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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" >
<title>BiodivOnto</title>
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<body><!-- Navigation Mobile type 2 -->
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<div><a href="#" class="f-heading f-22 link color-main mb-20">Featured</a></div>
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<style>
.header_16{
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<div class="row align-items-baseline">
<div class="col-lg-9 d-flex align-items-center f-18 medium">
<a href="https://openreview.net/pdf?id=GayhBSLEqud" target="blank"><div class="mr-15 logo color-white">BiodivOnto</div></a>
<a href="#Intro" class="mx-15 link color-white">Introduction</a>
<a href="#Method" class="mx-15 link color-white">Methodology</a>
<a href="#team" class="mx-15 link color-white">Team</a>
<a href="https://fusion.cs.uni-jena.de/fusion/" target="blank" class="mx-15 link color-white">FUSION</a>
</div>
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<a href="https://github.com/fusion-jena/BiodivOnto" target="blank" class="btn sm action-1">GitHub</a>
<a href="https://openreview.net/pdf?id=GayhBSLEqud" target="blank" class="btn sm action-1">Paper</a>
</div>
</div>
</div>
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<div class="row justify-content-center">
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<div class="col-lg-7 col-md-9 pt-40">
<div class="mb-3 logo d-block d-xl-none color-white logo_mobile">BiodivOnto</div>
<h1 class="mb-20 big" data-aos-duration="600" data-aos="fade-down" data-aos-delay="0">BiodivOnto: Towards a Core Ontology for Biodiversity </h1>
<div class="f-22 text-adaptive" data-aos-duration="600" data-aos="fade-down" data-aos-delay="300">
We aim to develop a core ontology for the biodiversity domain establishing links between the foundational and domain-specific ontologies.
</div>
<div class="mt-80 row blocks">
<div class="mt-30 col-sm-6" data-aos-duration="600" data-aos="fade-down" data-aos-delay="600">
<i class="f-50 fas fa-cogs"></i>
<div class="mt-30 mb-25 semibold f-20 title">Keywords</div>
<div class="text-adaptive">
Biodiversity. Knowledge Representation. Core Ontology.
</div>
</div>
</div>
</div>
<!--<div class="col-lg-5 col-md-3 d-flex align-items-center" data-aos-duration="600" data-aos="fade-down" data-aos-delay="1200">
<img srcset="i/[email protected] 2x" src="i/header_16_img.png" class="ml-30 mh-full img" alt="" />
</div>-->
</div>
</div>
</div>
</div>
</header>
<!-- Feature 37 -->
<section class="feature_37 bg-light pt-100 pb-65" id="Intro">
<div class="container px-xl-0">
<div class="row justify-content-between">
<div class="col-xl-1"></div>
<div class="col-lg-5 col-md-6 mb-50 mb-md-0" data-aos-duration="600" data-aos="fade-down" data-aos-delay="0">
<h2 class="mb-20 small">
Introduction
</h2>
<div class="mb-25 f-18 medium op-7 text-adaptive">
To preserve biodiversity, research to understand its underlying mechanisms is needed which requires integrated data. An increasing amount of heterogeneous data is generated and publicly shared in biodiversity research.
There are also a lot of efforts to semantically describe biodiversity datasets and research outputs. Multiple ontologies, like <a href='https://bioportal.bioontology.org/ontologies/ENVO'>ENVO</a> and <a href='https://bioportal.bioontology.org/ontologies/IOBC'>IOBC</a>, model specific parts of the domain.
However, in order to support integrative biodiversity research, there is a growing need to bridge between the more refined biodiversity concepts and general concepts provided by the foundational ontologies.
</div>
</div>
<div class="col-md-1"></div>
<div class="col-md-5" data-aos-duration="600" data-aos="fade-down" data-aos-delay="300">
<div class="mb-55 d-flex align-items-center advantage">
<i class="fas fa-check-circle color-gray f-26 lh-24 w-30 mr-20"></i>
<div class="f-14 semibold sp-20 title">We propose the design of a core ontology for the biodiversity domain using a semi-automatic approach.</div>
</div>
<div class="mb-55 d-flex align-items-center advantage">
<i class="fas fa-check-circle color-gray f-26 lh-24 w-30 mr-20"></i>
<div class="f-14 semibold sp-20 title">We make use of the fusion/merge strategy, where the new ontology is developed by assembling and reusing one or more ontologies</div>
</div>
<div class="mb-55 d-flex align-items-center advantage">
<i class="fas fa-check-circle color-gray f-26 lh-24 w-30 mr-20"></i>
<div class="f-14 semibold sp-20 title">Our design is guided by data from several databases in the biodiversity field.</div>
</div>
<div class="mb-55 d-flex align-items-center advantage">
<i class="fas fa-check-circle color-gray f-26 lh-24 w-30 mr-20"></i>
<div class="f-14 semibold sp-20 title">We develop a four-stage pipeline involving biodiversity experts and computer scientists at different phases.</div>
</div>
<div class="mb-55 d-flex align-items-center advantage">
<i class="fas fa-check-circle color-gray f-26 lh-24 w-30 mr-20"></i>
<div class="f-14 semibold sp-20 title">Using automated approaches of clustering and the help of biodiversity experts, we generate the list of core concepts.</div>
</div>
</div>
</div>
</div>
</section>
<!-- Content 6 -->
<style>
.content_6{
background-image:url(i/content_6_bg.png);
}
@media(-webkit-min-device-pixel-ratio: 1.25), (min-resolution: 120dpi){
.content_6{
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</style>
<section class="content_6 pt-125 pb-105" id="Method">
<div class="container px-xl-0 text-center color-white">
<div class="row justify-content-center">
<div class="col-lg-8 col-md-10" data-aos-duration="600" data-aos="fade-down" data-aos-delay="0">
<h2>Methodology</h2>
</div>
<div class="mt-35 col-xl-7 col-lg-8 col-md-10 f-22 text-adaptive" data-aos-duration="600" data-aos="fade-down" data-aos-delay="300">
How do we reach the final outcome, step by step ... </div>
</div>
</div>
</section>
<!-- Ecommerce 30 -->
<style>
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background-image:url(i/ecommerce_30_bg_2.jpg);
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background-image:url(i/ecommerce_30_bg_2.jpg);
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#ecommerce_30_block_1 .bg{
background-image:url(i/ecommerce_30_bg_221.png);
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background-image:url(i/ecommerce_30_bg_221.png);
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</style>
<section class="ecommerce_30 bg-light pt-85 pb-85 text-center text-md-left">
<div class="container px-xl-0">
<div class="row">
<div class="mt-15 mb-15 col-xl-8 col-md-6 d-md-flex align-items-stretch product big" id="ecommerce_30_block_1" data-aos-duration="600" data-aos="fade-down" data-aos-delay="0">
<div class="relative holder radius10">
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<div class="px-50 pt-50 pb-60 relative d-md-flex flex-column justify-content-between align-items-start h-full inner">
<div class="top">
<!--<div class="mb-2 f-14 color-heading semibold text-uppercase sp-20 subtitle">Step 1</div>-->
<p class="medium">The aim of this step is to get sufficient data sources from which we can extract relevant terms.</p>
<p class="medium">Keywords, such as ‘abundance’, ‘benthic’, ‘biomass’, ‘carbon’, ‘climate change’, ‘decomposition’, ‘earthworms’, ‘ecosystem’. </p>
<p class="medium">Semedico, BEFChina, and data.world. </p>
<p class="medium">Output: 100 abstracts, more than 50 tables.</p>
</div>
<!--<a href="#" class="btn action-2">Try Right Now</a>-->
</div>
</div>
</div>
<div class="mt-15 mb-15 col-xl-4 col-md-6 d-md-flex align-items-stretch product small" id="ecommerce_30_block_2" data-aos-duration="600" data-aos="fade-down" data-aos-delay="300">
<div class="relative holder radius10">
<div class="absolute bg"></div>
<div class="px-50 pt-50 pb-60 relative d-md-flex flex-column justify-content-between align-items-start h-full inner">
<div class="top">
<div class="mb-2 f-14 color-white semibold text-uppercase sp-20 subtitle">Step 1</div>
<h2 class="mb-60 small color-white">Data Acquisition</h2>
</div>
<a href="https://github.com/fusion-jena/BiodivOnto" target="blank" class="btn action-white"><span class="color-main">Try Right Now</span></a>
</div>
</div>
</div>
</div>
</div>
</section>
<style>
#ecommerce_31_block_1 .bg{
background-image:url(i/ecommerce_30_bg_31.png);
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#ecommerce_31_block_2 .bg{
background-image:url(i/ecommerce_30_bg_3.png);
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</style>
<section class="ecommerce_30 ecommerce_32 bg-light pt-85 pb-85 text-center text-md-left">
<div class="container px-xl-0">
<div class="row">
<div class="mt-15 mb-15 col-xl-8 col-md-6 d-md-flex align-items-stretch product big" id="ecommerce_31_block_1" data-aos-duration="600" data-aos="fade-down" data-aos-delay="0">
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<div class="px-50 pt-50 pb-60 relative d-md-flex flex-column justify-content-between align-items-start h-full inner">
<div class="top">
<!--<div class="mb-2 f-14 color-heading semibold text-uppercase sp-20 subtitle">Step 1</div>-->
<p class="medium">Manual annotation of the collected data following the annotation scheme in QEMP [1]</p>
<p class="medium">Ontologies: OBC, SWEET, ECOCORE, ECSO, CBO, BCO, and the Biodiversity A-Zdictionary</p>
<p class="medium">Compound keyword expanded: "photosynthetic O2 production" -> ["photosynthetic", "O2", "O2 production", "photosynthetic O2 production"]</p>
<p class="medium">Keywords from external sources are included: QEMP, AquaDiva [2] and Soil related [3]</p>
</div>
<!--<a href="#" class="btn action-2">Try Right Now</a>-->
</div>
</div>
</div>
<div class="mt-15 mb-15 col-xl-4 col-md-6 d-md-flex align-items-stretch product small" id="ecommerce_31_block_2" data-aos-duration="600" data-aos="fade-down" data-aos-delay="300">
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<div class="px-50 pt-50 pb-60 relative d-md-flex flex-column justify-content-between align-items-start h-full inner">
<div class="top">
<div class="mb-2 f-14 color-white semibold text-uppercase sp-20 subtitle">Step 2</div>
<h2 class="mb-60 small color-white">Keywords Extraction</h2>
</div>
<a href="https://github.com/fusion-jena/BiodivOnto" target="blank" class="btn action-white"><span class="color-main">Try Right Now</span></a>
</div>
</div>
</div>
</div>
</div>
</section>
<style>
#ecommerce_32_block_1 .bg{
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<section class="ecommerce_30 bg-light pt-85 pb-85 text-center text-md-left">
<div class="container px-xl-0">
<div class="row">
<div class="mt-15 mb-15 col-xl-8 col-md-6 d-md-flex align-items-stretch product big" id="ecommerce_32_block_1" data-aos-duration="600" data-aos="fade-down" data-aos-delay="0">
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<p class="medium">Keywords normalization.</p>
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<p class="medium">1107 unique keyword = 1.8 QEMP corpus. </p>
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<h2 class="mb-60 small color-white">Keywords Filtration</h2>
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<p class="medium">Distance-basedd clustering using word2vec [4] representation</p>
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<p class="medium">Word-Net [5] similarity measure among the final seeds. If Similarity 0.0 take the seed as a core concept, otherwise, check BioPortal for a common ancestor</p>
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<th class="color-heading f-14 semibold text-uppercase sp-20" scope="col">Terms sample inside category</th>
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<td class="color-heading"><a href='https://bioportal.bioontology.org/ontologies/ENVO'>ENVO</a>, <a href='https://bioportal.bioontology.org/ontologies/ECOCORE'>ECOCORE</a>, <a href='https://bioportal.bioontology.org/ontologies/ECSO'>ECSO</a>, <a href='https://bioportal.bioontology.org/ontologies/PATO'>PATO</a></td>
<td>groundwater, garden</td>
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<td class="color-heading"><a href='https://bioportal.bioontology.org/ontologies/ENVO'>ENVO</a>, <a href='https://bioportal.bioontology.org/ontologies/ECOCORE'>ECOCORE</a>, <a href='https://bioportal.bioontology.org/ontologies/ECSO'>ECSO</a>, <a href='https://bioportal.bioontology.org/ontologies/BCO'>BCO</a></td>
<td>mammal, insect</td>
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<td class="color-heading"><a href='https://bioportal.bioontology.org/ontologies/ENVO'>ENVO</a>, <a href='https://bioportal.bioontology.org/ontologies/PATO'>PATO</a>, <a href='https://bioportal.bioontology.org/ontologies/BCO'>BCO</a></td>
<td>decomposition, colonization</td>
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<td class="color-heading"><a href='https://bioportal.bioontology.org/ontologies/ENVO'>ENVO</a>,<a href='https://bioportal.bioontology.org/ontologies/PATO'>PATO</a>, <a href='https://bioportal.bioontology.org/ontologies/CBO'>CBO</a>, <a href='https://bioportal.bioontology.org/ontologies/ECSO'>ECSO</a></td>
<td>volume, age</td>
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<td>Landscape</td>
<td class="color-heading"><a href='https://bioportal.bioontology.org/ontologies/ENVO'>ENVO</a></td>
<td>grassland, forest</td>
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<td>Trait</td>
<td class="color-heading"><a href='https://bioportal.bioontology.org/ontologies/BCO'>BCO</a></td>
<td>texture, structure</td>
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<td>Ecosystem</td>
<td class="color-heading"><a href='https://bioportal.bioontology.org/ontologies/ENVO'>ENVO</a>, <a href='https://bioportal.bioontology.org/ontologies/ECOCORE'>ECOCORE</a>, <a href='https://bioportal.bioontology.org/ontologies/ECSO'>ECSO</a>, <a href='https://bioportal.bioontology.org/ontologies/PATO'>PATO</a></td>
<td>biome, habitat</td>
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<td>Matter</td>
<td class="color-heading"><a href='https://bioportal.bioontology.org/ontologies/ENVO'>ENVO</a>, <a href='https://bioportal.bioontology.org/ontologies/ECSO'>ECSO</a></td>
<td>carbon, H2O</td>
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The authors thank the Carl Zeiss Foundation for the financial support of the project “A Virtual Werkstatt for Digitization in the Sciences (K3, P5)” within the scope of the program line “Breakthroughs: Exploring Intelligent Systems for Digitization” - explore the basics, use applications”. Alsayed Algergawy’ work has been funded by the Deutsche Forschungsgemeinschaft (DFG) as part of CRC 1076 AquaDiva. Our sincere thanks to Tina Heger (Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB)) as the domain expert.
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References
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<ol>
<li>Löffler, F., Abdelmageed, N., Babalou, S., Kaur, P., König-Ries, B.: Tag me if you can! semantic annotation of biodiversity metadata with the qemp corpus and the biodivtagger. In: Proceedings of The 12th Language Resources and Evaluation Conference. pp. 4557–4564 (2020)</li>
<li>AquaDiva project <a href="http://www.aquadiva.uni-jena.de/">http://www.aquadiva.uni-jena.de/</a> </li>
<li>Udovenko, V., Algergawy, A.: Entity extraction in the ecological domain–a practical guide. BTW 2019–Workshopband (2019)</li>
<li>Goldberg, Y., Levy, O.: word2vec explained: deriving mikolov et al.’s negative sampling word-embedding method. arXiv preprint arXiv:1402.3722 (2014)</li>
<li>Pedersen, T., Patwardhan, S., Michelizzi, J., et al.: Wordnet: Similarity-measuring the relatedness of concepts. In: AAAI. vol. 4, pp. 25–29 (2004)</li>
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