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<!DOCTYPE html>
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<head>
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Phenopackets - Concepts and Technology
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<li class="sidebar-brand">
<a href="#top" onclick=$("#menu-close").click();>
<span>
<img src="site/PhenoPackets_Logo.png" style="height:50px;">
</span>
Phenopackets
</a>
</li>
<li>
<a href="#top" onclick=$("#menu-close").click();>Home</a>
</li>
<li>
<a href="#phenopackets-are" onclick=$("#menu-close").click();>About Phenopackets</a>
<ul>
<li>
<a href="#a-vision" onclick=$("#menu-close").click();>The Vision</a>
</li>
<li>
<a href="#a-technology" onclick=$("#menu-close").click();>The Technology</a>
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<a href="#a-community" onclick=$("#menu-close").click();>The Community</a>
</li>
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<a href="#contact" onclick=$("#menu-close").click();>Contact</a>
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</ul>
</nav>
<header id="top" class="header">
<div class="text-vertical-center">
<img src="site/PhenoPackets_Logo.png" style="margin-top:10px;">
<br>
<br>
<h1>Phenopackets</h1>
<h3><b>Open and Computable Bioinformation</b></h3>
<br>
<br>
<a href="#phenopackets-are" class="btn btn-dark btn-lg">
Learn More
</a>
</div>
</header>
<section id="phenopackets-are" class="services bg-primary">
<div class="container">
<div class="row row-inset">
<div class="col-lg-10 col-lg-offset-1 text-center">
<h2>Phenopackets Are …</h2>
<hr class="small">
<div class="row">
<div class="col-md-4 col-sm-12">
<div class="service-item">
<span class="fa-stack fa-4x">
<a href="#a-vision" class="btn-fa">
<i class="fa fa-circle fa-stack-2x"></i>
<i class="fa fa-lightbulb-o fa-stack-1x text-primary"></i>
</a>
</span>
<h4>
<strong>A Vision</strong>
</h4>
<p>
An open standard for sharing disease and phenotype information will improve
our ability to understand, diagnose, and treat both rare and common diseases.
A Phenopacket links detailed phenotype descriptions with disease, patient, and genetic information, enabling clinicians, biologists, and disease and drug researchers to build more complete models of disease.
The standard is designed to encourage wide adoption and synergy between the people, organizations and systems that comprise the joint effort to address human disease and biological understanding.
</p>
</div>
</div>
<div class="col-md-4 col-sm-12">
<div class="service-item">
<span class="fa-stack fa-4x">
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<i class="fa fa-circle fa-stack-2x"></i>
<i class="fa fa-cogs fa-stack-1x text-primary"></i>
</a>
</span>
<h4>
<strong>A Technology</strong>
</h4>
<p>
Phenopackets are represented as PXF (Phenotype Exchange Format) files, which may be encoded in JSON or YAML. Each packet associates a list of phenotypic abnormalities with a disease and patient, including details about age, sex, onset, and evidence.
PXF uses standard ontologies to ensure interoperability between diverse sources and consumers, to simplify text-mining, and to enable machine reasoning.
Software libraries supporting PXF have been written for Java, Python, and Javascript, and the open standard makes it easy to adapt to other languages, systems and applications.
</p>
</div>
</div>
<div class="col-md-4 col-sm-12">
<div class="service-item">
<span class="fa-stack fa-4x">
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<i class="fa fa-circle fa-stack-2x"></i>
<i class="fa fa-user-md fa-stack-1x text-primary"></i>
</a>
</span>
<h4>
<strong>A Community</strong>
</h4>
<p>
Phenopackets is an evolving standard jointly developed by researchers, clinicians, curators and authors. Journals, model organism databases, medical data repositories and commercial efforts are encouraged to adopt Phenopackets as a way to improve their use and publication of detailed and computable characterizations of disease. This will enable new modes of treatment and drug discovery, including translational research, precision medicine, and automated pipelines revealing knowledge in existing publications and databases.
</p>
</div>
</div>
</div>
<!--
<a href="#overview-detailed" class="btn btn-dark"
onclick=$("#overview-detailed").toggleClass('hidden');>
Details
</a>
-->
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<i class="fa fa-circle fa-stack-2x"></i>
<i class="fa fa-lightbulb-o fa-stack-1x text-primary"></i>
</span>
<h3>The Vision of Phenopackets</h3>
</div>
<div class="col-xs-7 xtext-center">
<p class="lead">
Using Phenopackets to communicate bioinformation ensures that knowledge is liberated and useable by the existing and nascent computational pipelines, databases and journals. This enables new possibilities for research, diagnosis and treatment. Some of the features of Phenopackets are listed below.
</p>
</div>
<div class="col-xs-5 xtext-center">
<ul>
<li>
Searchability, Comparability
</li>
<li>
Accessible outside paywalls and private data sources
</li>
<li>
Attributable and Citeable
</li>
<li>
Interoperable and Computable
</li>
<li>
Exchangeable across contexts and disciplines
</li>
</ul>
</div>
<div class="col-xs-12 text-center">
<a href="#a-vision-detailed" class="btn btn-dark"
onclick=$("#a-vision-detailed").toggleClass('hidden');>
Details
</a>
</div>
</div>
<div class="row hidden" id="a-vision-detailed">
<div class="col-xs-12">
<div id="a-vision-detailed-markdown" class="markdown">
</div>
</div>
</div>
</div>
</section>
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<div class="row row-inset">
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<i class="fa fa-circle fa-stack-2x"></i>
<i class="fa fa-cogs fa-stack-1x text-primary"></i>
</span>
<h3>The Technology of Phenopackets</h3>
<p class="lead">
Phenopackets are defined using a
<a href="https://github.com/phenopackets/phenopacket-schema" target="_blank">
protobuf schema
</a>
that allows implementations to be automatically generated for many languages. The phenopacket-schema build
process automatically produces language bindings for Java, Python and C++.
</p>
</div>
<div class="col-xs-12">
<p class="lead">
Source code and examples of Phenopackets technology may be found in the following GitHub repositories:
</p>
</div>
<div class="col-xs-12 text-center">
<div class="col-xs-4">
<ul class="list-unstyled">
<li>
<a href="https://github.com/phenopackets" target="_blank">
<i class="fa fa-github fa-fw"></i>
Phenopackets organization
</a>
</li>
</ul>
</div>
<div class="col-xs-4">
<ul class="list-unstyled">
<li>
<a href="https://github.com/phenopackets/phenopacket-schema" target="_blank">
<i class="fa fa-github fa-fw"></i>
Phenopacket schema
</a>
</li>
</ul>
</div>
<div class="col-xs-4">
<ul class="list-unstyled">
<li>
<a href="https://phenopacket-schema.readthedocs.io/en/latest/index.html" target="_blank">
<i class="fa fa-book fa-fw"></i>
Phenopacket schema documentation
</a>
</li>
</ul>
</div>
</div>
<!-- <hr class="small light">-->
<!-- <div class="col-xs-12">-->
<!-- <p class="lead">-->
<!-- A Google Summer of Code 2016 Project, the PhenoPacket Scraper, extracts ontology-linked phenopackets from published journal abstracts.-->
<!-- </p>-->
<!-- </div>-->
<!-- <div class="col-xs-6">-->
<!-- <ul class="list-unstyled">-->
<!-- <li>-->
<!-- <a href="https://github.com/monarch-initiative/phenopacket-scraper-core" target="_blank">-->
<!-- <i class="fa fa-github fa-fw"></i>-->
<!-- phenopacket-scraper-core-->
<!-- </a>-->
<!-- </li>-->
<!-- <li>-->
<!-- <a href="https://github.com/monarch-initiative/phenopacket-scraper-api" target="_blank">-->
<!-- <i class="fa fa-github fa-fw"></i>-->
<!-- phenopacket-scraper-api-->
<!-- </a>-->
<!-- </li>-->
<!-- </ul>-->
<!-- </div>-->
<!-- <div class="col-xs-6">-->
<!-- <ul class="list-unstyled">-->
<!-- <li>-->
<!-- <a href="https://github.com/monarch-initiative/phenopacket-scraper-webapp" target="_blank">-->
<!-- <i class="fa fa-github fa-fw"></i>-->
<!-- phenopacket-scraper-webapp-->
<!-- </a>-->
<!-- </li>-->
<!-- <li>-->
<!-- -->
<!-- </li>-->
<!-- </ul>-->
<!-- </div>-->
<!-- <div class="text-center">-->
<!-- <a href="#a-technology-detailed" class="btn btn-dark"-->
<!-- onclick=$("#a-technology-detailed").toggleClass('hidden');>-->
<!-- Details-->
<!-- </a>-->
<!-- </div>-->
</div>
<div class="row hidden" id="a-technology-detailed">
<div class="col-xs-12">
<div id="a-technology-detailed-markdown" class="markdown">
</div>
</div>
</div>
</div>
</section>
<section id="a-community" class="services bg-secondary">
<div class="container">
<div class="row row-inset">
<div class="col-xs-12 text-center">
<span class="fa-stack fa-4x xbg-primary">
<i class="fa fa-circle fa-stack-2x"></i>
<i class="fa fa-user-md fa-stack-1x text-primary"></i>
</span>
<h3>The Community of Phenopackets</h3>
<p class="lead">
Phenopackets were designed by, and intended to be used by, the diverse community of
researchers, data modelers, computer scientists, bioinformaticians, environmental
scientists, and clinicians dedicated to maximizing the value of existing and new data.
</p>
<a href="#a-community-detailed" class="btn btn-dark"
onclick=$("#a-community-detailed").toggleClass('hidden');>
Details
</a>
</div>
</div>
<div class="row hidden" id="a-community-detailed">
<div class="col-xs-12">
<div id="a-community-detailed-markdown" class="markdown">
</div>
</div>
</div>
</div>
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class="carousel slide"
data-ride="carousel"
data-type="multi"
data-interval="5000" id="myCarousel">
<div class="carousel-inner">
<div class="item active">
<div class="col-md-2 col-sm-6 col-xs-12 carousel-item">
<a href="http://www.orpha.net"class="img-responsive" target="_blank">
<img src="content/partners/logo-orphanet.png" class="img-responsive">
</a>
</div>
</div>
<div class="item">
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<a href="http://ga4gh.org/#/" target="_blank">
<img src="content/partners/logo-globalalliance.jpg" class="img-responsive">
</a>
</div>
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<div class="item">
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<a href="https://monarchinitiative.org" target="_blank">
<img src="content/partners/logo-monarch.png" class="img-responsive">
</a>
</div>
</div>
<div class="item">
<div class="col-md-2 col-sm-6 col-xs-12 carousel-item">
<a href="https://mondo.monarchinitiative.org" target="_blank">
<img src="content/partners/logo-mondo.png" class="img-responsive">
</a>
</div>
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<div class="item">
<div class="col-md-2 col-sm-6 col-xs-12 carousel-item">
<a href="http://human-phenotype-ontology.github.io" target="_blank">
<img src="content/partners/logo-hpo.png" class="img-responsive">
</a>
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<div class="item">
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<a href="http://geneontology.org" target="_blank">
<img src="content/partners/logo-clingen.png" class="img-responsive">
</a>
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<a class="left carousel-control" href="#myCarousel" data-slide="prev"><i class="glyphicon glyphicon-chevron-left"></i></a>
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<div class="container">
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<i class="fa fa-circle fa-stack-2x"></i>
<i class="fa fa-book fa-stack-1x text-primary"></i>
</span>
<h3>Documentation and References</h3>
</div>
<div class="col-xs-12 text-center">
<div class="col-xs-4">
<ul class="list-unstyled">
<li>
<a href="https://github.com/phenopackets" target="_blank">
<i class="fa fa-github fa-fw"></i>
Phenopackets organization
</a>
</li>
</ul>
</div>
<div class="col-xs-4">
<ul class="list-unstyled">
<li>
<a href="https://github.com/phenopackets/phenopacket-schema" target="_blank">
<i class="fa fa-github fa-fw"></i>
Phenopacket schema
</a>
</li>
</ul>
</div>
<div class="col-xs-4">
<ul class="list-unstyled">
<li>
<a href="https://phenopacket-schema.readthedocs.io/en/latest/index.html" target="_blank">
<i class="fa fa-book fa-fw"></i>
Phenopacket schema documentation
</a>
</li>
</ul>
</div>
</div>
<div class="col-xs-12">
<ul class="list-unstyled">
<li>
<i class="fa fa-external-link fa-fw"></i>Processing phenotype data using Phenopackets-API and PXFTools
<br>
<a href="https://www.open-bio.org/wiki/BOSC_2016" target="_blank">
BOSC 2016
</a>
<a href="https://f1000research.com/slides/5-1649" target=_blank>
Slides
</a>
<a href="https://www.youtube.com/watch?v=8UreKE1eGNY" target=_blank>
Video
</a>
</li>
<li>
<i class="fa fa-external-link fa-fw"></i>
Phenopackets: Making phenotype profiles FAIR++ for disease diagnosis and discovery
<br>
<a href="https://www.force11.org/meetings/force2016" target="_blank">
Force2016
</a>
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