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.
Description
More detailed information about this field from each metasource.
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.
metasource: Fairsharing.orgversion: FAIRsharing.org: Bio2RDF; Bio2RDF; DOI: https://doi.org/10.25504/FAIRsharing.6gz84c; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Webpage:
http://bio2rdf.orgWebpage
More detailed information about this field from each metasource.
http://bio2rdf.org
metasource: Fairsharing.orgversion: FAIRsharing.org: Bio2RDF; Bio2RDF; DOI: https://doi.org/10.25504/FAIRsharing.6gz84c; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence:
Name: bio2rdf Terms of UseLicence name
More detailed information about this field from each metasource.
bio2rdf Terms of Use
metasource: Fairsharing.orgversion: FAIRsharing.org: Bio2RDF; Bio2RDF; DOI: https://doi.org/10.25504/FAIRsharing.6gz84c; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
More detailed information about this field from each metasource.
https://github.com/bio2rdf/bio2rdf-scripts/wiki/Terms-of-use
metasource: Fairsharing.orgversion: FAIRsharing.org: Bio2RDF; Bio2RDF; DOI: https://doi.org/10.25504/FAIRsharing.6gz84c; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Bio2RDF: towards a mashup to build bioinformatics knowledge systems
PMID: 18472304
metasource: Fairsharing.org
version: FAIRsharing.org: Bio2RDF; Bio2RDF; DOI: https://doi.org/10.25504/FAIRsharing.6gz84c; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
Bio2RDF: towards a mashup to build bioinformatics knowledge systems
PMID: 18472304
metasource: Fairsharing.org
version: FAIRsharing.org: Bio2RDF; Bio2RDF; DOI: https://doi.org/10.25504/FAIRsharing.6gz84c; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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Bio2RDF: towards a mashup to build bioinformatics knowledge systems
PubMed citations: 191.
191 articles citing: Bio2RDF: towards a mashup to build bioinformatics knowledge systems
BETA: a comprehensive benchmark for computational drug-target prediction. PMID:35649342
Key observations in terms of management of electronic health records from a mHealth perspective. PMID:35449505
Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications. PMID:35402106
SmileGNN: Drug-Drug Interaction Prediction Based on the SMILES and Graph Neural Network. PMID:35207606
Drug-Drug Interaction Predictions via Knowledge Graph and Text Embedding: Instrument Validation Study. PMID:34185011
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Knowledge-Based Biomedical Data Science. PMID:33954284
MultiPaths: a python framework for analyzing multi-layer biological networks using diffusion algorithms. PMID:33367476
Does tetanus vaccination contribute to reduced severity of the COVID-19 infection? PMID:33341328
KGen: a knowledge graph generator from biomedical scientific literature. PMID:33317512
Constructing knowledge graphs and their biomedical applications. PMID:32637040
Data Integration in the Brazilian Public Health System for Tuberculosis: Use of the Semantic Web to Establish Interoperability. PMID:32628611
ABHD11, a new diacylglycerol lipase involved in weight gain regulation. PMID:32579589
Exploring Novel Computable Knowledge in Structured Drug Product Labels. PMID:32477661
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Enabling semantic queries across federated bioinformatics databases. PMID:31697362
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation. PMID:31685817
SinoPedia-A Linked Data Services platform for decentralized knowledge base. PMID:31374080
An effective biomedical data migration tool from resource description framework to JSON. PMID:31343683
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). PMID:30848456
An Approach to Share Self-Taught Knowledge between Home IoT Devices at the Edge. PMID:30781639
NBDC RDF portal: a comprehensive repository for semantic data in life sciences. PMID:30576482
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
Knowledge-based biomedical Data Science. PMID:30294517
Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. PMID:30085931
Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data. PMID:29982236
Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. PMID:29695735
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. PMID:29390967
DataMed - an open source discovery index for finding biomedical datasets. PMID:29346583
Biotea: semantics for Pubmed Central. PMID:29312824
Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature. PMID:29238346
A semantic-based workflow for biomedical literature annotation. PMID:29220478
BioSearch: a semantic search engine for Bio2RDF. PMID:29220451
Triage by ranking to support the curation of protein interactions. PMID:29220432
Predicate Oriented Pattern Analysis for Biomedical Knowledge Discovery. PMID:28983419
BioCarian: search engine for exploratory searches in heterogeneous biological databases. PMID:28969593
PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets. PMID:28931422
MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection. PMID:28929971
Towards precision medicine: discovering novel gynecological cancer biomarkers and pathways using linked data. PMID:28927463
RDFIO: extending Semantic MediaWiki for interoperable biomedical data management. PMID:28870259
Ontological interpretation of biomedical database content. PMID:28651575
Supporting inter-topic entity search for biomedical Linked Data based on heterogeneous relationships. PMID:28601712
Neuro-symbolic representation learning on biological knowledge graphs. PMID:28449114
Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations. PMID:28430977
Improving data workflow systems with cloud services and use of open data for bioinformatics research. PMID:28419324
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
GT2RDF: Semantic Representation of Genetic Testing Data. PMID:28269903
Using Drug Similarities for Discovery of Possible Adverse Reactions. PMID:28269889
SCALEUS: Semantic Web Services Integration for Biomedical Applications. PMID:28214993
SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. PMID:28178937
Protein Bioinformatics Databases and Resources. PMID:28150231
Consolidating drug data on a global scale using Linked Data. PMID:28109310
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. PMID:27927232
Text mining resources for the life sciences. PMID:27888231
Knowledge Representation and Management: a Linked Data Perspective. PMID:27830248
Knowledge Discovery from Biomedical Ontologies in Cross Domains. PMID:27548262
Using AberOWL for fast and scalable reasoning over BioPortal ontologies. PMID:27502585
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. PMID:27392431
The Orthology Ontology: development and applications. PMID:27259657
Generation of open biomedical datasets through ontology-driven transformation and integration processes. PMID:27255189
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases. PMID:27153650
A Querying Method over RDF-ized Health Level Seven v2.5 Messages Using Life Science Knowledge Resources. PMID:27050304
Wikidata as a semantic framework for the Gene Wiki initiative. PMID:26989148
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker. PMID:26640691
Dealing with the Data Deluge: Handling the Multitude Of Chemical Biology Data Sources. PMID:26609498
Automatic generation of bioinformatics tools for predicting protein-ligand binding sites. PMID:26545824
RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource. PMID:26500754
Nanopublications for exposing experimental data in the life-sciences: a Huntington's Disease case study. PMID:26464783
Data integration in biological research: an overview. PMID:26336651
Drug Normalization for Cancer Therapeutic and Druggable Genome Target Discovery. PMID:26306243
Neuroinformatics Software Applications Supporting Electronic Data Capture, Management, and Sharing for the Neuroimaging Community. PMID:26267019
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. PMID:26175801
SEEK: a systems biology data and model management platform. PMID:26160520
kpath: integration of metabolic pathway linked data. PMID:26055101
Next generation distributed computing for cancer research. PMID:25983539
Semantic enrichment of longitudinal clinical study data using the CDISC standards and the semantic statistics vocabularies. PMID:25973166
Implementation of linked data in the life sciences at BioHackathon 2011. PMID:25973165
Desiderata for an authoritative Representation of MeSH in RDF. PMID:25954433
Utilizing the Wikidata system to improve the quality of medical content in Wikipedia in diverse languages: a pilot study. PMID:25944105
Automatically exposing OpenLifeData via SADI semantic Web Services. PMID:25937881
Toward a complete dataset of drug-drug interaction information from publicly available sources. PMID:25917055
KaBOB: ontology-based semantic integration of biomedical databases. PMID:25903923
An evidence-based approach to identify aging-related genes in Caenorhabditis elegans. PMID:25888240
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. PMID:25877637
Dynamic integration of biological data sources using the data concierge. PMID:25825659
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Aber-OWL: a framework for ontology-based data access in biology. PMID:25627673
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PMID:25522365
Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study. PMID:25521637
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
GlycoRDF: an ontology to standardize glycomics data in RDF. PMID:25388145
Executing SADI services in Galaxy. PMID:25309716
Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives. PMID:25254202
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. PMID:25127889
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. PMID:24909153
Using semantic web technologies to annotate and align microarray designs. PMID:24904201
OWL reasoning framework over big biological knowledge network. PMID:24877076
TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model. PMID:24829452
Integrative approaches for predicting in vivo effects of chemicals from their structural descriptors and the results of short-term biological assays. PMID:24805064
BioTCM-SE: a semantic search engine for the information retrieval of modern biology and traditional Chinese medicine. PMID:24772189
MIRASS: medical informatics research activity support system using information mashup network. PMID:24700079
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. PMID:24618464
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. PMID:24602174
Toolboxes for a standardised and systematic study of glycans. PMID:24564482
An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines. PMID:24441647
The EBI RDF platform: linked open data for the life sciences. PMID:24413672
Extending the "web of drug identity" with knowledge extracted from United States product labels. PMID:24303301
Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying. PMID:24303249
Representing annotation compositionality and provenance for the Semantic Web. PMID:24268021
The semantic web in translational medicine: current applications and future directions. PMID:24197933
Toward knowledge support for analysis and interpretation of complex traits. PMID:24079802
GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework. PMID:24078711
NCBI2RDF: enabling full RDF-based access to NCBI databases. PMID:23984425
Using linked data for mining drug-drug interactions in electronic health records. PMID:23920643
An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics. PMID:23920613
Ontology-Based Querying with Bio2RDF's Linked Open Data. PMID:23735196
Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data. PMID:23734622
The ChEMBL database as linked open data. PMID:23657106
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
PharmaTrek: A Semantic Web Explorer for Open Innovation in Multitarget Drug Discovery. PMID:23548981
Applications of the InChI in cheminformatics with the CDK and Bioclipse. PMID:23497723
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
Chapter 1: Biomedical knowledge integration. PMID:23300416
Gene family matters: expanding the HGNC resource. PMID:23245209
Semantically enabling a genome-wide association study database. PMID:23244533
COEUS: "semantic web in a box" for biomedical applications. PMID:23244467
Taking Open Innovation to the Molecular Level - Strengths and Limitations. PMID:23226167
Biological databases for behavioral neurobiology. PMID:23195119
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. PMID:23161682
Text-mining solutions for biomedical research: enabling integrative biology. PMID:23150036
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
Assessing drug target association using semantic linked data. PMID:22859915
BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. PMID:22847375
Mining the pharmacogenomics literature--a survey of the state of the art. PMID:22833496
Using semantic web technologies for cohort identification from electronic health records for clinical research. PMID:22779040
Building a transnational biosurveillance network using semantic web technologies: requirements, design, and preliminary evaluation. PMID:22642960
AlliumMap-A comparative genomics resource for cultivated Allium vegetables. PMID:22559261
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. PMID:22541594
Towards linked open gene mutations data. PMID:22536974
Improving integrative searching of systems chemical biology data using semantic annotation. PMID:22401035
Exploring and linking biomedical resources through multidimensional semantic spaces. PMID:22373409
A semantic web framework to integrate cancer omics data with biological knowledge. PMID:22373303
Semantically enabling pharmacogenomic data for the realization of personalized medicine. PMID:22256869
Self-organizing ontology of biochemically relevant small molecules. PMID:22221313
Scenario driven data modelling: a method for integrating diverse sources of data and data streams. PMID:22165854
Mining relational paths in integrated biomedical data. PMID:22162991
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. PMID:22140103
CMLLite: a design philosophy for CML. PMID:21999395
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PMID:21991315
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. PMID:21976737
Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics. PMID:21791100
S3QL: a distributed domain specific language for controlled semantic integration of life sciences data. PMID:21756325
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. PMID:21632604
Developing a kidney and urinary pathway knowledge base. PMID:21624162
HyQue: evaluating hypotheses using Semantic Web technologies. PMID:21624158
The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. PMID:21624155
Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration. PMID:21595881
Linked open drug data for pharmaceutical research and development. PMID:21575203
Semantic Web integration of Cheminformatics resources with the SADI framework. PMID:21575200
Resource description framework technologies in chemistry. PMID:21569523
Linking NCBI to Wikipedia: a wiki-based approach. PMID:21516242
Finding complex biological relationships in recent PubMed articles using Bio-LDA. PMID:21448266
Linking the Resource Description Framework to cheminformatics and proteochemometrics. PMID:21388575
Biomedical semantics in the Semantic Web. PMID:21388570
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. PMID:21375767
Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases. PMID:21342584
Booly: a new data integration platform. PMID:20942966
At the intersection of public-health informatics and bioinformatics: using advanced Web technologies for phylogeography. PMID:20924230
PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. PMID:20858292
Exposing the cancer genome atlas as a SPARQL endpoint. PMID:20851208
Using views of Systems Biology Cloud: application for model building. PMID:20730508
WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications. PMID:20727184
Publishing Chinese medicine knowledge as Linked Data on the Web. PMID:20663193
RKB: a Semantic Web knowledge base for RNA. PMID:20626922
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. PMID:20478034
Word add-in for ontology recognition: semantic enrichment of scientific literature. PMID:20181245
BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature. PMID:19811635
Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies. PMID:19796400
BioGateway: a semantic systems biology tool for the life sciences. PMID:19796395
A journey to Semantic Web query federation in the life sciences. PMID:19796394
Translational informatics: enabling high-throughput research paradigms. PMID:19737991
Ultra-Structure database design methodology for managing systems biology data and analyses. PMID:19691849
Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. PMID:19426461
Adventures in semantic publishing: exemplar semantic enhancements of a research article. PMID:19381256
Semantic mashup of biomedical data. PMID:18703163
Extraction of semantic biomedical relations from text using conditional random fields. PMID:18433469
GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. PMID:18315859
Need help integrating and/or managing biomedical data?