https://dev.openphacts.org/

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      "_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.",
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        "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.",
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        "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.",
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       },
       {
        "_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"
       }
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       "prefLabel": "CARDIAC FAILURE ACUTE"
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       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "RENAL IMPAIRMENT"
      },
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       "_about": "http://aers.data2semantics.org/resource/diagnosis/HYPERURICAEMIA",
       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "HYPERURICAEMIA"
      },
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       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "TUMOUR LYSIS SYNDROME"
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       "_about": "http://aers.data2semantics.org/resource/diagnosis/LEFT_VENTRICULAR_DYSFUNCTION",
       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "LEFT VENTRICULAR DYSFUNCTION"
      },
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       "_about": "http://aers.data2semantics.org/resource/diagnosis/METABOLIC_ACIDOSIS",
       "inDataset": "http://aers.data2semantics.org/",
       "prefLabel": "METABOLIC ACIDOSIS"
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     ],
    },
    {
     "_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"
    },
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     "_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"
    }
   ],
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      <item href="http://ops.rsc.org/OPS379634">
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        <prefLabel>NEXAVAR</prefLabel>
        <reportedAdverseEvent>
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            <prefLabel>HEAD INJURY</prefLabel>
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          </item>
          <item href="http://aers.data2semantics.org/resource/diagnosis/SUPRAVENTRICULAR_TACHYCARDIA">
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          <!-- .. -->
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          </item>
          <!-- .. -->
        </drugInteraction>
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        <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>
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        <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>
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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

https://www.docker.com/

ops-docker

https://github.com/openphacts/ops-docker/

Docker Compose

https://docs.docker.com/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

# 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

API architecture

https://github.com/openphacts/ops-docker

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

https://hub.docker.com/r/openphacts/

https://github.com/openphacts/ops-docker

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

https://data.openphacts.org/

https://github.com/openphacts/ops-docker

Start the services

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

http://localhost:3001/  Explorer

http://localhost:3002/ REST API

http://localhost:3003/  SPARQL queries

http://localhost:3004/QueryExpander Identity Mapping

Using Open PHACTS from Workflows

BIOVIA Pipeline Pilot

https://exchange.sciencecloud.com/exchange/browse

Jean-Marc Neefs, Janssen

http://www.openphactsfoundation.org/workflow-tools-for-life-science-research-where-next/

Coming soon to a KNIME node near you

James A. Lumley, Eli Lilly

http://www.commonwl.org/

Common format for pipeline execution
Community-based standards effort
Implemented by multiple workflow engines
Defined with a schema, specification, tests
Designed for shared nothing cluster/cloud
Designed for containers (e.g. Docker)

Main focus: command line tools

#!/usr/bin/env cwl-runner
class: Workflow
inputs:
  - id: pairedEnds
    type:
      - type: array
        items: File
    description: list of files containing the first end of paired end reads in fasta or fastq format
outputs:
  - id: bam
    type: File
    source: "#samindex/bam_with_bai"
steps:
  - id: lobSTR
    run: lobSTR-tool.cwl
    inputs:
      - { id: p1, source: "#pairedEnds" }
      - { id: p2, source: "#p2" }
      - { id: output_prefix, source: "#output_prefix" }
      - { id: reference, source: "#reference" }
      - { id: rg-sample, source: "#rg-sample" }
      - { id: rg-lib, source: "#rg-lib" }
    outputs:
      - { id: bam }
      - { id: bam_stats }

  - id: samsort
    run: samtools-sort.cwl
    inputs:
      - { id: input, source: "#lobSTR/bam" }
      - { id: output_name, default: "aligned.sorted.bam" }
    outputs:
      - { id: output_file }

  - id: samindex
    run: samtools-index.cwl
    inputs:
      - { id: input, source: "#samsort/output_file" }
    outputs:
      - { id: bam_with_bai }

  - id: allelotype
    run: allelotype.cwl
    inputs:
      - { id: bam, source: "#samindex/bam_with_bai" }
      - { id: reference, source: "#reference" }
      - { id: output_prefix, source: "#output_prefix" }
      - { id: noise_model, source: "#noise_model" }
      - { id: strinfo, source: "#strinfo" }
    outputs:
      - { id: vcf }
      - { id: vcf_stats }

https://view.commonwl.org/

http://bioexcel.eu/software/workflows/