Open PHACTS

Architecture and
Docker install

 

Stian Soiland-Reyes, University of Manchester

http://orcid.org/0000-0001-9842-9718

@soilandreyes

Big Data Europe Webinar, 2016-07-06

This work has been done as part of the BioExcel CoE (www.bioexcel.eu),

a project funded by the EC H2020 program, EINFRA-5-2015 contract number 675728

Bringing together pharmacological data resources

in an integrated, interoperable infrastructure

Data sources integrated and linked together so that you can easily see the relationships between compounds, targets, pathways, diseases and tissues.

ChEBI, ChEMBL, ChemSpider, ConceptWiki, DisGeNET, DrugBank, FAERS, Gene Ontology, neXtProt, SureChEMBL, UniProt, WikiPathways

Data integration

Re-exposed as public API

{
 "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",
  "definition": "https://beta.openphacts.org/api-config",
  "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=json&_metadata=all%2Cviews%2Cformats%2Cexecution%2Cbindings%2Csite",
  "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"
  }
 }
}
<?xml version="1.0" encoding="utf-8"?>
<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"/>
  <extendedMetadataVersion 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&_metadata=all%2Cviews%2Cformats%2Cexecution%2Cbindings%2Csite"/>
  <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 .

Architecture

API architecture

Data loading

Linux Container technology

..light-weight "virtual" virtual machine

 

A container is started from a image

 

Images downloaded from Docker Hub

 

Dockerfile: Layer-based recipe

 

Philosophy: One service, one image → microservices

 

Cloud's best friend: scalable, reproducible, customizable

ops-docker

Docker Compose

Which images to download

 

Which data volumes to use

 

Which network ports are exposed

 

How are containers linked

 

How to start/stop the containers

$ docker-compose up -d
# Open PHACTS platform
# Docker Compose configuration

explorer:
  image: openphacts/explorer2
  ports:
    - "3001:3000"
  links:
    - api
  environment:
    - API_URL=http://localhost:3002
  #restart: always

api:
  image: openphacts/ops-linkeddataapi
  ports:
    - "3002:80"
  links:
    - ims
    - memcached
    - virtuoso:sparql

# SPARQL server
virtuoso:
  build: virtuoso-ops
  ports:
    - "3003:8890"
  volumes_from:
    - virtuosodata

virtuosodata:
  image: busybox
  volumes:
    - /virtuoso

mysqldata:
  image: busybox
  volumes:
    - /var/lib/mysql


mysql:
  image: mysql
  volumes_from:
    - mysqldata
  environment:
    - MYSQL_ROOT_PASSWORD=uCie0ahgah
    - MYSQL_DATABASE=ims
    - MYSQL_USER=ims
    - MYSQL_PASSWORD=ims

ims:
  image: openphacts/identitymappingservice
  ports:
    - "3004:8080"
  links:
    - mysql

memcached:
  image: memcached


mysqlstaging:
  container_name: ops-mysqlstaging
  image: openphacts/identitymappingservice-staging
  links:
    - mysql

# Populate RDF from virtuoso backup download
virtuosostaging:
  build: virtuosodata-frombackup
  volumes_from:
    - virtuosodata

# To customize RDF dataloading, comment OUT the above 'virtuosostaging' block,
# uncomment the below block, and then run
# docker-compose up -d virtuosostagingrdf
#
## BEGIN custom loading

### Download from data.openphacts.org
#openphactsrdf:
#  build: openphacts-rdf
#  volumes:
#    # To specify alternative data folder, use instad:
#    # - /media/big-SSD/download:/download
#    # - /media/big-SSD/staging:/staging
#    - /download
#    - /staging
#    # /download
#
### Load into virtuoso
#virtuosostagingrdf:
#  build: virtuosodata-fromrdf
#  volumes_from:
#    - virtuosodata
#    - openphactsrdf

### END custom loading



## Future services

#elasticsearch:
#  container_name: ops-elasticsearch
#  image: elasticsearch
##  TODO: Data loading
#ops-search:
# container_name: ops-search
# image: openphacts/ops-search

Data staging

Docker and data?

Docker Hub maximum image size: 10 GB

Open PHACTS data (compressed): ~30 GB

Open PHACTS data (installed): ~200 GB

 

Solution: Added staging Docker containers

Download from https://data.openphacts.org/

Verify consistency

Import into Virtuso and mySQL

data.openphacts.org

RDF datasets

RDF linksets

VoID metadata/provenance

 

mySQL-imported linksets

Virtuoso-imported datasets

 

→ Maven repository

release data as software

→Research Objects

propagate metadata

Try it!

Hardware requirements:

  • 150 GB of disk space (ideal: 250 GB)
  • 16 GB of RAM (ideal: 128 GB)
  • 4 CPU core (ideal: 8 cores)

 

Prerequisites:

What do I need?

Follow the GitHub tutorial exactly, customize later

 

Install latest Docker and Docker Compose

 

Just testing on Windows or OS X?

.. modify Docker's Linux VM to have enough disk and memory

 

Firewall? Different settings depend on your firewall details. 

 

Don't worry - Docker is containerized!

..you won't break your machine

Don't jump ahead..

Get the software

curl -L https://github.com/openphacts/ops-docker/archive/master.tar.gz | tar xzv
cd ops-docker-master
sudo docker-compose pull

Get the data

$ sudo docker-compose up --no-recreate -d mysqlstaging virtuosostaging

$ sudo docker-compose logs mysqlstaging virtuosostaging
ops-mysqlstaging | mySQL staging finished
ops-mysqlstaging exited with code 0

ops-virtuosostaging | 09:13:35 --> Backup file # 675 [0x3F02-0x74-0x8A]
ops-virtuosostaging | 09:13:36 --> Backup file # 676 [0x3F02-0x74-0x8A]
ops-virtuosostaging | 09:13:37 End of restoring from backup, 6751701 pages
ops-virtuosostaging | 09:13:37 Server exiting
ops-virtuosostaging | Loading completed
ops-virtuosostaging exited with code 0

Start the services

$ sudo docker-compose up --no-recreate -d
$ sudo docker-compose logs --tail=5

Using the services

http://localhost:3001/  Explorer

http://localhost:3002/  API

http://localhost:3003/  SPARQL

http://localhost:3004/QueryExpander Identity Mapping

What's next?

Custom data staging

Different Open PHACTS 2.1 licensing options:

 

Non-Commercial users: Everything

Commercial users: No DrugBank, partial SureChembl

Open PHACTS members: Full SureChembl

Microservices pr dataset

Most queries have separate fragments per dataset

..which could be executed on separate microservices

Better cloud scalability

Easier to test upgrades of individual datasets

 

But still need "API" layer to do Identity Mapping

and selecting datasets to query

BioExcel Workflow blocks

BioExcel approach: Spin up virtual machine when an Open PHACTS workflow is started

 

Workflow bound dynamically to VM instance(s)

Scalability (exclusive access)

Reproducibility (independent/fixed OPS install)

Tool descriptions - exposed in bio.tools

Customization

Make it easier to add third-party data:

datasets, linksets, queries, API calls

 

..so pharma industry can mix in their in-house data

.. so academics can upgrade and expand datasets

 

More tooling,

more documentation,

or more training?

Feedback

2016-07-06 Open PHACTS Docker

By Stian Soiland-Reyes

2016-07-06 Open PHACTS Docker

  • 1,471
Loading comments...

More from Stian Soiland-Reyes