Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[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_March_2017|March]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
== April 6, 2017 ==
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
=== AGR time spent ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
* Paul S asking about %time spent on AGR project
 
* Time spent on working groups, conference calls, AGR development
 
* Send estimates to Paul
 
  
=== SimpleMine ===
 
* Two tables added to SimpleMine for human orthology
 
* Now SimpleMine output has many columns (30+)
 
* We may want to give users the option to specify which output they want
 
* Users could specify groups of data (with checkboxes): gene IDs/names, phenotypes, orthology, etc.
 
* All checkboxes can be checked by default
 
  
=== Enrichment tools ===
+
==March 14, 2024==
* Raymond working on display for paper
 
  
=== Gene Ontology SObA graph ===
+
=== TAGC debrief ===
* Raymond, Juancarlos working on
 
* Working on paper
 
  
=== WormMine updates ===
+
==February 22, 2024==
* WS258 adding gene class
 
* WS259 adding more info (almost all meta data) on variations, laboratory and strains, RNAi phenotypes (hopefully)
 
* Expression data in WormMine is problematic
 
* Many genes being annotated to the same ~6 tissues or so
 
* Resulting in erroneous data for some genes
 
* Chris will send GitHub ticket to Todd
 
* Todd will discuss with Paulo today
 
  
=== Gene Ontology ===
+
===NER with LLMs===
* Some very complex terms becoming immediate children of root terms (e.g. "biological process")
 
* May be result of attempt to create logical definitions/equivalence axioms
 
* Raymond will discuss with Kimberly
 
  
 +
* 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%)
  
== April 13, 2017 ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
=== Methods in Molecular Biology chapter ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Chapter draft sent out Monday night
 
* Will send to Martin at MiMB by late next week
 
* Please take a look and send comments
 
* Authors check their sections and send figure legends to Chris
 
  
=== Progress report ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* If someone finds the 2016 report, send around to group
 
* May 1st deadline (need to verify)
 
  
=== 2017 IWM ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Early registration Deadline May 18th
 
  
=== Models for citace ===
 
* Wen will fit models to local citace, should be ready by tomorrow
 
  
=== Citace Upload ===
 
* Tuesday, April 25th, 10am
 
  
=== Enrichment tool ===
+
==February 15, 2024==
* Now available for gene ontology and phenotype on live site
 
* Paper being submitted soon
 
* Need to change "Tissue Enrichment Analysis" link title under WormBase Tools menu
 
  
=== SObA for Gene Ontology ===
+
=== Literature Migration to the Alliance ABC ===
* Data source was server on Berkeley BOP; thought it was public but were discouraged to use
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* Seth Carbon said we could use it but might not always be working; now it seems to be down or dysfunctional
+
===== 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 =====
* SObA for GO will be broken until we install our own local server (Raymond working on)
+
*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
  
=== Dumping data for upload, taking over for Karen ===
+
===== Manually validate paper - topic flags without curating =====
* Karen will take care of dumping and uploading the data for this upload
+
*Facet for topic
* Karen will review the molecule curation with other curators at the IWM
+
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
=== Datomic meeting ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* Matt, Sibyl, Adam, Todd, Juancarlos, Raymond sat in
+
* Search ABC with paper identifier
* Raymond: thought Datomic would take over from ACEDB completely, but it seems we will still use ACEDB for some time for e.g. FMap
+
* Migrate to Topic and Entity Editor
* Seems there should be an executive meeting about Datomic to make clear what it will be used for and what it won't be used for
+
* View all associated data
* Several web pages and widgets are now being served by Datomic
+
* Manually validate flags, if needed
* There's a question about how we now handle model changes going forward
 
* Juancarlos will send around link for newest Datomic querying tool; may require access for specific IP addresses
 
  
 +
=== 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?
  
== April 20, 2017 ==
+
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
=== Gene Ontology data for SObA ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
* Use of GO server; hasn't been reliable
 
* Raymond working on establishing our own server to host all GO data
 
* Raymond and Juancarlos will keep working on SObA representation of GO annotations
 
  
=== Progress Report ===
+
==February 1, 2024==
* WS259 can be used as the current reference
+
* Paul will ask Natalia to take care of pending reimbursements
* Paul will send around last year's progress report
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
* What was the last release that we referenced in last year's progress report? We'll say WS254
 
* Wen will generate numbers for WS254 (resurrect WS254 ACEDB)
 
* Opportunity to specify/narrow scope of project
 
* Want to push community/automated curation, with curators laying foundation of data models, forms
 
* Promote LEGO curation; need to learn what needs to be said about plan going forward/what we want to accomplish
 
  
=== LEGO curation ===
+
==January 25, 2024==
* Phenotype curation in LEGO? Need to review phenotype-to-GO pipeline
 
* Want/need a mapping of phenotype terms to GO process terms; may require context-dependent mapping (e.g. "dumpy" phenotype)
 
* We don't make direct associations of phenotypes to LEGO models, although we do have "inferred from mutant phenotype" evidence code
 
* Want a mechanism to automate conversion of WB annotations into LEGO models
 
* Want a display mechanism that is user friendly, convert hairball into pathway
 
* We could focus on a particular topic/disease and collectively contribute
 
* Do we want to write a proposal to take existing, granular annotations (e.g. at level of mutation details) and map to LEGO model?
 
* Can we integrate the micropublication pipeline into LEGO model generation?
 
* How to assess the confidence of assertions?
 
  
=== Follow up on transgene question from user ===
+
=== Curator Info on Curation Forms ===
* Karen will contact authors of paper
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
=== Citace upload ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
* Tuesday, Apr 25th, 10am
+
* 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.
  
== April 27, 2017 ==
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
=== Gene Ontology data for SObA ===
+
=== Update on NN Classification via the Alliance ===
* All GO annotation data loaded at Caltech (bigGO solr database, 54GB)
+
* Use of primary/not primary/not designated flag to filter papers
* 100 species, 922296 bioentity (protein, gene product ...)
+
* Secondary filter on papers with at least C. elegans as species
* [Testing site http://131.215.12.204/~raymond/cgi-bin/soba_biggo.cgi]
+
* 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