Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
−
==2012 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
−
 
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_January_2011|January]]
 
−
 
 
−
 
 
−
== February 2, 2012 ==
 
−
 
 
−
 
 
−
EPIC data into WormBase
 
−
*Daniela spoke to John Murray
 
−
*Need to modify model and display for data
 
−
*3D movies as ?Movie objects
 
−
 
 
−
 
 
−
Endrov
 
−
*Tom Burglin and student Johan Henriksson developed Endrov.net (http://www.endrov.net)
 
−
*May be able to incorporate Endrov visualizations of Blender model and cell lineage into WormBase website?
 
−
*Need to talk to Todd and Web team
 
−
 
 
−
 
 
−
Elsevier legal issues
 
−
*Science-direct website links to-and-from WormBase website
 
−
*Daniela still working with contacts at MGI (Mouse Genomics Institute/Jackson Labs) & Elsevier
 
−
*MGI already has established links with Elsevier
 
−
 
 
−
 
 
−
New ?Interaction model
 
−
*Update old objects and speak to web team about new model before officially incorporating new ?Interaction model
 
−
 
 
−
 
 
−
 
 
−
== February 9, 2012 ==
 
−
 
 
−
Interaction model
 
−
*Added some XREFs (in Interactor tag) and Chromatin_IP to Detection method
 
−
*Co-Immunoprecipitation would be captured under Detection method "Affinity Capture Western"
 
−
*Worked out changes needed for old *.ACE files to fit new model; will give to Juancarlos to script
 
−
 
 
−
 
 
−
Transgene
 
−
*Daniela, Juancarlos, and Karen imported Extrachromosomal array transgenes into the Transgene OA
 
−
*Extrachromosomal array transgenes for which authors have not provided a name will be named Expr####_Ex
 
−
*Maybe we will name according to paper e.g. "WBPaper########_Ex####"
 
−
*Daniela and Karen will discuss cost-benefit of objectifying Ex transgenes
 
−
*Rather than determine transgene sequence (or partial sequence), curators will (as they have been for Expr_pattern) add free-text describing the sequence
 
−
**This includes: primer sets, restriction digest sites, etc.
 
−
**Continue to place this info in the Reporter_gene tag
 
−
**Maybe add an additional free-text field (Sequence_info tag?)
 
−
 
 
−
 
 
−
Displaying curator names on new website
 
−
*Should we display curators' names on their curated objects?
 
−
*Currently only on concise description; why not do all objects?
 
−
*Keep curator name info only internal?
 
−
*Prevent curator names from being dumped for build/release?
 
−
*Should include 'Date-last-updated' Evidence dump
 
−
*Curator confirmed note could be placed in Tree View for all data types
 
−
 
 
−
 
 
−
Incremental Updates
 
−
*Should we perform incremental updates?
 
−
*Update as frequently as possible?
 
−
*Web display (of updates) served from Postgres/Tazendra?
 
−
*Serve RESTful widget from Caltech?
 
−
*Caltech in agreement about pushing forward with incremental updates
 
−
 
 
−
== February 16, 2012 ==
 
−
 
 
−
 
 
−
Gene product annotation for variation
 
−
*Variation affects gene product: absent, disfunctional, isoform-specific effects
 
−
*How is this best captured?
 
−
*Report as a phenotype? "RNA expression variant", "protein expression variant", etc...
 
−
*Capture as a gene_regulation event? Soon will be interaction object...
 
−
*Sequence ontology?
 
−
*Captured in ?Variation?
 
−
*Ask Hinxton/Mary Ann Tuli
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
−
Interaction model
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
−
*Old objects updated OK and read into ACEDB without problems
 
−
*Need to discuss updates with Web team
 
−
*Will send all updated *.ACE files with old Gene_regulaion, Interaction, and YH objects
 
−
*Add two zeros to the Interaction IDs in postgres OA tables once all current interaction objects uploaded to the Interaction OA
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
Transgene naming
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
−
*New extrachromosomal arrays will get "WBPaper###_Ex###" type of ID
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
SPELL Issues
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
*Problems coming up as data size increasing
 
−
*SPELL server at Amazon running at lowest paid instance ($1000/yr)
 
−
*4GB memory needed (more than 132-bit machine can provide) for loading data
 
−
*64-bit machine will cost $4000 per year
 
−
*Run SPELL on canopus? Yes but, have to take care of sys-admin issues
 
−
*$500/quarter for IMSS machine maintenance
 
−
*Talk to Matt Hibbs? Maybe need to optimize the process at that step
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
BioCreative/BioCurator meetings
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
*Kimberly working with DictyBase
 
−
*Kimberly will give 2 talks (CCC and molecular function automated curation)
 
−
*WormBase workflow; Kimberly will discuss with individual curators in March
 
−
*Arun submitted abstract
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
GO Consotrium meeting in a week and a half
+
==April 18th, 2024==
−
*Paul, Michael (Muller) and Kimberly going
+
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
 +
==April 11th, 2024==
 +
*Caltech WS293 ace files ready for the upload
  
−
Human diseases will be objectified
+
==April 4th, 2024==
 +
* Continued discussion on sustainability
 +
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
 +
** Data is still going to SPELL and enrichment analysis
 +
** Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
 +
* Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
 +
* Michael's presentation on LLMs - Named Entity Recognition (NER)
  
 +
==March 14, 2024==
  
 +
=== TAGC debrief ===
  
−
== February 23, 2012 ==
+
==February 22, 2024==
  
 +
===NER with LLMs===
  
−
BioCurator Meeting
+
* 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%)
−
*Karen, Arun, Kimberly, Michael and Yuling are going
 
−
*QCFast poster accepted for presentation
 
  
 +
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
  
−
GO Consortium meeting this weekend
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
*Things to bring up at meeting?
 
−
*Responses to questionnaires
 
  
 +
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
−
Purchase OA Domain name?
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
*Move to a more formal link aside from mangolassi
 
−
*wormbase domain name?
 
−
*Cost? ~$11/year
 
−
*"Ontology Annotator" may not be best name
 
−
*"Curatool" and "Biocuratool" available; the "curinator"? Curate at your "curinal"? ;)
 
−
*Currently only a static site
 
−
*GO Consortium may want to use the tool
 
  
  
−
GO Upload
 
−
*Going back and forth on deciding frequency of upload
 
−
*Currently back to two-month uploads
 
−
*We can certainly change frequency
 
−
*Two-month cycle for upload (in sync with WormBase) is too long of a cycle for GO curation
 
−
*Change GO curation upload to once per month (twice per month?)
 
−
*Things will change when curating through a GO curation interface
 
  
 +
==February 15, 2024==
  
−
SPELL server on Amazon
+
=== Literature Migration to the Alliance ABC ===
−
*1)Existing paid service doesn't seem to be stable
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
**Looking at log file did not reveal anything
+
===== 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 =====
−
**No reply from Matt Hibbs
+
*Facet for topic
−
*2)Amazon installation cannot be updated to WS229 because the dataset demands more memory
+
*Facet for automatic assertion
−
**Raymond tried to install a 64-bit machine (free); wouldn't work
+
**neural network method
−
*We're stuck without more technical support (wrt Amazon service)
+
*Facet for confidence level
−
*Host ourselves (on canopus?) until OICR will take over? (When OICR is ~done with Beta site)
+
**High
−
*Host through IMSS?
+
*Facet for manual assertion
−
*WormMart is the only function of caprica; maybe setup SPELL on caprica for time being (next couple of months)
+
**author assertion
−
*Will Gary Williams et al add more RNA-Seq data?
+
***ACKnowledge method
−
*Athena (8GB memory?)
+
**professional biocurator assertion
−
*Instead of virtual machines, have one machine that does everything
+
***curation tools method - NULL
−
*SPELL usage? Not very much, but several (consistent users (300-900 queries per month)
 
−
*Farm out to Matt Hibbs? Matt not serving data
 
−
*Who is in charge of SPELL at SGD? How does SGD feel about SPELL? Ask Mike Cherry
 
−
*Problem with hosting at OICR if SPELL needs tinkering...
 
−
*Can Wen access and manipulate if at OICR? Not easy
 
−
*SPELL has LOTS of data (millions of lines)
 
−
*Will try to run locally for short term; meanwhile look for more resilient plan
 
−
*Kimberly can ask Cara Delinsky (sp?) about SPELL
 
  
 +
===== Manually validate paper - topic flags without curating =====
 +
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
RNAi parsing script
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
*Wen would like to work on
+
* Search ABC with paper identifier
−
*Updated more than a year ago
+
* Migrate to Topic and Entity Editor
−
*Should be able to parse interaction data directly into OA
+
* View all associated data
−
*Would like to handle new variations and transgenes
+
* Manually validate flags, if needed
−
*Script should look in Postgres tables
 
−
*Still need to deal with DNA sequence text mapping to genome/genes
 
−
*Elbrus a very old machine; very slow
 
−
*Install ace-server on tazendra?
 
−
*Ideal: OA takes/handles bulk of data; just run a script on the side to handle mapping DNA sequence to the genome
 
−
*We will build the RNAi OA
 
  
 +
=== 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?
  
−
Transgene naming strategy
+
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
−
*We will stick to the Expr1234_Ex naming as naming after WBPaper was giving problems (i.e. dealing with 430 objects with no Paper attached and other minor issues).  
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
*For a complete record of the process check wiki: http://wiki.wormbase.org/index.php/Expression_Pattern#Exporting_Reporter_Gene_description_from_Expr_pattern_OA_to_Transgene_OA
 
  
 +
==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==
  
−
== March 1, 2012 ==
+
=== 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.
  
−
GO Meeting
+
* 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.
−
*Focused on annotation pipelines; improving efficiency/effectiveness
 
−
*How to make GO annotations more 'expressive'
 
−
*GO would like to move towards more expressive statements
 
−
*Example: If a gene is involved in a function or process, where in the cell does this take place
 
−
*Common Annotation Framework
 
−
*Current/future members of the GO network can annotate using the same version of GO, same tools and standards
 
−
*Quality controls checks: e.g. do you have all the fields necessary to make an annotation
 
−
*GO hopes to centralize all of the data handling, formatting
 
−
*LEGO - Logical Extensions of GO
 
−
*We should pilot how we want to handle this; similar to how concise descriptions are constructed
 
−
*WormBase curates phenotypes, pathways, etc.
 
−
*Defining useful relationships to curate/annotate: Cross-products with defined relations
 
−
*Pilot: Take subdomains, pathways, try extended version of curation on these
 
−
*How do we capture that fly eye development is relevant to human biology?
 
−
**Humans don't have compound eyes - not the point
 
−
**The pathways are the same or similar; EGF signaling
 
−
*WormBase Process curation could really benefit from GO's adoption of this strategy
 
−
*Need to consider what the "right" way to approach this issue; need good pilot
 
−
*Where is the value? How do we focus on this?
 
−
*Another annotation pipeline: Phylogenetic Annotation and INference Tool (PAINT)
 
−
**How best to make these inferences?
 
−
**What kind of inferences can you make about organismal- or organ-specific processes?
 
−
***Uberon has framework for interspecies anatomical comparisons
 
−
**PAINT tool for nematodes?
 
  
 +
* 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.
  
−
Upload for WS231
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
−
*Interaction file upload took several hours
 
−
*Check if virtual memory is being used
 
−
*Likely culprit is the extra data and XREFs in the Interactor_info hash
 
−
*Can objectify the Interactor_info to be a tag in the main ?Interaction model
 
−
*We should warn EBI/Hinxton about 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
  
−
WormBase Curator Interview next Thursday
+
* 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)
  
−
Migration of Reporter_gene object annotations from Expr_pattern OA to Transgene OA
+
=== UniProt ===
−
*Everything seems OK
+
* 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
  
−
SPELL
 
−
*Papers with less than three experiments, statistics calculations cause slow-down, memory limitations
 
−
*Now can bypass this problem
 
−
*We are now operating SPELL on our local machines
 
−
*Do Amazon instances function/behave differently than local server?
 
−
**Need to compare; find benefits & drawbacks
 
−
*Use Amazon server as a dynamic name server
 
−
*Users shouldn't notice a difference
 
−
*We won't need to ask Todd for anything; we can fix it ourselves
 
  
 +
==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.
  
−
GO Meeting breakout session
+
==January 4, 2024==
−
*Software architecture for upcoming GO expansion (CAT - Common Annotation Tool)
+
* ACKnowlegde pipeline help desk question:
−
*How does Textpresso integrate?
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*What kind of annotation would GO expect Textpresso to do?
+
* Citace upload, current deadline: Tuesday January 9th
−
*User will be able to do guided text mining operations
+
** All processes (dumps, etc.) will happen on the cloud machine
−
**Example: regular expressions, then HMM, then export to CAT
+
** Curators need to deposit their files in the appropriate locations for Wen
−
*No forseeable roadblocks
+
* Micropublication pipeline
−
*Maybe standardize all of the text mining types and methods behind them
+
** Ticketing system confusion
−
*Develop paper-viewer? Apart from CAT, text mining flow? Separate module
+
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 16:04, 18 April 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

April 18th, 2024

  • NNC pipeline being switched off locally and moving into the Alliance ABC.

April 11th, 2024

  • Caltech WS293 ace files ready for the upload

April 4th, 2024

  • Continued discussion on sustainability
  • CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
    • Data is still going to SPELL and enrichment analysis
    • Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
  • Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
  • Michael's presentation on LLMs - Named Entity Recognition (NER)

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
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