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]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2014|January]]
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2014|February]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_March_2014|March]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
== April 3, 2014 ==
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
=== WOBr ===
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
−
* Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser)
 
−
* As one-offs, Raymond can take newly generated GAFs from curators and process for testing.
 
  
−
=== Murray Expression datasets ===
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
−
* Still need to acquire primary expression data from Waterston lab
 
−
* Problems with handling inferred expression of genes in cells
 
−
* Thus inferred expression data will be removed
 
−
* Expression object will retain graphical representations supplied by Murray et al.
 
−
* A friendly reminder will be sent to Waterston requesting tabulated, processed primary expression data.
 
  
 +
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
== April 10, 2014 ==
+
==April 11th, 2024==
−
===Apologies===
+
*Caltech WS293 ace files ready for the upload
−
* Karen: attending impromptu OICR group meeting, won't be on the Caltech call.
 
−
=== BioCurator Meeting ===
 
−
[[ISB2014_group_notes]]
 
−
* many text mining tools
 
−
* many ontology systems, mapping ontologies
 
−
** Aging ontologies
 
−
** Anatomy ontology mapping (Uberon)
 
−
** Format convergence? OBO, OWL, RDF? Plugin for Protege to read OBO files
 
−
** How extensive is OWL? How much has OWL been applied to biology? OWL is being used for reasoning
 
−
* Community Annotation
 
−
** CANTO (Community ANotation TOol) workshop (Wen attended)
 
−
*** PombeBase use CANTO and works well
 
−
* Big data curation open discussion/workshop
 
−
** Enormous datasets (e.g. genome sequencing of all cancer patients)
 
−
** Data storage issue
 
−
** Data stability issue
 
−
** Clinical data, portal set up by Michael Cherry, ClinGen
 
−
* Lincoln's talk
 
−
** International Cancer Genome Consortium (ICGC) project (petabyte datasets)
 
−
** 10,000 cancer patients already sequenced (18 PB by 2018)
 
−
** Torent P2P data sharing
 
−
* BioCreative workshop
 
−
** Text mining
 
−
*** Pubtator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/index.cgi?user=User425569566)
 
−
**** Curates sentences, marks up entities, only applied to abstract
 
−
** GO annotation
 
−
*** GO Cat (http://eagl.unige.ch/GOCat/)
 
−
* Amazon "Mechanical Turk" community annotation
 
−
* EcoCyc, MetaCyc - pathway curation (will hear from Karen)
 
−
* Reactome
 
−
** May be a good tool for displaying TF-target gene interaction display (vs. Cytoscape)
 
−
** Add a Reactome display to WormBase?
 
−
* SPELL - anything to replace SPELL? No.
 
−
** Still lacking other tools for microarray and RNA-Seq data
 
−
=== Heartbleed SSL security issue ===
 
−
* Raymond updated all servers/machines
 
−
* All machines need to be rebooted
 
−
* Any user passwords should be changed
 
−
* Do we care about any non-root users? Best to change all passwords on machines that have been updated
 
−
=== BioGrid C. elegans physical interactions ===
 
−
* Kimberly has been using BioGrid's curation tool
 
−
* We have a table of C.elegans large scale genetic and physical interaction data
 
−
* We're still trying to get all data
 
−
=== Timestamps ===
 
−
* Curator evidence vs. history of curation
 
−
* Kevin and Juancarlos still looking for use-cases
 
−
* Need to consider for future database migration and potential use of a common central database
 
−
* Curators use timestamps for culling out bogus data objects/cleaning up data
 
  
−
== April 17, 2014 ==
+
==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)
  
−
=== Agenda ===
+
==March 14, 2024==
−
* BioGrid
 
−
* AmiGO
 
−
* Reactome
 
−
* BioCurator Meeting
 
−
* Fission Yeast phenotype onotology & PATO
 
  
−
===BioGrid followup===
+
=== TAGC debrief ===
−
* What are the roadblocks to protein-protein interaction curation and incorporation into WormBase?
 
−
* Chris, Kimberly, and Rose have communicated about C. elegans interaction data
 
−
* We will import BioGrid interactions, non-redundantly
 
−
* We are still sorting out some discrepancies regarding the Li et al 2004 Y2H interactome dataset
 
  
−
===AmiGO verification manager===
+
==February 22, 2024==
−
*The GO verification manager creates a co-annotation matrix that highlights GO annotation intersections.
 
−
* From the matrix, it is easy to see where there are no or many co-annotations. From this analysis, PomBase built rules for future annotation, where if an annotation is made that has already been shown to never have occurred in conjunction with another annotation, an alert is sent.
 
−
* The curator can then reassess the annotation, either fixing it, or adjusting the rules.
 
−
* Poster by PomBase Val Wood on GO annotation rules built through a co-annotation analysis.
 
−
* I'm (Karen) thinking this would be a good tool for analyzing and setting rules for phenotype annotation.
 
−
http://amigo2.berkeleybop.org/cgi-bin/amigo2/matrix
 
−
https://sourceforge.net/apps/trac/pombase/wiki/MatrixProject
 
−
http://build.berkeleybop.org/job/check-shared-annotations/lastBuild/console
 
−
* They can include worm checks in this project as well. I(Karen) don't know what we would need to do for that.
 
−
* Karen can send along Val's poster to anyone who wants to know more
 
  
−
===Reactome training sessions===
+
===NER with LLMs===
−
* Peter D'Eustacio is setting up WebEx training sessions for curating in Reactome for the different MODs- this includes WB, SGD, Flybase and PomBase, at least. 
 
−
* Right now the thought is that there will be a couple intro WebEx sessions, and eventually an in-person curate-athon (jamboree) where all curators will get together and do a shared project (place to be determined). 
 
−
* Karen will definitely be participating, but this can be open to anyone.
 
−
* Reactome data can be imported into WikiPathways, therefore the data can make the "round trip" back to WormBase
 
  
−
===Fission Yeast Phenotype Ontology (FYPO)/PATO===
+
* 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%)
−
* Should we move to PATO?
 
−
* The FYPO has recently been [http://bioinformatics.oxfordjournals.org/content/early/2013/06/03/bioinformatics.btt266.full#T1 published]<br>
 
−
* You can download the ontology on the OBOfoundry [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fypo here]<br>
 
−
* (to open it in oboedit, you need to set an advance setting to allow danglers)<br>
 
−
* At first it seems pretty chaotic, but after a bit I found it makes a lot of sense- the branches are all different views and access points to the phenotypes.
 
−
* The phenotypes themselves are composed of different ontologies, GO, ChEBI, CL (Cell) and PATO qualities, so terms from these ontologies are used as 'parent' terms. There is also, of course, the phenotype branch itself along with a quality branch.  I think this organization actually makes the ontology more accessible to people as it lends itself to being approached from different vantage points.
 
−
* I (Karen) think it would be good for us to invest in moving our phenotype ontology to be PATO compliant, and I think FYPO offers an excellent example for organizing it.
 
−
* Migrating the WB phenotype ontology to PATO is not trivial
 
  
−
=== ?Construct model ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* There's an issue with incorporating, for example, Mosci alleles and their display on the website
 
  
−
=== Monarch Initiative ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* Chris Mungall: mapping phenotypes across species
 
−
* http://monarchinitiative.org/
 
  
−
=== Testing complex data in a central curation database ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Juancarlos would like examples of potentially complex data curation to determine important data modeling considerations
 
  
−
== April 24, 2014 ==
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
  
−
=== Topics Curation ===
 
−
* Pathway curation
 
−
** WikiPathways, Reactome, LEGO
 
−
** Reactome training/jamboree coming up
 
−
* New topic: Chromosome segregation (mitotic/meiotic)
 
−
** Annotations extensions (from GO) could be used
 
  
−
=== Gene Ontology ===
 
−
* Paul Thomas visits next Tuesday, 10am PDT
 
−
** Video conference call? Skype, Google Hangout? Join Me (www.join.me)?
 
−
** LEGO demo
 
−
* Suzie Lewis proposed a once-a-quarter GO-consortium conference call
 
−
* We could talk about Textpresso curation tool
 
−
* Textpresso YouTube (or other?) video
 
−
* GO-central
 
−
** Need a table/grid view, ontology annotator view
 
−
** OWL format for LEGO database ('OWLification')
 
−
* Paul T., Suzie L., and Paul S. will discuss syncing with UniProt in July
 
−
** Protein2GO tool
 
−
** Entity annotation tool
 
−
** Central annotation and quality control
 
−
* Protege-compatible tool for GO consortium
 
−
* OBO-Edit will be supported until replaced
 
−
* Currently there is no GO-enrichment tool in WormBase; can we link out to relevant/good tools?
 
−
* Enrichment tool could be applied to other ontologies (e.g. phenotype) as well
 
−
* PAINT tool (Phylogenetic annotation) [http://wiki.geneontology.org/index.php/PAINT]
 
−
** Annotations of common ancestors based on shared GO annotations of homologs/paralogs etc.
 
−
** Software has improved in last year
 
−
** Best to do a quality control test
 
−
** "Summer of PAINT"?
 
−
** Tool has a user-inertia issue: easier to use when using often, harder when using rarely
 
  
−
=== WOBr status ===
+
==February 15, 2024==
−
* Various Gene-Association Files (GAFs) pending (life stage, disease, etc.)
 
−
* Raymond and Juancarlos making progress, should be released soon
 
−
* Some issues; e.g. a single GO term with >7000 children (!) causing problems for Amigo and WOBr
 
−
** We could enforce a cut-off for terms with too many annotations (for performance)
 
−
* Currently still running on local machine (juancarlos.wormbase.org)
 
−
* Will push to live site ASAP
 
−
* Terms that have no children will explicitly say so (to be clear to users)
 
−
* Will apply a "?+" symbol instead of just a "+" on the relevant expandable nodes of the tree
 
  
−
=== SPELL ===
+
=== Literature Migration to the Alliance ABC ===
−
* Michael Cherry/SGD considering rewriting SPELL
+
==== 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
  
−
=== HTML format for special characters in ACEDB ===
+
===== Manually validate paper - topic flags without curating =====
−
* ACEDB doesn't support special character display (in concise decriptions, for example)
+
*Facet for topic
−
* GitHub issue [https://github.com/WormBase/website/issues/2626]
+
*Facet for manual assertion
−
* Not clear that using HTML format ever worked
+
**professional biocurator assertion
−
* Daniela mentioned script "Find-weird-characters"(?) that would process dumped .ace files for special characters
+
***ABC - no data
−
* Ideally characters are converted during the dump
 
−
* Can we use Unicode for all special characters?
 
  
−
=== Strains, transgenes consistency with CGC ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* There have been discrepancies of transgene references in strains between WB and CGC
+
* Search ABC with paper identifier
−
* Karen working on cleaning up
+
* Migrate to Topic and Entity Editor
−
* Cause? E.g. authors mis-incorporating transgene info
+
* View all associated data
−
* Juancarlos wrote scripts to check the data across the two databases, finds discrepancies
+
* Manually validate flags, if needed
−
* Discrepancies can be sent to Aric at CGC
 
  
−
=== New England Area Parasitology/Helminthology meeting ===
+
=== PDF Storage ===
−
* Xiaodong attended, representing WormBase
+
* At the Alliance PDFs will be stored in Amazon s3
−
* Not many parasitologists using WB
+
* We are not planning to formally store back-up copies elsewhere
 +
* Is this okay with everyone?
  
−
=== Phentoype cross-product terms ===
+
==February 8, 2024==
−
* e.g. "bloated", "kinker", "roller"
+
* TAGC
−
* Fuzzy synonyms in PATO?
+
** Prominent announcement on the Alliance home page?
−
* Gary S. using GO and PATO
+
 
−
* Do we need to add quality terms to PATO?
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Approach: first fix slim terms, map slim terms
+
 
 +
==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
 +
** 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 16:04, 18 April 2024

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2017 Meetings

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2020 Meetings

2021 Meetings

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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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