Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
−
==February 10, 2011==
+
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 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]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
 +
 
 +
 
 +
==March 14, 2024==
  
−
*Should we have a Caltech project/site manager? We'll look at the issues to be solved first
+
=== TAGC debrief ===
  
−
*Todd would like to know more about what's going on at Caltech
+
==February 22, 2024==
−
**What would Todd like to know about? New ideas, data types?
 
−
**What can we communicate more effectively to Todd?
 
  
−
*Should we take minutes of Caltech WormBase group meetings and send around?
+
===NER with LLMs===
  
−
*Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
+
* 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%)
  
−
*Bitbucket use
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
**How do we see only what pertains to us, individually?
 
−
**Paul: good way to document bugs and fixes, problems/solutions
 
−
**Bitbucket Wiki - does that capture what people want/need to see?
 
−
**Who should Todd follow? What would Todd like to know about?
 
−
**Raymond: used for code development/versioning by OICR; may be the best use for Bitbucket
 
−
**Should we develop best practices guideline for Bitbucket use?
 
−
***Avoid posting topics that are too specific or too vague?
 
−
***What do we want most to get out of Bitbucket?
 
−
**Curation efforts? No
 
  
−
*SAB Meeting
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
**Not much feedback for literature curators
 
−
**User interface stuff took precedence
 
−
**Paul: Testing, spot-checking website for errors
 
−
**Web issues, e-mails from Gary and Oliver
 
  
−
*WormBase-wide conference call twice per month
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
**First & third Thursday of the month
 
−
**Starting next Thursday (2-17) @ 8:30am PST
 
−
**Web redesign meetings on Thursdays will have to be every other week? Do both same day?
 
  
−
*Raymond: WormBase mirrors
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
**Do we want to implement the Genome Browser for the mirror(s)? If practical
 
−
**It seems as though Caltech mirror has been crashing often
 
−
**Has the Caltech mirror been working for people lately? Yes, more or less
 
  
  
−
== February 17, 2011 ==
 
  
−
Interaction dumping script
+
==February 15, 2024==
−
*Spot check table
 
−
*Push changes to Git? Yes, to main branch
 
  
 +
=== 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
  
−
Interactions automatically downloaded to FTP every release? Yes
+
===== Manually validate paper - topic flags without curating =====
−
*People should check their own curation data
+
*Facet for topic
−
*Users query frequently?
+
*Facet for manual assertion
−
*Can WormMart work instead?
+
**professional biocurator assertion
−
*Ruihua - feature can be added
+
***ABC - no data
−
*Todd - good to have pre-defined queries generated automatically
 
−
*Parse/remove predicted interactions (400,000) from others during dump? Yes
 
−
*Paul - Wei Wei wants to help with updates - who should she contact at WB?
 
  
 +
===== 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
  
−
Ranjana - Solar flares causing static on phone? ;)
+
=== 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?
  
−
Newsletter for new website release? Yes
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
*Todd - 5 development milestones
 
−
**teleconference with Gary Ruvkun's lab next week
 
−
**Go live with Beta version in June (@IWM)
 
−
**Go live live with new site in September
 
−
**Retire old site at end of year
 
−
**Need outreach, documentation, screencasts
 
  
 +
==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.
  
−
BioGRID
+
==January 25, 2024==
−
*WormBase to BioGRID curation
 
−
*Issues of mapping interaction types: WB -> BioGRID vs. BioGRID -> WB
 
−
*Moving towards using WB interaction types
 
−
*Definitions of our interaction types
 
−
*Rose will propose to BioGRID community
 
−
*Physical interactions - BioGRID has a better format
 
−
**break physical interactions away from other interaction types?
 
−
**Kimberly can propose changes to model: YH separate from other interactions?
 
−
**Physical vs Genetic interactions? keep separate
 
−
*We need an interaction ontology, of some sort
 
−
*Who should Wei Wei contact, how to coordinate with Hinxton; getting data from FlyBase and SGD?
 
−
**Automation?
 
−
*Interaction pages - explain what the interaction is based on; provenance/reference
 
−
*Gene Orienteer shows data, but user has to link out
 
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
−
WormBase IWM souvenir?
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
*Computer stress ball? with new site address?
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
*bouncy ball?
 
−
*worm rubber band thing?
 
−
*Screen shield?
 
−
*Complementary iPads? ;)
 
−
*Antifungal socks? wristbands?
 
  
 +
* 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.
  
−
SPELL
+
* 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.
−
*new data doesn't load; problem runnning search engine; can load it on athena, not generalizable problem?
 
−
*OS was not complete with an update; try again
 
−
*two virtual machines working back and forth for support
 
−
*how often is SPELL being used? log?; had 6-7 users within two weeks complaining of SPELL problems
 
−
*Todd - can send Google analytic tool to put at bottom of page
 
−
*Wen - SPELL testing server; official and mirror; want a separate testing server for new releases; mirror on athena (Wen's working machine); Raymond says don't want to attract users to that machine; WB's running SPELL on altair; heavily loaded and has had problems; relying on athena may be problematic
 
−
*maybe we need analysis of all of our machines to see big picture; can we consolidate machines; make use of ones we have? If not we can get another machine.
 
−
*what type of machine do we need?
 
−
*Log of all machines with purchase date and functionality?
 
−
*Linux vs Mac curators? athena development machine;
 
−
*how much power do the scripts need? can check
 
−
*may not be appropriate as official server if main machine goes down
 
−
*WB and athena can run SPELL server, but not others. security problems?
 
−
*prefer work machine is readily re-bootable; reconfigure software easily without affecting other things that people rely on
 
−
*need 10GB space; 4GB memory? SPELL production server; want it stable for outside world; hardware designed for that purpose; farm it out to IMSS?
 
−
*complexity of the application; Linux can run multiple applications; caprica has SVM production and WormMart; understand demand of the application; requirements; development vs running scripts, how often? Efficient use of machines. Have 2 computers, getting a third; for WormMart need power; traffic suddenly increased yesterday; monitor traffic; not much personal experience with server maintenance; cluster needs lots of expertise
 
−
*building official sever of SPELL at OICR? Yes
 
  
 +
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
−
WormMart
+
=== Update on NN Classification via the Alliance ===
−
*with WormMart and WormBase, people just want to know if it's down, just to know to lessen frustration; Official statement from dev team
+
* Use of primary/not primary/not designated flag to filter papers
−
*WormMart - we give users testing url; can we just change WormBase link to that testing server?
+
* Secondary filter on papers with at least C. elegans as species
−
*going to change HTML to update users with most recent information; discuss with Lincoln, 5 datasets on testing server; remaining 3 datasets. if WormMart not working, put a message on main site
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
−
*it doesn't look good to have a link to a tool linked from a production server; if we don't trust the data we shouldn't put it up.  
+
* Next NN clasification scheduled for ~March
−
*would like to keep the html page as a testing server; could modify page
 
−
*if WormMart is working OK but not perfect, that's OK; Comment in the banner
 
−
*the html page is a useful tool to get feedback from users
 
  
 +
* 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.
  
−
== February 24, 2011 ==
+
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
CIT Computer Survey - done
+
=== 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.
  
−
CD/DVD burner not working (Wen)
+
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
−
Build Scripts:
 
−
*run @ OICR
 
−
*dynamic/static files
 
−
*problem: no one takes care of them
 
−
*curators should claim them and take care of them
 
−
**Gene interaction dump script claimed by Raymond and Xiaodong
 
−
**256 interaction objects empty (should not be); emptied during build?
 
−
*Monitor usage with new site
 
−
*Files (like FASTA, GFF) should be immediately available to users
 
−
*Page that links to the scripts (FTP)
 
−
*Need to define what we should have (common datasets)
 
−
**Example: Table with all genes, RNAi phenotype, genetic phenotype, etc.
 
−
**How many genes have been knocked out by RNAi?, etc.
 
−
**Metrics table on each species: #genes, #chromosomes, etc.
 
−
*Curators think about what data should be available
 
−
*Modifying existing script is easier than making new one
 
−
*Gary Williams already generates RNAi-phenotype-gene connections?
 
  
−
Snehal work half-time at WormBase?  
+
==January 11, 2024==
−
*Will interview
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
−
*UI testing?
+
** Curators should make sure that, when pasting special characters, the duplicate function works
−
*Curation? GO? Phenotype?
+
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
−
*Start April 15th - 8 months? (Sept.) maybe longer
+
** 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)
−
*Focus on particular papers?
+
* 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.
  
−
Physical Interaction model
+
==January 4, 2024==
−
*Have been discussing with Rose at BioGRID
+
* ACKnowlegde pipeline help desk question:
−
*Y2H, CoIPs, Pull downs, etc.
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*Store physical interactions in WB outside of GO curation
+
* Citace upload, current deadline: Tuesday January 9th
−
*Data model
+
** All processes (dumps, etc.) will happen on the cloud machine
−
**YH model vs Interaction model
+
** Curators need to deposit their files in the appropriate locations for Wen
−
**Physical interaction tag in current interaction model unused
+
* Micropublication pipeline
−
**Generalize YH model -> physical interaction model
+
** Ticketing system confusion
−
**Add experiment types
+
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics
−
**Issue: what do we do with existing physical interaction tag in interaction model?
 
−
**Split out different interaction types into individual classes?
 
−
**Separate into physical, genetic, predicted classes? Textpresso?
 
−
**Create separate classes for each experimental type? (Y2H, CoIP, etc.)  
 
−
**XREF Interaction to Physical interaction, Genetic interaction
 
−
**Goal is for cleanliness and completeness
 
−
**How to capture experimental-specific info in curation and database?
 
−
**Suppress Y2H import from BioGRID?
 
−
**Keep interaction models as they are?
 
−
**All curators: Review interaction models to see what they want on the curation end
 

Revision as of 18:18, 14 March 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


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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