Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
= 2014 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2014|January]]
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2014|February]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_March_2014|March]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_April_2014|April]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
== May 1, 2014 ==
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
=== Progress report ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
* Curation status freezes have been collected (daily?)
 
* These can be used for report
 
* Review grant proposal: milestones, quarterly updates, etc.
 
  
=== LEGO - Paul Thomas' visit ===
 
* We want to work on/think about importing WB GO annotations into LEGO format
 
* Is .OWL format the final destination of LEGO data for us? Yes, probably
 
* Will we be able to automate the process and eventually port to WikiPathways or other pathway visualizer?
 
* Extended evidence codes? For capturing methods?
 
* We need some trial LEGO curation to start working out the process
 
* There is a communal desire to achieve a common format for pathways, whether it be SBML, SBGN, LEGO, etc. or some hybrid
 
* We would like to play around with how to import/interpret/export .OWL files for our data
 
  
=== Pathway curation ===
+
==March 14, 2024==
* Topic curation: a single (or pair of) curator(s) focusing on pulling together and drawing a pathway for a topic
 
* Labs adopting a pathway? Outreach, community annotation
 
* Reaching out to experts to confirm or proof read our pathways
 
  
=== WormBase Ontology Browser (WOBr) ===
+
=== TAGC debrief ===
* http://juancarlos.wormbase.org/tools/ontology_browser
 
* Getting closer to completion
 
* Working out how to handle different relationships, e.g. "part_of", "has_part"
 
  
 +
==February 22, 2024==
  
 +
===NER with LLMs===
  
== May 8, 2014 ==
+
* 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%)
  
=== BioTapestry ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
* We may be able to use BioTapestry (from Davidson group) to visualize gene regulatory interactions
 
* Xiaodong testing out
 
  
=== Li et al 2004 Interactome ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Mostly sorted out now
 
* Missing gene references have been filled in
 
* "Noncore" interactions will be omitted from website
 
* Almost perfect correspondence between the published dataset and WB dataset
 
  
=== WOBr ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* Still making progress
 
* Incorporating life stage and disease annotations
 
* There appeared to be missing gene-phenotype annotations; Raymond contacted Kevin Howe
 
* Raymond will try to work on from Taiwan
 
  
=== Models ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Paul Davis deposited the most recent models revision (1.404) in the models CVS repository
 
* Curators should test their model changes
 
* ?Variation and ?Construct models still need work; data needs to be conformed to fit new models
 
* Questionable whether all the changes for ?Construct and ?Variation models and data can be made by the next upload (May 27th)
 
* ?Expr_pattern model being modified soon to accommodate annotation of specific conditions; working to be compatible with LEGO
 
  
=== Curation Progress Report ===
 
* Each curator can use the Curation Status Form to generate numbers for their datatype(s)
 
* Wen can install relevant versions of ACEDB (WS238 - WS243?) to pull annotation numbers
 
  
  
== May 15, 2014 ==
+
==February 15, 2024==
  
=== Progress Report ===
+
=== Literature Migration to the Alliance ABC ===
* Paul will send around format during or after the call
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* Whole contribution from Caltech (bio-curation) should be about a page
+
===== 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 =====
* A few sentences on each curation topic
+
*Facet for topic
* Some mention of models, WOBr, topic curation
+
*Facet for automatic assertion
* Next Thursday (May 22nd) local deadline (official deadline June 1)
+
**neural network method
* WS238 - WS243, March 2013 (beginning curation) to March 2014 (end of curation) 12 months/1 year
+
*Facet for confidence level
* Curation Status Form has stats from Aug 1 2013, we can look at numbers from Aug 1 2013 to May 1 2014, 9 months, can be extrapolated to a year
+
**High
 +
*Facet for manual assertion
 +
**author assertion
 +
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
=== BioTapestry ===
+
===== Manually validate paper - topic flags without curating =====
* Xiaodong sent around some sample gene regulatory network diagrams based on WB data
+
*Facet for topic
* How do we want to use this?
+
*Facet for manual assertion
* To what extent do we need time and place (spatio-temporal) information for a transcriptional regulation to use BioTapestry?
+
**professional biocurator assertion
* Can we generate spatial-agnostic/temporal-agnostic diagrams?
+
***ABC - no data
* Xiaodong will look into curation numbers for annotations that include spatial info, temporal info, or both
 
  
=== GO Meeting at Caltech ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* Need to reserve a room for next Tuesday/Wednesday, 10-15 people, all day (if possible)
+
* Search ABC with paper identifier
* Tech-oriented discussions of LEGO, GO, Textpresso
+
* 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?
  
== May 22, 2014 ==
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
=== Agenda ===
+
==February 1, 2024==
* Orion/LEGO/Textpresso meeting
+
* Paul will ask Natalia to take care of pending reimbursements
* Progress Report
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
  
=== GO/LEGO ===
+
==January 25, 2024==
* GO curation will eventually morph into LEGO curation
 
* Can we incoporate other WormBase data into LEGO? Hopefully, we'll have to see
 
* Would be good to have OA (e.g. Interaction OA) feed directly into LEGO/Orion/Noctua
 
* We are building pathways with various tools; long term curation goal not clear yet
 
* How could we represent other data in LEGO? Phenotype annotations? Expression patterns? Genetic interactions?
 
* Connecting tools like PAINT, OA, Textpresso, etc. to LEGO
 
* LEGO team worked with Juancarlos to get some LEGO tools/infrastucture (Noctua, Barista, Amigo) running at Caltech
 
* Mechanisms to seed LEGO diagrams is a priority
 
* LEGO team working with Michael to interface with Capella (Textpresso tool)
 
  
=== Progress Report ===
+
=== Curator Info on Curation Forms ===
* Curators should send their blurbs to Chris (in any format)
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* Chris will send plain text to Paul S.
 
  
=== Monarch Initiative ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
* http://monarchinitiative.org/
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
* Human diseases connected to phenotypes via genetic variants in various model organisms
 
  
=== Athena is crashing ===
+
* 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.
* Wen having trouble with Athena; difficult to reboot
 
* Data is backed up; Wen and Raymond will work on replacing Athena
 
  
=== WS244 Upload ===
+
* 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.
* Citace upload to Wen by Tuesday morning
 
  
=== BioGrid data ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
* Still waiting on curator timestamps and a dump of partially curated papers from BioGrid
 
* Will still need to compare genetic interaction datasets
 
* For large scale genetic interaction datasets in both databases, we will favor the WB version, import others (best mapping of terms possible)
 
  
=== 2004 Vidal Interactome Yeast-Two Hybrid Data ===
+
=== Update on NN Classification via the Alliance ===
* Chris has nearly finished sorting out official interactions from those removed
+
* Use of primary/not primary/not designated flag to filter papers
* Once done, we can import from later interactome datasets
+
* Secondary filter on papers with at least C. elegans as species
 +
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
 +
 
 +
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
 +
* NNC html pages will show NNC values together with species.
 +
* Show all C. elegans papers first and other species in a separate bin.
 +
 
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
 +
 
 +
=== UniProt ===
 +
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
 +
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
 +
 
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
 +
 
 +
 
 +
==January 11, 2024==
 +
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
 +
** Curators should make sure that, when pasting special characters, the duplicate function works
 +
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
 +
 
 +
==January 4, 2024==
 +
* ACKnowlegde pipeline help desk question:
 +
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 +
* Citace upload, current deadline: Tuesday January 9th
 +
** All processes (dumps, etc.) will happen on the cloud machine
 +
** Curators need to deposit their files in the appropriate locations for Wen
 +
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 18:18, 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