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Table 2 Structured vocabularies useful for BCTEO

From: Guidelines for managing data and processes in bone and cartilage tissue engineering

Name

Acronym

Definition

Ref.

Brenda Tissue Ontology

BTO

For the source of an enzyme: it comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multi-cellular organisms.

[26]

Common Anatomy Reference Ontology

CARO

For facilitating the interoperability between existing anatomy ontologies of different species, and providing a template for building new anatomy ontologies.

[27]

Chemical Entities of Biological Interest

CHEBI

For chemical compounds of biological relevance.

[28]

Cell Type

CL

For cell types.

[29]

eagle-i research Resource Ontology

ERO

For instruments, protocols, reagents, animal models and biospecimens.

[30]

Gene Ontology

GO

For the annotation of gene products with respect to their molecular function, cellular component, and biological role.

[31]

Protein-protein interaction

MI

For the annotation of experiments concerned with protein-protein interactions.

[32]

Measurement Method Ontology

MMO

For representing the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.

[33]

Microarray and Gene Expression Data Ontology

MO

Concepts, definitions, terms, and resources for standardized description of a microarray experiment

[34]

Medical Subject Headings (MeSH)

MSH

Terms from National Library of Medicine.

[35]

NCI Thesaurus

NCI Thesaurus

For clinical care, translational and basic research, and public information and administrative activities.

[36]

Ontology for Biomedical Investigations

OBI

For investigations: protocols and instrumentation, material, data generated and types of analysis performed on it.

[37]

Phenotype and Trait Ontology

PATO

For phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.

[38]

Physician Data Query

PDQ

Wide range of cancer topics, a listing of some 30,000 cancer clinical trials from around the world, a directory of genetics services professionals, the NCI Dictionary of Cancer Terms, and the NCI Drug Dictionary.

[39]

Systematized Nomenclature Of Medicine Clinical Terms

SNOMEDCT

For medical terms that are used internationally for recording clinical information. They are coded in computer processable mode.

[40]

NCBI organismal classification

TAXON

Taxonomic classification of living organisms and associated artifacts.

[41]

  1. All of them are available for browsing in the NCBO BioPortal web site.