Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 15: Line 15:
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2017|February]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
== March 2, 2017 ==
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
=== Expression Cluster SVM ===
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
* Started curating expression clusters in 2007
 
* Had been using text pattern match to identify expression cluster papers
 
* Now with more papers for positive and negative training set, shifting to SVM identification
 
* 540 positive papers, 900 negative papers for training
 
* Wen received first batch, roughly ~70% precision, possibly ~80-90% recall
 
* Wen reviewed papers from WormEXP (http://wormexp.zoologie.uni-kiel.de/wormexp/)
 
  
=== Karen's SBIR grant ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
* Looks like it will get funded
 
* Karen will need to become part time at WormBase (needs to be more than half time on SBIR)
 
* Paul put in a request for posting another curator position
 
** If anyone has ideas about a potential (part-time or full-time) curator, let Paul know
 
* Will need to consider re-allocation of curation responsibilities
 
* Molecule curation in maintenance mode, may require updating of mapping terms with our internal IDs
 
** Ranjana: want to incorporate molecules in disease curation for WB/AGR, can offer to take over maintenance
 
** Do other AGR members curate molecules? In some cases yes; don't capture metabolites
 
* Transgene curation could be distributed
 
** Karen will be working on more automated curation of transgenes from papers; maybe also for molecules
 
  
=== Metabolomics ===
 
* What would we like to see in WB for metabolomics?
 
* Marian Walhout lab created the WormFlux database (http://wormflux.umassmed.edu/)
 
* WB enzyme gene pages link out to respective gene pages on WormFlux
 
* How are enzymatic pathways represented in GO, or by phenotype info? What's the cross-talk?
 
  
=== Pathway representation ===
+
==March 14, 2024==
* What are the best ways to capture empirical evidence as support for pathway models?
 
* Want clear, granular evidence for each assertion in a model, but need to accommodate probabilistic statements
 
* How can micropublications be used to fill in the gaps?
 
  
=== SObA GO on human data ===
+
=== TAGC debrief ===
* What would be a good set of genes to test?
 
* If we omit IEAs (most from mouse), are we left with substantial data for human genes?
 
  
 +
==February 22, 2024==
  
== March 9, 2017 ==
+
===NER with LLMs===
  
=== Expression widget via Datomic ===
+
* 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%)
* Sibyl is working on delivering the Expression widget from Datomic
 
* Issue with gene expression "mountain" data
 
* AcePerl script/query underlying the data, may be incorrect and needs an update
 
  
=== Human GO SObA graph ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
* Working SObA graph for human gene ontology data:
 
** http://131.215.12.204/~raymond/cgi-bin/soba_go_hs.cgi?action=annotSummaryCytoscape&focusTermId=UniProtKB:O94905
 
* Running off GOLR server for now
 
* Would be great to have a SObA widget on AGR portal
 
* Will need to get widgets working on AGR portal
 
* Will be good to have, for now, a stand alone version
 
  
=== AGR update ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* SAB meeting on Tuesday (two days ago)
 
* Positive feedback
 
  
=== AGR database ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* Although official database has not been chosen, most portal processes are running just on memory, need to start storing things in a database
 
* The database used may be the stepping stone for eventual database migration for AGR
 
  
=== AGR Curator calls ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Karen asking about purpose of curator calls going forward
 
* Have covered a good number of topics, a few still yet to be covered: synteny browser, person curation
 
* Possibly have discussions about the functions of different (and possibly new) working groups
 
* Can revisit curation procedures
 
* Should curator calls happen independently of AGR to share thoughts and methods about curation
 
  
=== Methods in Molecular Biology chapter update ===
 
* Have received drafts for most sections
 
* Working on making them consistent and making figures legible
 
  
  
== March 16, 2017 ==
+
==February 15, 2024==
  
=== Funding opportunities ===
+
=== Literature Migration to the Alliance ABC ===
* Could we focus on curation for disease genes and work with other groups?
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* Maybe work with GO
+
===== 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 =====
* What diseases would rely more on worm research than others?
+
*Facet for topic
* Lots of disease models on neurodegeneration diseases testing herbal treatments and compounds to treat
+
*Facet for automatic assertion
* Parasitic nematode research? May not work out
+
**neural network method
* Really want to focus on what worm research informs about human disease
+
*Facet for confidence level
* What are the studies that focus on orthology to human disease genes?
+
**High
* If some funding is cut, there will likely be refunding in a targeted manner (e.g. Alzheimer's research)
+
*Facet for manual assertion
* Can we do Textpresso search for funding agencies?
+
**author assertion
* Much more funding is going to military research; could look at what could apply (Tropical diseases, responses to pathogen, etc.)
+
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
=== IWM swag ===
+
===== Manually validate paper - topic flags without curating =====
* Still have tattoos from last years TAGC meeting
+
*Facet for topic
* WormBase piggy bank?
+
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
=== Human GO SObA ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* Server that Raymond used originally is not appropriate
+
* Search ABC with paper identifier
* Will require some reworking of the backend code
+
* Migrate to Topic and Entity Editor
* Might be ready after the Biocuration meeting
+
* View all associated data
* Could use in AGR disease pages, showing enriched GO terms (from genes implicated in the disease)
+
* Manually validate flags, if needed
* Could have (instead of enriched terms) a graph of all gene annotations merged
 
* What is a reasonably sized list of items to manage in the human mind? 7 +/- 3? 20?
 
** Can define a cutoff at which point using SObA is helpful
 
  
=== Micropublications ===
+
=== PDF Storage ===
* Deadline for grant rebuttal?
+
* At the Alliance PDFs will be stored in Amazon s3
* Organization name at IWM will be: Micropublication biology
+
* We are not planning to formally store back-up copies elsewhere
* Each micropublication is intended as a curatable unit
+
* Is this okay with everyone?
* Shohei Mitani wants, for example, to submit 100 knockout phenotypes; should be 100 micropublications
 
** Tim concerned that 100 micropubs is too much, but that is probably OK
 
* Want to generate a "narrative" from multiple individual micropubs
 
* Can DOI's be part of another DOI? Are relationships between DOI's allowed?
 
  
=== AGR communication and data pipeline ===
+
==February 8, 2024==
* Discussion about number of calls and modes of communication
+
* TAGC
* There was concern about data pipeline demands becoming overwhelming, e.g. loading data for Intermine as well as AGR portal
+
** Prominent announcement on the Alliance home page?
* There are questions about which database will be used as an interim database, which could possibly become the standard database
 
* AGR members like the Datomic techonology, but are concerned about the non-open-source aspect
 
* Should we have an all-hands call once a month (or every two weeks) where working groups could present and discuss issues? Yes, Kimberly will email Stacia about this idea
 
* AGR PI's were in favor of having a technical meeting face-to-face; disease working group face-to-face meeting worked well
 
* There may be AGR working group meetings at Biocuration meeting
 
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
== March 23, 2017 ==
+
==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.
  
=== Biocuration meeting ===
+
==January 25, 2024==
* Mary Ann (or someone who is available) will present the micropublications poster
 
* Can share posters here: https://f1000research.com/channels/biocuration
 
  
=== Person curation AGR curator call ===
+
=== Curator Info on Curation Forms ===
* Person curation is topic of next AGR curator call (April 12th)
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* Cecilia can present on person curation (persons, paper-person connections)
 
* Karen can help
 
* Could discuss authors vs. persons in WormBase
 
* Chris can discuss experience with online chat service
 
  
=== Potential AGR all-hands call on April 5th ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
* Stacia Engel will let people know
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
* Would have short presentations from working groups
 
  
=== Karen part time as of April 1st ===
+
* 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.
* Grant came through (congratulations!), so Karen will be part time as of Apr 1
+
 
* Someone should take over transgene and molecule curation
+
* 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.
* Transgenes
+
 
** Relevant curators already have training on how to curate
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
** How much of these curation processes are on auto-pilot?
+
 
** CGC sends strain info (with trangenes) to Mary Ann
+
=== Update on NN Classification via the Alliance ===
** Can we automate the transgene-strain connections coming from CGC?
+
* Use of primary/not primary/not designated flag to filter papers
** Mary Ann can take over manual transgene curation
+
* Secondary filter on papers with at least C. elegans as species
** Could have summer student (undergard or high school) to help?
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
* Molecules
+
* Next NN clasification scheduled for ~March
** Ranjana, Wen, & Chris can take over molecule curation
+
 
** Should we automate the dumping process? Wen will take over dumping the data
+
* 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