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]]
  
−
= January 2015 =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
== January 8, 2015 ==
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
=== Community annotation===
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
−
* author participation
 
−
**Cecilia: still lots of work, need to manually process data submitted by authors
 
−
** old data kept for history and for comparison
 
−
** people mess up institution names - institution field on submission form being changed to a controlled vocabulary
 
−
** campus addresses also not standardized - will organize/create address fields, e.g., street address, mail-code, etc.,
 
−
** add example address
 
−
** ~10 author submissions a week
 
−
** most curation involves extracting people information from papers (~800 week), as automated as possible right now - people and affiliation are extracted from xml, but information still needs to be parsed
 
−
** can we mine author data from other sources (institution, laboratory); important to get laboratory address for sending strains; two sets of data- (1) easy- people associated with a laboratory, (2) difficult- people not in a registered lab
 
  
−
===Cross-product development===
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
Raymond
 
−
* embarking on cross-product generation- ex., male tail, versus hermaphrodite tail - better to have one 'tail' and add modifiers
 
−
* wants to move to OWL now; comment is that obo relationships are not directly translatable into OWL
 
−
* Uberon has elegans anatomy
 
  
−
Gary
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
* starting to work with Chris and Karen on developing cross-products, still in exploration phase
 
−
* not looking at OWL yet
 
−
* will get relationships from Raymond
 
  
−
===Sequence feature curation===
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
Daniela, Gary, Xiaodong, Mary Ann are validating papers as positive/negative in curation status form. As soon as ready, Mary Ann/Gary will start curating
 
  
−
===Rose alleles===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
* 150,000 new alleles, Mary Ann done just all bar 12 of them in time for WS247
 
−
* phenotypes were only reported for a small fraction
 
  
−
===CGC strains===
+
==April 18th, 2024==
−
Mary Ann received latest update, CGC very busy with strains generated through new gene engineering techniques
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
=== WB WBook chapters ===
+
==April 11th, 2024==
−
Main outline [https://docs.google.com/a/wormbase.org/document/d/1l6pExlCMI88pi_-djk8jt7IzNsMDV-nIEY9Z1gBNh-A/edit here]- note this document cannot be edited, people can create their own shared docs for their respective papers
+
*Caltech WS293 ace files ready for the upload
−
*Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly) 
 
−
[https://docs.google.com/a/wormbase.org/document/d/1mAxrqVIhxDNpkTUBmtu12sAo58pEG763tgASlzy-3JU/ here]
 
−
*Pathways and Processes (Karen)  [https://docs.google.com/a/wormbase.org/document/d/1maTRPoIdmbZqfnd-8jZ5dCYPGM2fF6ihk9ZMhjcVL1Y/edit?usp=drive_web here]
 
−
* Expression (Daniela)
 
  
−
===Micropublication===
+
==April 4th, 2024==
−
* Hobert- micropublication for expression = small facts, which are data that will never be published (Daniela working with Hobert on these)
+
* Continued discussion on sustainability
−
* Community annotation not linked to a publication
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
−
* a couple models for WB dealing with the micropubs
+
** Data is still going to SPELL and enrichment analysis
−
** WB captures all submissions blind and posts them
+
** 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.
−
** WB reviews submission - curators decide which micropubs have value
+
* Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
−
* need to establish microattributions to increase the value of submissions
+
* Michael's presentation on LLMs - Named Entity Recognition (NER)
−
* involve semi-peer review through automated fact review requests to scientists who've worked on the gene, cell, entity, etc.
 
−
* need to set up a pilot, to get a feel for the amount of participation/work this tool will be
 
  
−
=== Picture curation ===
+
==March 14, 2024==
−
*for topic curation
 
−
**want to annotate figures with genes - involves model change
 
−
**want dynamic display with slide show, different highlighted figures - need to work with webteam
 
−
* community voting - crowdsourcing - need to work with webteam
 
−
* WB-blessed image represented through wikipathways
 
  
−
===Kimberly===
+
=== TAGC debrief ===
−
Continuing work on the new GO model
 
  
−
===Juancarlos===
+
==February 22, 2024==
−
* management of automated descriptions with Ranjana
 
−
* phenotype requests through RNAi and allele phenotype done in december
 
  
−
===Automated descriptions===
+
===NER with LLMs===
−
* playing with pulling out useful data to add to description automation (James and Ranjana)
 
  
 +
* 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%)
  
−
== January 15, 2015 ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
=== New expression objects and pictures ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Cross-species comparison of developmental gene expression
 
−
* Have life stage annotation
 
−
* Microarray experiments
 
−
* Do we have data on significant differences from C. elegans? Can we get the analysis or algorithm?
 
  
−
=== Neuro anatomy ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* 3 ways to access neuro-connectivity data
 
−
* ACEDB, Kris Gunsalus' server at NYU (defunct), Nikhil Bhatla's connectivity browser
 
−
* We would like to adopt Nikhil's browser (for neural connectivity AND the cell lineage browser); we need to act before it disappears
 
  
−
=== FPKM RNA-Seq data display ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Should we suggest splitting the data display by tissue, life stage, treatment, etc.?
 
−
* Gary Williams is responsible; need to talk to him
 
  
−
=== Heavy metal toxicity/response ===
 
−
* New topic, all papers have been checked
 
−
* Need to send list of relevant genes to Hinxton
 
−
* Curators can now flag figures relevant as topic diagrams
 
  
−
=== Phenotype picture curation ===
 
−
* We will begin to collect pictures for phenotypes
 
−
* Will require model changes
 
  
−
=== Phenotype OA Strain fields ===
+
==February 15, 2024==
−
* "Parental strain" autocomplete field added to TAB 2 of Phenotype OA
 
−
* Plan is to put parental strains in the Phenotype_info hash
 
−
* Natural isolate strains can be directly annotated with phenotype?
 
  
−
=== BioCuration meeting in April ===
+
=== Literature Migration to the Alliance ABC ===
−
* Xiaodong is writing up an abstract, will send around before submission
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Xiaodong will run a curation tutorial for Chinese speakers
+
===== 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
  
−
==Jan 22, 2014==
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
=== ad hoc curation of tier III species (Mary Ann)===
+
* Search ABC with paper identifier
−
WBPaper00046176 describes Ctr- genes and alleles (fig 3). Although we do not curate this (and other tier III) species, should we place this information somewhere, on an ad hoc basis?
+
* Migrate to Topic and Entity Editor
−
http://tazendra.caltech.edu/~acedb/daniel/00046176_Wei14_temp.pdf
+
* View all associated data
 +
* Manually validate flags, if needed
  
−
Mins: Curate as much as existing models allow and hopefully expand at later date. The volume of this sort of data will increase as we encourage Community Curation.
+
=== PDF Storage ===
−
Don't seek out papers, but add data as they come along.
+
* At the Alliance PDFs will be stored in Amazon s3
−
Talk to Hinxton about adding gene models.
+
* We are not planning to formally store back-up copies elsewhere
 +
* Is this okay with everyone?
  
−
=== Complex Gene Loci (Mary Ann) ===
+
==February 8, 2024==
−
e.g. lin-15A/lin-15B
+
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
unc-17/cha-1
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
We should use existing Gene_cluster model and add new Type tag to differentiate between e.g. rrn Gene cluster and e.g. lin-15A lin-15B complex loci.  
+
==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.
  
−
nb. Maybe hard to discuss w/o Paul Davies.
+
==January 25, 2024==
  
−
===micropublication===
+
=== Curator Info on Curation Forms ===
−
*Daniela starting to work on author submission forms for expression patterns where people can submit images
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
*Requirements?  Paul says needs sequence - minimal important stuff, sequence, expression pattern, construct, reporter gene
+
 
−
*genome coordinates are ok for elegans, but not for other species whose genomes
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
*making a micropublication - identifier, research object identifier,
+
* 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 16:04, 18 April 2024

Previous Years

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2012 Meetings

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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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