standards > terminology artifact > DOI:10.25504/FAIRsharing.dpkb5f


ready Semanticscience Integrated Ontology

Abbreviation: SIO


General Information
The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.

Homepage https://github.com/MaastrichtU-IDS/semanticscience

Countries that developed this resource Canada , European Union , Japan , United States

Created in 2015

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How to cite this record FAIRsharing.org: SIO; Semanticscience Integrated Ontology; DOI: https://doi.org/10.25504/FAIRsharing.dpkb5f; Last edited: Jan. 8, 2020, 11:59 a.m.; Last accessed: Jan 27 2020 7:28 a.m.

Publication for citation  The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, Del Rio NR, Duck G, Furlong LI, Keath N, Klassen D, McCusker JP, Queralt-Rosinach N, Samwald M, Villanueva-Rosales N, Wilkinson MD, Hoehndorf R.; J Biomed Semantics ; 2014; 10.1186/2041-1480-5-14;


This record is maintained by micheldumontier  ORCID

Record updated: Jan. 8, 2020, 11:58 a.m. by The FAIRsharing Team.

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The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.

Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, Del Rio NR, Duck G, Furlong LI, Keath N, Klassen D, McCusker JP, Queralt-Rosinach N, Samwald M, Villanueva-Rosales N, Wilkinson MD, Hoehndorf R.
J Biomed Semantics 2014

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SIO Ontology Display

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Implementing Databases (3)
DisGeNET: a knowledge base for disease genomics
DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific literature, and covers the whole landscape of human diseases. The current version of DisGeNET (v 6.0) contains 628,685 gene-disease associations (GDAs), between 17,549 genes and 24,166 diseases, disorders, traits, and clinical or abnormal human phenotypes, and 210,498 variant-disease associations (VDAs), between 117,337 variants and 10,358 diseases, traits, and phenotypes. The data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype-phenotype relationships. The information is accessible through a web interface, a Cytoscape App, an RDF SPARQL endpoint, a REST API, and an R package.

Bio2RDF
Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.

DNA Modification Database
DNAmod is an open-source database (https://dnamod.hoffmanlab.org) that catalogues DNA modifications and provides a single source to learn about their properties. The database annotates the chemical properties and structures of all curated modified DNA bases, and a much larger list of candidate chemical entities. DNAmod includes manual annotations of available sequencing methods, descriptions of their occurrence in nature, and provides existing and suggested nomenclature. DNAmod enables researchers to rapidly review previous work, select mapping techniques, and track recent developments concerning modified bases of interest.

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