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General Biological Ontologies

• MIAPA Minimal Information for Biological and Biomedical Investigations.

Taxonomic Ontologies

• NCBI Taxonomy
• Teleost Taxonomy Ontology
• Amphibian Taxonomy Ontology
• Fly Taxonomy
• Taxonomic Rank Ontology

Ontologies for taxonomic, specimen, and species data

• The Darwin Core (sometimes abbreviated as DwC) is a standard designed to facilitate the exchange of information about the geographic occurrence of species and the existence of specimens in collections. Extensions to the Darwin Core provide a mechanism to share additional information, which may be discipline-specific, or beyond the commonly agreed upon scope of the Darwin Core itself.
• The TDWG ontology from Biodiversity Information Standards (TDWG), an international not-for-profit group that develops standards and protocols for sharing biodiversity data.

Ontologies for scientific observations and experiments

• Extensible Observation Ontology (OBOE) A formal and conceptual framework for describing the semantics of observational data sets. Madin J, Bowers S, Schildhauer M, Krivov S, Pennington D, Villa F. 2007. An ontology for describing and synthesizing ecological observation data. Ecological Informatics 2: 279-296.
• Open Geospatial Consortium Obervations and Measurements (O&M) The OpenGIS® Observations and Measurements Encoding Standard (O&M) defines an abstract model and an [www.w3.org/XML/Schema XML schema] encoding for observations and it provides support for common sampling strategies. O&M also provides a general framework for systems that deal in technical measurements in science and engineering.
• SONET The Scientific Observations Network. NSF proposal to develop ontologies at the observation rather than dataset level.
• Ontology for Biomedical Investigations, "an integrated ontology for the description of life-science and clinical investigations."

Ecological/Enviromental Ontologies

• Research and Observation oNTology SERONTO. This is the ontology being used by CEH and the ALTER to markup LTER data. Some slides on SERONTO. Documentation.
• Ecolingua With the intention of specifying an ontology for the description of ecological data, Brilhante and Robertson chose not to build the ontology from scratch, but to do it the `proper way', that is, by re-using publicly available ontologies of related fields and incorporating their specifications into Ecolingua. For this reason they turned to the library of sharable ontologies provided by the Ontolingua Server.
• Earth sciences ontology NASA Semantic Web for Earth and Environental Terminology (SWEET)
• The Environment Ontology (EnvO) - Describes classes such as 'coastal' and 'woodland' and how they relate between different ontologies

Trait and Phenotype Ontologies

• TraitNet General ontology for traits.
• Amphibian Ontology
• Animal Trait Ontology project - appears to only include ontology for pigs
• Mammalian Phenotype - based predominantly on mice and humans
• Human Phenotype Ontology
• Phenotypic Qualities (PATO)
• Zebrafish

Evolution Ontologies

• CDAO, "Comparative Data Analysis Ontology" and it is an initial tentative to formalize the most current used terms for evolutionary analysis in a single framework.

Cellular Ontologies

• Sequence Ontology (SO)
• Protein Ontology (PRO)
• Multiple Alignment Ontology (MAO)
• "quest for orthologs"
• homology ontology
• OBO relations ontology
• Ontology for Biomedical Investigations (OBI)

and many others.

Geological Ontologies

• Palaeointegration project provides extensive fossil and sedimentary rock databases that are searchable seamlessly from the GEON portal.

Community resources

• Open Biomedical Ontologies The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.
• NCBO BioPortal, indexes currently 170 ontologies with more than 720,000 concepts. There is also an ontology browser that, among other things, allows identifying ontologies by category.
• Ontology Lookup Service, hosted at the EBI. Fast search and lookup of more or less all BioPortal ontologies.
• NERC DataGrid vocabulary server The NDG vocabulary server provides access to lists of standardised terms that cover a broad spectrum of disciplines of relevance to the oceanographic and wider community.
• GBIF Vocabulary Server
• {https://www.nescent.org/sites/hive/Main_Page HIVE (Helping Interdisciplinary Vocabulary Engineering)] - this is currently in development
• Ontolingua - a distributed collaborative environment to browse, create, edit, modify, and use ontologies.

Links & Related resources

• PhyloCode, formal set of rules governing phylogenetic nomenclature.
• NeXML, an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process, and with a standards-compliant way to embed semantically rich metadata
• PhyloWS, a standardized web-service API to allow integration of phylogenetic data and service providers into the programmable web.

Links

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