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_2021|2021 Meetings]]
  
−
== April 6, 2017 ==
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
=== AGR time spent ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
* Paul S asking about %time spent on AGR project
 
−
* Time spent on working groups, conference calls, AGR development
 
−
* Send estimates to Paul
 
  
−
=== SimpleMine ===
+
==May 30th, 2024==
−
* Two tables added to SimpleMine for human orthology
+
===Entity association with references - Alliance ABC (Kimberly)===
−
* Now SimpleMine output has many columns (30+)
+
* Need to make sure we have the right classes in the ATP ontology for what WB wants to associate wrt transgenes
−
* We may want to give users the option to specify which output they want
+
** Variation
−
* Users could specify groups of data (with checkboxes): gene IDs/names, phenotypes, orthology, etc.
+
** Construct
−
* All checkboxes can be checked by default
+
** Transgene
 +
** Rearrangement
 +
* Suggestion: create a new child of allele: transgenic allele and use that for WB transgenes
 +
* Question: should affected genomic model be a child of entity?
  
−
=== Enrichment tools ===
+
===AWS costs===
−
* Raymond working on display for paper
 
  
−
=== Gene Ontology SObA graph ===
+
==May 23rd, 2024==
−
* Raymond, Juancarlos working on
+
*Publication bias workshop NINDS
−
* Working on paper
+
** Registered report -> the protocol is sent before publication
 +
** How many negative curated data? Do we want to pull this out?
 +
** Two billion dollars worth of research not published each year
 +
**Octopus.ac publishing platform
  
−
=== WormMine updates ===
+
==April 18th, 2024==
−
* WS258 adding gene class
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
−
* WS259 adding more info (almost all meta data) on variations, laboratory and strains, RNAi phenotypes (hopefully)
 
−
* Expression data in WormMine is problematic
 
−
* Many genes being annotated to the same ~6 tissues or so
 
−
* Resulting in erroneous data for some genes
 
−
* Chris will send GitHub ticket to Todd
 
−
* Todd will discuss with Paulo today
 
  
−
=== Gene Ontology ===
+
==April 11th, 2024==
−
* Some very complex terms becoming immediate children of root terms (e.g. "biological process")
+
*Caltech WS293 ace files ready for the upload
−
* May be result of attempt to create logical definitions/equivalence axioms
 
−
* Raymond will discuss with Kimberly
 
  
 +
==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)
  
−
== April 13, 2017 ==
+
==March 14, 2024==
  
−
=== Methods in Molecular Biology chapter ===
+
=== TAGC debrief ===
−
* Chapter draft sent out Monday night
 
−
* Will send to Martin at MiMB by late next week
 
−
* Please take a look and send comments
 
−
* Authors check their sections and send figure legends to Chris
 
  
−
=== Progress report ===
+
==February 22, 2024==
−
* If someone finds the 2016 report, send around to group
 
−
* May 1st deadline (need to verify)
 
  
−
=== 2017 IWM ===
+
===NER with LLMs===
−
* Early registration Deadline May 18th
 
  
−
=== Models for citace ===
+
* 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%)
−
* Wen will fit models to local citace, should be ready by tomorrow
 
  
−
=== Citace Upload ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* Tuesday, April 25th, 10am
 
  
−
=== Enrichment tool ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Now available for gene ontology and phenotype on live site
 
−
* Paper being submitted soon
 
−
* Need to change "Tissue Enrichment Analysis" link title under WormBase Tools menu
 
  
−
=== SObA for Gene Ontology ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Data source was server on Berkeley BOP; thought it was public but were discouraged to use
 
−
* Seth Carbon said we could use it but might not always be working; now it seems to be down or dysfunctional
 
−
* SObA for GO will be broken until we install our own local server (Raymond working on)
 
  
−
=== Dumping data for upload, taking over for Karen ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Karen will take care of dumping and uploading the data for this upload
 
−
* Karen will review the molecule curation with other curators at the IWM
 
  
−
=== Datomic meeting ===
 
−
* Matt, Sibyl, Adam, Todd, Juancarlos, Raymond sat in
 
−
* Raymond: thought Datomic would take over from ACEDB completely, but it seems we will still use ACEDB for some time for e.g. FMap
 
−
* Seems there should be an executive meeting about Datomic to make clear what it will be used for and what it won't be used for
 
−
* Several web pages and widgets are now being served by Datomic
 
−
* There's a question about how we now handle model changes going forward
 
−
* Juancarlos will send around link for newest Datomic querying tool; may require access for specific IP addresses
 
  
  
−
== April 20, 2017 ==
+
==February 15, 2024==
  
−
=== Gene Ontology data for SObA ===
+
=== Literature Migration to the Alliance ABC ===
−
* Use of GO server; hasn't been reliable
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Raymond working on establishing our own server to host all GO data
+
===== 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 =====
−
* Raymond and Juancarlos will keep working on SObA representation of GO annotations
+
*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
  
−
=== Progress Report ===
+
===== Manually validate paper - topic flags without curating =====
−
* WS259 can be used as the current reference
+
*Facet for topic
−
* Paul will send around last year's progress report
+
*Facet for manual assertion
−
* What was the last release that we referenced in last year's progress report? We'll say WS254
+
**professional biocurator assertion
−
* Wen will generate numbers for WS254 (resurrect WS254 ACEDB)
+
***ABC - no data
−
* Opportunity to specify/narrow scope of project
 
−
* Want to push community/automated curation, with curators laying foundation of data models, forms
 
−
* Promote LEGO curation; need to learn what needs to be said about plan going forward/what we want to accomplish
 
  
−
=== LEGO curation ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* Phenotype curation in LEGO? Need to review phenotype-to-GO pipeline
+
* Search ABC with paper identifier
−
* Want/need a mapping of phenotype terms to GO process terms; may require context-dependent mapping (e.g. "dumpy" phenotype)
+
* Migrate to Topic and Entity Editor
−
* We don't make direct associations of phenotypes to LEGO models, although we do have "inferred from mutant phenotype" evidence code
+
* View all associated data
−
* Want a mechanism to automate conversion of WB annotations into LEGO models
+
* Manually validate flags, if needed
−
* Want a display mechanism that is user friendly, convert hairball into pathway
 
−
* We could focus on a particular topic/disease and collectively contribute
 
−
* Do we want to write a proposal to take existing, granular annotations (e.g. at level of mutation details) and map to LEGO model?
 
−
* Can we integrate the micropublication pipeline into LEGO model generation?
 
−
* How to assess the confidence of assertions?
 
  
−
=== Follow up on transgene question from user ===
+
=== PDF Storage ===
−
* Karen will contact authors of paper
+
* 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?
  
−
=== Citace upload ===
+
==February 8, 2024==
−
* Tuesday, Apr 25th, 10am
+
* 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.
  
−
== April 27, 2017 ==
+
==January 25, 2024==
  
−
=== Gene Ontology data for SObA ===
+
=== Curator Info on Curation Forms ===
−
* All GO annotation data loaded at Caltech (bigGO solr database, 54GB)
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* 100 species, 922296 bioentity (protein, gene product ...)
 
−
* [http://131.215.12.204/~raymond/cgi-bin/soba_biggo.cgi Testing site], try
 
−
  let-23, KRas (human)
 
−
  eat-4, SLC17A7 (human)
 
−
* Heavy querying may cause the server to go down; need to check why
 
−
* ~7 hours to load
 
  
−
=== AGR lexica ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* Karen's SBIR, trying to get gene names from each AGR database
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
* Non-trivial, in some cases, to query out curated papers list
+
 
 +
* 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 18:12, 30 May 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

May 30th, 2024

Entity association with references - Alliance ABC (Kimberly)

  • Need to make sure we have the right classes in the ATP ontology for what WB wants to associate wrt transgenes
    • Variation
    • Construct
    • Transgene
    • Rearrangement
  • Suggestion: create a new child of allele: transgenic allele and use that for WB transgenes
  • Question: should affected genomic model be a child of entity?

AWS costs

May 23rd, 2024

  • Publication bias workshop NINDS
    • Registered report -> the protocol is sent before publication
    • How many negative curated data? Do we want to pull this out?
    • Two billion dollars worth of research not published each year
    • Octopus.ac publishing platform

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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