Difference between revisions of "WormBase-Caltech Weekly Calls"

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==June 11, 2009==
+
= Previous Years =
−
*Discussion of allele-paper connections
 
−
**Jolene has a Textpresso-based pipeline for identifying alleles in papers
 
−
**Alleles get associated with a paper if there is phenotypic or molecular data
 
−
**List of all alleles associated with a paper could possibly be passed on to Sanger for subsequent connection
 
  
−
*Discussion of gene-paper connections
+
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
−
**What criteria should be used for associating genes with papers?
 
−
**Currently being associated manually by a curator during first-pass
 
−
**Could Textpresso be harnessed for this task?
 
−
**There are different evidences attached to gene-paper connections
 
−
**Genes associated with a paper via Textpresso searches could be presented to the first-pass curator for approval in the first-pass form
 
−
**Need to fix current abstract-gene associating script to include proteins (e.g. PIE-1)
 
  
−
*Incorporate a customized Textpresso query on WormBase object pages so users could look for additional info if they want
+
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
−
**Data type curator could help design a useful query
 
  
−
*Other gene-object connections
+
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
−
**Develop a canned query for all objects that should be associated with the gene page
 
  
−
*Worm Meeting
+
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
−
**Pre-meeting - meeting rooms?
 
−
**Pre-meeting - practice talks for WormBase workshop
 
−
**Storage for swag - pavillion should be okay
 
  
−
==June 18, 2009==
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
−
*Worm Meeting and Pre-Meeting
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
−
**WormBase Help Desk Schedule - set for worm meeting
 
−
**Wen may need help carrying boxes of swag
 
−
**Do any Sanger or WashU people need rides to UCLA?
 
−
**Mary Alvarez is working on finding rooms for the pre-meeting
 
−
**Be prepared to report on curation status of your data type and what we might need
 
  
−
*Author contact information on first-pass form
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
−
**email goes to the first email address found by Textpresso
 
−
**Raymond - we do care where this data comes from
 
−
**Erich - can we send it to the designated corresponding author
 
−
**first-pass curation could capture the corresponding author
 
−
**if the email didn't go to the corresponding author, it may affect our response rate
 
−
**two-stage approach proposal
 
−
***respond to Bernard - we'll try to find corresponding author in the future and add his name to the comments field for now
 
−
***going forward, how best to determine corresponding author?
 
−
***keep track of IP address from which the data was sent?
 
−
***add text to email saying that authors may include their contact information in the comments box, if they wish
 
−
***Raymond will proof-read papers to check on corresponding author designation and email addresses
 
  
−
*Zfin visit - PATO progress, worth looking at
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
−
**Erich noted no genome browser - what is the issue?
 
−
**Their experience with getting figures from journals might be helpful.
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
==February 10, 2011==
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
*Should we have a Caltech project/site manager? We'll look at the issues to be solved first
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
*Todd would like to know more about what's going on at Caltech
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
**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?
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
*Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
*Bitbucket use
 
−
**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
+
==March 14, 2024==
−
**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
+
=== TAGC debrief ===
−
**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
+
==February 22, 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
 
  
 +
===NER with LLMs===
  
−
== February 17, 2011 ==
+
* 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%)
  
−
Interaction dumping script
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
*Spot check table
 
−
*Push changes to Git? Yes, to main branch
 
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
−
Interactions automatically downloaded to FTP every release? Yes
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
*People should check their own curation data
 
−
*Users query frequently?
 
−
*Can WormMart work instead?
 
−
*Ruihua - feature can be added
 
−
*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?
 
  
 +
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
Ranjana - Solar flares causing static on phone? ;)
 
  
  
−
Newsletter for new website release? Yes
+
==February 15, 2024==
−
*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
 
  
 +
=== 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
  
−
BioGRID
+
===== Manually validate paper - topic flags without curating =====
−
*WormBase to BioGRID curation
+
*Facet for topic
−
*Issues of mapping interaction types: WB -> BioGRID vs. BioGRID -> WB
+
*Facet for manual assertion
−
*Moving towards using WB interaction types
+
**professional biocurator assertion
−
*Definitions of our interaction types
+
***ABC - no data
−
*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
 
  
 +
===== 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
  
−
WormBase IWM souvenir?
+
=== PDF Storage ===
−
*Computer stress ball? with new site address?
+
* At the Alliance PDFs will be stored in Amazon s3
−
*bouncy ball?
+
* We are not planning to formally store back-up copies elsewhere
−
*worm rubber band thing?
+
* Is this okay with everyone?
−
*Screen shield?
 
−
*Complementary iPads? ;)
 
−
*Antifungal socks? wristbands?
 
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
SPELL
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
*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
 
  
 +
==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.
  
−
WormMart
+
==January 25, 2024==
−
*with WormMart and WormBase, people just want to know if it's down, just to know to lessen frustration; Official statement from dev team
+
 
−
*WormMart - we give users testing url; can we just change WormBase link to that testing server?
+
=== Curator Info on Curation Forms ===
−
*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
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
*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.  
+
 
−
*would like to keep the html page as a testing server; could modify page
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
*if WormMart is working OK but not perfect, that's OK; Comment in the banner
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
*the html page is a useful tool to get feedback from users
+
 
 +
* 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

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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