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?
• Ontology Definition Metamodel

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
  • BioPAX wiki
• 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
• HCLSIG BioRDF Subgroup
  • Meetings
• NCI Enterprise Vocabulary Services (EVS) - a set of services and resources that address NCI's needs for controlled vocabulary.
• Large Scale Distributed Information Systems (LSDIS): Ontologies and datasets
• Bio-Ontologies workshop has been a satellite meeting to the annual ISMB conference since 1998 as a Special Interest Group
• Intelligent Systems for Molecular Biology conference
• Semantic web approach to data integration - from University of Amsterdam Integrative Bioinformatics Unit (IBU)

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
  • FOAF Wiki
• RDF Site Summary - RSS 1.0
• Web Service Modeling Ontology - date and time, location, purchase ontologies, etc.
• Eat Drink Feel Good Markup Language @ xml.com
• Ontology directories:
  • SchemaWeb - A comprehensive directory of RDF schemas and OWL ontologies
  • DAML Ontology Library
  • Ontoware - ontology repository
  • Protégé-OWL Ontology library

Metadata applications

• Swoogle Search and metadata for semantic web
• 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.
• The Legume Information Network (LIN) This is a prototype to demonstrate the power of semantic-MOBY framework to integrate disparate data sources into a virtual legume information network.
• Pathway Knowledge Base @ Stanford - integrated human, ecoli and yeast pathway data in BioPAX format from Kegg, BioCyc and Reactome. The underlying data is stored in an RDF triple store and all queries are made directly on the BioPAX model. This has some drawbacks in terms of performance but has allowed us to preserve the semantics specified in the BioPAX model.
• Bibster - A Semantics-Based Bibliographic Peer-to-Peer System
• Ontoware - Semantic Web related software projects

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

• 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
• OWL Pizzas: Practical Experience of Teaching OWL-DL: Common Errors & Common Patterns (PDF)
• Ontology Design Patterns and Problems: Practical Ontology Engineering using Protege-OWL
• National Center for Biomedical Ontology

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