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]]
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_October_2012|October]]
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
== November 1, 2012 ==
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
SPELL data
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
*Including new RNA-seq datasets
 
−
*Comparing different RNA-seq datasets
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
Dedicated ~2 weeks for issues
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
*Dedicated time during release cycle to fix bugs and address GitHub issues
 
  
 +
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
Intermine
+
==April 11th, 2024==
−
*JD Wong started at WormBase this week; will focus on building WormBase instance of Intermine
+
*Caltech WS293 ace files ready for the upload
−
*Developed FlyBase Intermine instance
 
−
*Once in place, we can build pre-canned queries that we can embed in WormBase pages (maybe in response to help desk inquiries)
 
−
**E.g. Display meta information for a gene; "How many genes show this phenotype?"
 
−
*We have resources provisioned for building and hosting
 
−
*Low hanging fruit: access to ontologies, gene models, phenotypes, homology, orthology (things already made for Intermine)
 
−
*Focus first on central dogma stuff
 
  
 +
==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)
  
−
SAB Meeting
+
==March 14, 2024==
−
*January 28th, 29th, 2013
 
−
*At Caltech
 
  
 +
=== TAGC debrief ===
  
−
Concise description template
+
==February 22, 2024==
−
*Curator version versus a community (simpler) version
 
−
*1) Transfer info from elegans to other species
 
−
*2) Updates
 
−
*Easier to script when there is little information; harder when lots of info
 
  
 +
===NER with LLMs===
  
−
Pathways
+
* 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%)
−
*Karen spoke to Alex Pico
 
−
*There could be tagged for "WormBase-approved" pathways
 
−
*Would be good to have worm community also contribute; "Community Pathways" widget
 
−
*Conflict resolution? There could be many contributions to the same pathway
 
−
*Is there a way to pull up conflicting versions of a pathway?
 
−
*Open system: any registered user can modify any pathway
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
Community Annotation
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*Possibilities?
 
−
*Concise descriptions, pathways, what else?
 
−
*Expression patterns?
 
−
*Tables/templates of suggested data/types that authors could/should submit for a paper
 
−
*Annotation Apps? iPhone, Android, etc.
 
−
**Controlled vocabulary, virtual worm, AMIGO ontology browser, etc.
 
−
*Annotation on tablets, other mobile devices? Read only?
 
−
*Web app versus native app
 
−
*[http://www.openbadges.org Open Badges] for micro-attribution, incentives
 
−
*[http://about.orcid.org/ ORCID] for unique person IDs
 
−
*Possible Ontology Annotator version for community?
 
−
*Templates/forms would need to be very straight-forward and simple to use
 
−
*Maybe display a form alongside web display to inform users of how the two relate
 
−
*Training users: tutorials, workshops (2013 IWM?)
 
−
*Daily updates to website could be more satisfying for users
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
== November 8, 2012 ==
 
  
  
−
Construction
+
==February 15, 2024==
−
*Burning smell frequently
 
−
*Now cigarette smoke smell (maybe completely unrelated to construction, of course)
 
  
 +
=== 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
  
−
Curation Status Form
+
===== Manually validate paper - topic flags without curating =====
−
*http://mangolassi.caltech.edu/~postgres/cgi-bin/curation_status.cgi
+
*Facet for topic
−
*Curators cannot indicate both positive and negative for a data type per paper; conflict must be resolved by curators
+
*Facet for manual assertion
−
*One free text comment field (and one "pre-canned" comment field) per paper per data type
+
**professional biocurator assertion
−
*To what extent would a curator like to see all data for several papers at once? Likely only need to see one paper and one data type at a time
+
***ABC - no data
−
*The form provides a (unique) way for curators to "validate" a paper as "negative" for a data type
 
−
*It is important to decouple validation from curation, so we can capture both
 
−
*Ideal if each paper could be independently categorized according to flagging status, validation status, and curation status
 
−
*Papers can be identified as "Not Validated", "Validated Negative", "Validate Positive - Not Curated", or "Validate Positive - Curated"
 
−
*We will make adjustments to form to accomodate
 
  
 +
===== 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
  
−
Dead Genes
+
=== PDF Storage ===
−
*How do we/should we handle objects (e.g. interactions) that now refer to dead genes?
+
* At the Alliance PDFs will be stored in Amazon s3
−
*Would be best if we could keep the original gene reference with a downstream automated process (at dump, ACE build, webdisplay???) to convert to new IDs (if there are merges) or a remark indicating a dead gene
+
* We are not planning to formally store back-up copies elsewhere
−
*Will discuss more next week
+
* 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?
  
−
== November 15, 2012 ==
+
==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==
  
−
Scripts from Mary Ann
+
=== Curator Info on Curation Forms ===
−
*Script for recognizing alleles for Textpresso
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
*Mary Ann sent to James and Raymond
 
−
*James has been working on it
 
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
AQL/WQL Queries
+
* 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.
−
*HTML vs plain text output
 
−
*HTML output takes much longer than plain text and often times out
 
−
*Not optimal to give users AQL queries; will be better once Intermine is up and running
 
−
*User data requests are use-cases for Intermine
 
−
*Problem with web browsers timing out before AQL query can finish: this is a browser issue
 
  
 +
* 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.
  
−
Curation Statistics Tool
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Do curators want to see unions or intersections of specific flagging methods? Yes
 
−
*Will need to develop a visualization aside from the summary table
 
−
*Chris and Juancarlos will discuss offline
 
  
 +
=== 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
  
−
Human Disease tags for ?Gene model
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*Using common vocabulary
+
* NNC html pages will show NNC values together with species.
−
*Human_disease_info tag with subset tags : OMIM_ortholog, Potential_model_for, Experimental_model_for, and Human_disease_relevance
+
* Show all C. elegans papers first and other species in a separate bin.
  
−
<pre>
+
=== Travel Reimbursements ===
−
?Gene
+
* Still waiting on October travel reimbursement (Kimberly)
−
        Human_disease_info    OMIM_ortholog            ?Accession_number      #Evidence
+
* Still waiting on September and October travel reimbursements (Wen)
−
                              Potential_model_for      ?DO_term      XREF  Gene    #Evidence
 
−
                              Experimental_model_for    ?DO_term      XREF  Gene    #Evidence
 
−
                              Human_disease_relevance  ?Text      #Evidence
 
−
</pre>
 
  
−
*Change "?Accession_number" above to full database reference "?Database, ?Database_field, ?Accession_number"
+
=== UniProt ===
−
*And add tags to #Evidence hash?
+
* 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.
  
−
<pre>
+
==January 18, 2024==
−
?Evidence
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
−
            Inferred_from_sequence_orthology    ?Accession_number
 
−
            Inferred_from_mutant_phenotype      ?Variation
 
−
            Inferred_from_genetic_interaction    ?Accession_number
 
−
</pre>
 
  
−
*Evidence_code tag instead of using #Evidence hash?
 
  
 +
==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.
  
−
Automated, template-based draft concise descriptions
+
==January 4, 2024==
−
*Can make a student assignment for credit?
+
* 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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