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biosoda authored Sep 20, 2023
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<!doctype html>

<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">

<title>bioSODA</title>

<style>
body {
max-width: 800px;
margin: 0 auto;
padding: 0em;
background-color: #fff;
color: #000;
font-family: sans-serif;
line-height: 1.666em;
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header h1 {
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min-height: 55px;
width: 47%;
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a, a:link, a:visited, a:active, a:hover {
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<header>
<h1>bioSODA - biological search over databases</h1>
</header>
<p>"Complex bioinformatics databases hold enormous amounts of knowledge that can only be retrieved with technical know-how. The goal of this project is to develop an intuitive, Google-like search function designed to help identify new correlations in the stored data." NFP75 Big Data</p>



<h3>Web tools / interfaces</h3>
<div class="container">
<div class="item"><a href="http://biosoda.cloudlab.zhaw.ch:8083/soda/?page=demo" target="_blank">QALD4 (biomedical task)</a></div>
<div class="item"><a href="https://biosoda.expasy.org:4481/soda/?page=demo" target="_blank">Bgee and OMA (bioinformatics)</a></div>
<div class="item"><a href="http://biosoda.cloudlab.zhaw.ch:8084/soda/?page=demo" target="_blank">CORDIS (EU-funded projects)</a></div>

<div class="item"><a href="http://biosoda.cloudlab.zhaw.ch:8890/sparql" target="_blank">federation server - SPARQL frontend</a></div>

<div class="item"><a href="https://biosoda.expasy.org/build_biosodafrontend/" target="_blank">bioQuery - dynamic search interface with query catalog<br><img src="images/bioquery.png"></a></div>
<div class="item"><a href="https://biosoda.expasy.org/biosodaUX/" target="_blank">bioSodaUX - NLP search interface<br><br><img src="images/bioux.png"></a></div>



</div>

<h3>Resources / code</h3>
<div class="container">
<div class="item"><a href="https://github.com/anazhaw/Bio-SODA" target="_blank">Bio-SODA search engine and API (github)</a></div>

<div class="item"><a href="https://github.com/biosoda/bioquery" target="_blank">BioQuery web frontend (github)</a></div>

</div>

<h3>Publications</h3>
<div class="container">

<div class="item">
<a href="https://link.springer.com/protocol/10.1007/978-1-4939-9074-0_22" target="_blank">Semantic Integration and Enrichment of Heterogeneous Biological Databases</a>
<p>(Evolutionary Genomics pp 655-690, July 2019)</p>
</div>
<div class="item">
<a href="https://dx.doi.org/10.12688%2Ff1000research.21027.2" target="_blank">A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL</a>
<p>(online, October 2019)</p>
</div>
<div class="item">
<a href="https://doi.org/10.1093/database/baz106" target="_blank">Enabling Semantic Queries Across Federated Bioinformatics Databases</a>
<p>(Database, Volume 2019, November 2019, baz106)</p>
</div>
<div class="item">
<a href="https://serval.unil.ch/resource/serval:BIB_D64CBC923F3D.P002/REF" target="_blank">Enabling Complex Semantic Queries to Bioinformatics Databases through Intuitive Search Over Data</a>
<p>(Thesis, University of Lausanne, October 2020)</p>
</div>
<div class="item">
<a href="https://arxiv.org/abs/2104.13744" target="_blank">Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data</a>
<p>(33rd International Conference on Scientific and Statistical Database Management (SSDBM 2021), April 2021)</p>
</div>

</div>

<h3>Funding</h3>
<div class="container">
<div class="item"><a href="http://www.nfp75.ch/en/projects/module-3-applications/project-stockinger" target="_blank">NRP75 Big Data National Research Programme</a></div>

<div class="item"><a href="https://bigdata-dialog.ch/?_sfm_post_lang=en_US" target="_blank">BigData-Dialog</a></div>

</div>

<h3>Follow up project</h3>
<div class="container">
<div class="item"><a href="http://www.inode-project.eu/" target="_blank">INODE Intellignet Open Data Exploration - EU Horizon 2020</a></div>


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