text  #Evidence
 
−
* Going forward we can encourage people to micropublish if they want to submit personal communication
 
  
−
=== Blog posts for WormMine ===
+
=== Literature Migration to the Alliance ABC ===
−
* Not quite ready; Chris will contact Ranjana about it when ready
+
==== 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
  
−
=== WormMine templates ===
+
===== Manually validate paper - topic flags without curating =====
−
* Todd had encouraged development of template queries
+
*Facet for topic
−
* Older templates are still difficult to access and edit, but new queries going forward are OK
+
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
=== New Server ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* New WormBase server (@ Catlech) is online
+
* Search ABC with paper identifier
−
* Let Raymond know if anyone has uses for the server
+
* Migrate to Topic and Entity Editor
−
* Anything that needs to be running 24-7 (e.g. services) can be considered
+
* View all associated data
 +
* Manually validate flags, if needed
  
−
=== Supplement for AGR ===
+
=== PDF Storage ===
−
* Proposing tuning up of orthology calls
+
* At the Alliance PDFs will be stored in Amazon s3
−
* Paul S. wants to get Gene Orienteer back up, and have RNASeq analysis pipeline
+
* We are not planning to formally store back-up copies elsewhere
−
* Pull in WormNet data (predicted interactions)
+
* Is this okay with everyone?
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
== July 27, 2017 ==
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
=== AGR GO Slim ===
+
==February 1, 2024==
−
*Discussion of new AGR GO slim and representation of C. elegans genes
+
* Paul will ask Natalia to take care of pending reimbursements
−
*[https://github.com/geneontology/go-ontology/issues/13791 Modification to AGR slim]
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
*Key to graphs
 
−
**Red = AGR slim
 
−
**Orange = C. elegans orphans
 
−
**Multi-colors = Other organism orphans, as well
 
  
 +
==January 25, 2024==
  
−
== August 3, 2017 ==
+
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
=== WB grant ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* Progress (maintenance stuff) can be written as of last grant cycle
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
* Current projects and report the steady state
 
  
−
=== CRISPR alleles ===
+
* 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.
−
* Some authors not reporting CRISPR alleles with standard nomenclature
 
−
* Some in Paul's lab creating same knockin with same name (should be distinct). Mary Ann to update nomenclature guidelines.
 
−
* Some (e.g. Bruce Bowerman) knock-in GFP in frame and use RNAi against GFP to knockdown endogenous gene
 
−
** RNAi mapping pipeline not setup to handle this
 
−
** Could maybe use endogenous sequence near insertion site (not ideal, for off-target effects)
 
−
** Maybe best, once new ?Phenotype_experiment model is in place, to just refer to perturbed gene
 
  
−
=== Ontology Browser ===
+
* 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.
−
* Has been less stable lately; Raymond has needed to restart machine
+
 
−
* Being served from Dell server (in Braun building)
+
* 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
 +
** 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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