Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 17: Line 17:
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
= 2018 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
== January 4, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
=== WS264 Upload ===
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
* Citace upload to Wen, Tuesday January 16th, by 10am PST
 
* Upload to Hinxton on Jan 19th
 
  
=== Strain data import to AGR for disease ===
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
* Will begin to consider pulling in strains into AGR
 
* Will need to think about how genotypes are built and stored at other MODs
 
* We should encourage authors to include strain IDs
 
* Diseases are annotated to genes, alleles, and strains within WB
 
  
=== Curating phenotypes and diseases to strains or genotypes ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
* Should we generate a ?Genotype class to capture genotypes without a known strain name? Or to capture relevant/relative genotypes thought to be responsible for a phenotype or disease?
 
* We could create un-named strain objects, that use a new unique identifier as a primary identifier and represent the entire genotype of a strain used
 
** Introduction of a new ?Strain class attribute of a unique serial identifier (like WBStrain00001) would be very costly to implement; would need to consider how crucial this is before implementing
 
** We can, instead, use new strain (public) names like "WBPaper00012345_Strain1", etc. instead of creating new unique ID attribute for un-named strains
 
* When curating phenotypes to strains, we will want to specify what is the relevant/relative genotype that is causative/correlated with the disease or phenotype observation
 
** Would be best if the specification of the relevant genotype used controlled vocabularies (when possible) and free text (when needed); would need to work out the logistics/mechanics of such curation
 
** Transgene-phenotype curation currently specifies causative gene, but would be more complicated for strains
 
* Alternatively, we could create the ?Genotype class to represent the abstract "relative"/"relevant" genotype thought to be responsible for the phenotype or disease, and annotate directly to that ?Genotype object
 
* ?Strain approach:
 
** Use strain if named (but important to know if the control strain is not simply N2)
 
*** If control strain is simply N2, causative genotype (and respective components) can be inferred from strain genotype
 
*** If control strain is not N2, causative genotype and components would need to be specified at the moment of phenotype/disease curation (by mechanism to be worked out)
 
** If no strain name provided, create "un-named" strain that contains the entire genotype provided by authors
 
*** Control strain issues above would still need to be addressed
 
* ?Genotype approach:
 
** ?Genotype class could represent individual instances of relevant/relative genotypes that are suggested to be causative for a disease or phenotype
 
** ?Genotype objects would be created with formal construction, with DB associations to each component object (e.g. alleles, transgenes, etc.) as well as free text descriptions (for components with no corresponding DB object)
 
** Such ?Genotype objects could be used repeatedly throughout a paper when applicable, but would likely not be used in any other papers (we would likely accumulate redundant objects in the DB)
 
* We may want to consider strains with same public name that have diverged
 
** Apply new strain names with prefixes/suffixes? Create new strain objects? Keep original?
 
* Need to determine how each AGR member DB curates phenotypes or diseases to genotypes: is each "genotype" a relative or absolute genotype?
 
  
  
== January 11, 2018 ==
+
==March 14, 2024==
  
=== IWM swag ===
+
=== TAGC debrief ===
* Eppendorf tube openers with WormBase logo?
 
  
=== Update on AFP Form ===
+
==February 22, 2024==
*[https://docs.google.com/presentation/d/1anFOFRK9Ida1UEvrXWf2OBAJ9F4xyU4lWJGy-qr6wRU/edit#slide=id.p3 In-progress mock-up of new form]
 
*[https://docs.google.com/spreadsheets/d/1sS_uAjBJ2r5H90Lam62Ai0HunjwvfjnklkFNrDoNXeU/edit#gid=1929595460 Data type spreadsheet]
 
*[http://wiki.wormbase.org/index.php/First-pass_flagging_pipelines#Author_first-pass_form_revisions Curation forms info]
 
  
*Idea is to move from author flagging to author validation of text mining and data submission wherever possible
+
===NER with LLMs===
*Goal is to flag all data types in a paper and either curate at WB or share with a group that does curate that data
 
*SVM flags and author flags can/will be used as filters in TPC
 
*Provide examples of what we want for each type of data to help avoid confusion
 
* Recognize entities automatically and show list to author
 
** Species, strains, genes, alleles, transgenes, etc.
 
** Ask to verify or add unrecognized
 
** Could show known/existing objects with checkboxes
 
** Possibly include unrecognized pattern matching objects? Ask author to verify if these are real?
 
** For strains:
 
*** Show recorded genotype for verification; maybe ask to update/modify if needed?
 
** For transgenes:
 
*** When author submits new transgene, send them to a transgene form, or send them an email asking for details?
 
*** Form could be for both strain and transgene
 
* Mapping data: still ask for? Maybe for balancers, but no one is reporting that. Could still ask if there's interest
 
* Maybe provide option for author to save their progress and return to the form later
 
* Phenotypes
 
** Ask for allele, RNAi and overexpression phenotypes with links to Phenotype form
 
** Also ask for drug/chemical and environmental perturbations (call treatment?); store as free text for now, accommodate with new data model when available
 
* Gene site- and time-of-action, mosaic
 
** Appears to be confusion from authors about mosaics. Should we keep this?
 
** Will keep gene site-of-action and time-of-action; leave unchecked (no SVM, yet) but allow users to indicate
 
* Cell and anatomy data
 
** Cell function ("Cell ablation (laser/genetic) data, optogenetics")
 
** Ultrastructural analysis
 
* Interaction data
 
** Genetic interactions
 
** Physical interactions
 
** Functional complementation
 
* Comparative genomics
 
* Gene expression & regulation
 
  
 +
* 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
  
== January 18, 2018 ==
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
=== WormBase Tutorials ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* May be good to get (possibly anonymous) written questions or suggestions after presenting
 
* Wen will have Skype call with Yishi Jin
 
* Micropublications
 
** how do we peer-review single experiment? No supporting information to corroborate a larger story
 
** Is the greater benefit of peer-review that the whole story is assessed by reviewers
 
** Do MPs help or hurt reproducibility?
 
** Larger papers may have lots of poor experiments that don't get much attention but still pass peer review
 
** Dedicated peer review on single experiment may be more rigorous
 
** What are the criteria/minimal requirements to micropublish?
 
* Concise descriptions
 
** SimpleMine has multiple descriptions output; people asked about the different types
 
** Yishi Jin suggested that we remind users to update manually written descriptions
 
** Showing last-updated date is important
 
** Automated descriptions relies on primary data; will rely on forms and community submissions
 
** Microreviews? Would want to guide authors what data we want; provide a template?
 
* Public/community education issues
 
** Users shouldn't assume that WormBase is comprehensively up to date
 
* Wen will also present at MidWest meeting (Ann Arbor, MI) in April and Boulder, Colorado in May
 
** Will assess topic interest ahead of time
 
  
=== New Cytoscape display for interactions ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Sibyl developed a new Cytoscape display for interactions, now live with WS262 release
 
* Simplified colors and subtypes
 
* Redraw button to clean up the graph based on what you want to see
 
* Play around and let Sibyl and/or Chris know about issues
 
  
== January 25, 2018 ==
 
  
=== UCSF visit report ===
+
 
 +
==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
 +
** 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 18:18, 14 March 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


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