Ontologies, markup languages, controlled vocabularies, and thesauri

by Cao — last modified Nov 07, 2012 11:05 AM

Resources for domain ontologies and ontology organizations, markup languages, and controlled vocabularies and thesauri

Controlled Vocabularies and Thesauri

AGI GeoRef Thesaurus

American Geosciences Institute (AGI) GeoRef Thesaurus

http://www.agiweb.org/georef/about/thesaurus.html

EPA Glossaries and Keywords

United States Environmental Protection Agency glossaries and keyword lists

http://iaspub.epa.gov/sor_internet/registry/termreg/searchandretrieve/glossariesandkeywordlists/search.do

EIONET GEMET Thesaurus

European Environment Information and Observation Network GEneral Multilingual Environmental Thesaurus

http://www.eionet.europa.eu/gemet

LTER Controlled Vocabulary

The Long Term Ecological Research Network Controlled Vocabulary

http://vocab.lternet.edu/vocab/vocab/index.php

GCMD

NASA Global Change Master Directory

http://gcmd.nasa.gov/

Metadata Languages

EML

Ecological Metadata Language

http://knb.ecoinformatics.org/software/eml/

GeoSciML

Geoscience Markup Language

http://www.geosciml.org/

INSPIRE

Infrastructure for Spatial Information in the European Community

http://inspire.jrc.ec.europa.eu/index.cfm/pageid/2

NetCDF CF

NetCDF climate forecasting metadata

http://cf-pcmdi.llnl.gov/

Markup language for sharing data in a manner compatible with the NetCDF API. Basic concepts include standard units, coordinates, time and climatalogical statistics. Contains a list of 2427 standard names with canonical units and definitions.

Term relationships are not axiomatized in a formal logical model.

Foundational Ontologies

OBO Foundry

http://www.obofoundry.org/

BFO

Basic Formal Ontology

http://www.ifomis.org/bfo

DOLCE

A Descriptive Ontology for Linguistic and Cognitive Engineering

http://www.loa-cnr.it/DOLCE.html

SIO

SemanticScience Integrated Ontology

http://code.google.com/p/semanticscience/

Domain Ontologies

SWEET Ontologies

http://sweet.jpl.nasa.gov/

Earth and Environmental sciences "middle-level ontology" containing 4417 classes, 565 object properties, and 41 data type properties in 200+ ontologies.

CUAHSI-HIS Ontology

Hydrologic Ontology for Discovery (CUAHSI-HIS)

http://his.cuahsi.org/ontologyfiles.html

ENVO

Environment Ontology

http://environmentontology.org/

PATO: PATO Wiki

PATO has three phenotype ontologies:

(1) PATO: Phenotypic qualities that form the building blocks of phenotype descriptions; (2) Mammalian Phenotype; (3) Plant Trait.

These three ontologies can be downloaded from PATO Wiki(in XML format), or from OBO Foundry (in obo format: TO (plant_trait.obo) , MP (mammalian_phenotype.obo), PATO(quality.obo)).

Groups that are using PATO:

Phenoscape: https://www.phenoscape.org/wiki/Main_Page
ZFIN The Zebrafish Model Organism Database: http://zfin.org/
J. Sprague, D. Clements, T. Conlin, P. Edwards, K. Frazer, K. Schaper, E. Segerdell, P. Song, B. Sprunger, and M. Westerfield. The zebrafish information network (ZFIN): the zebrafish model organism database. Nucleic Acids Res., 31(1):241–243, 2003. (link)
FlyBase Consortium: The flybase database of the drosophila genome projects and community literature. Nucleic Acids Res., 30(1):106–108, 2002. (Link)

VSTO Ontology

Virtual Solar-Terrestrial Observatory ontology

http://vsto.org/forward.htm?forward=ontology

Ontology for solar, solar-terrestrial, and space physics concepts consisting of 302 classes, 40 object properties, and 35 data properties.

ChadoDatabase

http://biowiki.org/ChadoDatabase

Sections

Personal tools