Journal article Open Access

PaccMann: a web service for interpretable anticancer compound sensitivity prediction

Cadow, Joris; Born, Jannis; Manica, Matteo; Oskooei, Ali; Rodríguez Martínez, María


DCAT Export

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:duv="http://www.w3.org/ns/duv#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:frapo="http://purl.org/cerif/frapo/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="http://schema.org/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#">
  <rdf:Description rdf:about="https://zenodo.org/record/3935564">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/3935564</dct:identifier>
    <foaf:page rdf:resource="https://zenodo.org/record/3935564"/>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-4410-2805">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-4410-2805</dct:identifier>
        <foaf:name>Cadow, Joris</foaf:name>
        <foaf:givenName>Joris</foaf:givenName>
        <foaf:familyName>Cadow</foaf:familyName>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0001-8307-5670">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0001-8307-5670</dct:identifier>
        <foaf:name>Born, Jannis</foaf:name>
        <foaf:givenName>Jannis</foaf:givenName>
        <foaf:familyName>Born</foaf:familyName>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-8872-0269">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-8872-0269</dct:identifier>
        <foaf:name>Manica, Matteo</foaf:name>
        <foaf:givenName>Matteo</foaf:givenName>
        <foaf:familyName>Manica</foaf:familyName>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-8318-687X">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-8318-687X</dct:identifier>
        <foaf:name>Oskooei, Ali</foaf:name>
        <foaf:givenName>Ali</foaf:givenName>
        <foaf:familyName>Oskooei</foaf:familyName>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0003-3766-4233">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0003-3766-4233</dct:identifier>
        <foaf:name>Rodríguez Martínez, María</foaf:name>
        <foaf:givenName>María</foaf:givenName>
        <foaf:familyName>Rodríguez Martínez</foaf:familyName>
      </rdf:Description>
    </dct:creator>
    <dct:title>PaccMann: a web service for interpretable anticancer compound sensitivity prediction</dct:title>
    <dct:publisher>
      <foaf:Agent>
        <foaf:name>Zenodo</foaf:name>
      </foaf:Agent>
    </dct:publisher>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2020</dct:issued>
    <frapo:isFundedBy rdf:resource="info:eu-repo/grantAgreement/EC/H2020/826121/"/>
    <schema:funder>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </schema:funder>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2020-05-13</dct:issued>
    <dct:language rdf:resource="http://publications.europa.eu/resource/authority/language/ENG"/>
    <owl:sameAs rdf:resource="https://zenodo.org/record/3935564"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/3935564</skos:notation>
        <adms:schemeAgency>url</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <owl:sameAs rdf:resource="https://doi.org/10.1093/nar/gkaa327"/>
    <dct:isPartOf rdf:resource="https://zenodo.org/communities/ipc"/>
    <dct:description>&lt;p&gt;The identification of new targeted and personalized therapies for cancer requires the fast and accurate assessment of the drug efficacy of potential compounds against a particular biomolecular sample. It has been suggested that the integration of complementary sources of information might strengthen the accuracy of a drug efficacy prediction model. Here, we present a web-based platform for the Prediction of AntiCancer Compound sensitivity with Multimodal Attention-based Neural Networks (PaccMann). PaccMann is trained on public transcriptomic cell line profiles, compound structure information and drug sensitivity screenings, and outperforms state-of-the-art methods on anticancer drug sensitivity prediction. On the open-access web service (https://ibm.biz/paccmann-aas), users can select a known drug compound or design their own compound structure in an interactive editor, perform in-silico drug testing and investigate compound efficacy on publicly available or user-provided transcriptomic profiles. PaccMann leverages methods for model interpretability and outputs confidence scores as well as attention heatmaps that highlight the genes and chemical sub-structures that were more important to make a prediction, hence facilitating the understanding of the model&amp;rsquo;s decision making and the involved biochemical processes. We hope to serve the community with a toolbox for fast and efficient validation in drug repositioning or lead compound identification regimes.&lt;/p&gt;</dct:description>
    <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/>
    <dct:accessRights>
      <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess">
        <rdfs:label>Open Access</rdfs:label>
      </dct:RightsStatement>
    </dct:accessRights>
    <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL rdf:resource="https://doi.org/10.1093/nar/gkaa327">https://doi.org/10.1093/nar/gkaa327</dcat:accessURL>
        <dcat:byteSize>1178327</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/3935564/files/gkaa327_.pdf">https://zenodo.org/record/3935564/files/gkaa327_.pdf</dcat:downloadURL>
        <dcat:mediaType>application/pdf</dcat:mediaType>
      </dcat:Distribution>
    </dcat:distribution>
  </rdf:Description>
  <foaf:Project rdf:about="info:eu-repo/grantAgreement/EC/H2020/826121/">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">826121</dct:identifier>
    <dct:title>individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology</dct:title>
    <frapo:isAwardedBy>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </frapo:isAwardedBy>
  </foaf:Project>
</rdf:RDF>
42
38
views
downloads
Views 42
Downloads 38
Data volume 44.8 MB
Unique views 40
Unique downloads 37

Share

Cite as