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class="content"> <div class="container"> <div class="row"> <div class="main col-lg-8"> <article id="post-25475" class="post--single post-25475 post type-post status-publish format-standard has-post-thumbnail hentry category-frictionless-data category-open-knowledge category-open-research category-open-science category-open-software category-technical"> <p class="post__meta">December 9, 2019, by <a href="https://blog.okfn.org/author/lillywinfree/" title="Posts by Lilly Winfree" rel="author">Lilly Winfree</a> </p> <div class="entry-content"> <p><strong><i>This blog is part of a series showcasing projects developed during the 2019 Frictionless Data Tool Fund. </i></strong></p> <p><i><span style="font-weight: 400">The 2019 Frictionless Data Tool Fund provided four mini-grants of $5,000 to support individuals or organisations in developing an open tool for reproducible research built using the Frictionless Data specifications and software. This fund is part of the Frictionless Data for Reproducible Research project, which is funded by the Sloan Foundation. This project applies our work in Frictionless Data to data-driven research disciplines, in order to facilitate reproducible data workflows in research contexts. </span></i></p> <p><img class="size-medium wp-image-25476 aligncenter" src="https://blog.okfn.org/files/2019/12/FDdarwincore-300x149.png" alt="logo" width="300" height="149" /></p> <h2><span style="font-weight: 400">Frictionless DarwinCore, developed by André Heughebaert</span></h2> <p> </p> <p><span style="font-weight: 400">André Heughebaert is an open biodiversity data advocate in his work and his free time. He is </span><span style="font-weight: 400">an IT Software Engineer at the </span><a href="https://www.biodiversity.be/"><span style="font-weight: 400">Belgian Biodiversity Platform</span></a><span style="font-weight: 400"> and is also the </span><a href="https://www.gbif.org/en/country/BE/summary"><span style="font-weight: 400">Belgian </span></a><a href="https://www.gbif.org/"><span style="font-weight: 400">GBIF</span></a> <span style="font-weight: 400">(Global Biodiversity Information Facility) </span><a href="https://www.gbif.org/en/country/BE/summary"><span style="font-weight: 400">Node</span></a><span style="font-weight: 400"> manager.</span><span style="font-weight: 400"> During this time, he has worked with the </span><a href="https://dwc.tdwg.org/"><span style="font-weight: 400">Darwin Core Standards</span></a><span style="font-weight: 400"> and Open Biodiversity data on a daily basis. This work inspired him to apply for the Tool Fund, where he has developed a tool to convert DarwinCore Archives into Frictionless Data Packages.</span></p> <p> </p> <p><span style="font-weight: 400">The DarwinCore Archive (DwCA) is a standardised container for biodiversity data and metadata largely used amongst the GBIF community, which consists of more than 1,500 institutions around the world. The DwCA is used to publish biodiversity data about observations, collections specimens, species checklists and sampling events. However, this domain specific standard has some limitations, mainly the </span><a href="https://github.com/gbif/ipt/wiki/DwCAHowToGuide"><span style="font-weight: 400">star schema</span></a><span style="font-weight: 400"> (core table + extensions), rules that are sometimes too permissive, and a lack of controlled vocabularies for certain terms. These limitations encouraged André to investigate emerging open data standards. In 2016, he discovered Frictionless Data and published his </span><a href="https://datahub.io/andrejjh/junibis_dp"><span style="font-weight: 400">first data package</span></a><span style="font-weight: 400"> on historical data from 1815 Napoleonic Campaign of Belgium. He was then encouraged to create a tool that would, in part, build a bridge between these two open data ecosystems.</span></p> <p> </p> <p><span style="font-weight: 400">As a result, </span><a href="https://github.com/frictionlessdata/FrictionlessDarwinCore"><span style="font-weight: 400">the Frictionless DarwinCore tool</span></a><span style="font-weight: 400"> converts DwCA into Frictionless Data Packages, and also gives access to the vast Frictionless Data software ecosystem enabling constraints validation and support of a fully relational data schema. Technically speaking, the tool is implemented as a Python library, and is exposed as a Command Line Interface. The tool automatically converts:</span></p> <p><span style="font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen-Sans, Ubuntu, Cantarell, 'Helvetica Neue', sans-serif">* DwCA data schema into datapackage.json</span></p> <p><span style="font-weight: 400">* EML metadata into human readable markdown readme file</span></p> <p><span style="font-weight: 400">* data files are converted when necessary, this is when default values are described</span></p> <p><span style="font-weight: 400">The resulting zip file complies to both DarwinCore and Frictionless specifications. </span></p> <p><img loading="lazy" class="alignright wp-image-25477 size-full" src="https://blog.okfn.org/files/2019/12/FDdarwin1.png" alt="project architecture" width="747" height="591" /></p> <p> </p> <p> </p> <p> </p> <p><span style="font-weight: 400">André hopes that bridging the two standards will give an excellent opportunity for the GBIF community to provide open biodiversity data to a wider audience. He says this is also a good opportunity to discover the Frictionless Data specifications and assess their applicability to the biodiversity domain. In fact, on 9th October 2019, André presented the tool at a GBIF Global Nodes meeting. It was perceived by the nodes managers community as an exploratory and pioneering work. While the command line interface offers a simple user interface for non-programmers, others might prefer the more flexible and sophisticated Python API. André encourages anyone working with DarwinCore data, including all data publishers and data users of GBIF network, to try out the new tool. </span></p> <blockquote><p><span style="font-weight: 400">“I’m quite optimistic that the project will feed the necessary reflection on the evolution of our biodiversity standards and data flows.”</span></p></blockquote> <p><span style="font-weight: 400">To get started, installation of the tool is done through a single pip install command (full directions can be found in the </span><a href="https://github.com/frictionlessdata/FrictionlessDarwinCore#frictionless-darwin-core"><span style="font-weight: 400">project README</span></a><span style="font-weight: 400">). Central to the tool is a table of DarwinCore terms linking a Data Package type, format and constraints for every DwC term. The tool can be used as CLI directly from your terminal window or as Python Library for developers. The tool can work with either locally stored or online DwCA. Once converted to Tabular DataPackage, the DwC data can then be ingested and further processed by software such as Goodtables, OpenRefine or any other Frictionless Data software.</span></p> <p><span style="font-weight: 400">André has aspirations to take the Frictionless DarwinCore tool further by encaps</span><span style="font-weight: 400">ulating the tool in a web-service that will directly deliver Goodtables reports from a DwCA, which will make it even more user friendly. Additional ideas for further improvement would be including an import pathway for </span><span style="font-weight: 400">Da</span><span style="font-weight: 400">rwinCore data into </span><a style="font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen-Sans, Ubuntu, Cantarell, 'Helvetica Neue', sans-serif" href="http://openrefine.org/">Open Refine</a><span style="font-weight: 400">, which is a popular tool in the GBIF community. André’s long term hope is that the Data Package will become an optional format for data download on GBIF.org. </span></p> <p><img loading="lazy" class="aligncenter wp-image-25478 size-full" src="https://blog.okfn.org/files/2019/12/FDdarwin2.png" alt="workflow" width="620" height="683" /></p> <p><em><span style="font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen-Sans, Ubuntu, Cantarell, 'Helvetica Neue', sans-serif">Further reading:</span></em></p> <p><span style="font-weight: 400">Repository: </span><a style="font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen-Sans, Ubuntu, Cantarell, 'Helvetica Neue', sans-serif" href="https://github.com/frictionlessdata/FrictionlessDarwinCore">https://github.com/frictionlessdata/FrictionlessDarwinCore</a></p> <p><span style="font-weight: 400">Project blog: </span><a href="https://andrejjh.github.io/fdwc.github.io/"><span style="font-weight: 400">https://andrejjh.github.io/fdwc.github.io/</span></a></p>   <div class="molongui-clearfix"></div> <div id="mab-1821722040" class="m-a-box " data-plugin-release="4.6.18" data-plugin-version="lite" data-box-layout="slim" data-box-position="below" data-multiauthor="false" data-author-id="97703" data-author-type="user" data-author-archived=""> <div class="m-a-box-container"> <div class="m-a-box-tab m-a-box-content m-a-box-profile" data-profile-layout="layout-1" data-author-ref="user-97703" itemscope itemid="https://blog.okfn.org/author/lillywinfree/" itemtype="https://schema.org/Person" > <div class="m-a-box-content-top"> </div> <div class="m-a-box-content-middle">  <div class="m-a-box-item m-a-box-avatar" data-source="local"> <a class="m-a-box-avatar-url" href="https://blog.okfn.org/author/lillywinfree/"> <img width="150" height="150" src="https://blog.okfn.org/wp-content/files/2023/06/lilly-150x150.png" class="attachment-150x150 size-150x150" alt="" loading="lazy" itemprop="image" /> </a> </div>   <div class="m-a-box-item m-a-box-data">  <div class="m-a-box-name m-a-box-title"> <h5 > <a class="m-a-box-name-url " href="https://blog.okfn.org/author/lillywinfree/" > Lilly Winfree </a> </h5> </div>  <div class="m-a-box-item m-a-box-meta"> <script type="text/javascript" language="JavaScript"> if ( typeof window.ToggleAuthorshipData === 'undefined' ) { function ToggleAuthorshipData(id, author) { let box_selector = '#mab-' + id; let box = document.querySelector(box_selector); if ( box.getAttribute('data-multiauthor') ) box_selector = '#mab-' + id + ' [data-author-ref="' + author + '"]'; let label = document.querySelector(box_selector + ' ' + '.m-a-box-data-toggle'); label.innerHTML = ( label.text.trim() === "+ posts" ? 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Lilly believes that the future of research is open, and is using Frictionless Data tooling within the researcher community to make science more reproducible.</p> </div>  <div class="m-a-box-related" data-related-layout="layout-1"> <div class="m-a-box-item m-a-box-related-entries" style="display: none;"> <ul> <li> <div class="m-a-box-related-entry" > <div class="molongui-display-none" > <div >Lilly Winfree</div> <div >https://blog.okfn.org/author/lillywinfree/</div> </div> <div class="m-a-box-related-entry-title"> <i class="m-a-icon-doc"></i> <a class="molongui-remove-underline" href="https://blog.okfn.org/2022/07/05/frictionless-planet-and-lacuna-fund-discuss-gaps-in-climate-datasets-for-machine-learning/" > <span >Frictionless Planet and Lacuna Fund discuss gaps in climate datasets for machine learning</span> </a> </div> </div> </li> <li> <div class="m-a-box-related-entry" > <div class="molongui-display-none" > <div >Lilly Winfree</div> <div >https://blog.okfn.org/author/lillywinfree/</div> </div> <div class="m-a-box-related-entry-title"> <i class="m-a-icon-doc"></i> <a class="molongui-remove-underline" href="https://blog.okfn.org/2022/03/09/combining-data-skills-knowledge-and-networks-to-save-our-planet/" > <span >Combining Data Skills, Knowledge, and Networks to Save our Planet</span> </a> </div> </div> </li> <li> <div class="m-a-box-related-entry" > <div class="molongui-display-none" > <div >Lilly Winfree</div> <div >https://blog.okfn.org/author/lillywinfree/</div> </div> <div class="m-a-box-related-entry-title"> <i class="m-a-icon-doc"></i> <a class="molongui-remove-underline" href="https://blog.okfn.org/2020/11/18/dryad-and-frictionless-data-collaboration/" > <span >Dryad and Frictionless Data collaboration</span> </a> </div> </div> </li> <li> <div class="m-a-box-related-entry" > <div class="molongui-display-none" > <div >Lilly Winfree</div> <div >https://blog.okfn.org/author/lillywinfree/</div> </div> <div class="m-a-box-related-entry-title"> <i class="m-a-icon-doc"></i> <a class="molongui-remove-underline" href="https://blog.okfn.org/2020/10/08/announcing-the-new-frictionless-framework/" > <span >Announcing the New Frictionless Framework</span> </a> </div> </div> </li> </ul> </div> </div> </div> </div> <div class="m-a-box-content-bottom"></div> </div> </div> </div> </div> <footer class="entry-footer"> <span class="cat-links">Posted in: <a href="https://blog.okfn.org/category/okfn-projects/frictionless-data/" rel="category tag">Frictionless Data</a>, <a href="https://blog.okfn.org/category/open-knowledge/" rel="category tag">Open Knowledge</a>, <a href="https://blog.okfn.org/category/open-research/" rel="category tag">Open Research</a>, <a href="https://blog.okfn.org/category/open-science/" rel="category tag">Open Science</a>, <a href="https://blog.okfn.org/category/open-software/" rel="category tag">Open Software</a>, <a href="https://blog.okfn.org/category/technical/" rel="category tag">Technical</a></span> </footer> </article> </div> <div class="sidebar col-lg-4"> <aside class="author-info"> <a class="author-info_link" href="https://www.gravatar.com/ddf27d2815b3012cf25e82d8206d7c78"> <span class="author-info_thumbnail"><img alt='' src='https://blog.okfn.org/wp-content/files/2023/06/lilly.png' class='avatar avatar-80 photo' height='80' width='80' loading='lazy' /></span> </a> <h4 class="author-info_name"> About Lilly Winfree </h4> <p>Lilly is the Product Manager for the Frictionless Data for Reproducible Research project. She has her PhD in neuroscience from Oregon Health and Science University, where she researched brain injury in fruit flies and became an advocate for open science and open data. 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2018</a> <a href="https://blog.okfn.org/category/open-data-day/open-data-day-2020/" class="tag-cloud-link tag-link-2079 tag-link-position-17" style="font-size: 11.444444444444pt;" aria-label="Open Data Day 2020 (68 items)">Open Data Day 2020</a> <a href="https://blog.okfn.org/category/okfn-projects/open-definition/" class="tag-cloud-link tag-link-34 tag-link-position-18" style="font-size: 12.444444444444pt;" aria-label="Open Definition (84 items)">Open Definition</a> <a href="https://blog.okfn.org/category/open-geodata/" class="tag-cloud-link tag-link-36 tag-link-position-19" style="font-size: 8pt;" aria-label="Open Geodata (33 items)">Open Geodata</a> <a href="https://blog.okfn.org/category/open-glam/" class="tag-cloud-link tag-link-182 tag-link-position-20" style="font-size: 9.5555555555556pt;" aria-label="Open GLAM (46 items)">Open GLAM</a> <a href="https://blog.okfn.org/category/open-government-data/" class="tag-cloud-link tag-link-37 tag-link-position-21" style="font-size: 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aria-label="Talks (87 items)">Talks</a> <a href="https://blog.okfn.org/category/technical/" class="tag-cloud-link tag-link-54 tag-link-position-36" style="font-size: 10.444444444444pt;" aria-label="Technical (55 items)">Technical</a> <a href="https://blog.okfn.org/category/the-tech-we-want/" class="tag-cloud-link tag-link-2724 tag-link-position-37" style="font-size: 8.3333333333333pt;" aria-label="The Tech We Want (35 items)">The Tech We Want</a> <a href="https://blog.okfn.org/category/working-groups/wg-economics/" class="tag-cloud-link tag-link-73 tag-link-position-38" style="font-size: 8pt;" aria-label="WG Economics (33 items)">WG Economics</a> <a href="https://blog.okfn.org/category/working-groups/wg-eu-open-data/" class="tag-cloud-link tag-link-74 tag-link-position-39" style="font-size: 13.555555555556pt;" aria-label="WG EU Open Data (106 items)">WG EU Open Data</a> <a href="https://blog.okfn.org/category/working-groups/wg-open-data-in-science/" class="tag-cloud-link tag-link-78 tag-link-position-40" style="font-size: 8.1111111111111pt;" aria-label="WG Open Data in Science (34 items)">WG Open Data in Science</a> <a href="https://blog.okfn.org/category/working-groups/wg-open-government-data/" class="tag-cloud-link tag-link-80 tag-link-position-41" style="font-size: 15.666666666667pt;" aria-label="WG Open Government Data (166 items)">WG Open Government Data</a> <a href="https://blog.okfn.org/category/working-groups/wg-public-domain/" class="tag-cloud-link tag-link-82 tag-link-position-42" style="font-size: 8.5555555555556pt;" aria-label="WG Public Domain (37 items)">WG Public Domain</a> <a href="https://blog.okfn.org/category/okfn-projects/wdmmg/" class="tag-cloud-link tag-link-59 tag-link-position-43" style="font-size: 8.5555555555556pt;" aria-label="Where Does My Money Go (37 items)">Where Does My Money Go</a> <a href="https://blog.okfn.org/category/working-groups/" class="tag-cloud-link tag-link-60 tag-link-position-44" style="font-size: 14.333333333333pt;" aria-label="Working Groups (124 items)">Working Groups</a> <a href="https://blog.okfn.org/category/events/workshop/" class="tag-cloud-link tag-link-61 tag-link-position-45" style="font-size: 10pt;" aria-label="Workshop (50 items)">Workshop</a></div> </li><li id="block-6" class="widget widget_block"> <h5>Tools</h5> </li><li id="block-7" class="widget widget_block widget_media_image"> <figure class="wp-block-image size-full is-resized"><a href="https://opendatacommons.org" target="_blank"><img loading="lazy" src="https://blog.okfn.org/wp-content/files/2023/11/open-data-commons.png" alt="" class="wp-image-28853" width="146" height="46"/></a></figure> </li><li id="block-5" class="widget widget_block widget_media_image"> <figure class="wp-block-image size-full is-resized"><a href="https://opendefinition.org/" target="_blank"><img loading="lazy" src="https://blog.okfn.org/wp-content/files/2023/11/open-definition-1.png" alt="" class="wp-image-28852" width="166" height="47"/></a></figure> </li><li id="block-8" class="widget widget_block widget_media_image"> <figure class="wp-block-image size-full is-resized"><a href="https://opendataeditor.okfn.org" target="_blank"><img loading="lazy" src="https://blog.okfn.org/wp-content/files/2023/11/opendataeditor-landscape-full-1x.png" alt="" class="wp-image-28855" width="149" height="47"/></a></figure> </li><li id="block-9" class="widget widget_block widget_media_image"> <figure class="wp-block-image size-full is-resized"><a href="https://frictionlessdata.io" target="_blank"><img loading="lazy" src="https://blog.okfn.org/wp-content/files/2023/11/frictionlessdata-short-full-1x.png" alt="" class="wp-image-28854" width="159" height="47"/></a></figure> </li><li id="block-10" class="widget widget_block widget_media_image"> <figure class="wp-block-image size-full is-resized"><a href="https://ckan.org" target="_blank"><img loading="lazy" src="https://blog.okfn.org/wp-content/files/2023/11/CKAN-full.png" alt="" class="wp-image-28856" width="107" height="30"/></a></figure> </li><li id="block-14" class="widget widget_block"> <div style="height:10px" aria-hidden="true" class="wp-block-spacer"></div> </li><li id="block-11" class="widget widget_block"> <h5>Community</h5> </li><li id="block-12" class="widget widget_block widget_media_image"> <figure class="wp-block-image size-full is-resized"><a href="https://network.okfn.org/specialist/" target="_blank"><img loading="lazy" src="https://blog.okfn.org/wp-content/files/2023/11/global-directory.png" alt="" class="wp-image-28857" width="217" height="45"/></a></figure> </li><li id="block-13" class="widget widget_block widget_media_image"> <figure class="wp-block-image size-full is-resized"><a href="https://network.okfn.org/project/" target="_blank"><img loading="lazy" src="https://blog.okfn.org/wp-content/files/2023/11/project-repository.png" alt="" class="wp-image-28858" width="238" height="45"/></a></figure> </li><li id="block-15" class="widget widget_block widget_media_image"> <figure class="wp-block-image size-full is-resized"><a href="https://opendataday.org" target="_blank"><img loading="lazy" src="https://blog.okfn.org/wp-content/files/2023/11/ODD-logo-landscape-full-1x.png" alt="" class="wp-image-28859" width="231" height="37"/></a></figure> </li><li id="block-16" class="widget widget_block"> <div style="height:10px" aria-hidden="true" class="wp-block-spacer"></div> </li><li id="text-12" class="widget widget_text"> <div class="textwidget"><p style="text-align: center;"><a href="http://creativecommons.org/licenses/by/4.0/" rel="license"><img class="alignnone aligncenter" style="border-width: 3;" src="https://i.creativecommons.org/l/by/4.0/88x31.png" alt="Creative Commons License" /></a></p> <p style="text-align: center;">This work is licensed under a <a href="http://creativecommons.org/licenses/by/4.0/" rel="license">Creative Commons Attribution 4.0 International License</a>.</p></div> </li> </ul> </div> </div> </div> </main> 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