Synthetic Biology:Semantic web ontology/Examples

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
 * Benefits
 * Controlled vocabulary
 * Theory of content
 * Knowledge management: systematization, sharing, reusability
 * Data integration

Upper level ontologies

 * UMBEL (Upper Mapping and Binding Exchange Layer) - a lightweight, subject concept reference structure for the Web
 * 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
 * Basic Formal Ontology (BFO)

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

Life Sciences

 * Ontology Lookup Service (OLS)
 * List of ontologies
 * 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.
 * Creating the gene ontology resource: design and implementation
 * Ontology recapitulates philology - comment
 * Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
 * Properties: name, definition, isa, association, evidence
 * Yeast Hub - demonstrates how a life sciences data warehouse can be built using a native RDF data store (Sesame). This data warehouse allows integration of different types of yeast genome data provided by different resources in different formats including the tabular and RDF formats (paper).
 * Semantic Mining - semantic interoperability and data mining in medicine (ontologies).
 * Sequence Ontology: features on a nucleotide or protein sequence
 * BioPAX: biological pathway data
 * BioPAX wiki
 * Amino Acid Ontology - a small ontology of amino acids and their properties
 * 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 (Systems Biology Ontology)
 * 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
 * HCLS Ontology Task Force
 * Seed Ontology
 * HCLSIG BioRDF Subgroup: Meetings and Tasks
 * 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)
 * MIPE - Minimal Information for PCR Experiments, an XML schema for the exchange of PCR related data
 * Cell Cycle Ontology aims to extend the existing ontologies for cell cycle knowledge, to build a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects in OBO and OWL.
 * The National Center for Biomedical Ontology (NCBO): Resources, Wiki

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

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
 * DOAP Description of a Project is an XML/RDF vocabulary to describe open source projects.
 * vocab.org - a URI namespace for vocabularies
 * RDF Relationship - a vocabulary for describing relationships between people
 * RSS Wikipedia article
 * RDF Site Summary - RSS 1.0
 * Introduction to RSS newsfeeds @ ibm.com
 * RSS 2.0 Specification - non-RDF
 * Web Service Modeling Ontology - date and time, location, purchase ontologies, etc.
 * Eat Drink Feel Good Markup Language @ xml.com
 * Basic Geo Vocabulary
 * Ontology directories:
 * SchemaWeb - A comprehensive directory of RDF schemas and OWL ontologies
 * DAML Ontology Library
 * Ontoware - ontology repository
 * Protégé-OWL Ontology library
 * Knowledge Zone - search and browse ontologies
 * Game Ontology Project (GOP) is a framework for describing, analyzing and studying games
 * 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.
 * PSL (Process Specification Language) Ontology

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)
 * AKT Reference Ontology
 * 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.
 * Nokia Semantic Web R&D Server demo
 * RDF Query demo. RDFQ is a tool for knowledge discovery, rather than for knowledge management or knowledge manipulation.
 * 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.


 * 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.


 * 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.


 * Intellidimension Labs - A Collection of RDF Gateway Demos, Examples, and Experiments (Uniprot, etc)
 * Intellidimension Semantic Web Search


 * Semantic MOBY or Simple Semantic Web Architecture and Protocol
 * drives the search of Virtual Plant Information Network (VPIN) - a consortium of information resources using emerging semantic web services technologies
 * The Legume Information Network (LIN) is a prototype to demonstrate the power of semantic-MOBY framework to integrate disparate data sources into a virtual legume information network


 * 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
 * WordNet Wikipedia article
 * Ontaris is a searchable and browsable directory of semantic web data
 * DBLP Bibliography Database - a D2R server

Resources

 * Abstraction hierarchy
 * Parts are basic biological f(x)'s encoded via genetic material.
 * Devices provide human-defined f(x)'s using one or more parts.
 * Systems provide human-defined f(x)’s using one or more devices.
 * 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
 * Tutorial Materials: A Practical Introduction to Ontologies & OWL
 * Ontology Development 101 from m3t4.studio
 * National Center for Biomedical Ontology
 * Relations in biomedical ontologies - paper in Genome Biology
 * Are the current ontologies in biology good ontologies?
 * Synthetic biology: new engineering rules for an emerging discipline describes a possible hierarchy for synthetic biology inspired by computer engineering.
 * IFOMIS - Institute for Formal Ontology and Medical Information Science, Saarland University
 * Gene Ontology Next Generation: GONG project aims to make tools and procedures for easy migration of biological ontologies to formal languages like OWL and explore the issues related to maintenance of large biological ontologies. Also a blog.
 * Ontology Design Patterns are the application of the same concept as Software Design Patterns (SDPs) from Object Oriented Programming to ontology engineering.