BridgeDb Java 3.0.30 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.30 https://doi.org/10.5281/zenodo.18157075
"This release updates to BridgeDb Datasources 20260105 adding a few hundred more species and updates various dependencies and Maven plugins."
BridgeDb Java is the library that implements a Java API to access identifier mappings (e.g. from #ChEBI to #Wikidata, or from Ensembl to UniProt) from local files.
Any idea how to get the (#cheminformatics) structures for a #ChEBI ontology term? Like, how do I get all the terpenoids, CHEBI:26873?
https://www.ebi.ac.uk/ols4/ontologies/chebi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_26873?lang=en says there are 11,119 terpenoids but I see no way to download them.
Trying the web API, https://www.ebi.ac.uk/chebi/backend/api/public/ontology/all_children_in_path/?relation=has_functional_parent&entity=CHEBI%3A26873&three_star_only=false&page=1&size=15&download=false says there are 547 (482 if three_star_only=true).
With 'download=true' I get the data in full (unpaged) data in tsv format, with the same counts.
What am I missing?
BridgeDb Java 3.0.29 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.29
"This update release brings in BridgeDb Datasources 20270728, improves the backwards compatibility with old Apache Derby versions, adds a BridgeDb.getVersion() method, and updates various dependencies."
BridgeDb Java is the library that implements a Java API to access identifier mappings (e.g. from #ChEBI to #Wikidata, or from Ensembl to UniProt) from local files.
At the ChEBI 2.0 workshop, Muhammad Arsalan is presenting how ChEBI is using the Bioregistry to standardize its cross-references, generate URLs on their front-end, and more
BridgeDb Java 3.0.27 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.27
"This update release brings in BridgeDb Datasources 20240725, a new organism (Solanum tuberosum), and various small stability improvements."
BridgeDb Java is the library that implements a Java API to access identifier mappings (e.g. from #ChEBI to #Wikidata, or from Ensembl to UniProt) from local files (there is API support for online services too, but we need help maintaining this code).
I've published a detailed article about #ChatGPT hallucination minimization using predefined #SPARQL-based query templates scoped to Linked Open Data (LOD) Cloud Knowledge Graphs such as #UniProtKB, #RHEA, #chEBI, and #OMIM.
Read: https://www.linkedin.com/pulse/reducing-hallucinations-chatgpt-using-predefined-query-idehen-4qxje/ .
#HowTo #UseCase #VirtuosoRDBMS #SemanticWeb #LinkedData #KnowledgeGraph #AI #GenAI
In the fast-paced world of artificial intelligence, chatbots using language model strategies are becoming more common. However, these chatbots sometimes generate responses based on incorrect or fabricated information, a problem often referred to as “hallucinations.
Remodeling other groups data is attractive but in the long run a waste of time.
Working together to remodel with the other group however is great.
Which is why I am looking forward to #CHEBI 2.0 in the ontology layer.
Of course the same query with just a changed graph name and less whitespace works at https://sparql.rhea-db.org as well. Because both #ontobee and #rhea decided not to remodel #ChEBI (no matter how much we might have wanted to). This is real #interoperability
Applications session: Talk
3. Elisabeth Coudert talks about Annotation of biologically relevant ligands - such as substrates of enzymes, cofactors, activators, inhibitors as well as their binding site - in UniProt using ChEBI
The BridgeDb Project
Andrew Dalke
Bioregistry
Kingsley Uyi Idehen
Jerven
Biocuration 2023