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.

Upper level ontologies

Intermediate level ontologies

  • EXPO ontology represents different stages of an experiment and the relationships between these stages; used by the Robot Scientist (presentation slides as PDF)
    • controlled vocabulary of scientific experiments
    • formalized electronic representation of scientific experiments
    • unified standards for representation, annotation, storage, and access to experimental results
    • reasoning over experimental data and conclusions
  • Bibliographic data ontology
  • Ontology of Functions is included in the OWL version of the General Formal Ontology (see upper level ontologies)
  • FuGO Functional Genomics Ontology aims to provide consistent annotation of functional genomics experiments, regardless of the particular field of study (transcriptomics, proteomics and metabolomics, etc).
  • HyBrow ontology for representing biological processes at different levels of detail

Domain level ontologies

Life Sciences

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

Other

Metadata applications

  • Swoogle Search and metadata for semantic web
  • Semantical - open source Semantic Web-based search engine for searching W3C standard RDF ontologies and tags
  • 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.
  • Unified Medical Language System (UMLS) project develops and distributes multi-purpose, electronic "Knowledge Sources" and associated lexical programs for system developers. Researchers will find the UMLS products useful in investigating knowledge representation and retrieval questions.
    • Metathesaurus is a very large, multi-purpose, and multi-lingual vocabulary database that contains information about biomedical and health related concepts, their various names, and the relationships among them
    • Semantic Network provides a consistent categorization of all concepts represented in the UMLS Metathesaurus and to provide a set of useful relationships between these concepts.
    • The SPECIALIST lexicon has been developed to provide the lexical information needed for the SPECIALIST Natural Language Processing System (NLP). It is intended to be a general English lexicon that includes many biomedical terms.
    • MetamorphoSys is the UMLS installation wizard and customization tool included in each UMLS release.
  • SNOMED Clinical Terms® (SNOMED CT®) is the universal health care terminology that makes health care knowledge usable and accessible wherever and whenever it is needed (included in UMLS since 2003). SNOMED browser.
  • 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
  • Rdf Calendar from W3C
  • Nokia Semantic Web Server demo provides access to metadata describing products, documents, vocabularies, schemas, and other resources which is made available to Nokia customers and partners in a machine processable format. This server is intended for use primarily by automated systems and is not optimized for human use.
  • Intellidimension Labs - A Collection of RDF Gateway Demos, Examples, and Experiments (Uniprot, etc)
  • Semantic MOBY searches Virtual Plant Information Network (VPIN) - a consortium of information resources using emerging semantic web services technologies.
  • National Center for Biomedical Ontology:
    • A virtual library of Open Biomedical Ontologies (OBO).
    • A Web-based BioPortal to allow investigators and intelligent computer programs to access and use OBO.
    • Tools to assist biomedical investigators use ontologies accessible through BioPortal to annotate experimental data.
    • An online repository of OBO annotations on experimental data accessible via BioPortal known as Open Biomedical Data (OBD).
  • mSpace is an interaction model and software framework to help people access and explore information.
  • HyBrow is a prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge; it consists of:
    • a modeling framework with the ability to accommodate diverse biological information sources
    • an event-based ontology for representing biological processes at different levels of detail
    • a database to query information in the ontology
    • programs to perform hypothesis design and evaluation

Datasets

  • Yeast Hub RDF datasets
  • Open Directory RDF dump The Open Directory Project (DMOZ) is the largest, most comprehensive human-edited directory of the Web. It is constructed and maintained by a vast, global community of volunteer editors.
  • ChefMoz RDF files the project goal is to produce the most comprehensive guide to restaurants, by relying on a vast army 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

Resources

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