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moreover, all experimental datasets leading to publications in genomics must be deposited to public repositories and made available to the research community. These datasets are typically used by biologists for validating or enriching their experiments; their content is documented by metadata. However, emphasis on data sharing is not matched by accuracy in data documentation; metadata are not standardized across the sources and often unstructured and incomplete. In this paper, we propose a conceptual model of genomic metadata, whose purpose is to query the underlying data sources for locating relevant experimental datasets. First, we analyze the most typical metadata attributes of genomic sources and define their semantic properties. Then, we use a top-down method for building a global-as-view integrated schema, by abstracting the most important conceptual properties of genomic sources. 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src="https://media.springernature.com/w72/springer-static/cover-hires/book/978-3-319-69904-2?as=webp" srcset="https://media.springernature.com/w144/springer-static/cover-hires/book/978-3-319-69904-2?as=webp 2x" alt=""> </picture> <span class="app-article-masthead__journal-title ">Conceptual Modeling</span> </a> <span class="app-article-masthead__conference-info">(ER 2017) </span> </div> </div> </div> </section> </div> <div class="c-article-main u-container u-mt-24 u-mb-32 l-with-sidebar" id="main-content" data-component="article-container"> <main class="js-main-column u-serif c-chapter-body" data-track-component="chapter"> <article lang="en"> <div class="c-article-header"> <header> <div class="app-overview-section"> <ul class="c-article-author-list c-article-author-list--short" data-test="authors-list" data-component-authors-activator="authors-list"><li class="c-article-author-list__item"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Anna-Bernasconi" data-author-popup="auth-Anna-Bernasconi" data-corresp-id="c1">Anna Bernasconi<svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-mail-medium"></use></svg></a><sup class="u-js-hide"><a href="#Aff17">17</a></sup>, </li><li class="c-article-author-list__item"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Stefano-Ceri" data-author-popup="auth-Stefano-Ceri">Stefano Ceri</a><sup class="u-js-hide"><a href="#Aff17">17</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Alessandro-Campi" data-author-popup="auth-Alessandro-Campi">Alessandro Campi</a><sup class="u-js-hide"><a href="#Aff17">17</a></sup> & </li><li class="c-article-author-list__show-more" aria-label="Show all 4 authors for this article" title="Show all 4 authors for this article">…</li><li class="c-article-author-list__item"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Marco-Masseroli" data-author-popup="auth-Marco-Masseroli">Marco Masseroli</a><sup class="u-js-hide"><a href="#Aff17">17</a></sup> </li></ul><button aria-expanded="false" class="c-article-author-list__button"><svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-chevron-down-medium"></use></svg><span>Show authors</span></button> <div class="app-overview-section__separator app-overview-section__book-series"> <div class="app-book-series-listing"> <div> <svg class="app-book-series-listing__icon" width="24" height="24" aria-hidden="true" focusable="false"><use 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data-track="click" data-track-action="open conference" data-track-label="link">International Conference on Conceptual Modeling</a></li> </ul> </div> </div> <div class="app-overview-section__separator" data-test="article-metrics"> <div id="altmetric-container"> <ul class="app-article-metrics-bar u-list-reset" data-test="article-metrics"> <li class="app-article-metrics-bar__item" data-test="access-count"> <p class="app-article-metrics-bar__count"><svg class="u-icon app-article-metrics-bar__icon" width="24" height="24" aria-hidden="true" focusable="false"> <use xlink:href="#icon-eds-i-accesses-medium"></use> </svg>1882 <span class="app-article-metrics-bar__label">Accesses</span></p> </li> <li class="app-article-metrics-bar__item" data-test="citation-count"> <p class="app-article-metrics-bar__count"><svg class="u-icon app-article-metrics-bar__icon" width="24" height="24" aria-hidden="true" focusable="false"> <use xlink:href="#icon-eds-i-citations-medium"></use> </svg>28 <span class="app-article-metrics-bar__label"> <a href="http://citations.springer.com/item?doi=10.1007/978-3-319-69904-2_26" target="_blank" rel="noopener" title="Visit Springer Citations for full citation details" data-track="click" data-track-action="Citation count" data-track-label="link">Citations</a> </span></p> </li> </ul> </div> </div> </div> </header> </div> <div data-article-body="true" data-track-component="chapter body" class="c-article-body"> <section aria-labelledby="Abs1" data-title="Abstract" lang="en"><div class="c-article-section" id="Abs1-section"><h2 id="Abs1" class="c-article-section__title js-section-title js-c-reading-companion-sections-item"><span class="c-article-section__title-number"> </span>Abstract</h2><div class="c-article-section__content" id="Abs1-content"><p>Many repositories of open data for genomics, collected by world-wide consortia, are important enablers of biological research; moreover, all experimental datasets leading to publications in genomics must be deposited to public repositories and made available to the research community. These datasets are typically used by biologists for validating or enriching their experiments; their content is documented by metadata. However, emphasis on data sharing is not matched by accuracy in data documentation; metadata are not standardized across the sources and often unstructured and incomplete.</p><p>In this paper, we propose a conceptual model of genomic metadata, whose purpose is to query the underlying data sources for locating relevant experimental datasets. First, we analyze the most typical metadata attributes of genomic sources and define their semantic properties. Then, we use a top-down method for building a global-as-view integrated schema, by abstracting the most important conceptual properties of genomic sources. Finally, we describe the validation of the conceptual model by mapping it to three well-known data sources: TCGA, ENCODE, and Gene Expression Omnibus.</p></div></div></section> <div class="c-notes"> <p class="c-notes__text c-status-message--info"> <svg width="24" height="24" focusable="false" role="img" aria-hidden="true" class="c-status-message__icon"> <use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-info-filled-medium"></use> </svg> This is a preview of subscription content, <a id="test-login-banner-link" href="//wayf.springernature.com?redirect_uri=https%3A%2F%2Flink.springer.com%2Fchapter%2F10.1007%2F978-3-319-69904-2_26%3Ferror%3Dcookies_not_supported%26code%3D4c850f32-3747-4f78-91f7-74bc633d7422" data-track="click" data-track-action="login" data-track-label="link">log in via an institution</a> <svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon c-external-link__icon"> <use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-external-link-small"></use> </svg> to check access. </p> </div> <div data-test="access-chapter-mobile" class="app-article-access"> <h2 class="app-article-access__heading">Access this chapter</h2> <div class="u-ma-16 u-clear-both"> <a href="//wayf.springernature.com?redirect_uri=https%3A%2F%2Flink.springer.com%2Fchapter%2F10.1007%2F978-3-319-69904-2_26%3Ferror%3Dcookies_not_supported%26code%3D4c850f32-3747-4f78-91f7-74bc633d7422" class="u-button u-button--full-width u-button--primary u-justify-content-space-between c-pdf-download__link" data-track="click" data-track-action="institution access" data-track-label="button"> <span data-test="access-via-institution">Log in via an institution</span> <svg aria-hidden="true" focusable="false" width="16" height="16" class="u-icon"> <use xlink:href="#icon-eds-i-arrow-right-medium"></use> </svg> </a> </div> <div data-test="buy-box-mobile" class="u-mb-24"> </div> <div class="app-article-access__subscriptions"> <p><a href="https://www.springernature.com/gp/librarians/licensing/agc/ebooks">Institutional subscriptions <svg aria-hidden="true" focusable="false" width="24" height="24" class="u-icon"> <use xlink:href="#icon-eds-i-arrow-right-medium"></use> </svg> </a></p> </div> </div> <div data-test="cobranding-download"> </div> <section aria-labelledby="inline-recommendations" data-title="Inline Recommendations" class="c-article-recommendations" data-track-component="inline-recommendations"> <h3 class="c-article-recommendations-title" id="inline-recommendations">Similar content being viewed by others</h3> <div class="c-article-recommendations-list"> <div class="c-article-recommendations-list__item"> <article class="c-article-recommendations-card" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-article-recommendations-card__img"><img src="https://media.springernature.com/w92h120/springer-static/cover-hires/book/978-3-030-34146-6?as=webp" loading="lazy" alt=""></div> <div class="c-article-recommendations-card__main"> <h3 class="c-article-recommendations-card__heading" itemprop="name headline"> <a class="c-article-recommendations-card__link" itemprop="url" href="https://link.springer.com/10.1007/978-3-030-34146-6_8?fromPaywallRec=true" data-track="select_recommendations_1" data-track-context="inline recommendations" data-track-action="click recommendations inline - 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3" data-track-label="10.1007/978-3-031-17995-2_14">A Comprehensive Approach for the Conceptual Modeling of Genomic Data </a> </h3> <div class="c-article-meta-recommendations" data-test="recommendation-info"> <span class="c-article-meta-recommendations__item-type">Chapter</span> <span class="c-article-meta-recommendations__date">© 2022</span> </div> </div> </article> </div> </div> </section> <script> window.dataLayer = window.dataLayer || []; window.dataLayer.push({ recommendations: { recommender: 'semantic', model: 'specter', policy_id: 'NA', timestamp: 1732285139, embedded_user: 'null' } }); </script> <section data-title="Notes" lang="en"><div class="c-article-section" id="notes-section"><h2 id="notes" class="c-article-section__title js-section-title js-c-reading-companion-sections-item"><span class="c-article-section__title-number"> </span>Notes</h2><div class="c-article-section__content" id="notes-content"><ol class="c-article-footnote c-article-footnote--listed"><li class="c-article-footnote--listed__item" id="Fn1"><span class="c-article-footnote--listed__index">1.</span><div class="c-article-footnote--listed__content"><p><a href="https://software.broadinstitute.org/firecloud/">https://software.broadinstitute.org/firecloud/</a>.</p></div></li><li class="c-article-footnote--listed__item" id="Fn2"><span class="c-article-footnote--listed__index">2.</span><div class="c-article-footnote--listed__content"><p>Data-Driven Genomic Computing, <a href="http://www.bioinformatics.deib.polimi.it/geco/">http://www.bioinformatics.deib.polimi.it/geco/</a>, ERC Advanced Grant, 2016–2021.</p></div></li><li class="c-article-footnote--listed__item" id="Fn3"><span class="c-article-footnote--listed__index">3.</span><div class="c-article-footnote--listed__content"><p>At <a href="https://www.encodeproject.org/profiles/graph.svg">https://www.encodeproject.org/profiles/graph.svg</a> see the conceptual model of ENCODE, an ER schema with tens of entities and hundreds of relationships, which is neither readable nor supported by metadata for most concepts.</p></div></li><li class="c-article-footnote--listed__item" id="Fn4"><span class="c-article-footnote--listed__index">4.</span><div class="c-article-footnote--listed__content"><p><a href="http://www.bioinformatics.deib.polimi.it/GMQL/interfaces/">http://www.bioinformatics.deib.polimi.it/GMQL/interfaces/</a>.</p></div></li><li class="c-article-footnote--listed__item" id="Fn5"><span class="c-article-footnote--listed__index">5.</span><div class="c-article-footnote--listed__content"><p>We will use the BRENDA Tissue and Enzyme Source Ontology [<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 32" title="Schomburg, I., et al.: BRENDA in 2013: new options and contents in BRENDA. Nucleic Acids Res. 41(Database issue), D764–D772 (2013)" href="#ref-CR32" id="ref-link-section-d26320654e3558">32</a>] for tissues, the Cell Line Ontology [<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 31" title="Sarntivijai, S., et al.: CLO: the cell line ontology. J. Biomed. Semant. 5(1), 37 (2014)" href="#ref-CR31" id="ref-link-section-d26320654e3561">31</a>] for cell lines, and the Human Disease Ontology [<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 33" title="Schriml, L.M., et al.: Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res. 40(Database issue), 940–946 (2012)" href="#ref-CR33" id="ref-link-section-d26320654e3564">33</a>] for human diseases.</p></div></li><li class="c-article-footnote--listed__item" id="Fn6"><span class="c-article-footnote--listed__index">6.</span><div class="c-article-footnote--listed__content"><p><a href="http://www.uniprot.org/uniprot/">http://www.uniprot.org/uniprot/</a>.</p></div></li><li class="c-article-footnote--listed__item" id="Fn7"><span class="c-article-footnote--listed__index">7.</span><div class="c-article-footnote--listed__content"><p>Textual analysis to extract semantic information from the GEO repository is reported in [<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 12" title="Galeota, E., Pelizzola, M.: Ontology-based annotations and semantic relations in large-scale (epi)genomics data. Brief. Bioinform. 18(3), 403–412 (2017)" href="#ref-CR12" id="ref-link-section-d26320654e3958">12</a>]; we plan to reuse their library.</p></div></li><li class="c-article-footnote--listed__item" id="Fn8"><span class="c-article-footnote--listed__index">8.</span><div class="c-article-footnote--listed__content"><p>The metadata is provided in the NCI Genomic Data Commons portal, <a href="https://docs.gdc.cancer.gov/Data_Dictionary/viewer/">https://docs.gdc.cancer.gov/Data_Dictionary/viewer/</a>.</p></div></li><li class="c-article-footnote--listed__item" id="Fn9"><span class="c-article-footnote--listed__index">9.</span><div class="c-article-footnote--listed__content"><p>GEO information can be retrieved through the R package <i>GEOmetadb</i> [<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 37" title="Zhu, Y., et al.: Geometadb: powerful alternative search engine for the gene expression omnibus. Bioinformatics 24(23), 2798–2800 (2008)" href="#ref-CR37" id="ref-link-section-d26320654e4016">37</a>].</p></div></li></ol></div></div></section><div id="MagazineFulltextChapterBodySuffix"><section aria-labelledby="Bib1" data-title="References"><div class="c-article-section" id="Bib1-section"><h2 id="Bib1" class="c-article-section__title js-section-title js-c-reading-companion-sections-item"><span class="c-article-section__title-number"> </span>References</h2><div class="c-article-section__content" id="Bib1-content"><div data-container-section="references"><ol class="c-article-references" data-track-component="outbound reference" data-track-context="references section"><li class="c-article-references__item js-c-reading-companion-references-item" data-counter="1."><p class="c-article-references__text" id="ref-CR1">Adams, D., et al.: BLUEPRINT to decode the epigenetic signature written in blood. Nat. 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