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

{% block main_content %}
  <div class="mx-auto max-w-4xl px-4 py-8">
    <!-- Breadcrumbs -->
    <div class="breadcrumbs mb-4 text-sm">
      <ul>
        <li><a href="/">Home</a></li>
        <li>How to Cite enviPath</li>
      </ul>
    </div>

    <!-- 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"
          >
            <path
              stroke-linecap="round"
              stroke-linejoin="round"
              stroke-width="2"
              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{Hafner2024,
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>

        <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">
              Predicting Biodegradation Pathways Using a Hybrid Relative
              Reasoning Model
            </h3>
            <p class="mb-4 text-sm">
              <strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L.,
              Kramer, S.<br />
              <strong>Journal:</strong> Biotechnology and Bioengineering,
              110(3), 837-846<br />
              <strong>Year:</strong> 2013<br />
              <strong>DOI:</strong>
              <a
                href="https://doi.org/10.1002/bit.24744"
                target="_blank"
                class="link link-primary"
                >10.1002/bit.24744</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{wicker2013predicting,
  title={Predicting biodegradation pathways using a hybrid relative reasoning model},
  author={Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Kramer, Stefan},
  journal={Biotechnology and Bioengineering},
  volume={110},
  number={3},
  pages={837--846},
  year={2013},
  publisher={Wiley Online Library},
  doi={10.1002/bit.24744}
}</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">
          enviPath-Transformer (Latest ML Model)
        </h3>
        <div class="card bg-base-200 mb-6">
          <div class="card-body">
            <p class="mb-2 text-sm">
              If you use the Transformer-based prediction model, please cite:
            </p>
            <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>
        </div>

        <h3 class="mt-6 mb-3 text-xl font-semibold">
          Relative Reasoning Models
        </h3>
        <div class="card bg-base-200 mb-6">
          <div class="card-body">
            <p class="mb-2 text-sm">
              For relative reasoning and machine learning approaches:
            </p>
            <p class="mb-4 text-sm">
              <strong>Authors:</strong> Fenner, K., Gao, J., Kramer, S., Ellis,
              L., Wackett, L.<br />
              <strong>Journal:</strong> Environmental Science & Technology,
              42(15), 5761-5767<br />
              <strong>Year:</strong> 2008<br />
              <strong>DOI:</strong>
              <a
                href="https://doi.org/10.1021/es800408g"
                target="_blank"
                class="link link-primary"
                >10.1021/es800408g</a
              >
            </p>
          </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/"
              target="_blank"
              class="link link-primary"
            >
              enviPath Community - Publications Section
            </a>
          </li>
          <li>
            <a
              href="https://wiki.envipath.org/"
              target="_blank"
              class="link link-primary"
            >
              enviPath Documentation - References
            </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>
  </div>
{% endblock main_content %}