Synthetic Biology:Semantic web ontology/Examples

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(Upper level ontologies)
 
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==Upper level ontologies==
==Upper level ontologies==
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*[http://umbel.org/ UMBEL] (Upper Mapping and Binding Exchange Layer) - a lightweight, subject concept reference structure for the Web
*[[Wikipedia:Upper_ontology_(computer_science)|Upper ontology]] Wikipedia article
*[[Wikipedia:Upper_ontology_(computer_science)|Upper ontology]] Wikipedia article
*[http://suo.ieee.org/ SUO WG] Standard Upper Ontology Working Group
*[http://suo.ieee.org/ SUO WG] Standard Upper Ontology Working Group
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==Intermediate level ontologies==
==Intermediate level ontologies==
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*[http://sourceforge.net/projects/expo/ EXPO] ontology represents different stages of an experiment and the relationships between these stages; used by the [http://www.aber.ac.uk/compsci/Research/bio/robotsci/ Robot Scientist] ([http://bbu.uwcm.ac.uk/awbw2006/talks/LarisaSoldatova.pdf presentation slides] as PDF)
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*[http://expo.sourceforge.net/ EXPO] ontology represents different stages of an experiment and the relationships between these stages; used by the [http://www.aber.ac.uk/compsci/Research/bio/robotsci/ Robot Scientist] ([http://bbu.uwcm.ac.uk/awbw2006/talks/LarisaSoldatova.pdf presentation slides] as PDF)
**controlled vocabulary of scientific experiments
**controlled vocabulary of scientific experiments
**formalized electronic representation of scientific experiments
**formalized electronic representation of scientific experiments
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*[http://www.gameontology.org Game Ontology Project] (GOP) is a framework for describing, analyzing and studying games
*[http://www.gameontology.org Game Ontology Project] (GOP) is a framework for describing, analyzing and studying games
*[http://sioc-project.org/ontology SIOC ontology] - an open-standard machine readable format for expressing the information contained both explicitly and implicitly in internet discussion methods, of SIOC metadata producers for a number of popular blogging platforms and content management systems, and of storage and browsing / searching systems for leveraging this SIOC data.
*[http://sioc-project.org/ontology SIOC ontology] - an open-standard machine readable format for expressing the information contained both explicitly and implicitly in internet discussion methods, of SIOC metadata producers for a number of popular blogging platforms and content management systems, and of storage and browsing / searching systems for leveraging this SIOC data.
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*[http://www.mel.nist.gov/psl/ontology.html PSL (Process Specification Language) Ontology]
==Metadata applications==
==Metadata applications==
*[http://swoogle.umbc.edu/ Swoogle] Search and metadata for semantic web
*[http://swoogle.umbc.edu/ Swoogle] Search and metadata for semantic web
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*[http://sindice.com/search Sindice] - search the data web
*[http://semantical.org/ Semantical] - open source Semantic Web-based search engine for searching W3C standard RDF ontologies and tags
*[http://semantical.org/ Semantical] - open source Semantic Web-based search engine for searching W3C standard RDF ontologies and tags
*[http://triplestore.aktors.org/ AKT Triplestore]: is an RDF store containing information about the UK HE computer science community (view sources contain in triplestore or browse and query the triplestore)
*[http://triplestore.aktors.org/ AKT Triplestore]: is an RDF store containing information about the UK HE computer science community (view sources contain in triplestore or browse and query the triplestore)

Current revision

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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): Image:SBOv0.01.png

Other

Metadata applications

  • Swoogle Search and metadata for semantic web
  • Sindice - search the data web
  • Semantical - open source Semantic Web-based search engine for searching W3C standard RDF ontologies and tags
  • AKT Triplestore: is an RDF store containing information about the UK HE computer science community (view sources contain in triplestore or browse and query the triplestore)
  • Google Base
  • 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.
  • mSpace is an interaction model and software framework to help people access and explore information.
  • SWAN is a project to develop effective specialist knowledge bases for the Alzheimer Disease research community, using the Semantic Web technology
  • Radar Networks is "building technology for enriching content that will catalyze the evolution of a new dimension of the Web".
  • Cyc - formalized common knowledge

Life sciences

  • 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.
  • Pathway Knowledge Base (PKB) @ 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.
  • 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).
  • OBO Foundry is a collaborative experiment involving developers of science-based ontologies who have established a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain
  • 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
  • Ontaris is a searchable and browsable directory of semantic web data
  • DBLP Bibliography Database - a D2R server

Resources


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