{% extends "framework_modern.html" %}
{% load static %}

{% block main_content %}
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      <ul>
        <li><a href="/">Home</a></li>
        <li>How to Cite enviPath</li>
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    <!-- Main Content -->
    <div class="bg-base-100 rounded-lg p-8 shadow-xl">
      <h1 class="mb-6 text-4xl font-bold">How to Cite enviPath</h1>

      <div class="prose max-w-none">
        <p class="mb-6 text-lg">
          If you use enviPath in your research, please cite our work. Citations
          help us demonstrate the impact of our platform and support continued
          development and maintenance.
        </p>

        <div class="alert alert-info mb-8">
          <svg
            xmlns="http://www.w3.org/2000/svg"
            fill="none"
            viewBox="0 0 24 24"
            class="h-6 w-6 shrink-0 stroke-current"
          >
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              d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"
            ></path>
          </svg>
          <div>
            <h3 class="font-bold">Quick Reference</h3>
            <div class="text-sm">
              The citation depends on which specific tools or models you used.
              Please cite the relevant publications below.
            </div>
          </div>
        </div>

        <h2 class="mt-8 mb-4 text-2xl font-semibold">Main Platform Citation</h2>
        <p class="mb-4">
          If you use the enviPath platform in general, please cite:
        </p>

        <div class="card bg-base-200 mb-6">
          <div class="card-body">
            <h3 class="mb-2 font-semibold">
              Advancements in biotransformation pathway prediction:
              enhancements, datasets, and novel functionalities in enviPath
            </h3>
            <p class="mb-4 text-sm">
              <strong>Authors:</strong> Hafner, J., Lorsbach, T., Schmidt, S.,
              Brydon, L., Dost, K., Zhang, K., Fenner, K., and Wicker, J.<br />
              <strong>Journal:</strong> Journal of Cheminformatics, 16(1), 93<br />
              <strong>Year:</strong> 2024<br />
              <strong>DOI:</strong>
              <a
                href="https://doi.org/10.1186/s13321-024-00881-6"
                target="_blank"
                class="link link-primary"
                >10.1186/s13321-024-00881-6</a
              >
            </p>
            <div class="collapse-arrow bg-base-300 collapse">
              <input type="checkbox" />
              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
              <div class="collapse-content">
                <pre
                  class="overflow-x-auto text-xs"
                ><code>@ARTICLE{Hafner2024enviPath,
    title     = "Advancements in biotransformation pathway prediction:
                    enhancements, datasets, and novel functionalities in enviPath",
    author    = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and
                    Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner,
                    Kathrin and Wicker, J{\"o}rg",
    journal   = "J. Cheminform.",
    publisher = "Springer Science and Business Media LLC",
    volume    =  16,
    number    =  1,
    pages     = "93",
    month     =  aug,
    year      =  2024,
    doi       = "10.1186/s13321-024-00881-6"
}</code></pre>
              </div>
            </div>
          </div>
        </div>

        <div class="card bg-base-200 mb-6">
          <div class="card-body">
            <h3 class="mb-2 font-semibold">
              enviPath – The environmental contaminant biotransformation pathway
              resource
            </h3>
            <p class="mb-4 text-sm">
              <strong>Authors:</strong> Wicker, J., Lorsbach, T., Gütlein, M.,
              Schmid, E., Latino, D., Kramer, S., Fenner, K.<br />
              <strong>Journal:</strong> Nucleic Acids Research, 44(D1),
              D502-D508<br />
              <strong>Year:</strong> 2016<br />
              <strong>DOI:</strong>
              <a
                href="https://doi.org/10.1093/nar/gkv1229"
                target="_blank"
                class="link link-primary"
                >10.1093/nar/gkv1229</a
              >
            </p>
            <div class="collapse-arrow bg-base-300 collapse">
              <input type="checkbox" />
              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
              <div class="collapse-content">
                <pre
                  class="overflow-x-auto text-xs"
                ><code>@ARTICLE{Wicker2016enviPath,
    title = "enviPath – The environmental contaminant biotransformation pathway resource",
    author = "Wicker, J{\"o}rg and Lorsbach, Tim and Gütlein, Martin and Schmid,
                  Emanuel and Latino, Diogo and Kramer, Stefan and Fenner, Kathrin",
    journal = "Nucleic Acids Research",
    volume = 44,
    number = "D1",
    pages = "D502-D508",
    year = 2016,
    month = jan,
    doi = "10.1093/nar/gkv1229"
}</code></pre>
              </div>
            </div>
          </div>
        </div>

        <h2 class="mt-8 mb-4 text-2xl font-semibold">
          Pathway Prediction System
        </h2>
        <p class="mb-4">
          If you use the pathway prediction functionality, please also cite:
        </p>

        <div class="card bg-base-200 mb-6">
          <div class="card-body">
            <h3 class="mb-2 font-semibold">
              A Hybrid Machine Learning and Knowledge Based Approach to Limit
              Combinatorial Explosion in Biodegradation Prediction
            </h3>
            <p class="mb-4 text-sm">
              <strong>Authors:</strong> Wicker, J., Fenner, K., Kramer, S.<br />
              <strong>Book:</strong> Computational Sustainability, 75-97<br />
              <strong>Year:</strong> 2016<br />
              <strong>DOI:</strong>
              <a
                href="https://doi.org/10.1007/978-3-319-31858-5_5"
                target="_blank"
                class="link link-primary"
                >10.1007/978-3-319-31858-5_5</a
              >
            </p>
            <div class="collapse-arrow bg-base-300 collapse">
              <input type="checkbox" />
              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
              <div class="collapse-content">
                <pre class="overflow-x-auto text-xs"><code>@INBOOK{Wicker2016ML,
    title="A Hybrid Machine Learning and Knowledge Based Approach to
                      Limit Combinatorial Explosion in Biodegradation Prediction",
    author="Wicker, J{\"o}rg and Fenner, Kathrin and Kramer, Stefan",
    editor="L{\"a}ssig, J{\"o}rg and Kersting, Kristian and Morik, Katharina",
    bookTitle="Computational Sustainability",
    year=2016,
    publisher="Springer International Publishing",
    pages="75--97",
    doi="10.1007/978-3-319-31858-5_5"
}</code></pre>
              </div>
            </div>
          </div>
        </div>

        <div class="card bg-base-200 mb-6">
          <div class="card-body">
            <h3 class="mb-2 font-semibold">
              Predictive modeling of biodegradation pathways using transformer
              architectures
            </h3>
            <p class="mb-4 text-sm">
              <strong>Authors:</strong> Brydon, L., Zhang, K., Dobbie, G.,
              Taškova, K., and Wicker, J.<br />
              <strong>Journal:</strong> Journal of Cheminformatics, 17(1), 21<br />
              <strong>Year:</strong> 2025<br />
              <strong>DOI:</strong>
              <a
                href="https://doi.org/10.1186/s13321-025-00969-7"
                target="_blank"
                class="link link-primary"
                >10.1186/s13321-025-00969-7</a
              >
            </p>
            <div class="collapse-arrow bg-base-300 collapse">
              <input type="checkbox" />
              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
              <div class="collapse-content">
                <pre
                  class="overflow-x-auto text-xs"
                ><code>@article{Brydon2025Transformer,
    title = "Predictive modeling of biodegradation pathways using transformer architectures",
    author = "Brydon, Liam and Zhang, Kunyang and Dobbie, Gillian and
                  Ta\v{s}kova, Katerina and Wicker, J{\"o}rg Simon",
    journal = "Journal of Cheminformatics",
    volume = 17,
    number = 1,
    pages = "1--16",
    year = 2025,
    month = feb,
    doi = "10.1186/s13321-025-00969-7",
}</code></pre>
              </div>
            </div>
          </div>
        </div>

        <h2 class="mt-8 mb-4 text-2xl font-semibold">
          Machine Learning Models
        </h2>

        <h3 class="mt-6 mb-3 text-xl font-semibold">
          Relative Reasoning Models
        </h3>
        <p class="mb-4">
          For relative reasoning and machine learning approaches, please cite:
        </p>
        <div class="card bg-base-200 mb-6">
          <div class="card-body">
            <h3 class="mb-2 font-semibold">
              Predicting biodegradation products and pathways: a hybrid
              knowledge- and machine learning-based approach
            </h3>
            <p class="mb-4 text-sm">
              <strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L.,
              Wackett, L., Kramer, S.<br />
              <strong>Journal:</strong> Bioinformatics, 26(6), 814-821<br />
              <strong>Year:</strong> 2010<br />
              <strong>DOI:</strong>
              <a
                href="https://doi.org/10.1093/bioinformatics/btq024"
                target="_blank"
                class="link link-primary"
                >10.1093/bioinformatics/btq024</a
              >
            </p>
            <div class="collapse-arrow bg-base-300 collapse">
              <input type="checkbox" />
              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
              <div class="collapse-content">
                <pre class="overflow-x-auto text-xs"><code>@ARTICLE{Wicker2010,
    title = "Predicting biodegradation products and pathways:
                  a hybrid knowledge- and machine learning-based approach",
    author = "Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Wackett, Larry and Kramer, Stefan",
    journal = "Bioinformatics",
    volume = 26,
    number = 6,
    pages = "814-821",
    year = 2010,
    month = jan,
    doi = "10.1093/bioinformatics/btq024"
}</code></pre>
              </div>
            </div>
          </div>
        </div>

        <div class="card bg-base-200 mb-6">
          <div class="card-body">
            <h3 class="mb-2 font-semibold">
              Data-driven extraction of relative reasoning rules to limit
              combinatorial explosion in biodegradation pathway prediction
            </h3>
            <p class="mb-4 text-sm">
              <strong>Authors:</strong> Fenner, K., Junfeng, G., Kramer, S.,
              Ellis, L., Wackett, L.<br />
              <strong>Journal:</strong> Bioinformatics, 26(18), 2079-2085<br />
              <strong>Year:</strong> 2008<br />
              <strong>DOI:</strong>
              <a
                href="https://doi.org/10.1093/bioinformatics/btn378"
                target="_blank"
                class="link link-primary"
                >10.1093/bioinformatics/btn378</a
              >
            </p>
            <div class="collapse-arrow bg-base-300 collapse">
              <input type="checkbox" />
              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
              <div class="collapse-content">
                <pre
                  class="overflow-x-auto text-xs"
                ><code>@ARTICLE{Fenner2008Reason,
    title = "Data-driven extraction of relative reasoning rules to
                  limit combinatorial explosion in biodegradation pathway prediction",
    author = "Fenner, Kathrin and Gao, Junfeng and Kramer, Stefan and Ellis, Lynda and Wackett, Larry",
    journal = "Bioinformatics",
    volume = 24,
    number = 18,
    pages = "2079-2085",
    year = 2008,
    month = 07,
    doi = "10.1093/bioinformatics/btn378"
}</code></pre>
              </div>
            </div>
          </div>
        </div>

        <h2 class="mt-8 mb-4 text-2xl font-semibold">
          Package-Specific Citations
        </h2>
        <p class="mb-4">
          If you use data from a specific package within enviPath, please also
          acknowledge the package creators and cite any relevant publications
          associated with that package. Package-specific citation information is
          available on each package's detail page.
        </p>

        <h2 class="mt-8 mb-4 text-2xl font-semibold">
          Example Acknowledgment Text
        </h2>
        <p class="mb-4">
          You may use the following text in your acknowledgments section:
        </p>

        <div class="card bg-base-200 mb-6">
          <div class="card-body">
            <p class="text-sm italic">
              "Biotransformation pathway predictions were performed using
              enviPath (<a
                href="https://envipath.org"
                target="_blank"
                class="link link-primary"
                >https://envipath.org</a
              >), a database and prediction system for microbial
              biotransformation of organic environmental contaminants."
            </p>
          </div>
        </div>

        <h2 class="mt-8 mb-4 text-2xl font-semibold">Additional Resources</h2>
        <p class="mb-4">
          For a complete list of publications related to enviPath, please visit:
        </p>
        <ul class="mb-6 list-inside list-disc space-y-2">
          <li>
            <a
              href="https://community.envipath.org/t/envipath-publications/"
              target="_blank"
              class="link link-primary"
            >
              enviPath Community - Publications Section
            </a>
          </li>
        </ul>

        <div class="alert alert-success mt-8">
          <svg
            xmlns="http://www.w3.org/2000/svg"
            fill="none"
            viewBox="0 0 24 24"
            class="h-6 w-6 shrink-0 stroke-current"
          >
            <path
              stroke-linecap="round"
              stroke-linejoin="round"
              stroke-width="2"
              d="M9 12l2 2 4-4m6 2a9 9 0 11-18 0 9 9 0 0118 0z"
            />
          </svg>
          <div>
            <h3 class="font-bold">Thank You!</h3>
            <div class="text-sm">
              Thank you for citing enviPath. Your citations help demonstrate the
              impact of our work and enable us to continue providing this
              resource to the scientific community.
            </div>
          </div>
        </div>

        <div class="divider my-8"></div>

        <h2 class="mt-8 mb-4 text-2xl font-semibold">Questions?</h2>
        <p class="mb-4">
          If you're unsure which papers to cite or have questions about
          citations, please
          <a href="/contact" class="link link-primary">contact us</a> or ask on
          our
          <a
            href="https://community.envipath.org/"
            target="_blank"
            class="link link-primary"
            >community forums</a
          >.
        </p>
      </div>
    </div>
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{% endblock main_content %}