Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
= 2015 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2015|January]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2015|February]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
= April 2015 =
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
== April 2, 2015 ==
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
* Adding Species information to nightly geneace dumps
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
** Michael Paulini is adding Species information for the WBGene IDs in the genes.ace file
 
−
** Does anyone want Species information for any of the other files
 
−
** For list of files, see: ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
= March 2015 =
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
== March 5, 2015 ==
+
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
=== New curation topic for WS249 ===
+
==April 4th, 2024==
−
* We will do Lipid Metabolism for WS249
+
* 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)
  
−
=== Paper ID converter tool ===
+
==March 14, 2024==
−
* Juancarlos built a simple CGI to convert a list of PubMed IDs to WBPaper IDs
 
−
* http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=PapIdToWBPaper
 
−
* Would other curators use this or a more comprehensive tool?
 
−
* What ID types would curators want to convert between?
 
  
−
=== GO data model change ===
+
=== TAGC debrief ===
−
* Change for WS248
 
−
* More detail with each annotation
 
−
* Pipeline for data incorporation into the build has changed; path goes through Caltech/Postgres for QC
 
−
* Changes to gene association file has implications for automated descriptions
 
−
* Do we want to include PAINT annotations for automated descriptions?
 
−
** Based on phylogenetic evidence codes
 
−
** Yes, could be a great benefit to the automated descriptions
 
−
** New GO annotations include a Panther tree node
 
−
** Should we include both manually annotated data AND PAINT data in automated descriptions equally? Should look at examples and check how we want to handle
 
−
* Clickable (linkable) evidence throughout the description?
 
  
−
=== International meeting give-aways ===
+
==February 22, 2024==
−
* Worm pick holders (pencil grips) with WormBase logos; can they be printed on?
 
−
* T-shirts and/or hats/caps; personalized for curators
 
  
−
=== Topic & Regional meeting abstracts ===
+
===NER with LLMs===
−
* Usually we receive the data for these meeting abstracts in a non-standardized format; makes it difficult/time-consuming to parse
 
−
* Would be good to request submissions in standard format
 
−
* Good to maybe go through GSA pipeline?
 
  
−
=== NIH request for info on sustaining bio-databases ===
+
* 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%)
−
* NIH requesting info on:
 
−
** best practices
 
−
** collaborations/partnerships
 
−
** efficiency
 
−
** alternative funding sources
 
−
*** requiring a DB funding allocation in individual grant applications?
 
−
** medical application
 
−
* What benefit do databases provide?
 
−
** Differential usefulness: transient DBs versus maintained, broader impact DBs
 
−
* Should MODs merge?
 
−
* So much has changed in terms of database and web technology since online bio DBs began
 
−
* Value distinction of manually curated annotations
 
−
* How much redundancy is there between DB effort?
 
−
* How do we assess the value of WormBase (or any DB) for academia and industry?
 
−
* We should assess the scientific value to determine monetary value
 
−
** Promote the benefit of transparency and reproducibility
 
  
−
=== Micropublication ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* We can introduce the idea at the international meeting
 
−
* May be nice to group all micropublications into a single official publication
 
−
* Maybe use "Gene Expression" journal for gene expression data as a pilot
 
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
== March 12, 2015 ==
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
=== Historical_gene tag ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Issues came up with layered hash references in ACEDB when converting to Datomic
 
−
* Changing line from "Historical_gene  ?Gene  #Evidence" to "Historical_gene  ?Gene  Text"
 
−
* Affects ?Interaction, ?Expr_pattern, ?Antibody, ?Construct, and ?WBProcess
 
  
−
=== WormBook Chapters ===
 
−
* Do we want/need a separate chapter/section on the new WormBase Ontology Browser?
 
−
** Maybe only need a few small paragraphs in other relevant chapters, should be sufficient
 
−
* Gene Function & Interaction chapter almost complete
 
−
** Need to finish intro for phenotypes
 
−
** Need to add predicted & regulatory interaction descriptions
 
  
−
=== Topic OA reminder ===
 
−
* The 'primary'/'nonprimary' paper status is updated automatically every night by a cron job
 
−
* The "Curation Status Omit" toggle button on TAB 3 was intended to flag nonprimary papers, but is no longer needed for that; only for rare noncuratable, primary, relevant articles (e.g. Methods papers)
 
  
−
=== Cloud bio-data storage ===
+
==February 15, 2024==
−
* Cloud has potential advantage of distributed colocation; robust for queries, performance etc.
 
  
−
=== Modeling user-submitted data ===
+
=== Literature Migration to the Alliance ABC ===
−
* How should we distinguish user-submitted data from curator-submitted data?
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Should we distinguish at the data model level, with a new tag for example? Probably only need to apply WBPerson evidence, etc.
+
===== 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 =====
−
* This issue came up with user-submitted/user-edited concise descriptions
+
*Facet for topic
−
* The distinction can be made explicit exclusively at the display (web page) level
+
*Facet for automatic assertion
−
* There could be a toggle in the OA to indicate user-submitted data
+
**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
  
−
== March 19, 2015 ==
+
=== 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?
  
−
=== WormBook Chapters ===
+
==February 8, 2024==
−
* Most chapters mostly complete as a draft
+
* TAGC
−
* Paul S. working on introduction
+
** Prominent announcement on the Alliance home page?
−
* Process chapter may not fill a chapter; also pending some website updates
 
−
* Person/author section can be added to nomenclature section
 
  
−
=== Mapping Bio-Annotations to Process ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Can we achieve automated mapping of annotations to processes?
 
−
* e.g. phenotype-to-process mapping, site-of-action (cells and genes) mapping to process
 
−
* Some phenotypes are indicative of a process, but some cannot be unambiguously mapped
 
−
* Some processes can be mapped to based on sequence homology (e.g. Wnt signaling) rather than phenotype
 
  
−
=== GO Physical interactions into WormBase ===
+
==February 1, 2024==
−
* Several (~400) papers in curation status form are considered "curated" for physical interactions via the GO pipeline
+
* Paul will ask Natalia to take care of pending reimbursements
−
* We would like to import these annotations into WormBase
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
* Directionality information has been lost in the GO annotations
 
−
* We want to re-curate the interactions to capture detection method and directionality
 
−
* We could import all interactions in bulk without detection method or directionality with flag indicating a need to re-curate with additional information
 
  
−
=== Topic curation ===
+
==January 25, 2024==
−
* Reminder for curators to check their lipid metabolism papers
 
−
* Daniela working with web team to create a Pictures widget on Topic pages to display pathway/topic images (with permission)
 
  
−
=== Interaction-based phenotypes ===
+
=== Curator Info on Curation Forms ===
−
* On staging, Sibyl has added an "Interaction-based Phenotypes" table in the Gene page Phenotypes widget
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* This phenotype data is taken exclusively from genetic interaction objects to associate the gene with the phenotype
 
  
 +
=== 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.
  
−
== March 26, 2015 ==
+
* 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.
  
−
=== Community submission forms ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
* Micropublication
 
−
** People may submit expression data directly, with future citation (e.g. DOI)
 
−
** Data submissions will need to adhere to some criteria providing evidence and reviewed by Paul, Daniela, and some other reviewer
 
−
** Form could be recycled for published data submission
 
−
** Forms remember user e-mails from IP used; makes easier to fill out subsequent submissions
 
−
** Daniela will talk to Daniel about assigning DOIs
 
−
** Can these be indexed by PubMed, etc.? Daniela discussing with Caltech librarians
 
−
* We should focus on promoting/pushing one data type submission so as not to overwhelm the community; focus on others later
 
−
* Concise description forms
 
−
** Want to send automated descriptions (or existing manual descriptions) to users to quality check based on their expert (published) knowledge
 
−
** User will use form to submit edits to descriptions
 
−
** Do we want/need users to stick to automated description format/guidelines?
 
−
** We could have direct links to forms from the Overview widget on gene pages
 
  
−
=== Funding Supplement Dedicated to Interoperability between MODs ===
+
=== Update on NN Classification via the Alliance ===
−
* Textpresso can be used to create common text mining pipelines across databases
+
* Use of primary/not primary/not designated flag to filter papers
−
* Combining concise descriptions or taking advantage of other MOD data
+
* Secondary filter on papers with at least C. elegans as species
−
* Supplement funding application due in April (soon)
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
  
−
=== Database migration ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
* Hope to have a pilot of new databases (Datomic?) done by mid-Fall
+
* NNC html pages will show NNC values together with species.
 +
* Show all C. elegans papers first and other species in a separate bin.
  
−
=== Global correlation of RNAseq gene expression data ===
+
=== Travel Reimbursements ===
−
* All pairs of genes could have a correlation calculation performed (based on RNAseq) and displayed on WormBase
+
* Still waiting on October travel reimbursement (Kimberly)
−
* Significant correlations could be a type of interaction/association
+
* 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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