after the break, Miranda Carlsson presented her work on ChEBI ontology enrichment. Her preprint is up on @biorxivpreprint: "ChEBI-N - Enrichment Analysis with the ChEBI Ontology" https://doi.org/10.64898/2026.10.14.758784
ChEBI-N - Enrichment Analysis with the ChEBI Ontology
Introduction Biological and chemical ontologies are structured representations that can be used to map entities such as metabolites onto broader chemical and biological categories. Enrichment analysis applied to such ontologies identifies classes whose representation within a set deviates from an expected background distribution, helping to interpret complex metabolomics measurements. Objectives This study aimed to develop a tool for ChEBI (Chemical Entities of Biological Interest) ontology-based enrichment analysis, named ChEBI-N (ChEBI eNrichment). It is a successor of the previous tool BiNChE, with new features that broaden its applicability. Methods We reimplemented BiNChE and extended it to accept SMILES or InChI strings as well as ChEBI IDs. These broaden applicability to datasets with entities that are not yet present in ChEBI. We also constructed organism-specific background populations. Results We demonstrate the tool on three published metabolomics datasets covering wine, cheese, and human plasma samples. ChEBI-N correctly highlighted relevant enriched classes in all three datasets, such as flavonoids in the wine dataset and fatty acid classes in the cheese dataset. Comparing organism-specific and full-ChEBI backgrounds shows that restricted backgrounds reduce the inflated significance of generic classes, although the most enriched classes remain largely consistent. Conclusion ChEBI-N is an extended successor to BiNChE for ontology-based enrichment analysis of metabolomics data, offering a hypothesis-generating complement to existing metabolomics analysis pipelines. Availability ChEBI-N is freely available at [chebin.hastingslab.org][1] or as a Python package (pypi.org/project/chebin), with source code at github.com/ontology-tools/chebin, archived at Zenodo (doi:10.5281/zenodo.23264219) and Software Heritage (swh:1:rev: 133a41792704eb7f1db746f36a5ae97e9247b2b7). ### Competing Interest Statement The authors have declared no competing interest. SNF, 10002786 [1]: https://chebin.hastingslab.org
www.biorxiv.org
November 5, 2026 at 9:57 AM
after the break, Miranda Carlsson presented her work on ChEBI ontology enrichment. Her preprint is up on @biorxivpreprint: "ChEBI-N - Enrichment Analysis with the ChEBI Ontology" https://doi.org/10.64898/2026.10.14.758784
Чебурашка
[Chebi: My Fluffy Friend]
[Chebi: My Fluffy Friend]
October 31, 2026 at 7:10 PM
Чебурашка
[Chebi: My Fluffy Friend]
[Chebi: My Fluffy Friend]
today the third #onto4chem2026 starts with a presentation by Noel O'Boyle (EMBL-EBI) about ChEBI, the @elixir_europe resource. It starts with where things were at the Ontologies4Chem meeting last year, also here in Limburg/DE
Follow Noel here: @baoilleach
Follow Noel here: @baoilleach
November 5, 2026 at 8:05 AM
today the third #onto4chem2026 starts with a presentation by Noel O'Boyle (EMBL-EBI) about ChEBI, the @elixir_europe resource. It starts with where things were at the Ontologies4Chem meeting last year, also here in Limburg/DE
Follow Noel here: @baoilleach
Follow Noel here: @baoilleach
the 2nd and 3rd #onto4chem2026 presentations by Simon Flügel and Charlotte Tumescheit show new approaches to classify ChEBI molecules (including the "toxic" role). Lot's of discussions follow on the use of SMILES in deep learning approaches. The rule based approach reminded me of LISP.
November 5, 2026 at 9:13 AM
the 2nd and 3rd #onto4chem2026 presentations by Simon Flügel and Charlotte Tumescheit show new approaches to classify ChEBI molecules (including the "toxic" role). Lot's of discussions follow on the use of SMILES in deep learning approaches. The rule based approach reminded me of LISP.
NISPO: "NISPO achieved 98.1% OPSIN round-trip accuracy on a held-out benchmark of 103 million PubChem compounds."
Openclature:"Round-trip accuracy PubChem: 99.76%"
Orthonym: "On 2.2 million selected molecules from ChEBI, QM9, PubChem and ZINC22, it named 97.37% correctly"
Openclature:"Round-trip accuracy PubChem: 99.76%"
Orthonym: "On 2.2 million selected molecules from ChEBI, QM9, PubChem and ZINC22, it named 97.37% correctly"
mstdn.science
October 25, 2026 at 6:44 AM
NISPO: "NISPO achieved 98.1% OPSIN round-trip accuracy on a held-out benchmark of 103 million PubChem compounds."
Openclature:"Round-trip accuracy PubChem: 99.76%"
Orthonym: "On 2.2 million selected molecules from ChEBI, QM9, PubChem and ZINC22, it named 97.37% correctly"
Openclature:"Round-trip accuracy PubChem: 99.76%"
Orthonym: "On 2.2 million selected molecules from ChEBI, QM9, PubChem and ZINC22, it named 97.37% correctly"
ChEBI-N - Enrichment Analysis with the ChEBI Ontology https://www.biorxiv.org/content/10.64898/2026.10.14.758784v1
October 20, 2026 at 5:46 PM
ChEBI-N - Enrichment Analysis with the ChEBI Ontology https://www.biorxiv.org/content/10.64898/2026.10.14.758784v1
ChEBI-N - Enrichment Analysis with the ChEBI Ontology https://www.biorxiv.org/content/10.64898/2026.10.14.758784v1
October 20, 2026 at 5:46 PM
ChEBI-N - Enrichment Analysis with the ChEBI Ontology https://www.biorxiv.org/content/10.64898/2026.10.14.758784v1
🧪 Same molecule, different names? ChEBI from @ebi.embl.org gives chemical entities shared identifiers and connects them by structure and biological role—helping bring chemistry datasets together.
openknowledgegraphs.com/resource/che...
#KnowledgeGraphs #OpenScience
openknowledgegraphs.com/resource/che...
#KnowledgeGraphs #OpenScience
ChEBI - Open Knowledge Graphs
database and ontology of molecular entities focused on small chemical compounds
openknowledgegraphs.com
October 1, 2026 at 6:30 PM
🧪 Same molecule, different names? ChEBI from @ebi.embl.org gives chemical entities shared identifiers and connects them by structure and biological role—helping bring chemistry datasets together.
openknowledgegraphs.com/resource/che...
#KnowledgeGraphs #OpenScience
openknowledgegraphs.com/resource/che...
#KnowledgeGraphs #OpenScience
#Chibi #HisuianTyplosion #Pokémon OC drawin, did an extra version with flames this time! I'm quite happy with the colours I ended up choosing for them! Wawa :3 💜
September 17, 2026 at 11:30 AM
#Chibi #HisuianTyplosion #Pokémon OC drawin, did an extra version with flames this time! I'm quite happy with the colours I ended up choosing for them! Wawa :3 💜
Thank you to all the participants and trainers who helped us put @ebi.embl.org resources into practise at today's workshop.
In just six hours, we've used ChEBI, ChEMBL, @pdbeurope.bsky.social, and @uniprotkb.bsky.social as workflows to investigate drug interactions with a protein target.
🧬🖥️📊
In just six hours, we've used ChEBI, ChEMBL, @pdbeurope.bsky.social, and @uniprotkb.bsky.social as workflows to investigate drug interactions with a protein target.
🧬🖥️📊
September 10, 2026 at 12:31 PM
Thank you to all the participants and trainers who helped us put @ebi.embl.org resources into practise at today's workshop.
In just six hours, we've used ChEBI, ChEMBL, @pdbeurope.bsky.social, and @uniprotkb.bsky.social as workflows to investigate drug interactions with a protein target.
🧬🖥️📊
In just six hours, we've used ChEBI, ChEMBL, @pdbeurope.bsky.social, and @uniprotkb.bsky.social as workflows to investigate drug interactions with a protein target.
🧬🖥️📊
icymi: ChEBI is hiring a curator! "Open Position: Chemistry Curator" https://chembl.blogspot.com/2026/08/open-position-chemistry-curator.html
#chemistry #openscience
#chemistry #openscience
Open Position: Chemistry Curator
We are looking for a talented scientist with a flair for data curation to be responsible for the quality of chemical and associated data in...
chembl.blogspot.com
September 4, 2026 at 7:51 PM
icymi: ChEBI is hiring a curator! "Open Position: Chemistry Curator" https://chembl.blogspot.com/2026/08/open-position-chemistry-curator.html
#chemistry #openscience
#chemistry #openscience
blogged today about ChEBI, data properties in OWL ontologies, computational chemistry, atomic numbers, and basis sets
https://cthoyt.com/2026/09/04/chebi-atomic-numbers.html
all part of @NFDI4Chem
#obo #owl #chebi #obofoundry #NFDI #NFDI4Chem
https://cthoyt.com/2026/09/04/chebi-atomic-numbers.html
all part of @NFDI4Chem
#obo #owl #chebi #obofoundry #NFDI #NFDI4Chem
September 4, 2026 at 7:23 PM
blogged today about ChEBI, data properties in OWL ontologies, computational chemistry, atomic numbers, and basis sets
https://cthoyt.com/2026/09/04/chebi-atomic-numbers.html
all part of @NFDI4Chem
#obo #owl #chebi #obofoundry #NFDI #NFDI4Chem
https://cthoyt.com/2026/09/04/chebi-atomic-numbers.html
all part of @NFDI4Chem
#obo #owl #chebi #obofoundry #NFDI #NFDI4Chem
🫂🦋🥰🐈⬛🌷🥰
Cheburashka Chebi My Fluffy Friend
ALT: Cheburashka Chebi My Fluffy Friend
static.klipy.com
August 28, 2026 at 5:18 AM
🫂🦋🥰🐈⬛🌷🥰
Chebi (c. 645-650 AD) was a ruler of the Eastern Turkic Khaganate.
He was the last khagan of the Eastern Turkic Khaganate. #ButIAmYourServant
He was the last khagan of the Eastern Turkic Khaganate. #ButIAmYourServant
First Turkic (Göktürk) Khaganate: Chebi (c. 645-650 AD)
Following up on First Turkic (Göktürk) Khaganate: Qilibi (c. 639-647 AD), this post covers Chebi.
www.linkedin.com
August 27, 2026 at 4:02 PM
Chebi (c. 645-650 AD) was a ruler of the Eastern Turkic Khaganate.
He was the last khagan of the Eastern Turkic Khaganate. #ButIAmYourServant
He was the last khagan of the Eastern Turkic Khaganate. #ButIAmYourServant
Qilibi (c. 639-647 AD), a ruler of the Eastern Turkic Khaganate, was the son of Tughruq.
He was succeeded by Chebi (c. 645-650 AD), the last khagan of the Eastern Turkic Khaganate. #ButIAmYourServant
He was succeeded by Chebi (c. 645-650 AD), the last khagan of the Eastern Turkic Khaganate. #ButIAmYourServant
First Turkic (Göktürk) Khaganate: Qilibi (c. 639-647 AD)
Following up on First Turkic (Göktürk) Khaganate: Illig (c. 620-630 AD), this post covers Qilibi.
www.linkedin.com
August 26, 2026 at 5:01 PM
Qilibi (c. 639-647 AD), a ruler of the Eastern Turkic Khaganate, was the son of Tughruq.
He was succeeded by Chebi (c. 645-650 AD), the last khagan of the Eastern Turkic Khaganate. #ButIAmYourServant
He was succeeded by Chebi (c. 645-650 AD), the last khagan of the Eastern Turkic Khaganate. #ButIAmYourServant
Illig (c. 620-630 AD), a ruler of the Eastern Turkic Khaganate, was the son of Yami and Poshi.
He was succeeded by Qilibi (c. 639-647 AD), who was then succeeded by Chebi (c. 645-650 AD). #ButIAmYourServant
He was succeeded by Qilibi (c. 639-647 AD), who was then succeeded by Chebi (c. 645-650 AD). #ButIAmYourServant
First Turkic (Göktürk) Khaganate: Illig (c. 620-630 AD)
Following up on First Turkic (Göktürk) Khaganate: Chuluo (c. 619-620 AD), this post covers Illig.
www.linkedin.com
August 26, 2026 at 4:13 PM
Illig (c. 620-630 AD), a ruler of the Eastern Turkic Khaganate, was the son of Yami and Poshi.
He was succeeded by Qilibi (c. 639-647 AD), who was then succeeded by Chebi (c. 645-650 AD). #ButIAmYourServant
He was succeeded by Qilibi (c. 639-647 AD), who was then succeeded by Chebi (c. 645-650 AD). #ButIAmYourServant
Of course, when the shorts come out in their respective years, Cheburashka became very popular as Mickey Mouse as his fame still became well known in his home country of Russia. He also became very popular in Japan as he is referred there in affection as 'Chebi-chan.'
August 16, 2026 at 10:32 PM
Of course, when the shorts come out in their respective years, Cheburashka became very popular as Mickey Mouse as his fame still became well known in his home country of Russia. He also became very popular in Japan as he is referred there in affection as 'Chebi-chan.'
Job ID: JR4291
Extract: The Chemical Biology Services Team at EMBL-EBI seeks a scientist for data curation in the ChEBI database, ensuring high-quality chemical data.
Extract: The Chemical Biology Services Team at EMBL-EBI seeks a scientist for data curation in the ChEBI database, ensuring high-quality chemical data.
August 13, 2026 at 12:05 PM
Job ID: JR4291
Extract: The Chemical Biology Services Team at EMBL-EBI seeks a scientist for data curation in the ChEBI database, ensuring high-quality chemical data.
Extract: The Chemical Biology Services Team at EMBL-EBI seeks a scientist for data curation in the ChEBI database, ensuring high-quality chemical data.
April 1, 2024 at 12:36 AM
I’m not sure which came first off the top of my head but Tony Jaa’s Tom-Yum-Goong/The Protector came out around the same time as Oldboy and had a vertical version of the one take hallway fight that’s way crazier. youtu.be/CQaRfXMxh6Y?...
The Protector Restaurant Fight Sequence HD YouTube
YouTube video by Aziz Chebi
youtu.be
March 3, 2025 at 5:53 AM
I’m not sure which came first off the top of my head but Tony Jaa’s Tom-Yum-Goong/The Protector came out around the same time as Oldboy and had a vertical version of the one take hallway fight that’s way crazier. youtu.be/CQaRfXMxh6Y?...
Nice! As Metaboverse uses ChEBI, have you considered using Rhea or Rhea annotations from UniProt too?
March 25, 2025 at 10:48 AM
Nice! As Metaboverse uses ChEBI, have you considered using Rhea or Rhea annotations from UniProt too?
Chebi Cms :3 💗
#digitalart #vgen #artist #chibi #chibiart #commissions #artcommissions #artcommission #commissionsopen #opencommissions #cute #cuteart #aesthetic #illust #illustrations #skeb
#digitalart #vgen #artist #chibi #chibiart #commissions #artcommissions #artcommission #commissionsopen #opencommissions #cute #cuteart #aesthetic #illust #illustrations #skeb
December 23, 2025 at 8:23 AM
Chopper Pilot: "We're heading toward the giant cherry blossom girl now!"
(Chebi knocks the helicopter down to the ground)
(Chebi knocks the helicopter down to the ground)
May 22, 2026 at 1:48 PM
Chopper Pilot: "We're heading toward the giant cherry blossom girl now!"
(Chebi knocks the helicopter down to the ground)
(Chebi knocks the helicopter down to the ground)