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]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
  
−
==2011 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_February_2011|February]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_March_2011|March]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_April_2011|April]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_May_2011|May]]
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
−
== June 2, 2011 ==
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
−
Website (Todd)
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
−
*Wrapped up support for all classes (display, etc.)
 
−
*Have one person volunteer to look at potential problems for a particular page?
 
−
**Send e-mail out to curators, etc.
 
−
**People volunteer for a page
 
−
**Reviewers send feedback to Todd/Web Team
 
−
**Google Document for signing up for looking at pages
 
−
*Todd
 
−
**Setting up production environment
 
−
**Will have dedicated set of servers
 
−
*Abby
 
−
**Debugging behavior of web app
 
−
**Stress testing dynamic loading of content
 
−
*Once exposed to worm community at International Meeting, can develop focus groups to enhance/improve features
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
Computer Security breach
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
−
*Sandbox/Fedora machine hacked
 
−
*Limited infection/compromised machines
 
−
*Raymond and Juancarlos working on it
 
−
*Textpresso-dev affected
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
−
Virtual Worm Site
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
−
*Make link on WormBase homepage
 
−
*Announce on homepage
 
−
*Fold into new web site release
 
−
*Will add note to site about how the model may be integrated into WormBase
 
−
*Chris will discuss more detail with Todd at/after International Meeting
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
Expression pattern OA
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
−
*Juancarlos and Daniela have to fix a couple of things
 
−
*Should be live soon
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
New Tazendra Login
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
*New password
 
−
*Raymond: Assume that once logged into another machine, your keystrokes could be monitored
 
−
*Don't ssh or scp to another machine (or type any passwords) while logged into a machine other than your own
 
−
*Limit off-site access?
 
−
*Setup dedicated machine (with open Port 22) for logging into and then ssh'ing or scp'ing to other machines from
 
−
*Consider security audit (what machines are operating and which ports are open)
 
−
*VPN, should always use VPN if accessing machines from a public WiFi spot
 
  
  
−
Textpresso-dev
+
==March 14, 2024==
−
*(Michael) need to make textpresso-dev more redundant to address need for access
 
−
*Security fixes, etc.
 
−
*Switched off right now (up again a couple hours later -- J)
 
  
 +
=== TAGC debrief ===
  
 +
==February 22, 2024==
  
−
== June 9, 2011 ==
+
===NER with LLMs===
  
−
Tazendra reinstallation (Juancarlos)
+
* 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%)
−
*Raymond and Juancarlos working on now
 
−
*Will be running on slower sandbox until next week (slightly noticeable)
 
−
*Hardware will be swapped (fast machine has 4G ram + 4 cores ; slower machine has 2G ram + 2 cores)
 
−
*Shouldn't affect work of curators
 
−
*Curators should make note if Tazendra feels slower than usual and document
 
−
*Ubuntu slower than Fedora for postgres queries, for some reason?
 
−
*Upgrade tazendra more frequently in future?
 
−
*Should restore tazendra up to the point when there was the security breach and go from there
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
Expression pattern OA is live (Daniela)
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*Working well and ready to use
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
BioGRID curation coordination (Kimberly)
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
*Focusing on Wnt pathway papers
 
−
*Still need to work out some details of curation sharing/prioritization
 
−
*They want to follow up on using Textpresso tools
 
  
  
−
Aldrin Montana here next week (Karen)
 
−
*Talk to Karen if you want to talk to him
 
−
*Karen can make a schedule
 
  
 +
==February 15, 2024==
  
−
Wiki setup for curation status (Karen)
+
=== Literature Migration to the Alliance ABC ===
−
*Flagged papers, how many have been taken care of
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
*Details of false positive flags
+
===== 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 =====
−
*Used to take Andrei's flags as gold standards
+
*Facet for topic
−
*Textpresso/SVM success/fail rates
+
*Facet for automatic assertion
−
*How do the numbers affect the curation pipeline?
+
**neural network method
−
*What is the ultimate goal? Meet needs/wants of users?
+
*Facet for confidence level
−
*Full disclosure/transparency to users as to what has or hasn't been curated
+
**High
−
*Generate feedback from user community
+
*Facet for manual assertion
−
*Paper stats vs. data type stats
+
**author assertion
−
*Difficult to determine the false negative rates without a study
+
***ACKnowledge method
−
*Use Textpresso tools to identify SVM false negatives?
+
**professional biocurator assertion
−
*First need to generate estimates
+
***curation tools method - NULL
−
*Tell users "We have 90% recall" vs. "We only get 30% recall" for example
 
−
*Would be great to have an automated way to report the numbers/stats
 
−
*Should include criteria for finding/flagging papers?
 
−
*Provide more refined flagging info to author first-pass forms, and authors correct
 
−
*Add info to WBPaper pages including possible data types and what's been curated?
 
−
*This data is useful for NIH reporting
 
  
 +
===== Manually validate paper - topic flags without curating =====
 +
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
International Meeting Help Desk
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
*Do we need a computer for users?
+
* Search ABC with paper identifier
−
*Curators will bring their own laptops
+
* Migrate to Topic and Entity Editor
−
*Wireless internet should be fine
+
* 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?
  
−
WormBase laptop?
+
==February 8, 2024==
−
*Had been discussed previously
+
* TAGC
−
*Most curators ended up getting their own laptop
+
** Prominent announcement on the Alliance home page?
−
*Laptops are relatively cheap these days (~$300?)
 
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
Post-International Meeting WormBase meeting
+
==February 1, 2024==
−
*Conference room reserved
+
* 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?
  
−
== June 16, 2011 ==
+
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
Tazendra
+
* 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.
−
*Tazendra back on normal hardware
 
−
*Should be running normally
 
−
*Let Juancarlos know otherwise
 
  
 +
* 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.
  
−
Scripting requests?
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Raymond can start taking requests
 
−
*Large-scale data set processing
 
−
*Querying ACeDB
 
  
 +
=== 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
  
−
Ask Karen @ wormbase.org account
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
*If you need an account for WormBase login, talk to Karen
+
* 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)
  
−
Interaction meeting review
+
=== UniProt ===
−
*Genetic interaction examples
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
*Adding new genetic interaction types tags
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
*Separating Physical interaction from interaction tag
+
* 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
  
−
GSA Go-term markup
 
−
*Need to discuss with SGD
 
  
 +
==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.
  
−
Karen spoke to Alex Pico @ WikiPathways
+
==January 4, 2024==
−
*New tool to click on pathway and navigate, highlight genes, etc.
+
* ACKnowlegde pipeline help desk question:
−
*May be able to integrate into pathway widget in WormBase
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*WikiPathways working with Reactome, WikiGenes
+
* Citace upload, current deadline: Tuesday January 9th
−
*Incorporate community curation?
+
** 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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