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Existing ontologies

Pointers to existing ontologies

Just what is Ontology, Anyway

 

Ontology Design Patterns

 

 

Generic

Dublin Core

http://dublincore.org/documents/usageguide/

 

http://dublincore.org/documents/usageguide/elements.shtml

 

http://rdfs.org/ns/void-guide voiD is a vocabulary and a set of instructions that enables the discovery and usage of linked datasets. A dataset is a collection of data, published and maintained by a single provider, available as RDF, and accessible, for example, through dereferenceable HTTP URIs or a SPARQL endpoint.

Chemistry, biology

 

The Open Biomedical Ontologies

http://www.obofoundry.org/

The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles forontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.

 

The Ontology Lookup Service

http://www.ebi.ac.uk/ontology-lookup/

The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format. The OLS can integrate any ontology available in the Open Biomedical Ontology (OBO) format.

 

NCBO BioPortal

http://bioportal.bioontology.org/

 

Use BioPortal to access and share ontologies that are actively used in biomedical communities.

 

 

NCI Enterprise Vocabulary Services (EVS)

http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncithesaurus

NCI EVS provides a set of services and resources, including NCI Thesaurus and NCI Metathesaurus, that facilitate the standardization of terminology across the Institute and the larger biomedical community.
The NCI Thesaurus is an ontology-like vocabulary that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships. The Thesaurus currently contains over 34,000 concepts, structured into 20 taxonomic trees.

 

NTP Pathology Code Tables

tables

 

MESH - Medical subjects headings

http://www.nlm.nih.gov/mesh/meshhome.html

 

High throughput data

 

MGED Society standards

http://www.mged.org/

 

 

MicroArray and Gene Expression - MAGE

http://www.mged.org/Workgroups/MAGE/mage.html

 

 

EMTREE Thesaurus

 http://www.amazon.com/EMTREE-Thesaurus-2004-Emtree/dp/0444516301/ref=dp_ob_title_bk/180-9873719-1232821

 EMTREE, the Life Science Thesaurus, is a sophisticated, hierarchically structured controlled vocabulary arranged in a cascading "tree" and used for subject indexing in EMBASE, EMBASE.com, and customer-specific solutions. The printed EMTREE includes more than 46,000 drug and medical terms, 10,000 numeric codes and over 200,000 synonyms. It incorporates MeSH terms used by the National Library of Medicine, as well as almost 20,000 CAS registry numbers assigned by the Chemical Abstracts Service. In 2004 a significant number of general biological terms have been added. This three-volume set is an indispensable tool for both novice and experienced searchers. The 2004 edition of the EMTREE Life Science Thesaurus incorporates several enhancements, including over 1,000 new general biological terms.

 

Chemical Entities of Biological Interest (ChEBI)

http://www.ebi.ac.uk/chebi/

Freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

ChEBI encompasses an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified.

ChEBI uses nomenclature, symbolism and terminology endorsed by the following international scientific bodies:

 

ChemAxiom

http://bitbucket.org/na303/

A set of extensible ontology modules for the domain of chemistry. Modules of potential interest to OpenTox :

  • ChemAxiomDomain : Fundamental concepts in the chemical domain, like substance, molecule;

  • ChemAxiomDescriptor : An ontology of descriptors for computational chemistry and QSAR/QSPR;

  • ChemAxiomProp : An ontology of chemical and materials properties. It contains a list of over 150 properties togethe with definitions of their symbols

Nico Adams, Edward O. Cannon & Peter Murray-Rust, ChemAxiom – An Ontological Framework for Chemistry in Science

 

QSAR Descriptors and Algorithms

Blue Obelisk descriptor dictionary

 

Statistics,data mining

 

The Statistical Core Vocabulary (scovo)

http://sw.joanneum.at/scovo/schema.html

[RDF-Schema] vocabulary for representing statistical data on the Web

The Statistical Core Vocabulary (scovo) lets you describe statistical information on the Web of Data. Three basic concepts are used:

  • a dataset, representing the container of some data, such as a table holding some data in its cells;
  • a data item, representing a single piece of data (e.g. a cell in a table);
  • a dimension, representing some kind of unit of a single piece of data (for example a time period, location, etc.)

 

Data Mining

Data mining ontology (DMO_ http://www.e-lico.eu/?q=dmo
OntoDM  http://kt.ijs.si/panovp/OntoDM
KDDOnto KDDONTO: An Ontology for Discovery and Composition of KDD Algorithms . Ontology-driven KDD Process Composition

 

Measurement units

http://www.w3.org/2007/ont/unit

 https://forge.morfeo-project.org/wiki_en/index.php/Measurement_Units_Ontology

Formats, available software

 

Software

 The JSR 275 Java packages for modeling and working with measurement units. The JSR-275 specifies one or more Java packages for the programmatic handling of physical quantities and their expression as numbers of units.

Linked Data

 

Tim Berners-Lee outlined four principles of Linked Data in his Design Issues: Linked Data note, paraphrased along the following lines:

  1. Use URIs to identify things.
  2. Use HTTP URIs so that these things can be referred to and looked up ("dereference") by people and user agents.
  3. Provide useful information (i.e., a structured description — metadata) about the thing when its URI is dereferenced.
  4. Include links to other, related URIs in the exposed data to improve discovery of other related information on the Web.

Tim Berners-Lee gave a presentation on Linked Data at the TED 2009 conference.

 

 

 

 

 

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