#geneontology — Public Fediverse posts

🐰🧬 The Easter bunny delivered early! The March 2026 Gene Ontology release is here with some impressive goodies:

📊 38,560 GO terms
🔬 8,883,119 annotations
🌍 5,557 species
💾 1,703,116 gene products

Your functional genomics just got a spring upgrade! Whether you're doing pathway analysis or comparative studies, this release has you covered.

🔗 current.geneontology.org
💬 https://community.alliancegenome.org/t/8648

#GeneOntology #Bioinformatics #OpenScience #FunctionalGenomics #Research #OpenData #AcademicMastodon

Congratulations to PhD student Daiqing Chen for her poster award at ASMB for "The MatriGO Project: Systematic Curation and Refinement of ECM-related Terms in #GeneOntology" #UIC #MatrixBiology #Science

🧬 Can we map the evolutionary history of plant genes through network analysis?

🔗 Hayai-Annotation: A functional gene prediction tool that integrates orthologs and gene ontology for network analysis in plant species. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.12.011

📚 CSBJ: https://www.csbj.org/

#PlantGenomics #GeneAnnotation #Bioinformatics #Orthologs #RShiny #GeneOntology #ComparativeGenomics #NetworkBiology #Genetics

Talking about remodeling other people's data. There used to be #GeneOntology rdf published by #uniprot that looked nothing like what the GO published. We stopped doing that a long time ago (https://www.uniprot.org/release-notes/2015-03-04-release) and while GO in #OWL is not that easy to query in #SPARQL I can at least use the same queries internally and externally.

As part of a FlyBase and GO consortium project focused on ncRNAs, we have created GO terms to annotate primary GO:0140990 and secondary GO:0140965 piRNA processing, piRNA-mediated retrotransposon silencing by heterochromatin formation GO:0141006 and piRNA-mediated retrotransposon silencing by mRNA destabilization GO:0141009. We welcome any feedback to improve the coverage and accuracy of these annotations.

#GeneOntology #piRNA #noncodingRNA @go

We have a new paper in #AppsPlantSci's upcoming #Bioinformatics issue: GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data with Emily Sessa, Rishi Masalia, @arrigon, and Jessie Pelosi

https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/aps3.11536

#GeneOntology #iamabotanist

Hey Twitterverse, if you work on Fly, Mouse, Rat, Yeast, Worm, Frog, or Zebrafish and/or the #GeneOntology, and use the Alliance resource- now’s your chance to tell us what you like (or what you don’t!). The #alliance is looking for YOUR input! #UserSurvey
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RT @alliancegenome
Got thoughts on the Alliance? Share them with us by taking the 2023 Alliance User Survey! We've added a question this year especially for our model organism…
https://twitter.com/alliancegenome/status/1650592524585652225

Many of the #GeneOntology contributors are #curators, who carefully pull data from literature and make it available on our site- but there are many similar opportunities working with other #ontologies! Here's a fantastic position with EBI working to curate #phenotypes- apply now!
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RT @EMBLEBIjobs
CLOSING: Scientific Curator

Join the PARADIGM initiative, a brand new project in collaboration with @sangerinstitute @Cambridge_Uni @Unio…
https://twitter.com/EMBLEBIjobs/status/1643931562537545728

Just in time for #WisdomWednesday: @ensembl's Variant Effect Predictor now displays #GeneOntology #annotations with links directly to @QuickGO_EBI- making the VEP tool even more fantastic!!

Read this quick blog post to learn more:
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RT @ensembl
Check out our new blogpost here (https://buff.ly/3Ke5GCx ) on the new Gene Ontology function now available in @ensembl VEP.
@news4go #variant #gene #annotator #bioinformatics
https://twitter.com/ensembl/status/1643619058468769792

Today’s #WisdomWednesday tidbit: if you’re trying to reproduce an older #GeneOntology #EnrichmentAnalysis or need to see what the ontology looked like at a specific point in time, etc., you can find past GO releases going back nearly 20 years at http://release.geneontology.org

Don't miss this great #OpenAccess #review in @Non_Coding_RNA about #MicroRNA resources- it has a wonderful section about the contributions and use of the #GeneOntology for examining #transcriptomic data: DOI: 10.3390/ncrna9020018
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RT @UCLgene
Fantastic to see my previous student, Diana Luna Buitrago, writing this great review of microRNA analysis tools: Insights into Online microRNA Bioinformatics Tools https://www.mdpi.com/2311-553X/9/…
https://twitter.com/UCLgene/status/1632682509069680641

The #GeneOntology provides #OpenAccess information on the functions of genes to support research in many fields. We have over 500k #GOannotations for M. #tuberculosis gene products, taxon:1773 & descendants. Find them on @QuickGO_EBI:
https://www.ebi.ac.uk/QuickGO/annotations?taxonId=1773&taxonUsage=descendants

#WorldTBDay #EndTB
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RT @UNYearbook
In 1947–48, the annual death rate from tuberculosis was 4–5 million people, with 40–50…
https://twitter.com/UNYearbook/status/1639322450935545873

Read the #OpenAccess paper at DOI:10.1371/journal.pgen.1010656

For more info about the PANTHER Classification System featured in Fig 4, visit http://www.pantherdb.org/about.jsp
PANTHER also powers the #GeneOntology #EnrichmentAnalysis on our homepage http://geneontology.org 2/2

Here's one of the latest in a flurry of fantastic papers that use #GeneOntology: in @FrontiersIn #CellandDevBio, Schäfer et al. examine USH1C/harmonin's role in the cWnt pathway, a step in understanding #UsherSyndrome. Keep up the great work and thanks for citing us!

Today's #WisdomWednesday tidbit is another frequent flyer on our Helpdesk.

Q: What's the best way to get high-quality #GeneOntology annotations for a novel/underannotated organism?

A: Just submit the transcriptome to @NCBI!
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RT @NCBI
RefSeq release 217 is now available! This full release contains new annotations for 33 species, including: slow loris (pictured), common vampire bat, blue catfish, California two-spot octopus, and more! Che…
https://twitter.com/NCBI/status/1635748054996320256

It's #Friday, it's #InternationalBagpipeDay, AND there's a new #GeneOntology Release- definitely one of the best days of the year so far!

The March 2023 GO Release (2023-03-06) is now available. Find it at
http://current.geneontology.org/
http://release.geneontology.org/2023-03-06
https://doi.org/10.5281/zenodo.7709866

When a novel #MolecularFunction or #BiologicalProcess is published our network of #biocurators usually find it-but we highly encourage authors/researchers to contact us about their novel research, or even if they find errors/omissions in the #GeneOntology (mistakes happen!) 2/4

In a wonderful #OpenAccess paper in @VirusesMDPI, Lim et al. use #GeneOntology to look at how the #alphavirus Ross River virus (RRV) impacts infected as well as bystander cell populations. Read more at https://www.mdpi.com/2043164

#HappyValentineDay! We're also halfway through #AmericanHeartMonth. #DidYouKnow our prolific contributing group @UCLgene is responsible for 3000 #cardiovascular #GOTerms? Many of their >45k manual #GeneOntology annotations to >5k human #proteins are❤️-related from @TheBHF funding

Here's a really interesting new paper from @SciReports: Kim et al. examined early molecular features in #tauopathy using generative adversarial networks to analyze bulk #RNAseq... and of course they used #GeneOntology too! #neuroscience #research doi: 10.1038/s41598-023-28081-6

Here's a great #DotPlot showing #GeneOntology terms from van Kuijk et al., with a very nice use of the GO in their new @ESC_Journals #CardiovascularResearch paper!
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RT @SluimerJudith
But what do they do? Gene ontology suggests common and different functions related to risk factors for cardiovascular disease (lipids, inflammation)
https://twitter.com/SluimerJudith/status/1620743440106651651

#WisdomWednesday: Have you ever noticed drastic changes in the amount of #GeneOntology #annotations for your organism? Many of these changes involve the electronically inferred (@ecoontology code IEA). Of the current 7,503,460 total annotations, 1,703,348 are IEAs.

1/3

#WisdomWednesday: Have you ever been working with the #geneontology, somehow wound up with a list of GO IDs (the numerical identifier) but actually need the #GOTerm (the #HumanReadable part)? You can use an instance of @intermine and have your new list in a few simple steps!!
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Did your #NewYearResolution involve publishing more? If so & you're using the #geneontology, #GOannotations or other GO products, cite at least two GO papers:
PMCID: PMC3037419
PMCID: PMC7779012
GO is #CCby40. Find our #CitationPolicy at http://geneontology.org/docs/go-citation-policy #WisdomWednesday

Absolutely fantastic new paper from Marie Brasseur & @leeselab in @BioMedCentral featuring Gammarus fossarum - a wonderful demonstration of the #geneontology in use (thanks for the citation!) @VascoElbrecht @rksalis @weiss_martina @Daniel_G1978 #goannotation
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RT @leeselab
New study by our @unidue team & @Leibniz_LIB on #multiplestressor impacts lead by Marie Brasseur 🎉. We herein focused on #transcriptomic analysis of the #freshwater k…
https://twitter.com/leeselab/status/1601184358370459648

Gene length bias strikes again (is everything in #bioinformatics biased by gene length, GC content, or both?):
Aging is associated with a systemic length-associated transcriptome imbalance
https://www.nature.com/articles/s43587-022-00317-6
#AgingBiology #GeneLength #GeneOntology

Ever wonder what the #evidencecode in a #goannotation means? It describes the evidence used to pair a #geneontology term to the #geneproduct or #complex. Although many @ecoontology terms are for manual annotations by breathing #biocurators, some #goannotations are #computational.
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RT @EBItraining
Want to learn how functional annotation of #protein sequences is automated? Join our #webinar next week to learn how it works with @unipro…
https://twitter.com/EBItraining/status/1598628130025095170

#TipTuesday: The #geneontology can be #cited by doi (or release version, e.g. 2022-11-03)!

Snag the doi for the #latestrelease at http://current.geneontology.org/metadata/release-archive-doi.json

To represent all releases, use http://doi.org/10.5281/zenodo.1205166 which will resolve to the latest release.

http://geneontology.org/docs/go-citation-policy/
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RT @RIOJournal
🔝Best practices on how identifiers should be used & how they…
https://twitter.com/RIOJournal/status/1594626274647248896

New #mastadon account, new feature! We're going to highlight #newpublications that feature (AND *importantly* #cite!!) the #geneontology. First winner is Marina Brasó-Vives et. al, who examined gene duplication in amphioxus vs. vertebrate genomes in #GenomeBiology. Read more at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02808-6