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        <article-title>Finding drugs with common downstream e ects, using direction information in biological pathways</article-title>
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      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Ryan A. Miller</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jonathan Melius</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Nuno Nunes</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Egon L. Willighagen</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Peter Woollard</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Chris T. Evelo</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Computational Biology, GlaxoSmithKline</institution>
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          <addr-line>Stevenage</addr-line>
          ,
          <country country="UK">UK</country>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University</institution>
          ,
          <country country="NL">The Netherlands</country>
        </aff>
        <aff id="aff2">
          <label>2</label>
          <institution>Maastricht Centre for Systems Biology (MaCSBio), Maastricht University</institution>
          ,
          <country country="NL">The Netherlands</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Drugs aim at compensating for a biological process or processes that are not behaving as desired. Drugs frequently do this by binding to proteins in pathways, causing immediate or downstream changes in the pathway a ecting the biological process. WikiPathways is an open resource for curating biological pathways. Interactions in the pathway, capture information that connects biological entities. WikiPathways RDF representation captures the participants of a speci c interaction, the type of interaction (inhibition, stimulation, catalysis, etc.), and also the direction of the interaction. The increasing availability of this directionality enables answering a new class of research questions programmatically. For instance, this knowledge can be used to show how a combination of two drugs a ects common downstream processes. This list of drug combinations with common downstream e ects is important because drug combination therapies may be used to minimize the side e ects of single drug treatments where higher doses need to be administered. We will present work that answers this question by combining data from WikiPathways, ChEMBL, and Uniprot. ChEMBL is used to extend the knowledge base with drug data annotations linking drugs to protein targets in the pathway. While Uniprots endpoint is used to map ChEMBL target information to Uniprot IDs. The interaction directional information de nes what is upstream and downstream in the pathway of the protein targets. Analysis of the combined data results in a list of drug combinations that share common downstream e ects. The analysis was implemented as a series of queries against the SPARQL endpoints of ChEMBL, Uniprot, and WikiPathways.</p>
      </abstract>
      <kwd-group>
        <kwd>Semantic Web</kwd>
        <kwd>biological pathways</kwd>
        <kwd>network extension</kwd>
      </kwd-group>
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