Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(793 intermediate revisions by 13 users not shown)
Line 21: Line 21:
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
==March 14, 2024==
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
=== TAGC debrief ===
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
==February 22, 2024==
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
===NER with LLMs===
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
* 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%)
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
 +
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
==July 9th, 2020==
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
===Gene names issue in SimpleMine and other mining tools===
 
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
 
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
 
*Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
 
*Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
 
*Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
 
**single public name is assigned to multiple WBgene ID, Wen has a list of these genes
 
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
 
**overlapped or dicistronic, but has a single sequence name, examples:
 
    exos-4.1 and tin-9.2 (B0564.1)
 
    eat-18 and lev-10 (Y105E8A.7)
 
    cha-1 and unc-17 (ZC416.8)
 
  
**simple confusion from authors, ex. mdh-1 and mdh-2
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
 
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
 
*Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools. They will also write a microPub explaining this issue to the community.
 
  
===Wormicloud===
 
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
 
*Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
 
*Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.
 
  
===Noctua 2.0 form ready to use===
 
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
 
  
===Nightly names service updates to postgres===
+
==February 15, 2024==
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.
 
  
 +
=== 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
  
==July 16th, 2020==
+
===== Manually validate paper - topic flags without curating =====
===Citing ontologies and their versions===
+
*Facet for topic
*Came up in the context of the Alliance: It would be best practice to provide users with the list of ontologies used and their versions/date.
+
*Facet for manual assertion
*If WB ontology developers could make sure their ontology file headers (WB anatomy ontology, WB life stage, etc.) conformed to obo file header specifications, then it would be easy to pull in version and date information into the Alliance.
+
**professional biocurator assertion
*Some useful links
+
***ABC - no data
**http://www.obofoundry.org/principles/fp-004-versioning.html
 
**http://obo-dashboard-test.ontodev.com/ (you can see that wbbt, wbls version metadata attribute is generating a warning).
 
**Note: OBO-foundry may not have been updated, but good practice to check your headers, anyway.
 
* Chris worked with Nico yesterday to update the ODK version for WBbt and WBls; versioning should be fine now (once the OBO dashboard runs again (hasn't run since February))
 
* Important point: the GitHub release version date tag (e.g. "v2020-06-30") needs to match the ODK release date (as stored in the OBO and OWL file headers)
 
** There are some existing mismatches, Chris is cataloging them now
 
  
=== Gene Name Sanitizer ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* Would be good to always (when possible) make users aware of name ambiguities
+
* Search ABC with paper identifier
* Wen will keep the "Multiple Output" section at the bottom of SimpleMine output
+
* Migrate to Topic and Entity Editor
* The gene name sanitizer will be built as a stand alone tool
+
* View all associated data
* Important to include history of gene names
+
* Manually validate flags, if needed
  
=== Tools linking to SimpleMine ===
+
=== PDF Storage ===
* Vennter and other tools link to SimpleMine with hard coded field/column names; we should have more dynamic/robust linking without relying on hard coded field names
+
* 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?
  
== July 23rd, 2020 ==
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
=== Alliance pathway working group ===
+
==February 1, 2024==
* Integrating pathways from GO-CAM, Reactome, Meta-cyc
+
* Paul will ask Natalia to take care of pending reimbursements
* Raymond, Chris interested
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
* Laurent-Philippe wants to work on user-friendly displays of GO-CAM models
 
  
=== Working on Alliance paralogs ===
+
==January 25, 2024==
* In the works
 
  
=== Summer project ===
+
=== Curator Info on Curation Forms ===
* Neuronal regulation of dauer formation
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* Fernando has been collecting literature
 
* Will work on GO-CAMs and build a relevant model(s)
 
  
=== Disk failures ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
* Brought down wobr1, wobr2, spica
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
* Raymond has upgraded OS from 8-year old OS, beefed up hardware
 
* wobr1 and wobr2 are back to full function
 
* Having trouble bringing back spica on the network
 
  
=== WormMine updates ===
+
* 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.
* Paulo working on importing new classes: SO_term, disease_model_annotation, transgene, construct, molecule, wbprocess, interaction
 
* Chris is working with Paulo to move them in; talk to Paulo and/or Chris if interested in discussing
 
* Spreadsheet to map ACEDB/XML attributes to ACEDB attributes: https://docs.google.com/spreadsheets/d/1-fpzVU3rblN3Rp38wQjd3121z3rVkxmR9_i5T0EIPNo/edit?usp=sharing
 
* Still have some loader headaches
 
* Do we know the usage stats of WormMine?
 
* BlueGenes
 
** New interface coming; in the works, not sure when it will be fully functional
 
** Lacks some useful features in the current Intermine (Intermine devs are aware and working on it)
 
** Does BlueGenes have better loading? Don't know
 
  
=== WB move to Chen building ===
+
* 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.
* Need to sort out what will get moved over; will be more limited space
 
* How late can move happen? If all is OK, move will happen 2nd week of January 2021
 
  
=== Caltech BBE retreat ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
* Will be online; may be more accessible
 
* Wen will submit a request to present on the Alliance
 
  
=== WormBase Webinars ===
+
=== Update on NN Classification via the Alliance ===
* Could run a WormMine webinar in September
+
* Use of primary/not primary/not designated flag to filter papers
** 30-45 minute webinar with 15 minutes of questions and discussion
+
* Secondary filter on papers with at least C. elegans as species
** Would be good have people register
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
* Chris has slot at Worcester Area Worm Meeting and Boston Area Worm Meeting coming up (late in 2020); these will likely be virtual
+
* Next NN clasification scheduled for ~March
  
=== Gene Name Sanitizer ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
* Juancarlos and Wen are working on tool prototype
+
* NNC html pages will show NNC values together with species.
* Prototype recognizes ambiguous gene names/IDs and returns them to the user
+
* Show all C. elegans papers first and other species in a separate bin.
* Will return HTML or single download file with a status/classification column
 
* Four types:
 
** good/valid (unambiguous match to a live gene)
 
** ambiguous (matches multiple genes)
 
** invalid (unambiguous match to dead or suppressed gene)
 
** not found (no match)
 
  
 +
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
== July 30, 2020 ==
+
=== 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.
  
=== Gene Name Sanitizer ===
+
==January 18, 2024==
* Currently there are many cases where even live C. elegans gene IDs result in an "Ambiguous - Split" status that doesn't return a matching gene ID
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
* This happens with 647 live C. elegans (N2) gene IDs, all of which do not have any indication of ambiguity when uploading to SimpleMine or WormMine, or sample searching in the WormBase website interface
 
* Many (all?) cases involve an existing, live, valid gene having been split at some point to create an adjacent gene model but the original gene retained its identity
 
* It would be good to still make sure people are aware of this split, but still provide a "suggested" matching gene (i.e. the actual same input gene ID); also "Ambiguous" may not be the appropriate word
 
* There are also cases where there really is an ambiguity (e.g. a name matches the "Public_name" of one gene but the "Other_name" of another gene) but we still might want to return a suggested mapping to the "most likely" gene match, e.g. the gene where the input matches the public name
 
* Maybe we can have multiple columns in the output to provide the gene IDs of other matches
 
* We could have a core "suggested" match/mapping gene ID column, plus a column to indicate "siblings of a split", "Matches to public name", "Matches to sequence name", "Matches to other name"
 
* Chris will draw up some mockups with examples
 
  
=== Help Desk ===
 
* https://github.com/WormBase/website/issues/7803
 
* Hi, I was wondering if there is a way to search for maternally versus zygotically enriched splice variants of a gene. I was looking through the RNAseq data and am not sure how to pull that out. I'm specifically looking at afd-1, but any help on that would be great!
 
* Ask Gary Williams
 
  
=== Summer project ===
+
==January 11, 2024==
* Fernando has made curation progress on neural control of dauer development (couple papers)
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
* Acquiring list of papers is important:  
+
** Curators should make sure that, when pasting special characters, the duplicate function works
** [https://pubmed.ncbi.nlm.nih.gov/2006412/ Bargmann (1991)] ablation paper; start at beginning
+
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
** WormBook chapter (old but good)
+
** 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)
** WormAtlas, check references
+
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
** Look at Nikhil Bhatla's worm web tools and references (wormweb.org)
+
** 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
* Ablation, mosaic analysis
+
** Raymond: simply set up forwarding at our end?
* Maybe add a Wiki page for methodology for addressing questions of cell function
+
* 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?)
** Address necessity/sufficiency issues
+
* 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.
** Address cell autonomous/cell nonautonomous experiments
+
* Valerio would like to use an alliancegenome.org email address for the openAI account
** What are basic approaches and their caveats?
+
* 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