NFDI4Biodiversity
Source: /files/meta/Used_Ontologies_at_NFDI.xlsx (sheet: NFDI4Biodiversity)
| Ontology ID | Ontology | Domain | License | Format | developed / reused / only indexed / only evaluated | Modularity | GFbio | Obofoundry | OLS URL | Bioportal | Github | File URL | Other URL | Description | Useful Links: | OBO Foundry | NCBO BioPortal | OLS ontology search | GFBio Terminology Service | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BCO | Biological Collections Ontology | biology | CC0 1.0 | owl | reused | BFO | https://terminologies.gfbio.org/terminology/BCO | https://obofoundry.org/ontology/bco.html | https://www.ebi.ac.uk/ols/ontologies/bco | https://bioportal.bioontology.org/ontologies/BCO | https://github.com/BiodiversityOntologies/bco | https://bioportal.bioontology.org/ontologies/BCO | The biological collection ontology includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of "samples". Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers. | Comments: | Please (also) check out the DataPlant sheet, there is some overlap ... Gruss, Steffen | |||||
| CHEBI | Chemical Entities of Biological Interest Ontology | chemistry | CC BY 4.0 | owl | reused | https://terminologies.gfbio.org/terminology/CHEBI | https://obofoundry.org/ontology/chebi.html | https://www.ebi.ac.uk/ols/ontologies/chebi | https://bioportal.bioontology.org/ontologies/CHEBI | https://github.com/ebi-chebi/ChEBI | https://bioportal.bioontology.org/ontologies/CHEBI | http://www.ebi.ac.uk/chebi | A structured classification of chemical compounds of biological relevance. | |||||||
| ENVO | Environment Ontology | environmental | CC0 1.0 | owl | reused | BFO | https://terminologies.gfbio.org/terminology/ENVO | https://obofoundry.org/ontology/envo.html | https://www.ebi.ac.uk/ols/ontologies/envo | https://bioportal.bioontology.org/ontologies/ENVO | https://github.com/EnvironmentOntology/envo | https://raw.githubusercontent.com/EnvironmentOntology/envo/master/envo.owl | http://environmentontology.org/ | The most up-to-date information about ENVO is available here: http://www.obofoundry.org/ontology/envo.html EnvO is an OBO Foundry and Library ontology for the concise, controlled description of environmental entities such as ecosystems, environmental processes, and environmental qualities. It closely interoperates with a broad collection of other OBO ontologies and is used in a diverse range of projects. | ||||||
| FLOPO | Flora Phenotype Ontology | anatomical | CC BY 3.0 | owl | reused | https://terminologies.gfbio.org/terminology/FLOPOO | https://obofoundry.org/ontology/flopo.html | https://www.ebi.ac.uk/ols/ontologies/flopo | https://bioportal.bioontology.org/ontologies/FLOPO | https://github.com/flora-phenotype-ontology/flopoontology | https://github.com/flora-phenotype-ontology/flopoontology/tree/master/ontology | The Flora Phenotype Ontology is an ontology of phenotypes reported in Floras. The original version was developed at the pro-iBiosphere Hackathon in Leiden. This is the pre-classified version of the ontology; the original OWL file is at https://github.com/flora-phenotype-ontology/flopoontology/blob/master/ontology/flopo.owl The Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kews African Floras. Every class in the ontology has at least one taxon annotation. The (draft) taxon annotation are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/ | ||||||||
| NCBITAXON | National Center for Biotechnology Information Organismal Classification | biology | CC0 1.0 | owl | reused | OIO, DCTERMS, IAO | https://terminologies.gfbio.org/terminology/NCBITAXON | https://obofoundry.org/ontology/ncbitaxon.html | https://www.ebi.ac.uk/ols/ontologies/ncbitaxon | https://bioportal.bioontology.org/ontologies/NCBITAXON | https://github.com/obophenotype/ncbitaxon | https://bioportal.bioontology.org/ontologies/NCBITAXON | https://www.ncbi.nlm.nih.gov/taxonomy | The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. | ||||||
| OBOE | The Extensible Observation Ontology | environmental | CC BY 3.0 | owl | reused | https://terminologies.gfbio.org/terminology/OBOE | https://bioportal.bioontology.org/ontologies/OBOE | https://github.com/NCEAS/oboe | https://bioportal.bioontology.org/ontologies/OBOE | The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations. | ||||||||||
| PATO | Phenotypic Quality Ontology | anatomical | CC BY 3.0 | owl | reused | BFO | https://terminologies.gfbio.org/terminology/PATO | https://obofoundry.org/ontology/pato.html | https://www.ebi.ac.uk/ols/ontologies/pato | https://bioportal.bioontology.org/ontologies/PATO | https://github.com/pato-ontology/pato/ | https://bioportal.bioontology.org/ontologies/PATO | Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested. | |||||||
| PO | Plant Ontology | biology | CC BY 4.0 | owl | reused | BFO | https://terminologies.gfbio.org/terminology/PO | https://obofoundry.org/ontology/po.html | https://www.ebi.ac.uk/ols/ontologies/po | https://bioportal.bioontology.org/ontologies/PO | https://github.com/Planteome/plant-ontology | https://bioportal.bioontology.org/ontologies/PO | The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. | |||||||
| PTO | Plant Trait Ontology | anatomical | CC BY 4.0 | owl | reused | BFO | https://terminologies.gfbio.org/terminology/PTO | https://obofoundry.org/ontology/to.html | https://www.ebi.ac.uk/ols/ontologies/to | https://bioportal.bioontology.org/ontologies/PTO | https://github.com/Planteome/plant-trait-ontology | https://bioportal.bioontology.org/ontologies/PTO | A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part. | |||||||
| QUDT | Quantity, Unit, Dimension and Type | other | CC BY 4.0 | owl | reused | OBO_compatible | https://terminologies.gfbio.org/terminology/QUDT | https://bioportal.bioontology.org/ontologies/QUDT | https://github.com/qudt/qudt-public-repo | https://github.com/qudt/qudt-public-repo/releases | The QUDT collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units. | |||||||||
| SWEET | Semantic Web for Earth and Environment Technology Ontology | geo-sciences | CC0 1.0 | owl | reused | https://terminologies.gfbio.org/terminology/SWEET | https://bioportal.bioontology.org/ontologies/SWEET | https://github.com/ESIPFed/sweet | https://bioportal.bioontology.org/ontologies/SWEET | |||||||||||
| ETS | Ecological Trait-data Standard | biology | CC BY 4.0 | owl | reused | https://terminologies.gfbio.org/terminology/ETS | https://github.com/EcologicalTraitData/ETS | https://terminologies.gfbio.org/terms/ets/pages/ | The Ecological Trait-data Standard defines terms for the use in datasets containing quantitative and qualitative functional traits. | |||||||||||
| RECORDBASIS | GFBio Agreed Vocabulary for RecordBasis | biology | CC0 1.0 | owl | reused | https://terminologies.gfbio.org/terminology/RECORDBASIS | https://terminologies.gfbio.org/terms/recordbasis/ | A controlled vocabulary (Terminology) "BasisOfRecords" or "RecordBasis" (DwC: "The specific nature of the data record."). Based on GBIF/ DwC and BiNHum/ABCD. | ||||||||||||
| BOHLMANN | Bohlmann Ontology | biology | CC0 1.0 | owl | reused | https://terminologies.gfbio.org/terminology/BOHLMANN | https://terminologies.gfbio.org/terms/bohlmann/ | An ontology listing the natural substances that occurr in the plant family of Compositae (Asteraceae). | ||||||||||||
| TRICHOPTERA | Trichoptera Ontology | biology | owl | reused | https://terminologies.gfbio.org/terminology/TRICHOPTERA | Working list: taxon names of the order Trichoptera (caddisflies; Insecta). | ||||||||||||||
| THYSANOPTERA | Thysanoptera Ontology | biology | owl | reused | https://terminologies.gfbio.org/terminology/THYSANOPTERA | Working list: taxon names of the order Thysanoptera (Insecta). | ||||||||||||||
| RIVERS_DE | German River Names | geo-sciences | GeoNutzV | owl | reused | https://terminologies.gfbio.org/terminology/RIVERS_DE | https://terminologies.gfbio.org/terms/rivers_de/ | A controlled vocabulary of the names of rivers in Germany and their connections, extracted from the Shape File provided by the environmental authority of the Federal Republic of Germany: Umweltbundesamt (UBA). | ||||||||||||
| ITIS | Integrated Taxonomic Information System | biology | CC0 1.0 | owl | reused | https://terminologies.gfbio.org/terminology/ITIS | https://www.itis.gov/; https://www.gbif.org/dataset/9ca92552-f23a-41a8-a140-01abaa31c931 | The White House Subcommittee on Biodiversity and Ecosystem Dynamics has identified systematics as a research priority that is fundamental to ecosystem management and biodiversity conservation. This primary need identified by the Subcommittee requires improvements in the organization of, and access to, standardized nomenclature. ITIS (originally referred to as the Interagency Taxonomic Information System) was designed to fulfill these requirements. In the future, the ITIS will provide taxonomic data and a directory of taxonomic expertise that will support the system. The ITIS is the result of a partnership of federal agencies formed to satisfy their mutual needs for scientifically credible taxonomic information. Since its inception, ITIS has gained valuable new partners and undergone a name change; ITIS now stands for the Integrated Taxonomic Information System. | ||||||||||||
| KINGDOM | Kingdom Ontology | biology | CC0 1.0 | owl | reused | https://terminologies.gfbio.org/terminology/KINGDOM | https://terminologies.gfbio.org/terms/kingdom | A controlled vocabulary (Terminology) for biological taxa "Higher Classification - Kingdom (=Regnum)". Based on GBIF and CoL. | ||||||||||||
| ORIBATIDA | Oribatida Ontology | biology | CC0 1.0 | owl | reused | https://terminologies.gfbio.org/terminology/ORIBATIDA | https://terminologies.gfbio.org/terms/oribatida/ | Working list: taxon names of the order Oribatida (moss- or beetle-mites). | ||||||||||||
| IHO | IHO World Seas | geo-sciences | CC BY 4.0 | owl | reused | imports GEO and GEONAMES | https://terminologies.gfbio.org/terminology/IHO | https://terminologies.gfbio.org/terms/iho/ | https://www.marineregions.org/sources.php#iho | A hierarchy of the world oceans, seas and sea regions, based on the publication "Limits of Oceans & Seas, Special Publication No. 23" (1953) by the International Hydrographic Organization (IHO), extracted from the Shape Files (version 2 [2017]) available on http://www.marineregions.org and provided by Flanders Marine Institute (VLIZ). | ||||||||||
| GEONAMES | The Geonames geographical database | geo-sciences | CC BY 4.0 | owl | reused | https://terminologies.gfbio.org/terminology/GEONAMES | https://www.geonames.org/ontology/ontology_v3.3.rdf | http://www.geonames.org/ | The GeoNames geographical database is available for download free of charge under a creative commons attribution license. It contains over 10 million geographical names and consists of over 9 million unique features whereof 2.8 million populated places and 5.5 million alternate names. All features are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes. Only information from Germany is available right now. | |||||||||||
| ISOCOUNTRIES | ISO3166 Countries and Subdivisions | general | MIT | owl | reused | https://terminologies.gfbio.org/terminology/ISOCOUNTRIES | https://www.omg.org/spec/LCC/Countries/ISO3166-1-CountryCodes/ | https://databus.dbpedia.org/ontologies/omg.org/spec--LCC--Countries--ISO3166-1-CountryCodes/2021.04.19-031153 | A thersaurus of countries (ISO 3166-1) and country subdivisions (ISO 3166-2) with labels and alternative names in various languages, hierarchical connections between regions and subregions, and links to Wikidata and Geonames. | |||||||||||
| LIT_I | The lithologs rock names ontology for igneous rocks | geo-sciences | ODbL v1.0 | skos | reused | https://terminologies.gfbio.org/terminology/LIT_I | http://www.lithologs.net/skos/igneous_rocks/all | The lithologs ontology for igneous rocks provides SKOSified information on the classification of igneous rocks extracted from the IUGS recommendations published by Le Maitre (ed.)(2002): Igneous rocks: a classification and glossary of terms |