forked from enviPath/enviPy
298 lines
10 KiB
HTML
298 lines
10 KiB
HTML
{% extends "framework_modern.html" %}
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{% load static %}
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{% block main_content %}
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<div class="mx-auto max-w-4xl px-4 py-8">
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<!-- Breadcrumbs -->
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<div class="breadcrumbs mb-4 text-sm">
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<ul>
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<li><a href="/">Home</a></li>
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<li>How to Cite enviPath</li>
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</ul>
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</div>
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<!-- Main Content -->
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<div class="bg-base-100 rounded-lg p-8 shadow-xl">
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<h1 class="mb-6 text-4xl font-bold">How to Cite enviPath</h1>
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<div class="prose max-w-none">
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<p class="mb-6 text-lg">
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If you use enviPath in your research, please cite our work. Citations
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help us demonstrate the impact of our platform and support continued
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development and maintenance.
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</p>
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<div class="alert alert-info mb-8">
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<svg
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xmlns="http://www.w3.org/2000/svg"
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fill="none"
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viewBox="0 0 24 24"
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class="h-6 w-6 shrink-0 stroke-current"
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>
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<path
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stroke-linecap="round"
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stroke-linejoin="round"
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stroke-width="2"
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d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"
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></path>
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</svg>
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<div>
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<h3 class="font-bold">Quick Reference</h3>
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<div class="text-sm">
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The citation depends on which specific tools or models you used.
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Please cite the relevant publications below.
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</div>
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</div>
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</div>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">Main Platform Citation</h2>
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<p class="mb-4">
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If you use the enviPath platform in general, please cite:
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</p>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<h3 class="mb-2 font-semibold">
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Advancements in biotransformation pathway prediction:
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enhancements, datasets, and novel functionalities in enviPath
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</h3>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Hafner, J., Lorsbach, T., Schmidt, S.,
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Brydon, L., Dost, K., Zhang, K., Fenner, K., and Wicker, J.<br />
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<strong>Journal:</strong> Journal of Cheminformatics, 16(1), 93<br />
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<strong>Year:</strong> 2024<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1186/s13321-024-00881-6"
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target="_blank"
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class="link link-primary"
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>10.1186/s13321-024-00881-6</a
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>
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</p>
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<div class="collapse-arrow bg-base-300 collapse">
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<input type="checkbox" />
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<div class="collapse-title text-sm font-medium">Show BibTeX</div>
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<div class="collapse-content">
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<pre class="overflow-x-auto text-xs"><code>@ARTICLE{Hafner2024,
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title = "Advancements in biotransformation pathway prediction:
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enhancements, datasets, and novel functionalities in enviPath",
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author = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and
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Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner,
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Kathrin and Wicker, J{\"o}rg",
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journal = "J. Cheminform.",
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publisher = "Springer Science and Business Media LLC",
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volume = 16,
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number = 1,
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pages = "93",
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month = aug,
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year = 2024,
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doi = "10.1186/s13321-024-00881-6"
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}</code></pre>
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</div>
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</div>
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</div>
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</div>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">
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Pathway Prediction System
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</h2>
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<p class="mb-4">
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If you use the pathway prediction functionality, please also cite:
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</p>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<h3 class="mb-2 font-semibold">
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Predicting Biodegradation Pathways Using a Hybrid Relative
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Reasoning Model
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</h3>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L.,
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Kramer, S.<br />
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<strong>Journal:</strong> Biotechnology and Bioengineering,
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110(3), 837-846<br />
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<strong>Year:</strong> 2013<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1002/bit.24744"
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target="_blank"
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class="link link-primary"
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>10.1002/bit.24744</a
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>
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</p>
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<div class="collapse-arrow bg-base-300 collapse">
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<input type="checkbox" />
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<div class="collapse-title text-sm font-medium">Show BibTeX</div>
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<div class="collapse-content">
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<pre
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class="overflow-x-auto text-xs"
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><code>@article{wicker2013predicting,
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title={Predicting biodegradation pathways using a hybrid relative reasoning model},
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author={Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Kramer, Stefan},
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journal={Biotechnology and Bioengineering},
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volume={110},
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number={3},
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pages={837--846},
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year={2013},
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publisher={Wiley Online Library},
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doi={10.1002/bit.24744}
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}</code></pre>
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</div>
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</div>
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</div>
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</div>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">
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Machine Learning Models
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</h2>
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<h3 class="mt-6 mb-3 text-xl font-semibold">
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enviPath-Transformer (Latest ML Model)
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</h3>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<p class="mb-2 text-sm">
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If you use the Transformer-based prediction model, please cite:
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</p>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Brydon, L., Zhang, K., Dobbie, G.,
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Taškova, K., and Wicker, J.<br />
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<strong>Journal:</strong> Journal of Cheminformatics, 17(1), 21<br />
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<strong>Year:</strong> 2025<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1186/s13321-025-00969-7"
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target="_blank"
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class="link link-primary"
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>10.1186/s13321-025-00969-7</a
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>
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</p>
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</div>
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</div>
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<h3 class="mt-6 mb-3 text-xl font-semibold">
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Relative Reasoning Models
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</h3>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<p class="mb-2 text-sm">
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For relative reasoning and machine learning approaches:
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</p>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Fenner, K., Gao, J., Kramer, S., Ellis,
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L., Wackett, L.<br />
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<strong>Journal:</strong> Environmental Science & Technology,
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42(15), 5761-5767<br />
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<strong>Year:</strong> 2008<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1021/es800408g"
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target="_blank"
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class="link link-primary"
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>10.1021/es800408g</a
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>
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</p>
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</div>
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</div>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">
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Package-Specific Citations
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</h2>
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<p class="mb-4">
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If you use data from a specific package within enviPath, please also
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acknowledge the package creators and cite any relevant publications
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associated with that package. Package-specific citation information is
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available on each package's detail page.
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</p>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">
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Example Acknowledgment Text
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</h2>
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<p class="mb-4">
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You may use the following text in your acknowledgments section:
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</p>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<p class="text-sm italic">
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"Biotransformation pathway predictions were performed using
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enviPath (<a
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href="https://envipath.org"
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target="_blank"
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class="link link-primary"
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>https://envipath.org</a
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>), a database and prediction system for microbial
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biotransformation of organic environmental contaminants."
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</p>
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</div>
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</div>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">Additional Resources</h2>
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<p class="mb-4">
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For a complete list of publications related to enviPath, please visit:
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</p>
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<ul class="mb-6 list-inside list-disc space-y-2">
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<li>
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<a
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href="https://community.envipath.org/"
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target="_blank"
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class="link link-primary"
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>
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enviPath Community - Publications Section
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</a>
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</li>
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<li>
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<a
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href="https://wiki.envipath.org/"
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target="_blank"
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class="link link-primary"
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>
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enviPath Documentation - References
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</a>
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</li>
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</ul>
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<div class="alert alert-success mt-8">
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<svg
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xmlns="http://www.w3.org/2000/svg"
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fill="none"
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viewBox="0 0 24 24"
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class="h-6 w-6 shrink-0 stroke-current"
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>
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<path
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stroke-linecap="round"
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stroke-linejoin="round"
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stroke-width="2"
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d="M9 12l2 2 4-4m6 2a9 9 0 11-18 0 9 9 0 0118 0z"
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/>
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</svg>
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<div>
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<h3 class="font-bold">Thank You!</h3>
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<div class="text-sm">
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Thank you for citing enviPath. Your citations help demonstrate the
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impact of our work and enable us to continue providing this
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resource to the scientific community.
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</div>
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</div>
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</div>
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<div class="divider my-8"></div>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">Questions?</h2>
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<p class="mb-4">
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If you're unsure which papers to cite or have questions about
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citations, please
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<a href="/contact" class="link link-primary">contact us</a> or ask on
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our
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<a
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href="https://community.envipath.org/"
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target="_blank"
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class="link link-primary"
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>community forums</a
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>.
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</p>
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</div>
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</div>
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</div>
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{% endblock main_content %}
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