Synthetic Biology:Semantic web ontology/Examples

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Ontology - essentially, a formal description of objects and their interrelationships Described using RDF Schema and/or OWL.

• Wikipedia ontology article
• What is an ontology?

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
• Yeast Hub - edit, load and query various RDF datasets
• 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
• HCLS Wiki

Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the Registry website):

Upper ontologies

• Upper ontology Wikipedia article
• SUO WG Standard Upper Ontology Working Group
• SUMO Suggested Upper Merged Ontology
  • SUMO Wikipedia article
  • Downloads - ontology browser, virus ontology, etc
  • Online SUMO browser
• OpenCyc an upper ontology for all of human consensus reality.
  • OpenCyc Wikipedia article
• General Formal Ontology

Other

• 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
• DOAC Description of a career
  • Description of a Career Wikipedia article
• FOAF Friend of a Friend
  • FOAF Wikipedia article
• Web Service Modeling Ontology - date and time, location, purchase ontologies, etc.
• Eat Drink Feel Good Markup Language @ xml.com

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.

Datasets

• 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.
• Wikipedia³ is a conversion of the English Wikipedia into RDF.
• ConceptNet is a semantic network, a freely available commonsense knowledgebase and natural-language-processing toolkit
• WordNet is a semantic lexicon for the English language
  • WordNet Wikipedia article

Resources

1. GO annotation wiki (from Sri)
2. Ontology Development 101: A Guide to Creating Your First Ontology - what is an ontology and why we need it
3. Protégé OWL Tutorial (PDF)
4. Manchester Pizza Finder
5. National Center for Biomedical Ontology

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