Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
= 2021 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
+
==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)
  
−
== April 1, 2021 ==
+
==March 14, 2024==
  
−
=== Antibodies ===
+
=== TAGC debrief ===
−
* Alignment of the antibody class to Alliance:
 
−
** Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
 
−
*** Other animal is sometimes used for older annotations, e.g. authors say that the antibodies were raised both  in rats and rabbits. Standard practice would create 2 records, one for the rat antibody and one for the rabbit.
 
−
*** Possible pseudonym was used when  a curator was not able to unambiguously assign a previous antibody to a record. (we have a Other name -synonym- tag to capture unambiguous ones). When moving to remarks we can keep a controlled vocabulary for easy future parsing, e.g. “possible_pseudonym:”
 
−
** Antigen field: currently separated into Protein, peptide, and other_antigen (e.g.: homogenate of early C.elegans embryos, sperm). Propose to use just one antigen field to capture antigen info.
 
  
−
All changes proposed above were approved by the group
+
==February 22, 2024==
  
−
=== textpress-dev clean up ===
+
===NER with LLMs===
−
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
 
−
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
 
−
* Direct access may be possible via Caltech VPN
 
−
* Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines
 
  
−
=== Braun servers ===
+
* 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%)
−
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
 
−
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
 
  
−
=== Citace upload ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* Next Friday, April 9th, by end of the day
 
−
* Wen will contact Paul Davis for the frozen WS280 models file
 
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
== April 8, 2021 ==
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
=== Braun server outage ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Raymond fixed; now Spica, wobr and wobr2 are back up
 
  
−
=== Textpresso API ===
 
−
* Was down yesterday affecting WormiCloud; Michael has fixed
 
−
* Valerio will learn how to manage the API for the future
 
  
−
=== Grant opportunities ===
 
−
* Possibilities to apply for supplements
 
−
* May 15th deadline
 
−
* Druggable genome project
 
−
** Pharos: https://pharos.nih.gov/
 
−
** could we contribute?
 
−
* Visualization, tools, etc.
 
−
* Automated person descriptions?
 
−
* Automated descriptions for proteins, ion channels, druggable targets, etc.?
 
  
−
=== New WS280 ONTOLOGY FTP directory ===
+
==February 15, 2024==
−
* Changes requested here: https://github.com/WormBase/website/issues/7900
 
−
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
 
−
* Known issues (Chris will report):
 
−
** Ontology files are provided as ".gaf" in addition to ".obo"; we need to remove the ".gaf" OBO files
 
−
** Some files are duplicated and/or have inappropriate file extensions
 
  
−
=== Odd characters in Postgres ===
+
=== Literature Migration to the Alliance ABC ===
−
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
+
===== 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 =====
−
* We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
+
*Facet for topic
−
* Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters
+
*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
  
−
== April 15, 2021 ==
+
===== 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
  
−
=== Special characters in Postgres/OA ===
+
=== PDF Storage ===
−
* Juancarlos working on/proposing a plan to store UTF-8 characters in Postgres and the OA which would then get converted, at dumping, to HTML entities (e.g. α) for the ACE files
+
* At the Alliance PDFs will be stored in Amazon s3
−
* There is still a bit of cleanup needed to fix or remove special characters (not necessarily UTF-8) that apparently got munged upon copy/pasting into the OA in the past
+
* We are not planning to formally store back-up copies elsewhere
−
* Note: copy/paste from a PDF often works fine, but sometimes does not work as expected so manual intervention would be needed (e.g. entering Greek characters by hand in UTF-8 format)
+
* Is this okay with everyone?
−
* Would copy/pasting from HTML be better than PDF?
 
−
* For Person curation it would be good to be able to faithfully store and display appropriate foreign characters (e.g. Chinese characters, Danish characters, etc.)
 
−
* Mangolassi script called "get_summary_characters.pl" located here: /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters
 
−
** Juancarlos will modify script to take a data type code as an argument on the command line and return all Postgres tables (and their respective PGIDs) that have special characters, e.g.
 
−
*** $ ./get_summary_characters.pl exp
 
−
*** $ ./get_summary_characters.pl int
 
−
*** $ ./get_summary_characters.pl grg
 
−
*** Juancarlos will email everyone once it's ready
 
−
* Action items:
 
−
** Juancarlos will update the "get_summary_characters.pl" script as described above
 
−
** Curators should use the "get_summary_characters.pl" to look for (potentially) bad characters in their OAs/Postgres tables
 
−
** Need to perform bulk (automated) replacement of existing HTML entities into corresponding UTF-8 characters
 
−
** Curators will need to work with Juancarlos for each OA to modify the dumper
 
−
** Juancarlos will write (or append to existing) Postgres/OA dumping scripts to:
 
−
*** 1) Convert UTF-8 characters to HTML entities in ACE files
 
−
*** 2) Convert special quote and hyphen characters into simple versions that don't need special handling
 
  
−
=== CeNGEN pictures ===
+
==February 8, 2024==
−
* Model change went in to accommodate images from the CeNGEN project
+
* TAGC
−
* Want gene page images for CeNGEN data; have the specifications for such images been worked out? Maybe not yet
+
** Prominent announcement on the Alliance home page?
−
* Raymond and Daniela will work with data producers to acquire images when ready
 
  
−
=== Supplement opportunities ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Money available for software development to "harden" existing software
 
−
* Might be possible to make Eduardo's single cell analysis tools more sustainable
 
−
* Could make WormiCloud adapted to Alliance?
 
  
−
=== Student project for Textpresso ===
+
==February 1, 2024==
−
* Create tool to allow user to submit text and return a list of similar papers
+
* Paul will ask Natalia to take care of pending reimbursements
−
* Use cases:
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
** curator wants an alert to find papers similar to what they've curated
+
 
−
** look for potential reviewers of a paper based on similar text content
+
==January 25, 2024==
 +
 
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
 +
 
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
 +
 
 +
* The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
 +
 
 +
* I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
 +
 
 +
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
 +
 
 +
=== Update on NN Classification via the Alliance ===
 +
* Use of primary/not primary/not designated flag to filter papers
 +
* Secondary filter on papers with at least C. elegans as species
 +
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
 +
 
 +
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
 +
* NNC html pages will show NNC values together with species.
 +
* Show all C. elegans papers first and other species in a separate bin.
 +
 
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
 +
 
 +
=== UniProt ===
 +
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
 +
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
 +
 
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
 +
 
 +
 
 +
==January 11, 2024==
 +
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
 +
** Curators should make sure that, when pasting special characters, the duplicate function works
 +
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
 +
 
 +
==January 4, 2024==
 +
* ACKnowlegde pipeline help desk question:
 +
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 +
* Citace upload, current deadline: Tuesday January 9th
 +
** All processes (dumps, etc.) will happen on the cloud machine
 +
** Curators need to deposit their files in the appropriate locations for Wen
 +
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 18:05, 11 April 2024

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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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