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<!DOCTYPE html>
<html>
<title>DEBBIE Project</title>
<meta charset="UTF-8">
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<body>
<!-- Navbar (sit on top) -->
<div class="top">
  <div class="w3-bar w3-white w3-wide w3-padding w3-card">
    <img src="images/flyer.png" width="60" height="60"></a>
    <!-- Float links to the right. Hide them on small screens -->
    <div class="w3-right">
      <a href="https://projectdebbie.github.io/#about" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">About</a>
      <a href="https://bioportal.bioontology.org/ontologies/DEB" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">Ontology</a>
      <a href="https://debbie.bsc.es/search/" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">Database</a>
      <a href="https://github.com/ProjectDebbie" class="w3-bar-item w3-button w3-padding-16">GitHub</a>
      <a href="https://projectdebbie.github.io/documentation.html" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">Documentation</a>
      <a href="https://projectdebbie.github.io/#research" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">Research&Team</a>
      <a href="https://projectdebbie.github.io/contact.html" class="w3-bar-item w3-button w3-padding-16">Contact</a>
    </div>
  </div>
</div>
<br>
<!-- Header -->
<header class="w3-display-container w3-content w3-wide w3-center" style="max-width:1245px; min-width:1245px;" id="home">
  <img class="w3-image w3-center" style="border-radius: 25px;" src="images/Debbie_long.png" alt="Debbie_img">
</header>

<!-- Page content max-width:1564px -->
<div class="w3-content w3-padding w3-white" style="max-width:1300px; min-width: 1300px;">

  <!-- About Section -->
  <div class="w3-container w3-padding-16 w3-white" id="about" >
    <h2 class="w3-border-bottom w3-border-light-grey w3-padding-16">About</h2>
    <p>The Database of Experimental Biomaterials and their Biological Effect (DEBBIE) was an <a href="https://cordis.europa.eu/project/id/751277"> EU Horizon 2020 funded project </a> to develop an open access database of
            biomaterials automatically curated from the scientific literature. DEBBIE
            was designed to facilitate a more efficient access to the large literature in the field, generate
            a comprehensive map of research activity and findings, and enable evidence-based selection of materials for
            medical applications.
    </p>
    <p>Beyond the development of database, the project was dedicated to the creation, adaptation and optimization of
            text mining tools for the biomaterials domain. These tools, including the DEBBIE retrieval and annotation
            pipeline (see illustration below), are openly available for download and use through the
            project’s <a href="https://github.com/ProjectDebbie/DEBBIE_pipeline"> GitHub repositories</a>.
    </p>
    <br>
    <center><img class="w3-image w3-center w3-padding-16" src="images/Biocuration_pipeline_20200123.png" alt="Pipeline" width="650" height="300"></center>
  </div>
  <br>
   <!-- Ontology Section -->
  <div class="w3-container w3-padding-16" style="border-radius: 25px; background-color: #F7F7F7;" id="ontology">
    <h2 class="w3-border-bottom w3-border-light-grey w3-padding-16"">Ontology</h2>
    <p> <a href="https://bioportal.bioontology.org/ontologies/DEB">The Devices, Experimental scaffolds and
    Biomaterials Ontology (DEB)</a> is an open resource for organizing information about biomaterials,
    their design, manufacture and biological testing. It was developed using text analysis for identifying
    ontology terms from a biomaterials gold standard corpus, systematically curated to represent the domain’s lexicon.
    Topics covered by DEB were validated by members of the biomaterials research community.
    </p>
    <p>DEB may be used
    for searching terms, performing annotations for machine learning applications, standardized meta-data indexing
    and other cross-disciplinary data exploitation.
    If you are a biomaterials scientist, we encourage and welcome your input to this effort! You can flag new terms, definitions and errors through
    the 'issues' tab in <a href="https://github.com/ProjectDebbie/Ontology_DEB"> DEB's GitHub repository</a>.
        <br>
        <br>
        <p>In addition, below you can find the static and dynamic visualization of the ontology.</p>
        <br>
        <div class="w3-row-padding">
          <div class="w3-col l6 m6 w3-margin-bottom w3-margin-top">
            <div class="w3-display-container w3-center">
              <a href="http://owlgred.lumii.lv/online_visualization/pbqt"><img src="images/static_ontology.png" alt="static" style="height:300px; border:1px solid #021a40;"></a>
              <center><p>Static Visualization on <a href="http://owlgred.lumii.lv/online_visualization/pbqt">OWLGrEd</a></p></center>
            </div>
          </div>
          <div class="w3-col l6 m6 w3-margin-bottom w3-margin-top">
            <div class="w3-display-container w3-center">
              <a href="http://visualdataweb.de/webvowl/#iri=https://raw.githubusercontent.com/ProjectDebbie/Ontology_DEB/20191001/DEB_20191001.owl"><img src="images/dynamic.png" alt="dynamic" style=" height:300px; filter:brightness(110%);border:1px solid #021a40;" ></a>
              <center><p>Dynamic Visualization on <a href="http://visualdataweb.de/webvowl/#iri=https://raw.githubusercontent.com/ProjectDebbie/Ontology_DEB/20191001/DEB_20191001.owl">WebVOWL</a></p></center>
            </div>
          </div>
        </div>
    </p>
  </div>
    <!-- Database Section -->
  <div class="w3-container w3-padding-16" id="database">
    <h2 class="w3-border-bottom w3-border-light-grey w3-padding-16">Database</h2>
    <p>
      An experimental version of DEBBIE is now openly available for browsing. It is still under development,
        but we consider it a minimal viability product and are welcoming the feedback and comments of the
                                                                   research community.
    </p>
    <p>
      The current version of the database contains abstracts automatically retrieved from PubMed,
         which were classified as ‘relevant’ to the areas of implants, medical devices, and experimental scaffolds.
           The abstracts were then annotated using our novel
         <a href="https://github.com/ProjectDebbie/Biomaterials_annotator"> data model </a> which includes multiple
         lexical resources. The annotations are finally stored a NoSQL database, with each of the annotated concept
           labelled by one or more of the following categories:
    </p>
      <!-- list of superclasses -->
      <ul class="list" style="padding-left: 150px;">
      <!--row 1 -->
        <li>Biomaterial</li>
        <li>Medical Application</li>
        <li>Study Type</li>
      <!--row 2 -->
        <li>Manufactured Object</li>
        <li>Associated Biological Process</li>
        <li>Tissue Type</li>
      <!--row 3 -->
        <li>Structure</li>
        <li>Effect on Biological System</li>
        <li>Cell Type</li>
      <!--row 4 -->
        <li>Material Processing</li>
        <li>Adverse Effects</li>
        <li>Animal Model</li>
      <!--row 5 -->
        <li>Manufactured Object Features</li>
        <li>Biologically Active Substance</li>
        <li>Research Technique</li>
      </ul>
    <p>
    Users can access the information with a simple and highly institutive keyword search through the following link:
    </p>
  <br>
    <center><button style="background-color:#3995F9;font-size:20px;color:white; padding: 10px 32px;
  text-align: center;"><a href="http://debbie.bsc.es/search/">DEBBIE Database</a></button></center>
  </div>
  <br>
  <br>

<!-- Research Section -->
<div class="w3-container w3-padding-16" style="border-radius: 25px; background-color: #F7F7F7;" id="research">
    <h2 class="w3-border-bottom w3-border-light-grey w3-padding-16">Research</h2>
    <div class="w3-row-padding">
      <div class="w3-col l3 s3 m3 w3-margin-bottom w3-center">
        <a href="https://towardsdatascience.com/could-data-analysis-prevent-unnecessary-suffering-lessons-to-learn-from-the-vaginal-mesh-scandal-793086d6bbcc"><img src="images/veg_mesh_word_cloud.png" alt="osnat_medium_article1" style="width:95%"></a>
        <p><a href="https://towardsdatascience.com/could-data-analysis-prevent-unnecessary-suffering-lessons-to-learn-from-the-vaginal-mesh-scandal-793086d6bbcc">Could data analysis prevent unnecessary suffering? Lessons to learn from the vaginal mesh scandal.</a></p>
        <p class="w3-opacity">Medium, December 2019</p>
      </div>
      <div class="w3-col l3 s3 m3 w3-margin-bottom w3-center">
        <a href="https://onlinelibrary.wiley.com/doi/10.1002/adfm.201909910"><img src="images/TOC_20200209.png" alt="osnat_medium_article1" style="width:90%"></a>
        <p><a href="https://onlinelibrary.wiley.com/doi/10.1002/adfm.201909910">The Devices, Experimental Scaffolds, and Biomaterials Ontology (DEB): A Tool for Mapping, Annotation, and Analysis of Biomaterials' Data</a></p>
        <p class="w3-opacity">Advanced Functional Materials, February 2020</p>
      </div>
      <div class="w3-col l3 s3 m3 w3-margin-bottom w3-center">
        <a href="https://www.nature.com/articles/s41578-020-0215-z"><img src="images/nature0820.jpeg" alt="osnat_medium_article1" style="width:85%"></a>
        <p><a href="https://www.nature.com/articles/s41578-020-0215-z">Time to kick-start text mining for biomaterials</a></p>
        <p class="w3-opacity">Nature Reviews Materials, August 2020</p>
      </div>
      <div class="w3-col l3 s3 m3 w3-margin-bottom w3-center">
        <a href="https://www.aclweb.org/anthology/2021.sdp-1.5/"><img src="images/Biomaterials_Annotator.png" alt="osnat_medium_article1" style="width:103%"></a>
        <p><a href="https://www.aclweb.org/anthology/2021.sdp-1.5/">The Biomaterials Annotator: a system for ontology-based concept annotation of biomaterials text</a></p>
        <p class="w3-opacity">Association for Computational Linguistics, June 2021</p>
      </div>
      <div class="w3-col l3 m3 s3 w3-margin-bottom">
      </div>
      <div class="w3-col l3 m3 s3 w3-margin-bottom">
      </div>
    </div>
</div>

<!-- Team Section -->
  <div class="w3-container w3-padding-16" id="team">
    <h2 class="w3-border-bottom w3-border-light-grey w3-padding-16">Team</h2>
  <div class="w3-row-padding">
    <div class="w3-col l3 m3 s3 w3-margin-bottom w3-center">
      <img src="images/osnat_hakimi.jpg" alt="Osnat" style="width:70%;">
      <h3>Osnat Hakimi</h3>
      <p class="w3-opacity">Project Leader</p>
      <p>Osnat is a Bosch-Aymerich tenure tracked fellow at the Universitat Internacional de Catalunya and a visitor to the Barcelona Supercomputing Center</p>
      <!--<p><button class="w3-button w3-blue w3-block">Contact</button></p> -->
      <p class="w3-opacity"></p>
    </div>
    <div class="w3-col l3 m3 s3 w3-margin-bottom w3-center">
      <img src="images/javi.jpeg" alt="javi" style="width:68%">
      <h3>Javier Corvi</h3>
      <p class="w3-opacity">Bioinformatics Researcher</p>
      <p>Javi is a Research Engineer at the Barcelona Supercomputing Center</p>
      <p class="w3-opacity"></p>
    </div>
    <div class="w3-col l3 m3 s3 w3-margin-bottom w3-center">
      <img src="images/austin.jpg" alt="austin" style="width:70%">
      <h3>Austin McKitrick</h3>
      <p class="w3-opacity">Research Assistant</p>
      <p>Austin is a Masters Student in Bioinformatics for Health Sciences at Universitat Pompeu Fabra (UPF) in Barcelona</p>
      <p class="w3-opacity"></p>
    </div>
    <div class="w3-col l3 m3 s3 w3-margin-bottom w3-center">
      <img src="images/CFL_square.jpg" alt="carla" style="width:68%">
      <h3>Carla V. Fuenteslópez</h3>
      <p class="w3-opacity">Collaborator</p>
      <p>Carla is a DPhil Student studying Engineering Science at the University of Oxford</p>
      <p class="w3-opacity"></p>
    </div>
  </div>
</div>

<div class="w3-container w3-padding-16" id="team">
    <h2 class="w3-border-bottom w3-border-light-grey w3-padding-16">Scientific Advisors</h2>
  <div class="w3-row-padding">
    <div class="w3-col l3 m3 s3 w3-margin-bottom w3-center">
      <img src="images/MPGinebra.jpeg" alt="osnat" style="width:70%;">
      <h3>Maria-Pau Ginebra</h3>
      <p>Maria-Pau leads the Department of Materials Science and Engineering at the Universitat Politècnica de Catalunya</p>
      <!--<p><button class="w3-button w3-blue w3-block">Contact</button></p> -->
      <p class="w3-opacity"></p>
    </div>
    <div class="w3-col l3 m3 s3 w3-margin-bottom w3-center">
      <img src="images/MKrallinger.jpeg" alt="austin" style="width:70%">
      <h3>Martin Krallinger</h3>
      <p>Martin leads the Text Mining Unit at the Barcelona Supercomputing Center</p>
      <p class="w3-opacity"></p>
    </div>
    <div class="w3-col l3 m3 s3 w3-margin-bottom w3-center">
      <img src="images/Gelpi.jpeg" alt="carla" style="width:70%;">
      <h3>Josep Gelpi</h3>
      <p>Josep leads the Computational Team for the National Institute of Bioinformatics at the Barcelona Supercomputing Center</p>
      <p class="w3-opacity"></p>
    </div>
    <div class="w3-col l3 m3 s3 w3-margin-bottom w3-center">
      <img src="images/AlexPerera.jpeg" alt="javi" style="width:67%;">
      <h3>Alexandre Perera Lluna</h3>
      <p>Alexandre leads the Bioinformatics and Biomedical Signals Laboratory (B2S) at the Universitat Politècnica de Catalunya</p>
      <p class="w3-opacity"></p>
    </div>
  </div>
</div>


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 <p> This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 751277
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