Stian Soiland-Reyes
eScience lab, University of Manchester
@soilandreyes
http://orcid.org/0000-0001-9842-9718
2015-09-18
This work is licensed under a
Creative Commons Attribution 4.0 International License.
Multiple domains:
Bioinformatics (genes, proteins, pathways)
Chemistry (molecules)
Pharmaceutical (compounds, patents)
Medical (diseases, trials)
Uniprot
Chembl
DrugBank
DisGeNet
ChemSpider
GeneOntology
WikiPathways
...
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ns0:reportedAdverseEvent <http://aers.data2semantics.org/resource/diagnosis/TUMOUR_LYSIS_SYNDROME> ;
ns0:reportedAdverseEvent <http://aers.data2semantics.org/resource/diagnosis/LEFT_VENTRICULAR_DYSFUNCTION> ;
ns0:reportedAdverseEvent <http://aers.data2semantics.org/resource/diagnosis/METABOLIC_ACIDOSIS> .
<http://bio2rdf.org/drugbank:DB00398>
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> ;
<http://bio2rdf.org/drugbank_vocabulary:metabolism> "Sorafenib is metabolized primarily in the liver, undergoing oxidative metabolism, mediated by CYP3A4, as well as glucuronidation mediated by UGT1A9. Sorafenib accounts for approximately 70-85% of the circulating analytes in plasma at steady- state. Eight metabolites of sorafenib have been identified, of which five have been detected in plasma. The main circulating metabolite of sorafenib in plasma, the pyridine N-oxide, shows <i>in vitro</i> potency similar to that of sorafenib. This metabolite comprises approximately 9-16% of circulating analytes at steady-state."@en ;
<http://bio2rdf.org/drugbank_vocabulary:toxicity> "The highest dose of sorafenib studied clinically is 800 mg twice daily. The adverse reactions observed at this dose were primarily diarrhea and dermatologic events. No information is available on symptoms of acute overdose in animals because of the saturation of absorption in oral acute toxicity studies conducted in animals."@en ;
<http://bio2rdf.org/drugbank_vocabulary:description> "Sorafenib (rINN), marketed as Nexavar by Bayer, is a drug approved for the treatment of advanced renal cell carcinoma (primary kidney cancer). It has also received \"Fast Track\" designation by the FDA for the treatment of advanced hepatocellular carcinoma (primary liver cancer), and has since performed well in Phase III trials.\nSorafenib is a small molecular inhibitor of Raf kinase, PDGF (platelet-derived growth factor), VEGF receptor 2 & 3 kinases and c Kit the receptor for Stem cell factor. A growing number of drugs target most of these pathways. The originality of Sorafenib lays in its simultaneous targeting of the Raf/Mek/Erk pathway."@en ;
<http://bio2rdf.org/drugbank_vocabulary:proteinBinding> "99.5% bound to plasma proteins."@en ;
<http://bio2rdf.org/drugbank_vocabulary:genericName> "Sorafenib"@en ;
<http://bio2rdf.org/drugbank_vocabulary:drugType> "investigational"@en ;
<http://bio2rdf.org/drugbank_vocabulary:drugType> "approved"@en ;
ns0:drugInteraction <http://bio2rdf.org/drugbank_resource:DB00398_DB00755> ;
ns0:drugInteraction <http://bio2rdf.org/drugbank_resource:DB00398_DB00958> ;
ns0:drugInteraction <http://bio2rdf.org/drugbank_resource:DB00398_DB06414> ;
ns0:drugInteraction <http://bio2rdf.org/drugbank_resource:DB00072_DB00398> ;
ns0:drugInteraction <http://bio2rdf.org/drugbank_resource:DB00112_DB00398> .
<http://bio2rdf.org/drugbank_resource:DB00072_DB00398>
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> ;
ns0:interactingDrug <http://bio2rdf.org/drugbank:DB00072> ;
<http://bio2rdf.org/drugbank_vocabulary:text> "DDI between Trastuzumab and Sorafenib - Trastuzumab may increase the risk of neutropenia and anemia. Monitor closely for signs and symptoms of adverse events."@en .
<http://bio2rdf.org/drugbank_resource:DB00112_DB00398>
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> ;
ns0:interactingDrug <http://bio2rdf.org/drugbank:DB00112> ;
<http://bio2rdf.org/drugbank_vocabulary:text> "DDI between Bevacizumab and Sorafenib - Monitor therapy due to increased adverse effects of sorafenib, especially hand-foot skin reaction."@en .
*Really: Is it sensible to combine data associated with these two molecules?
:chembl_rdf_dataset a void:Dataset ;
dcterms:title "The ChEMBL Database" ;
dcterms:description "ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs." ;
pav:createdBy <http://orcid.org/0000-0003-2634-7400> ;
pav:createdOn "2009-10-28T00:00:00.000Z"^^xsd:dateTime ;
pav:lastUpdateOn "2015-01-14T00:00:00.000Z"^^xsd:dateTime ;
dcat:landingPage <https://www.ebi.ac.uk/chembl> ;
foaf:page <ftp://ftp.ebi.ac.uk/pub/databases/chembl/> ;
dcterms:license <http://creativecommons.org/licenses/by-sa/3.0/> ;
void:uriSpace "http://rdf.ebi.ac.uk/resource/chembl/" ;
pav:version "20.1" ;
pav:previousVersion <http://rdf.ebi.ac.uk/dataset/chembl/20.0/void.ttl#chembl_rdf_dataset> ;
dcterms:publisher <https://www.ebi.ac.uk/> ;
dcterms:created "2009-10-28T00:00:00.000Z"^^xsd:dateTime ;
dcterms:modified "2015-01-14T00:00:00.000Z"^^xsd:dateTime ;
void:subset :chembl_rdf_target_relation_dataset , :chembl_rdf_cell_line_dataset , :chembl_rdf_molhierarchy_dataset , :chembl_rdf_bindingsite_dataset , :chembl_rdf_moa_dataset , :chembl_rdf_molecule_dataset , :chembl_rdf_biocmpt_dataset , :chembl_rdf_target_dataset , :chembl_rdf_targetcmpt_dataset , :chembl_rdf_assay_dataset , :chembl_rdf_activity_dataset , :chembl_rdf_document_dataset , :chembl_rdf_journal_dataset , :chembl_rdf_protclass_dataset , :chembl_rdf_source_dataset , :chembl_rdf_unichem_dataset ;
void:vocabulary <http://purl.org/ontology/bibo> , <http://www.bioassayontology.org/bao> , <http://semanticscience.org/ontology/cheminf.owl> , <http://purl.org/spar/cito> , <http://purl.org/dc/terms> , <http://www.w3.org/2002/07/owl> , <http://www.w3.org/1999/02/22-rdf-syntax-ns> , <http://www.w3.org/2000/01/rdf-schema> , <http://semanticscience.org/ontology/sio.owl> , <http://www.w3.org/2004/02/skos/core> , <http://www.w3.org/2001/XMLSchema> ;
void:exampleResource chembl_molecule:CHEMBL941 ;
void:sparqlEndpoint <http://www.ebi.ac.uk/rdf/services/chembl/sparql> ;
voag:frequencyOfChange freq:quarterly .
:molecule_chebi_linkset a void:Linkset ;
dcterms:title "The ChEMBL Molecule to ChEBI Molecule Linkset" ;
dcterms:description "The ChEMBL Molecule to ChEBI Molecule Linkset" ;
dcterms:publisher <http://www.ebi.ac.uk/> ;
dcterms:license <http://creativecommons.org/licenses/by-sa/3.0/> ;
dcterms:issued "2015-01-27T15:29:59.000Z"^^xsd:dateTime ;
void:dataDump <ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.1/chembl_20.1_molecule_chebi_ls.ttl.gz> ;
void:subjectsTarget :chembl_rdf_molecule_dataset ;
void:objectsTarget :chebi_dataset ;
void:linkPredicate skos:exactMatch ;
dul:expresses sio:CHEMINF_000059 ;
pav:authoredBy <http://orcid.org/0000-0003-2634-7400> ;
pav:authoredOn "2015-09-09T09:53:07.000+01:00"^^xsd:dateTime ;
pav:createdBy <http://orcid.org/0000-0003-2634-7400> ;
pav:createdOn "2015-09-09T09:53:07.000+01:00"^^xsd:dateTime .
:chembl_singletarget_targetcmpt_linkset a void:Linkset ;
dcterms:title "The ChEMBL Single Protein Target to Target Component Linkset" ;
dcterms:description "The ChEMBL Single Protein Target to Target Component Linkset maps ChEMBL targets that are single proteins to their equivalent target component (a simple 1:1 mapping)." ;
dcterms:publisher <http://www.ebi.ac.uk/> ;
dcterms:license <http://creativecommons.org/licenses/by-sa/3.0/> ;
dcterms:issued "2015-09-09T09:53:07.000+01:00"^^xsd:dateTime ;
void:dataDump <ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.1/chembl_20.1_singletarget_targetcmpt_ls.ttl.gz> ;
void:subjectsTarget :chembl_rdf_target_dataset ;
void:objectsTarget :chembl_rdf_targetcmpt_dataset ;
void:linkPredicate skos:exactMatch ;
dul:expresses sio:SIO_010043 ;
pav:authoredBy <http://orcid.org/0000-0003-2634-7400> ;
pav:authoredOn "2015-09-09T09:53:07.000+01:00"^^xsd:dateTime ;
pav:createdBy <http://orcid.org/0000-0003-2634-7400> ;
pav:createdOn "2015-09-09T09:53:07.000+01:00"^^xsd:dateTime .
API: Text Query to URI
ElasticSearch-based
Indexes triple stores by SPARQL
Selects label-like properties
TODO: Integrate with Identity mapping service
Dataset update - Mirror and load RDF @dev
Ontology changes - Edit queries
URI changes - Update linksets and IMS
Manual testing - does it still integrate?
Maven project per dataset/linkset, which:
- Downloads dataset from upstream
- Clean/filter data
- Versioned, licensed
Built by Jenkins CI
- Deploys to Maven repository
TODO: Make a Research Object,
add provenance/VoID
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>wagon-maven-plugin</artifactId>
<version>1.0</version>
<executions>
<execution>
<id>download-rdf</id>
<phase>generate-resources</phase>
<goals>
<goal>download</goal>
</goals>
<configuration>
<includes>*.ttl.gz</includes>
<url>http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/${chembl.version}</url>
<toDir>${project.build.outputDirectory}/data/${project.artifactId}</toDir>
</configuration>
</execution>
Linux container technology
Download images from Docker Hub
Philosophy: One application per container
1) Data staging
- Downloads from http://data.openphacts.org/1.5/
2) Starts linked Docker containers
3) Customizable per container
Provides: Explorer, API, Virtuoso, IMS