Bio2RDF: Towards a mashup to build bioinformatics knowledge systems

By F. Belleau, Marc-Alexandre Nolin, N. Tourigny, P. Rigault, J. Morissette. Journal of Biomedical Informatics, 2008

861 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a51badd5461c1650b2bfba7d0a5a89949186fb67

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Citations in the corpus

The EBI RDF platform: linked open data for the life sciences (2014, background): “Availability: http://www.ebi.ac.uk/rdf Contact: jupp@ebi.ac.uk Received on October 10, 2013; revised on November 22, 2013; accepted on December 23, 2013”
Linked Data - The Story So Far (2009, neutral): “The content of the cloud is diverse in nature, comprising data about geographic locations, people, companies, books (Bizer & Cyganiak & Gauss, 2007), scientific publications (Van de Sompel et al., 2009), films (Hassanzadeh & Consens, 2009), music, television and radio programmes (Kobilarov et al, 20”
DBpedia SPARQL Benchmark - Performance Assessment with Real Queries on Real Data (2011, background): “Examples of such knowledge bases are curated bio-medical ontologies such as those contained in Bio2RDF [2] as well as knowledge bases extracted from unstructured or semi-structured sources such as DBpedia [10] or LinkedGeoData [1].”
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases (2015, methodology): “…knowledge representation and reasoning in the scientific research, and the same design pattern has been implemented in the Bio2RDF mash-up system [22, 23] and the Semantic Automated Discovery and Integration (SADI) [50, 51] The SPARQL query returned 72 different compounds listed in Additional…”
Domain-specific Knowledge Extraction from the Web of Data (2018, background): “Linked Data also contains datasets capturing knowledge for specific domains such as life science (Bio2RDF [Belleau et al. 2008]), entertainment (BBC program [Kobilarov et al. 2009]), and education (DBLP1).”
A Review of Relational Machine Learning for Knowledge Graphs (2015, background): “For instance, Bio2RDF [36], Neurocommons [37], and LinkedLifeData [38] are knowledge graphs that integrate multiple sources of biomedical information.”
Sindice.com: a document-oriented lookup index for open linked data (2008, background): “Projects such as Bio2RDF [Belleau et al. 2007] provide real-time mapping and consolidation of identifiers over vast amounts of bioscience databases.”
Linked Data: Evolving the Web into a Global Data Space (2011, methodology): “In particular, the Bio2RDF project [11] has interlinked more than 30 widely used data sets, including UniProt (the Universal Protein Resource), KEGG (the Kyoto Encyclopedia of Genes and Genomes), CAS (the Chemical Abstracts Service), PubMed, and the Gene Ontology.”
Open PHACTS: semantic interoperability for drug discovery. (2012, neutral): “These include Bio2RDF [14], Chem2-Bio2RDF [15], LinkedLifeData (http://linkedlifedata.com/), Open-Tox [16], the World Wide Web Consortium Semantic Web Health Care and Life Sciences Interest Group (http://www.w3.org/blog/ hcls/) and others [17,18].”
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes (2015, background): “This implies that the DisGeNET RDF resources are linked out to other external resources in the Linking Open Data Cloud such as UniProt and several datasets from the Bio2RDF (48) and Linked Life Data (49) subnetworks, spanning the information on genotype-phenotype associations in the Semantic Web and”
The ChEMBL database as linked open data (2013, methodology): “The Linked Data server used by Bio2RDF has been reconfigured for ChEMBL to provide URL based services for standard URI resolution, along with textual and link-based searches [28].”
Why Linked Data is Not Enough for Scientists (2010, neutral): “Bio2RDF [35] provides ‘‘rdfized’’ access to information from data sources such as Kegg, PDB, MGI and HGNC.”
A Survey on Knowledge Graph-Based Recommender Systems (2020, background): “…Freebase Google’s Knowledge Graph [18] Cross-Domain Web data Facebooks Entities Graph [41] Cross-Domain Wikipedia, Facebook data [42] Bio2RDF [25] Biological Domain Public bioinformatics databases, NCBIs databases KnowLife [43] Biomedical Domain Scientiﬁc literature, Web portals…”
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format (2011, methodology): “It is noted that the Bio2RDF project (16) has already been providing a subset of PDB data in the RDF format based on the Bio2RDF ontology (http://bio2rdf.”