Open PHACTS architecture

Stian Soiland-Reyes

eScience lab, University of Manchester
@soilandreyes
http://orcid.org/0000-0001-9842-9718

2015-09-18

Linked Data for pharma

Multiple domains:

 

Bioinformatics (genes, proteins, pathways)

Chemistry (molecules)

Pharmaceutical (compounds, patents)

Medical (diseases, trials)

Loads of Linked Data available

Uniprot

Chembl

DrugBank

DisGeNet

ChemSpider

GeneOntology

WikiPathways

...

Integrating data mirror

Re-exposed as public APIs

{
 "format": "linked-data-api",
 "version": "1.5",
 "result": {
  "_about": "https://beta.openphacts.org/1.5/compound?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5&app_id=161aeb7d&app_key=bbcba81896020f0b95e3dd35b55e3345&_format=json",
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  "linkPredicate": "http://www.w3.org/2004/02/skos/core#exactMatch",
  "activeLens": "Default",
  "primaryTopic": {
   "_about": "http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5",
   "inDataset": "http://www.conceptwiki.org",
   "exactMatch": [    
     {
      "_about": "http://bio2rdf.org/drugbank:DB00398",
      "description_en": "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.",
      "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.",
      "drugType_en": [
       "investigational",
       "approved"
      ],
      "drugType": [
       "investigational",
       "approved"
      ],
      "genericName_en": "Sorafenib",
      "genericName": "Sorafenib",
      "metabolism_en": "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 in vitro potency similar to that of sorafenib. This metabolite comprises approximately 9-16% of circulating analytes at steady-state.",
      "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 in vitro potency similar to that of sorafenib. This metabolite comprises approximately 9-16% of circulating analytes at steady-state.",
      "proteinBinding_en": "99.5% bound to plasma proteins.",
      "proteinBinding": "99.5% bound to plasma proteins.",
      "toxicity_en": "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.",
      "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.",
      "inDataset": "http://www.openphacts.org/bio2rdf/drugbank",
      "drugInteraction": [
       {
        "_about": "http://bio2rdf.org/drugbank_resource:DB00398_DB00755",
        "text_en": "DDI between Sorafenib and Tretinoin - The strong CYP2C8 inhibitor, Sorafenib, may decrease the metabolism and clearance of oral Tretinoin. Consider alternate therapy or monitor for changes in Tretinoin effectiveness and adverse/toxic effects if Sorafenib is initiated, discontinued to dose changed.",
        "text": "DDI between Sorafenib and Tretinoin - The strong CYP2C8 inhibitor, Sorafenib, may decrease the metabolism and clearance of oral Tretinoin. Consider alternate therapy or monitor for changes in Tretinoin effectiveness and adverse/toxic effects if Sorafenib is initiated, discontinued to dose changed.",
        "inDataset": "http://www.openphacts.org/bio2rdf/drugbank",
        "interactingDrug": "http://bio2rdf.org/drugbank:DB00755"
       },
       {
        "_about": "http://bio2rdf.org/drugbank_resource:DB00398_DB00958",
        "text_en": "DDI between Sorafenib and Carboplatin - Sorafenib may enhance the adverse/toxic effect of carboplatin. Concurrent use of sorafenib with carboplatin and placlitaxel in patients with squamous cell lung cancer is contraindicated. The use of this combination in other settings is not specifically contraindicated, but any such use should be approached with added caution.",
        "text": "DDI between Sorafenib and Carboplatin - Sorafenib may enhance the adverse/toxic effect of carboplatin. Concurrent use of sorafenib with carboplatin and placlitaxel in patients with squamous cell lung cancer is contraindicated. The use of this combination in other settings is not specifically contraindicated, but any such use should be approached with added caution.",
        "inDataset": "http://www.openphacts.org/bio2rdf/drugbank",
        "interactingDrug": "http://bio2rdf.org/drugbank:DB00958"
       },
       {
        "_about": "http://bio2rdf.org/drugbank_resource:DB00398_DB06414",
        "text_en": "DDI between Sorafenib and Etravirine - Sorafebib, when used concomitantly with etravirine, may experience a decrease in serum concentration. It is recommended to avoid concurrent therapy.",
        "text": "DDI between Sorafenib and Etravirine - Sorafebib, when used concomitantly with etravirine, may experience a decrease in serum concentration. It is recommended to avoid concurrent therapy.",
        "inDataset": "http://www.openphacts.org/bio2rdf/drugbank",
        "interactingDrug": "http://bio2rdf.org/drugbank:DB06414"
       },
       {
        "_about": "http://bio2rdf.org/drugbank_resource:DB00072_DB00398",
        "text_en": "DDI between Trastuzumab and Sorafenib - Trastuzumab may increase the risk of neutropenia and anemia. Monitor closely for signs and symptoms of adverse events.",
        "text": "DDI between Trastuzumab and Sorafenib - Trastuzumab may increase the risk of neutropenia and anemia. Monitor closely for signs and symptoms of adverse events.",
        "inDataset": "http://www.openphacts.org/bio2rdf/drugbank",
        "interactingDrug": "http://bio2rdf.org/drugbank:DB00072"
       },
       {
        "_about": "http://bio2rdf.org/drugbank_resource:DB00112_DB00398",
        "text_en": "DDI between Bevacizumab and Sorafenib - Monitor therapy due to increased adverse effects of sorafenib, especially hand-foot skin reaction.",
        "text": "DDI between Bevacizumab and Sorafenib - Monitor therapy due to increased adverse effects of sorafenib, especially hand-foot skin reaction.",
        "inDataset": "http://www.openphacts.org/bio2rdf/drugbank",
        "interactingDrug": "http://bio2rdf.org/drugbank:DB00112"
       }
      ]
     },
    {
     "_about": "http://aers.data2semantics.org/resource/drug/SORAFENIB",
     "inDataset": "http://aers.data2semantics.org/",
     "reportedAdverseEvent": [
      {
       "_about": "http://aers.data2semantics.org/resource/diagnosis/CARDIAC_FAILURE_ACUTE",
       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "CARDIAC FAILURE ACUTE"
      },
      {
       "_about": "http://aers.data2semantics.org/resource/diagnosis/RENAL_IMPAIRMENT",
       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "RENAL IMPAIRMENT"
      },
      {
       "_about": "http://aers.data2semantics.org/resource/diagnosis/HYPERURICAEMIA",
       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "HYPERURICAEMIA"
      },
      {
       "_about": "http://aers.data2semantics.org/resource/diagnosis/TUMOUR_LYSIS_SYNDROME",
       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "TUMOUR LYSIS SYNDROME"
      },
      {
       "_about": "http://aers.data2semantics.org/resource/diagnosis/LEFT_VENTRICULAR_DYSFUNCTION",
       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "LEFT VENTRICULAR DYSFUNCTION"
      },
      {
       "_about": "http://aers.data2semantics.org/resource/diagnosis/METABOLIC_ACIDOSIS",
       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "METABOLIC ACIDOSIS"
      }
     ],
    },
    {
     "_about": "http://rdf.ebi.ac.uk/resource/chembl/molecule/CHEMBL1336",
     "mw_freebase": 464.82,
     "inDataset": "http://www.ebi.ac.uk/chembl",
     "type": "http://rdf.ebi.ac.uk/terms/chembl#SmallMolecule"
    },
    {
     "_about": "http://ops.rsc.org/OPS379634",
     "inDataset": "http://ops.rsc.org",
     "hba": 7,
     "hbd": 3,
     "inchi": "InChI=1S/C21H16ClF3N4O3/c1-26-19(30)18-11-15(8-9-27-18)32-14-5-2-12(3-6-14)28-20(31)29-13-4-7-17(22)16(10-13)21(23,24)25/h2-11H,1H3,(H,26,30)(H2,28,29,31)",
     "inchikey": "MLDQJTXFUGDVEO-UHFFFAOYSA-N",
     "logp": 5.158,
     "molformula": "C21H16ClF3N4O3",
     "molweight": 464.825,
     "psa": 92.35,
     "ro5_violations": 1,
     "rtb": 5,
     "smiles": "CNC(=O)C1=NC=CC(=C1)OC2=CC=C(C=C2)NC(=O)NC3=CC(=C(C=C3)Cl)C(F)(F)F"
    }
   ],
   "prefLabel_en": "Sorafenib",
   "prefLabel": "Sorafenib",
   "isPrimaryTopicOf": "https://beta.openphacts.org/1.5/compound?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5&app_id=161aeb7d&app_key=bbcba81896020f0b95e3dd35b55e3345&_format=json"
  }
 }
}
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<result format="linked-data-api" version="1.5" href="https://beta.openphacts.org/1.5/compound?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5&app_id=161aeb7d&app_key=bbcba81896020f0b95e3dd35b55e3345&_format=xml">
  <primaryTopic href="http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5">
    <prefLabel xml:lang="en">Sorafenib</prefLabel>
    <exactMatch>
      <item href="http://rdf.ebi.ac.uk/resource/chembl/molecule/CHEMBL1336">
        <type href="http://rdf.ebi.ac.uk/terms/chembl#SmallMolecule"/>
        <inDataset href="http://www.ebi.ac.uk/chembl"/>
        <mw_freebase datatype="double">464.82</mw_freebase>
      </item>
      <item href="http://ops.rsc.org/OPS379634">
        <smiles>CNC(=O)C1=NC=CC(=C1)OC2=CC=C(C=C2)NC(=O)NC3=CC(=C(C=C3)Cl)C(F)(F)F</smiles>
        <rtb datatype="double">5.0</rtb>
        <ro5_violations datatype="double">1.0</ro5_violations>
        <psa datatype="double">92.35</psa>
        <molweight datatype="double">464.825</molweight>
        <molformula>C21H16ClF3N4O3</molformula>
        <logp datatype="double">5.158</logp>
        <inchikey>MLDQJTXFUGDVEO-UHFFFAOYSA-N</inchikey>
        <inchi>InChI=1S/C21H16ClF3N4O3/c1-26-19(30)18-11-15(8-9-27-18)32-14-5-2-12(3-6-14)28-20(31)29-13-4-7-17(22)16(10-13)21(23,24)25/h2-11H,1H3,(H,26,30)(H2,28,29,31)</inchi>
        <hbd datatype="double">3.0</hbd>
        <hba datatype="double">7.0</hba>
        <inDataset href="http://ops.rsc.org"/>
      </item>      
      <item href="http://aers.data2semantics.org/resource/drug/NEXAVAR">
        <prefLabel>NEXAVAR</prefLabel>
        <reportedAdverseEvent>
          <item href="http://aers.data2semantics.org/resource/diagnosis/HEAD_INJURY">
            <prefLabel>HEAD INJURY</prefLabel>
            <inDataset href="http://aers.data2semantics.org/"/>
          </item>
          <item href="http://aers.data2semantics.org/resource/diagnosis/SUPRAVENTRICULAR_TACHYCARDIA">
            <prefLabel>SUPRAVENTRICULAR TACHYCARDIA</prefLabel>
            <inDataset href="http://aers.data2semantics.org/"/>
          </item>
          <!-- .. -->
        </reportedAdverseEvent>
        <inDataset href="http://aers.data2semantics.org/"/>
      </item>
      <item href="http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5"/>
      <item href="http://bio2rdf.org/drugbank:DB00398">
        <drugInteraction>
          <item href="http://bio2rdf.org/drugbank_resource:DB00398_DB00755">
            <interactingDrug href="http://bio2rdf.org/drugbank:DB00755"/>
            <inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/>
            <text xml:lang="en">DDI between Sorafenib and Tretinoin - The strong CYP2C8 inhibitor, Sorafenib, may decrease the metabolism and clearance of oral Tretinoin. Consider alternate therapy or monitor for changes in Tretinoin effectiveness and adverse/toxic effects if Sorafenib is initiated, discontinued to dose changed.</text>
          </item>
          <item href="http://bio2rdf.org/drugbank_resource:DB00398_DB00958">
            <interactingDrug href="http://bio2rdf.org/drugbank:DB00958"/>
            <inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/>
            <text xml:lang="en">DDI between Sorafenib and Carboplatin - Sorafenib may enhance the adverse/toxic effect of carboplatin. Concurrent use of sorafenib with carboplatin and placlitaxel in patients with squamous cell lung cancer is contraindicated. The use of this combination in other settings is not specifically contraindicated, but any such use should be approached with added caution.</text>
          </item>
          <!-- .. -->
        </drugInteraction>
        <inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/>
        <toxicity xml:lang="en">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.</toxicity>
        <proteinBinding xml:lang="en">99.5% bound to plasma proteins.</proteinBinding>
        <metabolism xml:lang="en">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.</metabolism>
        <genericName xml:lang="en">Sorafenib</genericName>
        <drugType>
          <item xml:lang="en">investigational</item>
          <item xml:lang="en">approved</item>
        </drugType>
        <description xml:lang="en">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.
Sorafenib 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.</description>
      </item>
    </exactMatch>
    <inDataset href="http://www.conceptwiki.org"/>
  </primaryTopic>
  <activeLens>Default</activeLens>
  <linkPredicate href="http://www.w3.org/2004/02/skos/core#exactMatch"/>
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  <definition href="https://beta.openphacts.org/api-config"/>
</result>
@prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix skos:  <http://www.w3.org/2004/02/skos/core#> .
@prefix void:  <http://rdfs.org/ns/void#> .
@prefix foaf:  <http://xmlns.com/foaf/0.1/> .
@prefix ns0:  <http://www.openphacts.org/api#> .
@prefix ns1:  <http://bio2rdf.org/> .
@prefix ns2:  <http://rdf.ebi.ac.uk/terms/chembl#> .
@prefix chembl1336:  <http://rdf.ebi.ac.uk/resource/chembl/molecule/CHEMBL1336#> .
@prefix linked-data:  <http://purl.org/linked-data/api/vocab#> .
@prefix msg0:  <http://www.openphacts.org/api/> .

<http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5>
        skos:exactMatch        <http://aers.data2semantics.org/resource/drug/NEXAVAR> ;
        skos:exactMatch        <http://aers.data2semantics.org/resource/drug/SORAFENIB> ;
        skos:exactMatch        <http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5> ;
        skos:exactMatch        <http://bio2rdf.org/drugbank:DB00398> ;
        skos:exactMatch        <http://rdf.ebi.ac.uk/resource/chembl/molecule/CHEMBL1336> ;
        skos:exactMatch        <http://ops.rsc.org/OPS379634> ;
        skos:prefLabel         "Sorafenib"@en ;
        void:inDataset         <http://www.conceptwiki.org> ;
        foaf:isPrimaryTopicOf  <https://beta.openphacts.org/1.5/compound?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5&app_id=161aeb7d&app_key=bbcba81896020f0b95e3dd35b55e3345&_format=ttl> .

<https://beta.openphacts.org/1.5/compound?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5&app_id=161aeb7d&app_key=bbcba81896020f0b95e3dd35b55e3345&_format=ttl>
        foaf:primaryTopic       <http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5> ;
        linked-data:definition  <https://beta.openphacts.org/api-config> ;
        msg0:activeLens         "Default" ;
        void:linkPredicate      skos:exactMatch ;
        linked-data:extendedMetadataVersion  <https://beta.openphacts.org/1.5/compound?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5&app_id=161aeb7d&app_key=bbcba81896020f0b95e3dd35b55e3345&_format=ttl&_metadata=all%2Cviews%2Cformats%2Cexecution%2Cbindings%2Csite> .

<http://ops.rsc.org/OPS379634>
        void:inDataset      <http://ops.rsc.org> ;
        ns0:smiles          "CNC(=O)C1=NC=CC(=C1)OC2=CC=C(C=C2)NC(=O)NC3=CC(=C(C=C3)Cl)C(F)(F)F" ;
        ns0:inchi           "InChI=1S/C21H16ClF3N4O3/c1-26-19(30)18-11-15(8-9-27-18)32-14-5-2-12(3-6-14)28-20(31)29-13-4-7-17(22)16(10-13)21(23,24)25/h2-11H,1H3,(H,26,30)(H2,28,29,31)" ;
        ns0:inchikey        "MLDQJTXFUGDVEO-UHFFFAOYSA-N" ;
        ns0:logp            "5.158"^^<http://www.w3.org/2001/XMLSchema#double> ;
        ns0:hba             "7.0"^^<http://www.w3.org/2001/XMLSchema#double> ;
        ns0:hbd             "3.0"^^<http://www.w3.org/2001/XMLSchema#double> ;
        ns0:ro5_violations  "1.0"^^<http://www.w3.org/2001/XMLSchema#double> ;
        ns0:psa             "92.35"^^<http://www.w3.org/2001/XMLSchema#double> ;
        ns0:rtb             "5.0"^^<http://www.w3.org/2001/XMLSchema#double> ;
        ns0:molweight       "464.825"^^<http://www.w3.org/2001/XMLSchema#double> ;
        ns0:molformula      "C21H16ClF3N4O3" .

<http://bio2rdf.org/drugbank_resource:DB00398_DB00755>
        void:inDataset       <http://www.openphacts.org/bio2rdf/drugbank> ;
        ns0:interactingDrug  <http://bio2rdf.org/drugbank:DB00755> ;
        <http://bio2rdf.org/drugbank_vocabulary:text>  "DDI between Sorafenib and Tretinoin - The strong CYP2C8 inhibitor, Sorafenib, may decrease the metabolism and clearance of oral Tretinoin. Consider alternate therapy or monitor for changes in Tretinoin effectiveness and adverse/toxic effects if Sorafenib is initiated, discontinued to dose changed."@en .

<http://bio2rdf.org/drugbank_resource:DB00398_DB00958>
        void:inDataset       <http://www.openphacts.org/bio2rdf/drugbank> ;
        ns0:interactingDrug  <http://bio2rdf.org/drugbank:DB00958> ;
        <http://bio2rdf.org/drugbank_vocabulary:text>  "DDI between Sorafenib and Carboplatin - Sorafenib may enhance the adverse/toxic effect of carboplatin. Concurrent use of sorafenib with carboplatin and placlitaxel in patients with squamous cell lung cancer is contraindicated. The use of this combination in other settings is not specifically contraindicated, but any such use should be approached with added caution."@en .

<http://bio2rdf.org/drugbank_resource:DB00398_DB06414>
        void:inDataset       <http://www.openphacts.org/bio2rdf/drugbank> ;
        ns0:interactingDrug  <http://bio2rdf.org/drugbank:DB06414> ;
        <http://bio2rdf.org/drugbank_vocabulary:text>  "DDI between Sorafenib and Etravirine - Sorafebib, when used concomitantly with etravirine, may experience a decrease in serum concentration. It is recommended to avoid concurrent therapy."@en .

<http://aers.data2semantics.org/resource/drug/NEXAVAR>
        skos:prefLabel            "NEXAVAR" ;
        void:inDataset            <http://aers.data2semantics.org/> ;
        ns0:reportedAdverseEvent  <http://aers.data2semantics.org/resource/diagnosis/HEAD_INJURY> ;
        ns0:reportedAdverseEvent  <http://aers.data2semantics.org/resource/diagnosis/SUPRAVENTRICULAR_TACHYCARDIA> ;
        ns0:reportedAdverseEvent  <http://aers.data2semantics.org/resource/diagnosis/SWOLLEN_TONGUE> ;
        # ...  
        ns0:reportedAdverseEvent  <http://aers.data2semantics.org/resource/diagnosis/APHAGIA> ;
        ns0:reportedAdverseEvent  <http://aers.data2semantics.org/resource/diagnosis/LIVER_FUNCTION_TEST_ABNORMAL> .

<http://aers.data2semantics.org/resource/drug/SORAFENIB>
        skos:prefLabel            "SORAFENIB" ;
        void:inDataset            <http://aers.data2semantics.org/> ;
        ns0:reportedAdverseEvent  <http://aers.data2semantics.org/resource/diagnosis/CARDIAC_FAILURE_ACUTE> ;
        ns0:reportedAdverseEvent  <http://aers.data2semantics.org/resource/diagnosis/RENAL_IMPAIRMENT> ;
        ns0:reportedAdverseEvent  <http://aers.data2semantics.org/resource/diagnosis/HYPERURICAEMIA> ;
        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 .

Data loading

The identity problem

Are These Two Molecules The Same(*)?

*Really: Is it sensible to combine data associated with these two molecules?

ims ConceptWiki ConceptWiki Uniprot Uniprot ConceptWiki--Uniprot ConceptWiki--Uniprot ConceptWiki--Uniprot HMDB HMDB ConceptWiki--HMDB ChEBI ChEBI ConceptWiki--ChEBI Chembl_Compound Chembl_Compound ConceptWiki--Chembl_Compound ConceptWiki--Chembl_Compound Chemspider Chemspider ConceptWiki--Chemspider DrugBank DrugBank ConceptWiki--DrugBank ConceptWiki--DrugBank ConceptWiki--DrugBank DrugBank_Target DrugBank_Target ConceptWiki--DrugBank_Target Enzyme_Nomenclature Enzyme_Nomenclature ConceptWiki--Enzyme_Nomenclature Bioontology_MESH Bioontology_MESH ConceptWiki--Bioontology_MESH ConceptWiki--Bioontology_MESH ConceptWiki--Bioontology_MESH ConceptWiki--Bioontology_MESH Bioontology_UMLS_NCIM Bioontology_UMLS_NCIM ConceptWiki--Bioontology_UMLS_NCIM ConceptWiki--Bioontology_UMLS_NCIM ConceptWiki--Bioontology_UMLS_NCIM ConceptWiki--Bioontology_UMLS_NCIM Protein_Data_Bank Protein_Data_Bank ConceptWiki--Protein_Data_Bank ConceptWiki--Protein_Data_Bank Protein_Data_Bank_Ligand Protein_Data_Bank_Ligand ConceptWiki--Protein_Data_Bank_Ligand GeneOntology GeneOntology ConceptWiki--GeneOntology WikiPathways WikiPathways ConceptWiki--WikiPathways Ensembl Ensembl Ensembl--Ensembl Ensembl--Ensembl Ensembl--Uniprot Ensembl--Enzyme_Nomenclature Ensembl--Protein_Data_Bank BioGrid BioGrid Ensembl--BioGrid Embl Embl Ensembl--Embl FlyBase FlyBase Ensembl--FlyBase GenBank GenBank Ensembl--GenBank HGNC_Accession_number HGNC_Accession_number Ensembl--HGNC_Accession_number InterPro InterPro Ensembl--InterPro IPI IPI Ensembl--IPI Entrez_Gene Entrez_Gene Ensembl--Entrez_Gene Locus_Reference_Genomic Locus_Reference_Genomic Ensembl--Locus_Reference_Genomic Ensembl--Locus_Reference_Genomic MGI MGI Ensembl--MGI mirBase_sequence mirBase_sequence Ensembl--mirBase_sequence MEROPS MEROPS Ensembl--MEROPS Orphanet Orphanet Ensembl--Orphanet RefSeq RefSeq Ensembl--RefSeq RGD RGD Ensembl--RGD Rfam Rfam Ensembl--Rfam UniParc UniParc Ensembl--UniParc ZFIN ZFIN Ensembl--ZFIN Uniprot--Ensembl Chembl_Target_Components Chembl_Target_Components Uniprot--Chembl_Target_Components Uniprot--Protein_Data_Bank Uniprot--FlyBase Uniprot--IPI Uniprot--Entrez_Gene Uniprot--MGI Uniprot--RefSeq Uniprot--RGD Uniprot--ZFIN Drugbank_Target_v4 Drugbank_Target_v4 Uniprot--Drugbank_Target_v4 SGD SGD Uniprot--SGD OMIM OMIM Uniprot--OMIM UniGene UniGene Uniprot--UniGene WormBase WormBase Uniprot--WormBase Drugbank Drugbank AERS AERS Drugbank--AERS CAS CAS HMDB--CAS KEGG KEGG HMDB--KEGG PubChem PubChem HMDB--PubChem Wikipedia Wikipedia HMDB--Wikipedia Chembl_Target_Component Chembl_Target_Component Chembl_Target_Components--Chembl_Target_Component Bioontology_UMLS_NCIM--Bioontology_MESH Human_Disease_Ontology Human_Disease_Ontology Bioontology_UMLS_NCIM--Human_Disease_Ontology Pathway_Ontology Pathway_Ontology WikiPathways--Pathway_Ontology HGNC HGNC HGNC_Accession_number--HGNC OPS_CRS OPS_CRS OPS_CRS--HMDB OPS_CRS--ChEBI OPS_CRS--Chembl_Compound OPS_CRS--Chemspider OPS_CRS--DrugBank OPS_CRS--Bioontology_MESH OPS_CRS--OPS_CRS OPS_CRS--OPS_CRS OPS_CRS--OPS_CRS OPS_CRS--OPS_CRS OPS_CRS--OPS_CRS OPS_CRS--OPS_CRS

Following transitives

VoID linkset descriptions

: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 .

How do we find those identifiers?

Next: ops-search

API: Text Query to URI

ElasticSearch-based

Indexes triple stores by SPARQL

Selects label-like properties

 

TODO: Integrate with Identity mapping service

How do we load data?

Manual ad-hoc approach

Dataset update - Mirror and load RDF @dev

Ontology changes - Edit queries

URI changes -  Update linksets and IMS

Manual testing - does it still integrate?

Next: Maven data builds

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>

Continuous data integration

Running Open PHACTS on Docker

Docker overview

Linux container technology

Download images from Docker Hub

 

Philosophy: One application per container

 

ops-docker

%3 rdf RDF/SPARQL (Virtuoso) ims Identity Mapping Service mysql mySQL ims->mysql web Explorer api Linked Data API web->api api->rdf api->ims rsc Chemical Structure Search api->rsc conceptwiki Identity Resolution Service (ConceptWiki) api->conceptwiki

Docker Compose

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

2015-09-18 Open PHACTS architecture

By Stian Soiland-Reyes

2015-09-18 Open PHACTS architecture

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