Live and recent posts from across the Fediverse tagged #geneontology, aggregated by home.social.
🧬 Gene Ontology Release 2026-06-19 is live - with breaking changes!
🚨 File URLs & names changed - automated downloads are likely broken right now if you didn't already update your code!
📊 38,263 GO terms
🔬 14,736,040 annotations
🌍 171 species
Need migration help? Check the @AllianceGenome forum: https://community.alliancegenome.org/t/8689
🔗 current.geneontology.org
📖 DOI: 10.5281/zenodo.20943148
#GeneOntology #Bioinformatics #OpenScience #AcademicMastodon #Research
🐰🧬 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
Excellent talk by Rund Tawfiq on a systems view of GO annotations, considering not each GO term and each protein separately, but the coverage of consistent functions over a genome. #ismbeccb2025 #GeneOntology
https://www.biorxiv.org/content/10.1101/2025.07.14.664848v1
Valverde et al. analyzed 15 years of Gene Ontology evolution, finding that GO changes not just incrementally, but also via major, curator-driven restructurings, underscoring the need for version-aware, multi-layer models to ensure reproducibility and interpretability.
🔗 doi.org/10.1093/molbev/msaf148
Current me: Ugh, human GO terms are annotated with Uniprot, current data has Entrez, when I generate the GO annotation object I'll have to convert as part of the process.
Past me: Human GO terms are annotated with Uniprot, when we ingest this data, we should be able to provide a mapping table so that the final GO annotation object uses whatever gene IDs we want.
Current me: Thanks past me! Glad I looked at the help and the code for that function first!
🧬 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
Working with #GeneOntology annotations today for a #bioinformatics analysis of cytokines (we'll see what actually turns up when you just measure 225 cytokines).
So, remap genes to terms using our {gocats} python library, and then read in the new annotations for use in {categoryCompare2}.
Somehow, I always forget that I wrote a function specifically for importing the {gocats} generated stuff into the annotation format. 🤦♂️
https://github.com/MoseleyBioinformaticsLab/categoryCompare2/blob/main/R/gocats.R#L13
Happy #DNADay2024!
Today's @AllianceGenome forum post highlights some of the close ties between the Human Genome Project and the #GeneOntology: both Dr. David Botstein and Dr. Paul Thomas.
https://community.alliancegenome.org/t/happy-dna-day-close-ties-between-the-hgp-go/7642
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.
Bioinformatics and system biology approach to identify the influences of SARS-CoV-2 on metabolic unhealthy obese patients. https://doi.org/10.3389/fmolb.2023.1274463 #SarsCov2 #MetabolicUnhealthyObese #DifferentiallyExpressedGenes #GeneOntology #ProteinProteinNetwork
📊 We now offer Gene Ontology annotations for Hierarchical Orthologous Groups, enabling both extant and ancestral GO enrichments. Dive into functional genomics with ease! #GeneOntology #OMAUpdate2024
What a feeling getting one of our Senior High School students to the point where they are re-running an analysis using `snakemake`, our #GeneOntology mapping package `gocats`, and hypergeometric enrichments from `categoryCompare2`.
So much hand holding through de-compressing things, reading error messages together, installing various bits and pieces, and modifying the `$PATH`!
But the look on their face when it runs! Hooked. And this is just the prelude to their actual research project. 😉
Results are up for the FlyBase Community Advisory Group #GeneOntology (GO) survey https://wiki.flybase.org/wiki/File:FlyBase_Gene_Ontology_(GO)_Survey.pdf, which asked about how GO annotations are used, highlighted resources and tools of interest and asked about prioritization of curation projects.
Want to help (and influence) FlyBase by joining #FCAG https://wiki.flybase.org/wiki/FlyBase:Community_Advisory_Group Please go to the registration form http://flybase.org/static/fcag.
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
The influence of COVID-19 on colorectal cancer was investigated using bioinformatics and systems biology techniques. https://doi.org/10.3389/fmed.2023.1169562 #Covid19 #ColorectalCancer #DifferentiallyExpressedGenes #GeneOntology #Protein–ProteinInteraction
Not only does this MOD issue of #Genetics have the #GeneOntology Consortium’s brand new, super exciting article, but the cover art is FANTASTIC 😉!! Find our new GO paper here: https://doi.org/10.1093/genetics/iyad031 #NewPaper
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RT @GeneticsGSA
A new issue of #GENETICS is out today! It features our 2nd annual collection of Model Organism Database articles from @news4go @ZFINmod @Xenbase @yeastgenome @MaizeGDB @ratgenome. Cozy cover a…
https://twitter.com/GeneticsGSA/status/1654153164935815168
Huge thanks to @DisProt_db for hosting the #GeneOntology consortium meeting and sharing their beautiful city with us! Have a safe trip home from #Padova for everyone leaving today. It’s been an amazing meeting with tons of great formal (and informal) discussions!
After all those years, WHY didn't you tell me about recursive queries in #SPARQL that find all the descendants of a term in an ontology? https://gist.github.com/lindenb/2b0239f2237ce835fe2d2ddfc9ebeb02
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
The #GeneOntology is thrilled to be one of the founding Global Core Biodata Resources, a status neatly described by Guy Cochrane in his fantastic #biocuration2024 keynote as indicating a “keystone species” in the ecosystem of biodata resources.
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RT @biocuration2023
Best way to start the end of the conference : Day 4
Our last keynote speaker : Guy Cochrane on Global Biodata Coalition (GBC)
Forum has been formed to overcome the ex…
https://twitter.com/biocuration2023/status/1651121819758239745
Wow! The room is absolutely packed for another amazing talk by a #GeneOntology member: @wormbase’s Kimberly Van Auken presenting on WB’s ACKnowledge pipeline, which uses #AI to aid fact extraction in community curation #biocuration2023
Wonderful speech from Patrick Masson to kick off #biocuration2023 on the #GeneOntology’s GO-CAM Models!
You may know about the #GeneOntology, but do you know about the Disease Ontology? Follow DO on slack!
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RT @diseaseontology
Join our slack group and stay up to date with the Disease Ontology:
https://join.slack.com/t/humandiseaseontology/shared_invite/zt-1sw9fbq8m-V0xQSN67tMkBrmvkJYcK2A
#DiseaseOntologySlack
https://twitter.com/diseaseontology/status/1646960074563244059
BioMart- of course we all know you can get #GeneOntology annotations with this great tool, but here's a fantastic #tweetorial about converting gene IDs!
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RT @ensembl
1/ Do you have a list of @ensembl IDs that you want to convert to IDs from other databases?
Here's how you can retrieve the @NCBI gene IDs from a list of #Ensembl IDs. A thread...🧵
#genomics #bioinformatics #tweetorial #Ensembltraining 🧬
https://twitter.com/ensembl/status/1646497467909767169
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
It's past #AprilFoolsDay so trust us- we have new data! The April 2023 #GeneOntology Release (2023-04-01) is now available!
http://current.geneontology.org/
http://release.geneontology.org/2023-04-01
https://doi.org/10.5281/zenodo.7796232
43,093 GO terms
7,442,411 annotations
1,502,221 gene products
5,291 species
#ThrowbackThursday Can you believe it's been nearly 10 years since our #GeneOntology Consortium meeting in #Cambridge right after Biocuration2013? We are certainly looking forward to seeing many of the same faces-and some new ones-next month in Padua right after #biocuration2023!
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
Can't recommend this free 2-day #GeneOntology workshop enough!! If you can get to Rome the week after #biocuration2023, sign up now. Space is limited and yes the instructors are absolutely fantastic! @UCLgene @MINT_database
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RT @MINT_database
Join the Rome-UCL bioinformatics workshop in May @BiologiaUniRM2 with Ruth Lovering @UCLgene and Luana Licata @MINT_database
Registration free but essential: https://tinyurl.com/UCL-Rome-bio…
https://twitter.com/MINT_database/status/1638141695844921346
Today's #thursdaytreat is a #tweetorial!! Here's a common question our #GeneOntology #Helpdesk has been getting lately:
I have a list of GO IDs, now what's the easiest way to get the GO term names?
#GOtermnames #Bioinformatics #computationalbiology
1/8
Today's #thursdaytreat is a #tweetorial!! Here's a common question our #GeneOntology #Helpdesk has been getting lately:
I have a list of GO IDs, now what's the easiest way to get the GO term names?
#GOtermnames #Bioinformatics #computationalbiology
1/8
On this #InternationalWomensDay2023, we'd like to recognize two of the #GeneOntology's founding PIs: Judy Blake at @jacksonlab and Suzi Lewis at BBOP @BerkeleyLab. Although both are retired, the foundation they worked to create continues to influence #Science every day #IWD2023
Drop us a DM, email us or swing by our #github Helpdesk: https://github.com/geneontology/helpdesk/discussions. If you think we're missing a GO Term, gather the info mentioned at http://geneontology.org/docs/contributing-to-go-terms/ to help us improve the #GeneOntology 3/4
We are constantly updating, improving, and re-evaluating annotations & ontology. This is another reason it's important to include GO versions with any publications or work involving the #GeneOntology. Hopefully future studies will show there's a unique keanumycin activity! 4/4
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
Congratulations to our friends at @FlyBaseDotOrg, who are very active in contributing to the #GeneOntology at many levels!
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RT @MArbeitman
Congratulations to our colleagues recognized for their outstanding community service at #Dros23--Dr Thomas Brody @interactivefly, Dr James Thompson for Drosophila Information Services (https://www.ou.edu/journals/dis/), and Flybase Curatorial Team @FlyBaseDotOrg 🧵1/4
https://twitter.com/MArbeitman/status/1632800803823169536
#FunFactFriday Did you know the #GeneOntology Consortium began in 1998 as a collaboration between @yeastgenome @FlyBaseDotOrg and @mgi_mouse (MGD)? The GOC continues to be an amazing, fun group to be involved with. We look forward to seeing many of you at our Spring 2023 meeting!
GOC Members: remember to register for this year's Spring #GeneOntology Consortium #conference in Padua, Italy in April- right after #biocuration2023! Check your email for the invitation. Only 3 weeks until registration deadline!
#SaveTheDate! The Spring 2023 #GeneOntology Consortium meeting will be held (in person!) on April 27-29th in Padova, Italy, directly after the #biocuration2023 conference. Details and registration link will be sent out shortly.
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
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