Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
==March 14, 2024==
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
=== TAGC debrief ===
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
==February 22, 2024==
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
===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%)
  
== June 4, 2020 ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
=== Citace (tentative) upload ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 
* Citace upload to Hinxton on Friday, July 10th
 
  
=== Caltech reopening ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* Paul looking to get plan approved
 
* People that want to come to campus need to watch training video
 
* Masks available in Paul's lab
 
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 
* Also, need to submit who you were in contact with for contact tracing
 
* Form is used all week, and hold on to it until asked to be submitted
 
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
 
  
=== Nameserver ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Nameserver was down
 
* CIT curators would still like to have a single form to interact with
 
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 
* Hinxton is pulling in CGC strains, how often?
 
* Caltech could possibly get a block of IDs
 
  
=== Alliance SimpleMine ===
 
* Any updates? 3.1 feature freeze is tomorrow
 
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
 
  
  
== June 11, 2020 ==
+
==February 15, 2024==
  
=== Name Service ===
+
=== Literature Migration to the Alliance ABC ===
* Testing site now up; linked to Mangolassi
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* CGI from Juancarlos not accepting all characters, including double quotes like "
+
===== 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 =====
* Example submission that fails via CGI
+
*Facet for topic
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
+
*Facet for automatic assertion
* Juancarlos will look into and try to fix
+
**neural network method
 +
*Facet for confidence level
 +
**High
 +
*Facet for manual assertion
 +
**author assertion
 +
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
=== Alliance Literature group ===
+
===== Manually validate paper - topic flags without curating =====
* Textpresso vs. OntoMate vs. PubMed
+
*Facet for topic
* Still some confusion about what the different tasks can be performed in each tool
+
*Facet for manual assertion
* Working on collecting different use cases on spreadsheet
+
**professional biocurator assertion
* Sentence-based search is big strength of Textpresso
+
***ABC - no data
* At latest meeting performed some large searches for OntoMate and Textpresso
 
* Literature acquisition: still needs work
 
** Using SVM vs. Textpresso search to find relevant papers
 
** Species based SVM? Currently use string matching to derive different corpora
 
** Finding genes and determining which species those genes belong to?
 
  
=== Alliance priorities? ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* Transcription regulatory networks
+
* Search ABC with paper identifier
* Interactions can focus on network viewer eventually
+
* Migrate to Topic and Entity Editor
** May want different versions/flavors of interaction viewers
+
* View all associated data
** May also want to work closely with GO and GO-CAMs
+
* Manually validate flags, if needed
* Gene descriptions can focus on information poor genes, protein domains, etc.
 
  
=== Sandbox visual cues ===
+
=== PDF Storage ===
* Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
+
* At the Alliance PDFs will be stored in Amazon s3
* AFP and Micropub dev sites have indicators
+
* We are not planning to formally store back-up copies elsewhere
* Could play with changing the background color? Maybe too hard to look at?
+
* Is this okay with everyone?
* Change the color of the title of the form, e.g. the OA?
 
* Will add red text "Development Site" at top of the OA form
 
  
=== Evidence Code Ontology ===
+
==February 8, 2024==
* Kimberly and Juancarlos have worked on a parser
+
* TAGC
* Will load into ACEDB soon
+
** Prominent announcement on the Alliance home page?
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
== June 18, 2020 ==
+
==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.
  
=== Undergrad phenotype submissions ===
+
==January 25, 2024==
* Chris gave presentation to Lina Dahlberg's class about community phenotype curation
 
* Class took survey about experience with presentation and experience trying to curate worm phenotypes
 
** Survey results: https://www.dropbox.com/s/00cit5aitv8yu27/Dahlberg_class_survey_results.xlsx?dl=0
 
** Some students didn't benefit, but most did; nice feedback!
 
** Lina intends to publish/micropublish the survey results so please don't share
 
* Since April 24, the class has submitted 171 annotations from 23 papers (some redundant and some still under review)
 
  
=== Special characters in OA/Postgres ===
+
=== Curator Info on Curation Forms ===
* There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
 
* It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
 
* Juancarlos wrote Perl script on Mangolassi at:
 
** /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters/get_summary_characters.pl
 
** Will find bad characters and their pgids for a given Postgres table
 
** Will find bad data and their pgids for the same table
 
** People can query their data tables for these characters
 
* Chris & Wen will work on compiling a list of bad characters that tend to come up
 
  
=== Citace upload ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
* July 10th citace-to-Hinxton upload
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
* July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th
 
  
 +
* 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.
  
== June 25, 2020 ==
+
* 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.
  
=== Caltech Summer Student ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
* Paul has new summer student
 
** Molecular lesion curation, maybe
 
** Are early stops more or less likely to be null mutations?
 
** Alleles are flagged as null in WB in the context of phenotypes
 
** Would be good to query Postgres for null alleles and work from there
 
* Fernando
 
** Anatomy function
 
** GO curation? Curating transcription factors?
 
*** Checking for consistent curation
 
  
=== Worm Community Diversity Meeting ===
+
=== Update on NN Classification via the Alliance ===
* Organized by Ahna Skop and Dana Miller
+
* Use of primary/not primary/not designated flag to filter papers
* Invite posted on Facebook "C. elegans Researchers" group
+
* Secondary filter on papers with at least C. elegans as species
* Two meetings held: one Thursday (June 18th), one Friday (June 19th)
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
* Chris attended last Friday (June 19th)
+
* Next NN clasification scheduled for ~March
* Worm Board looking to take input and ideas from this meeting and incorporate into meetings and events
 
* One idea was to document and track outreach efforts and what people have learned from them and organize them in a central location, maybe WormBase or Worm Community Forum
 
* Also, there was a suggestion to have a tool that could inform potential students of worm labs in their respective local area
 
** Ask Todd; he used to have a map of researchers; Todd had asked Cecilia to curate lab location and institution
 
* Person and Laboratory addresses in ACEDB have a different format, so looking to reconcile
 
* Do we know how many labs are still viable? Check for a paper verified in the last 5 years, or requested strains from the CGC recently
 
** Most labs were real
 
  
=== C_elegans Slack group ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
* Called "C_elegans"
+
* NNC html pages will show NNC values together with species.
* Chris made a "WormBase" channel for people to post questions, comments
+
* Show all C. elegans papers first and other species in a separate bin.
* Chris will look into inviting everyone and possibly integrating with help@wormbase.org email list
 
  
=== WormBase Outreach Webinars ===
+
=== Travel Reimbursements ===
* While travel is still restricted, we should consider WormBase webinars
+
* Still waiting on October travel reimbursement (Kimberly)
* Scott working on a JBrowse webinar
+
* Still waiting on September and October travel reimbursements (Wen)
* Could have a different topic each month
 
* Should collect topics to cover and assign speakers (maybe multiple speakers per topic; keep it lively)
 
* Should set up a schedule
 
* How should we advertise? Can post on blog, twitter, etc.
 
  
=== New transcripts expanding gene range ===
+
=== UniProt ===
* Will bring up at next week's site-wide call
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
* Possibly due to incorporation of newer nanopore reads
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
* Many genes coming in WS277 have expanded well beyond the gene limits as seen in WS276
+
* Stavros escalates the issue on Hinxton Standup.
** Example genes: pes-2.2, pck-2, herc-1, atic-1
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
* Has several repercussions:
 
** WormBase does not submit alleles affecting more than one gene; with these gene expansions suddenly alleles once only affecting a single gene are now affecting two genes, and so are now omitted from loading into the Alliance (including any phenotype and/or disease annotations)
 
** Some expanded genes are now being attributed with thousands of alleles/variants
 
  
=== Citace upload ===
+
==January 18, 2024==
* Upload files to Spica/Wen by Tuesday (June 30th) 10am
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
* Wen will clean up folders in Spica (older files from WS277 not cleared out for some reason)
 
  
==July 9th, 2020==
 
===Gene names issue in SimpleMine and other mining tools===
 
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
 
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
 
*Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
 
*Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
 
*Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
 
**single public name is assigned to multiple WBgene ID.(you listed up these cases in the word file you attached)
 
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
 
**overlapped or dicistronic, but has a single sequence name, examples:
 
    exos-4.1 and tin-9.2 (B0564.1)
 
    eat-18 and lev-10 (Y105E8A.7)
 
    cha-1 and unc-17 (ZC416.8)
 
  
**simple confusion from authors, ex. mdh-1 and mdh-2
+
==January 11, 2024==
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
+
** Curators should make sure that, when pasting special characters, the duplicate function works
*Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data minign tools. They will also write a microPub explaining this issue to the community.
+
* 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.
  
===Wormicloud===
+
==January 4, 2024==
*Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud  
+
* ACKnowlegde pipeline help desk question:
*With a pair of keywords can generate a graph that plots trends of occurence across the years in publication abstracts
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 
+
* Citace upload, current deadline: Tuesday January 9th
===Noctua 2.0 form ready to use===
+
** All processes (dumps, etc.) will happen on the cloud machine
*Caltech summer student will try using Noctua initially for duaer (neuronal signaling) pathways
+
** 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 18:18, 14 March 2024

Previous Years

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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


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