Main ontology
 bio-zen.owl 1.01 - Stable. You can use this URL to import the ontology into other ontologies.
Last update: 09 Nov 2006
A previous version (associated with the article in 'Journal of Web Semantics') is also available: previous version of bio-zen.owl
download the bio-zen manual (.pdf)
Download the PHP BioPAX-to-bio-zen converter prototype. You need PHP, MySQL and the RDF API for PHP to run it. Conversions of BIND, Reactome, Ecocyc and the SBML model repository will soon be available for download.
 bio-zen discussion forum at Google Groups
Data
Reactome Version 19 in bio-zen format: reactome-bio-zen-13-Dec-2006.zip (18 MB)
Reactome is a curated resource of core pathways and reactions in biology. See reactome.org for more information.
Ontology extensions
bio-zen-plus.owl - Development version (updated periodically). bio-zen-plus is an extension of the main bio-zen ontology that adds selected constructs from the FOAF, SIOC (Semantically Interlinked Online Communities) and Creative Commons ontology, plus some additional concepts for representing basic scientific discourse.
Last update: Dec 2006
Concept package extensions
The concept package extensions add concepts and taxonomies from other projects to the basic bio-zen framework. They are represented using the SKOS vocabulary. Many of the extensions are derived from taxonomies found in the Open Biomedical Ontologies collection.
Last update: 18 Oct 2006
bio-zen-EVIDENCE.owl - extension to the bio-zen ontology that adds all concepts from the Evidence Codes Ontology (150 KB, this ontology also imports the main bio-zen ontology)
bio-zen-MESH.owl - extension to the bio-zen ontology that adds all concepts from MeSH (16 MB, this ontology also imports the main bio-zen ontology) download temporarily disabled because of high server load, please download zipped version
bio-zen-MESH.zip - zipped version of the MeSH extension for download (1,6 MB)
bio-zen-GO.owl - extension to the bio-zen ontology that adds all non-obsolete concepts from the Gene Ontology (17 MB, this ontology also imports the main bio-zen ontology) download temporarily disabled because of high server load, please download zipped version
bio-zen-GO.zip - zipped version of the Gene Ontology extension for download (1 MB)
bio-zen-CELLTYPE.owl - extension to the bio-zen ontology that adds all non-obsolete concepts from the celltype ontology (450 KB, this ontology also imports the main bio-zen ontology)
bio-zen-CHEBI.owl - extension to the bio-zen ontology that adds all non-obsolete concepts from the ChEBI (Chemical entities of biological interest) (11 MB, this ontology also imports the main bio-zen ontology) download temporarily disabled because of high server load, please download zipped version
bio-zen-CHEBI.zip - zipped version of the ChEBI extension for download (600 KB)
bio-zen-TAXONOMY.zip - zipped version of an extension to the bio-zen ontology that adds all non-obsolete concepts from the NCBI Taxonomy (7,5 MB, 150 MB when uncompressed, this ontology also imports the main bio-zen ontology)
bio-zen-SEQUENCE.owl - extension to the bio-zen ontology that adds all non-obsolete concepts from the Sequence Ontology (700 KB, this ontology also imports the main bio-zen ontology)
bio-zen-SEQUENCE.zip - zipped version of the Sequence Ontology extension for download (50 KB)
bio-zen-MOLTYPE.owl - extension to the bio-zen ontology that adds all concepts from INOH Molecule role/type ontology 2.11 (7 MB, this ontology also imports the main bio-zen ontology) download temporarily disabled because of high server load, please download zipped version
bio-zen-MOLTYPE.zip - zipped version of the molecular type extension for download (350 KB)
Planned:
bio-zen-HUMAN-DISEASE.owl - - extension to the bio-zen ontology that adds all concepts from Disease Ontology
Neuronames, CATH Protein Structure Classification, microarray annotations...
BIND database in OWL
The Biomolecular Interaction Network Database (BIND) is a vast database of interactions between DNA, RNA, proteins and small molecules. Here you can download the data from the BIND database in the ontology web language (OWL). Please note that the data in these files are derived from the PSI-MI version of the BIND database, which does not contain all of the annotations in the database.
This download contains several files. Each file holds data for one taxon, identified by the Entrez Taxonomy ID. Each file contains a maximum of 200 datasets.
Download BIND-OWL-2006-12.zip (10 MB, Version from 7. Dec 2006)
Previous version: BIND-OWL-2006-5-beta.zip (4 MB, Version from 15. May 2006)
(Each file holds data that was derived from one publication)
The original files in .XML format can be downloaded from http://bind.ca (requires cost-free registration). You can also download the BIND PSI-MI XML -> OWL converter that was used for this conversion (XQuery file):
Download PSI-MI-to-BioPAX.xquery
You can view the content of the .OWL files with any OWL ontology editor, e.g. Stanfords Protégé Editor. XQueries can be run with the Saxon XQuery Processor
Please note: the conversion can be very slow for files that are larger than 1 MB. The OWL files have no namespace defined yet.
This ontology is based on BioPAX.
PDSP Ki Database in OWL
The PDSP Ki Database is "a unique resource in the public domain which provides information on the abilities of drugs to interact with an expanding number of molecular targets. The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes."
The OWL version of the PDSP Ki Database is enriched with annotation that is not contained in the original database (annotation with NCBI Taxonomy ID and IUPHAR receptor codes). This ontology is based on BioPAX.
kidb.zip - Data from the PDSP Ki Database in OWL format (800 KB)
Voltage Gated Potassium Channel Database in OWL
Not available for public download. Please contact  Matthias Samwald if you are interested.
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