Graphs

This page contains descriptions of all the RDF graphs.

A-Type Graphs

Imported graphs:

http://rdf.biogateway.eu/graph/taxon – taxonomic entities

Sources: http://purl.obolibrary.org/obo/ncbitaxon.owl

http://rdf.biogateway.eu/graph/go – biological processes, cellular components, and molecular functions entities

Sources: http://purl.obolibrary.org/obo/go/go-basic.owl

http://rdf.biogateway.eu/graph/mi – molecular interactions entities

Sources: http://purl.obolibrary.org/obo/mi.owl

http://rdf.biogateway.eu/graph/omim – disease entities

Sources: http://purl.bioontology.org/ontology/OMIM/submissions/23/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb

BGW Graphs

http://rdf.biogateway.eu/graph/prot – defines protein entities

Sources: http://uniprot.org/uniprot/, Reference Proteome filtered; H. sapiens + 19 model organisms

Classes: Subclasses of http://semanticscience.org/resource/SIO_010043 (protein), correspond to UniProt entries

URI examples: http://uniprot.org/uniprot/P04637

Instances: Correspond to particular isoforms, identified by UniParc IDs

URI examples: http://uniprot.org/uniparc/UPI0000456A12 (corresponds to P04637-2)

Properties:

http://purl.obolibrary.org/obo/RO_0000052 “characteristic of”

http://schema.org/evidenceLevel “has evidence level”

http://schema.org/evidenceOrigin “has evidence origin”

http://semanticscience.org/resource/SIO_000253 “has source”

http://semanticscience.org/resource/SIO_000772 “has evidence”

http://www.w3.org/1999/02/22-rdf-syntax-ns#type “is instance of”

http://www.w3.org/2000/01/rdf-schema#subClassOf “is subclass of”

http://www.w3.org/2004/02/skos/core#altLabel “has synonym”

http://www.w3.org/2004/02/skos/core#closeMatch “has close match”

http://www.w3.org/2004/02/skos/core#definition “has definition”

http://www.w3.org/2004/02/skos/core#prefLabel “has name”

http://rdf.biogateway.eu/graph/gene – defines gene entities

Sources: http://uniprot.org/uniprot/, Reference Proteome filtered; H. sapiens + 19 model organisms

Classes: Subclasses of http://semanticscience.org/resource/SIO_010035 (gene)

Semantically these entities are defined by the sets of translation products they encode and logistically by the preferred gene names (as used in ‘http://uniprot.org/uniprot/’) conditioned on the biological species

URI examples:

http://rdf.biogateway.eu/gene/9606/TP53

Instances:

Correspond to the associated NCBI and Ensembl entries

URI examples:

http://rdf.biogateway.eu/gene/9606/TP53#ENSG00000141510

http://rdf.biogateway.eu/gene/9606/TP53#7157

Properties:

http://purl.obolibrary.org/obo/RO_0000052 “characteristic of”

http://schema.org/evidenceOrigin “has evidence origin”

http://semanticscience.org/resource/SIO_000253 “has source”

http://semanticscience.org/resource/SIO_010078 “encodes”

http://www.w3.org/1999/02/22-rdf-syntax-ns#type “is instance of”

http://www.w3.org/2000/01/rdf-schema#subClassOf “is subclass of”

http://www.w3.org/2004/02/skos/core#altLabel “has synonym”

http://www.w3.org/2004/02/skos/core#closeMatch “has close match”

http://www.w3.org/2004/02/skos/core#definition “has definition”

http://www.w3.org/2004/02/skos/core#prefLabel “has name”

http://rdf.biogateway.eu/graph/crm – defines cis-regulatory module entities

Sources:

http://218.8.241.248:8080/SEA3/; H. sapiens

http://acgt.cs.tau.ac.il/focs/; H. sapiens

http://biocc.hrbmu.edu.cn/DiseaseEnhancer/; H. sapiens

http://bioinfo.vanderbilt.edu/AE/HACER; H. sapiens

http://enhanceratlas.net/scenhancer/; H. sapiens

http://health.tsinghua.edu.cn/jianglab/endisease/; H. sapiens

http://lcbb.swjtu.edu.cn/EnhancerDB/; H. sapiens

http://lcbb.swjtu.edu.cn/EnhFFL/; H. sapiens

http://lcbb.swjtu.edu.cn/TiED/; H. sapiens

https://asntech.org/dbsuper/; H. sapiens

https://egg2.wustl.edu/roadmap/; H. sapiens

https://enhancer.lbl.gov/; H. sapiens

https://fantom.gsc.riken.jp/5/; H. sapiens

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=geneHancer; H. sapiens

https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeBroadHmm&db=hg19; H. sapiens

https://screen.encodeproject.org/; H. sapiens

https://w3id.org/biolink/vocab/supporting_data_source; H. sapiens

https://webs.iiitd.edu.in/raghava/cancerend/; H. sapiens

https://www.cmm.in.tum.de/public/paper/GenoSTAN/; H. sapiens

https://www.ensembl.org/Homo_sapiens/Info/Index; H. sapiens

https://www.ncbi.nlm.nih.gov/refseq/; H. sapiens

http://www.computationalbiology.cn/RAEdb/index.php; H. sapiens

http://www.enhanceratlas.org/indexv2.php; H. sapiens

http://www.licpathway.net/ENdb/; H. sapiens

http://www.licpathway.net/sedb/; H. sapiens

http://yiplab.cse.cuhk.edu.hk/jeme/; H. sapiens

Classes:

Subclasses of http://purl.obolibrary.org/obo/SO_0000727 (cis-regulatory module)

URI examples:

http://rdf.biogateway.eu/crm/9606/CRMHS00000005752

Instances:

Views on the class derived from a particular source, carry the corresponding metadata

URI examples:

http://rdf.biogateway.eu/crm/9606/CRMHS00000005752#cancerend

Properties:

http://purl.obolibrary.org/obo/CLO_0037208 “derived from anatomic part”

http://purl.obolibrary.org/obo/CLO_0037209 “derived from cell”

http://purl.obolibrary.org/obo/CLO_0037210 “derived from cell line”

http://purl.obolibrary.org/obo/OGI_1000003 “end point of interval”

http://purl.obolibrary.org/obo/OGI_1000004 “start point of interval”

http://purl.obolibrary.org/obo/RO_0000052 “characteristic of”

http://purl.obolibrary.org/obo/RO_0001025 “located in”

http://purl.obolibrary.org/obo/RO_0002331 “involved in”

http://purl.obolibrary.org/obo/RO_0002428 “involved in regulation of”

http://purl.obolibrary.org/obo/RO_0002436 “molecularly interacts with”

http://purl.org/dc/terms/hasVersion “has version”

http://schema.org/evidenceOrigin “has evidence origin”

http://semanticscience.org/resource/SIO_000253 “has source”

http://semanticscience.org/resource/SIO_000772 “has evidence”

https://w3id.org/linkml/is_a “is a”

http://www.w3.org/1999/02/22-rdf-syntax-ns#type “is instance of”

http://www.w3.org/2000/01/rdf-schema#isDefinedBy “is defined by”

http://www.w3.org/2000/01/rdf-schema#subClassOf “is subclass of”

http://www.w3.org/2004/02/skos/core#altLabel “has synonym”

http://www.w3.org/2004/02/skos/core#closeMatch “has close match”

http://www.w3.org/2004/02/skos/core#definition “has definition”

http://www.w3.org/2004/02/skos/core#exactMatch “has exact match”

http://www.w3.org/2004/02/skos/core#prefLabel “has name”

http://rdf.biogateway.eu/graph/tad – defines topologically associated domain entities

Sources:

http://3dgenome.fsm.northwestern.edu/index.html; H. sapiens

http://dna.cs.miami.edu/TADKB/; H. sapiens

Classes:

Subclasses of http://purl.obolibrary.org/obo/SO_0002304 (topologically associated domain)

URI examples:

http://rdf.biogateway.eu/tad/9606/TADHS00000000001

Instances:

Views on the class derived from a particular source, carry the corresponding metadata

URI examples:

http://rdf.biogateway.eu/tad/9606/TADHS00000000001#3dgb

Properties:

http://purl.obolibrary.org/obo/CLO_0037208 “derived from anatomic part”

http://purl.obolibrary.org/obo/CLO_0037209 “derived from cell”

http://purl.obolibrary.org/obo/CLO_0037210 “derived from cell line”

http://purl.obolibrary.org/obo/OGI_1000003 “end point of interval”

http://purl.obolibrary.org/obo/OGI_1000004 “start point of interval”

http://purl.obolibrary.org/obo/RO_0000052 “characteristic of”

http://purl.obolibrary.org/obo/RO_0001025 “located in”

http://purl.org/dc/terms/hasVersion “has version”

http://schema.org/evidenceOrigin “has evidence origin”

http://semanticscience.org/resource/SIO_000253 “has source”

http://semanticscience.org/resource/SIO_000772 “has evidence”

https://w3id.org/linkml/is_a “is a”

http://www.w3.org/1999/02/22-rdf-syntax-ns#type “is instance of”

http://www.w3.org/2000/01/rdf-schema#isDefinedBy “is defined by”

http://www.w3.org/2000/01/rdf-schema#subClassOf “is subclass of”

http://www.w3.org/2004/02/skos/core#altLabel “has synonym”

http://www.w3.org/2004/02/skos/core#definition “has definition”

http://www.w3.org/2004/02/skos/core#exactMatch “has exact match”

http://www.w3.org/2004/02/skos/core#prefLabel “has name”

B-type graphs

All entities are modeled as subclasses of http://www.w3.org/1999/02/22-rdf-syntax-ns#Statement with instances conditioned on the source

http://rdf.biogateway.eu/graph/ortho – orthology relations among proteins

Sources:

https://www.orthodb.org/; H. sapiens + 19 model organisms

URI examples:

http://rdf.biogateway.eu/ortho/uniprot!P02340–uniprot!P04637 (class)

http://rdf.biogateway.eu/ortho/uniprot!P02340–uniprot!P04637#orthodb (instance)

Properties:

http://purl.obolibrary.org/obo/BFO_0000050 “is part of”

http://schema.org/memberOf “is member of”

http://semanticscience.org/resource/SIO_000253 “has source”

http://semanticscience.org/resource/SIO_000558 “is orthologous to”

http://www.w3.org/1999/02/22-rdf-syntax-ns#object “has object”

http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate “has predicate”

http://www.w3.org/1999/02/22-rdf-syntax-ns#subject “has subject”

http://www.w3.org/1999/02/22-rdf-syntax-ns#type “is instance of”

http://www.w3.org/2000/01/rdf-schema#subClassOf “is subclass of”

http://www.w3.org/2004/02/skos/core#definition “has definition”

http://www.w3.org/2004/02/skos/core#prefLabel “has name”

http://rdf.biogateway.eu/graph/gene2phen – gene-phenotype interactions currently limited to diseases

Sources:

http://uniprot.org/uniprot/; H. sapiens

URI examples:

http://rdf.biogateway.eu/gene-phen/gene!TP53–omim!151623 (class)

http://rdf.biogateway.eu/gene-phen/gene!TP53–omim!151623#uniprot (instance)

Properties:

http://purl.obolibrary.org/obo/RO_0002331 “involved in”

http://schema.org/evidenceOrigin “has evidence origin”

http://semanticscience.org/resource/SIO_000253 “has source”

http://www.w3.org/1999/02/22-rdf-syntax-ns#object “has object”

http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate “has predicate”

http://www.w3.org/1999/02/22-rdf-syntax-ns#subject “has subject”

http://www.w3.org/1999/02/22-rdf-syntax-ns#type “is instance of”

http://www.w3.org/2000/01/rdf-schema#subClassOf “is subclass of”

http://www.w3.org/2002/07/owl#versionInfo “current version”

http://www.w3.org/2004/02/skos/core#definition “has definition”

http://www.w3.org/2004/02/skos/core#prefLabel “has name”

http://rdf.biogateway.eu/graph/prot2bp – interactions between proteins and biological processes

Sources:

http://identifiers.org/goa; H. sapiens + 19 model organisms

URI examples:

http://rdf.biogateway.eu/prot-onto/uniprot!P04637–obo!GO_0000122 (class)

http://rdf.biogateway.eu/prot-onto/uniprot!P04637–obo!GO_0000122#goa (instance)