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]]
  
== January 9, 2014 ==
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
=== AGENDA ===
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
* Apologies from Mary Ann - in Strasboug. Might try and Skype in. - Mary Ann joined in at the end of the call.
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
* Curation of protein complexes - will wait until Chris can join in.
 
* Set up a time next week to go over what more needs to be done for the construct/variation/transgene class - Main people being Mary Ann, Daniela, Chris, and Karen, others are welcome. Visit the construct model requests [http://wiki.wormbase.org/index.php/WormBase_Model:Construct here]
 
* Raymond gave an update on WObr. Juancarlos has learned enough Catalyst to create a workable ontology browser on the caltech wormbase sandbox.
 
**The browser can accommodate all ontologies used by Caltech curators (all GO, Phenotype, Anatomy, Life Stage, Disease)
 
**A browser will be on each respective ontology page;
 
***direct and indirect gene connections will be displayed in a list format
 
***there was a request that the gene connections to ontology terms display the indirect annotations with direct annotations in parenths
 
**various ontology browsers can be in their own widgets where desired.
 
**still need to set up the search function from the main wb search
 
*  Caltech Models due Thursday 16 January 2014
 
* Caltech WS242 data due into Citace by Tuesday Jan 28.
 
*  Biocuration 2014
 
**http://biocuration2014.events.oicr.on.ca/biocuration
 
**M. Tuli, X. Wang interested in attending.
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
== January 16, 2014 ==
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
=== AGENDA ===
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
* WOBr discussion
 
* Author-person issues
 
* Timeline for construct model
 
* Topic Curation
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
=== Author/Person issues ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
*User was looking for papers for a specific person
 
*Person was an author, but did not have a WBPerson object
 
*Cecilia will contact user
 
*Make author names searchable? ~32,000 authors without a person object
 
*How many authors (without a WBPerson) have multiple (5+?) papers?
 
*Proposal 1: make WBPersons for authors with 5 or more articles, and/or sort results of a search by number of publications
 
*Proposal 2: Search for WBPerson (no autocomplete function); if no WBPerson, look up authors (prioritized search)
 
  
  
=== Timeline for ?Construct model ===
+
==March 14, 2024==
*For WS243?
 
*Mapping primers used for expression constructs or reporters
 
*Integration of sequence features
 
*Examples of the new Crispr/CAS (genome editing) alleles (curated with flanking sequences)
 
*AddGene plasmids etc.
 
*Karen will move ahead with the ?Construct model just for the context of genome-editing alleles
 
*Other contexts can be added later
 
  
 +
=== TAGC debrief ===
  
=== Topic Curation ===
+
==February 22, 2024==
*Is there a way to update curators if a new paper is added to the current focus topic?
 
*No, but curators can just send around an e-mail and/or query through the topic OA and curation status form
 
  
 +
===NER with LLMs===
  
=== WormBase Ontology Browser (WOBr) ===
+
* 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%)
*Juancarlos can now modify WormBase widgets, but would need to learn how ACEDB is handled, if required
 
*We want to workout a pipeline for widget/website modifications, proposals etc.
 
*WOBr is not working off of ACEDB
 
*Note: WOBr is going to be a widget on the Ontology Term page (all other ACEDB-based info will be present on page)
 
*General structure:
 
**Testing site: http://juancarlos.wormbase.org/tools/ontology_browser
 
**Two entry points: 1. Homepage "Tools" menu (tree-like view from root terms), 2. Specific ontology term page (WOBr widget)
 
**Data present: ontology term objects, associated genes
 
*Association files needed: Disease, Life stage
 
*Curators are now testing and commenting on WOBr
 
*Difficult to implement: display of evidence codes, sorting by species
 
**Will consider for second generation WOBr
 
*Do we want species-specific WOBr? C. elegans WOBr? Yes, probably; not clear how to implement
 
**WormBase ontologies are currently species-agnostic
 
**Maybe we should have species-specific ontology terms/pages
 
*When displaying the number of associated gene products, we could/should? distinguish the number of gene products from C. elegans versus other species (or ALL species)
 
*Direct vs. indirect/inferred annotations, how to display at different points? Ignore numbers for ancestor terms? Speed is an issue
 
*The new Solr update may allow for precalculated/precached number calculations, which should improve speed
 
  
== January 23, 2014 ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
=== AGENDA ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
* Biocuration 2014
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
** Mary Ann's flights are booked.
 
** Shall we ask for a WormBase booth/helpdesk table?
 
  
=== Biocuration Meeting April 2014, OICR, Toronto, CA ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
* http://biocuration2014.events.oicr.on.ca/biocuration
 
* Mary Ann going
 
* Xiaodong may go, present info presented at IWM
 
* Wen considering, may want to see what's up for RNAseq etc.
 
* February 10, 2014 is abstract deadline, March registration deadline
 
* More WormBase curators?
 
* Registration discount for "International Society for Biocuration" members
 
  
=== Topic Curation ===
 
  
* Considerations for WS243
+
==February 15, 2024==
* Innate immunity, response to pathogens?
 
* Good to work on something for which a WormBook chapter exists
 
* Jonathan Ewbank, "Signaling in the immune response" 2006 WormBook chapter
 
* Creg Darby, "Interactions with microbial pathogens" 2005 WormBook chapter
 
* Action items: Look over two WormBook chapters, collect relevant genes and send to EBI/Hinxton, collect relevant papers
 
* What are the distinct challenges for EBI/Hinxton? Is it the number of genes? Number of protein coding genes? Are we sticking to "Core" species only? Which ones?
 
  
=== Upload ===
+
=== 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
  
* Tuesday morning 10am, 1-28-2014 deadline
+
===== Manually validate paper - topic flags without curating =====
* Models available tomorrow (Friday 1-24-2014)
+
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
== January 30, 2014 ==
+
===== 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
  
=== AGENDA ===
+
=== PDF Storage ===
* lin-15
+
* At the Alliance PDFs will be stored in Amazon s3
* Models deadline
+
* We are not planning to formally store back-up copies elsewhere
* Curating pseudogenes
+
* Is this okay with everyone?
* Part-time help
 
  
=== lin-15 - Creating a page for it ===
+
==February 8, 2024==
<pre>
+
* TAGC
Karen:
+
** Prominent announcement on the Alliance home page?
*Should it be considered a gene or can we fix up it up better as an operon?
 
It has been assigned to operon CEOPX140, but searching for
 
lin-15 in the operon class does not work,  is there an other_name tag in the operon
 
class to store 'lin-15'.
 
*'lin-15' is frequently published object. Although many people in the field know
 
that it is a complex locus comprised of two separate genes, lin-15A and lin-15B,
 
many people do not.
 
*There are many lin-15AB alleles, e.g., n765. Where in WB can we see that one
 
allele affects more than one gene, is this something a lin-15 operon page can
 
display?  
 
  
</pre>
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
<pre>
 
Mary Ann:
 
*There are no plans to kill the lin-15 gene object at this time.
 
*I agree that the operon object is rather vague. That it is the lin-15 operon
 
could currently only be curated in the Description tag, which is not ideal.
 
Should we propose a Name (or similar) tag for the ?Operon model?
 
*The operon object is linked from lin-15A and lin-15B and is visible in the
 
Overview on their respective Gene Summary pages.
 
</pre>
 
  
<pre>
+
==February 1, 2024==
Tim Schedl:
+
* Paul will ask Natalia to take care of pending reimbursements
I think there should be a lin-15 page that explains the original allele/
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
why it was called lin-15 and then refers the user to the lin-15A and lin-15B
 
pages. The lin-15 page need not have any/much other information, although
 
a description of the define allele would be useful.
 
Just killing the lin-15 page might lead to confusion for someone who
 
does not know the history (which is the majority of current worm researchers).
 
</pre>
 
  
* Mary Ann would like to attribute as many strains as possible to lin-15A or lin-15B
+
==January 25, 2024==
* lin-15 is the only gene/locus with ONLY a "Public_name"
 
* Can lin-15 be the CGC name? What about synonyms/"Other_names"
 
* Should the operon of lin-15 be called "lin-15"? Can we apply descriptions to operons?
 
* Proposal: create a "Name" tag for operons?
 
* Important: We need a page for the "lin-15" entity, for historical reasons at least, either as a gene or an operon (something else?)
 
* Allele attribution, e.g. n765? others?
 
  
=== Models deadline ===
+
=== Curator Info on Curation Forms ===
* Models deadline first conference call of the (upload) month?
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* Proposal to EBI
 
** First conference call of the "Upload" month (3rd conference call of the cycle, usually), finalize models
 
** Paul Davis has 1 week to finish the models.wrm file and tag it for the official release
 
** Once tagged, the "final" models.wrm file can be tested by curators for ~1 week before data upload for citace build by Wen
 
  
=== Curating Pseudogenes (Kimberly) ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
*Two cases have come up recently wrt functional annotation of pseudogenes.
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
*drh-2 - a Dicer-related helicase for which there is apparently protein evidence and some functional studies (although it is part of an operon)
 
***klp-10 - a kinesin-related protein that lacks a critical motif was recently converted to a pseudogene
 
*Pseudogene status is listed discreetly under Type in the summary box display, but I wonder if we need to communicate this information more prominently and/or explain the classification in the concise description (CD). 
 
*Typically, we haven't written CDs for genes WB classifies as pseudogenes, but in the case of drh-2, there are papers that suggest it is functional.
 
*How best to reconcile all this data?  Should we contact authors of the papers?  What should we do with experimental data attached to pseudogenes?
 
*Consensus: users should have access to all relevant information, including any conflicting evidence (in a concise description) and why a gene should or shouldn't be considered a pseudogene
 
  
=== Part-time help ===
+
* 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.
* Part-time help (undergrads, etc.); Paul was wondering if we thought we could use any
+
 
* Mary Ann: allele curation, check through papers for true positives (appropriate for undergrads)
+
* 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.
** Could undergrads at Caltech use the Hinxton curation tools? Would they need a "sponsored" account or something?
+
 
** Or, more simply, papers could be scanned for data and results sent to Mary Ann
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
* Karen: downloading papers and supplemental information (high school students could do this)
+
 
 +
=== 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
 +
** 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

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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