Synthetic Biology:Semantic web ontology/Examples: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
| Line 8: | Line 8: | ||
==Life Sciences== | ==Life Sciences== | ||
*[http://geneontology.org/ Gene Ontology] provides a controlled vocabulary to describe gene and gene product attributes in any organism. GO terms are organized in directed acyclic graphs (DAGs), which differ from hierarchies in that a 'child' (more specialized term) can have many 'parents' (less specialized terms). GO terms are connected by 'is a' (generalizations) and 'part of' (composition) relationships. | |||
**Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd | |||
**Properties: name, definition, isa, association, evidence | |||
*[http://song.sourceforge.net/so.shtml Sequence Ontology]: features on a nucleotide or protein sequence | |||
*[http://www.biopax.org/ BioPAX]: biological pathway data | |||
*[http://www.isb-sib.ch/~ejain/rdf/ UniProt] protein sequence and annotation data in RDF format. [http://www.isb-sib.ch/~ejain/rdf/owl/ UniProt OWL Ontology] | |||
*[http://sbml.org/documents/ SBML] uses [http://www.cellml.org/specifications/archive/metadata/20011102/cellml_metadata_specification.html CellML metadata] to describe its elements. See also a [http://www.sbml.org/forums/index.php?t=msg&goto=1435&rid=0#msg_1435 message] on SBML forum. | |||
*[http://biomodels.net/ BioModels] database and Systems Biology Ontologies (SBO) project | |||
*[http://obo.sourceforge.net/ Open Biomedical Ontologies] | |||
*[http://anil.cchmc.org/Bio-Ontologies.html Bio-Ontologies] | |||
*[http://www.bioinfo.de/isb/2002/02/0017/main.html Ontologies for molecular biology and bioinformatics] | |||
*[http://mged.sourceforge.net/ontologies/ Microarray Gene Expression Society (MGED) Ontology] | |||
*[http://www.schemaweb.info/ RDF Schemas directory] | |||
*[http://www.co-ode.org/ontologies/ CO-ODE ontology examples] | |||
**[http://smi-protege.stanford.edu:8080/KnowledgeZone/ KnowledgeZone] - peer reviewed ontology library | |||
*[http://www.onto-med.de/ Onto-Med] research group: ontologies in medicine | |||
Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the [http://parts2.mit.edu/r/parts/partsdb/index.cgi Registry website]): | Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the [http://parts2.mit.edu/r/parts/partsdb/index.cgi Registry website]): | ||
Revision as of 13:09, 26 April 2006
Ontology - essentially, a formal description of objects and their interrelationships Described using RDF Schema and/or OWL.
Life Sciences
- Gene Ontology provides a controlled vocabulary to describe gene and gene product attributes in any organism. GO terms are organized in directed acyclic graphs (DAGs), which differ from hierarchies in that a 'child' (more specialized term) can have many 'parents' (less specialized terms). GO terms are connected by 'is a' (generalizations) and 'part of' (composition) relationships.
- Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
- Properties: name, definition, isa, association, evidence
- Sequence Ontology: features on a nucleotide or protein sequence
- BioPAX: biological pathway data
- UniProt protein sequence and annotation data in RDF format. UniProt OWL Ontology
- SBML uses CellML metadata to describe its elements. See also a message on SBML forum.
- BioModels database and Systems Biology Ontologies (SBO) project
- Open Biomedical Ontologies
- Bio-Ontologies
- Ontologies for molecular biology and bioinformatics
- Microarray Gene Expression Society (MGED) Ontology
- RDF Schemas directory
- CO-ODE ontology examples
- KnowledgeZone - peer reviewed ontology library
- Onto-Med research group: ontologies in medicine
Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the Registry website):
Upper ontologies
- SUO WG Standard Upper Ontology Working Group
- SUMO Suggested Upper Merged Ontology
- SUMO Wikipedia article
- Dublin Core provides a vocabulary to describe bibliographic metadata
- Introduction to Dublin Core @ xml.com
- Namespace: http://purl.org/dc/elements/1.1/
- Properties: title, creator, publisher, identifier
- WordNet is a semantic lexicon for the English language
- WordNet Wikipedia article
- OpenCyc an upper ontology for all of human consensus reality.
- OpenCyc Wikipedia article
- General Formal Ontology
Metadata applications
- Google Base
- Biozon - a unified biological resource on DNA sequences, proteins, complexes and cellular pathways. The information in Biozon is logically represented as a graph in which nodes represent some unit of data, and edges indicate a relationship between two nodes.
- Open Directory RDF dump The Open Directory Project is the largest, most comprehensive human-edited directory of the Web. It is constructed and maintained by a vast, global community of volunteer editors.
Resources
- GO annotation wiki (from Sri)
- Ontology Development 101: A Guide to Creating Your First Ontology - what is an ontology and why we need it
- Protégé OWL Tutorial (PDF)
- Manchester Pizza Finder
- National Center for Biomedical Ontology
This site is hosted on OpenWetWare and can be edited by all members of the Synthetic Biology community.
Making life better, one part at a time.
