TreatmentBank

<!DOCTYPE html> <html class="no-js" lang="en"> <head> <meta charset="UTF-8"> <meta name="viewport" content="width=device-width, initial-scale=1"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title>TreatmentBank - Plazi</title> <script>(function(d,e){d[e]=d[e].replace("no-js","js");})(document.documentElement,"className");</script> <meta name="description" content="TreatmentBank is a service to liberate data from scholarly publications and disseminate it as FAIR data"> <link rel="stylesheet" href="/css/style.css"> <link rel="alternate" type="application/rss+xml" href="/treatmentbank/index.xml" title="Plazi"> <link rel="shortcut icon" href="/img/favicon_io/favicon.ico"> <link rel="stylesheet" href="https://unpkg.com/leaflet@1.7.1/dist/leaflet.css" integrity="sha512-xodZBNTC5n17Xt2atTPuE1HxjVMSvLVW9ocqUKLsCC5CXdbqCmblAshOMAS6/keqq/sMZMZ19scR4PsZChSR7A==" crossorigin=""/>  <script src="https://unpkg.com/leaflet@1.7.1/dist/leaflet.js" integrity="sha512-XQoYMqMTK8LvdxXYG3nZ448hOEQiglfqkJs1NOQV44cWnUrBc8PkAOcXy20w0vlaXaVUearIOBhiXZ5V3ynxwA==" crossorigin=""></script> <link rel="stylesheet" href="/css/plazi_styles.css"> <link rel="stylesheet" href="/css/expanding-search.css"> </head> <body class="body"> <div class="container container--outer"> <header class="header"> <div class="container header__container"> <div class="logo logo--mixed"> <div class="logo__item logo__imagebox"> <a class="logo__link" href="/" title="Plazi" rel="home"> <img class="logo__img" src="/img/logo-main.png" alt="Plazi"> </a> </div> <div class="search-box"> <input id="searchInput" type="text" class="search-input" placeholder="search…"> <a class="search-btn" href="#"></a> <ul id="searchResults"></ul> </div> </div>  <nav class="menu"> <button class="menu__btn" aria-haspopup="true" aria-expanded="false" tabindex="0"> <span class="menu__btn-title" tabindex="-1">Menu</span> </button> <ul class="menu__list"> <li class="menu__item"> <a class="menu__link" href="/treatmentbank/"><span class="menu__text">treatmentbank</span></a> </li> <li class="menu__item"> <a class="menu__link" href="/blr/"><span class="menu__text">Biodiversity Literature Repository</span></a> </li> <li class="menu__item"> <a class="menu__link" href="/services/"><span class="menu__text">Services</span></a> </li> <li class="menu__item"> <a class="menu__link" href="/how-to-participate/"><span class="menu__text">How to Participate</span></a> </li> <li class="menu__item"> <a class="menu__link" href="/about/"><span class="menu__text">About</span></a> </li> <li class="menu__item"> <a class="menu__link" href="/15-years/"><span class="menu__text">15 Years</span></a> </li> </ul> </nav>  </div> </header> <div class="wrapper flex"> <div class="primary"> <ol class="nav navbar-nav"> <li> <a href="https://plazi.org/">Home</a> </li> <li class="active"> <a href="https://plazi.org/treatmentbank/">TreatmentBank</a> </li> </ol> <br style="clear:both" />  <main class="main list" role="main"> <header class="main__header"> <h1 class="main__title">TreatmentBank</h1> </header> <div class="content main__content clearfix"> <p><img src="img/tb-logo.png" alt="Treatment Bank"></p> <div class="widget-search widget">  <form class="widget-search__form" role="search" target="_blank" method="get" action="https://tb.plazi.org/GgServer/search"> <label>  <input class="searchInput" type="search" placeholder="find treatments…" id="fullText.ftQuery" name="fullText.ftQuery" aria-label="find treatments…"> </label> <input id="searchBtn" class="searchBtn" type="submit" value="Search"> </form> <div id="search_results"></div> </div> <script> const search = function(e) { const q = document.getElementById('q') const search_results = document.getElementById('search_results') //const tb = 'https://tb.plazi.org/GgServer/search?fullText.matchMode=prefix&fullText.ftQuery=' + q.value fetch(`https://test.zenodeo.org/v3/treatments?q=${q.value}`) .then(function(response) { if (!response.ok) { throw new Error('HTTP error, status = ' + response.status); } return response.json(); }) .then(function(response) { let res = '<h2>Treatments search results</h2>' response.item.records.forEach(r => { res += `<details> <summary>${r.treatmentTitle}</summary> <p>${r.articleTitle}, ${r.journalTitle}</p> </details>` }) search_results.innerHTML = res }) e.stopPropagation() e.preventDefault() } window.onload = function(e) { // const searchBtn = document.getElementById('searchBtn') // searchBtn.addEventListener('click', search) }() </script> <b>GoldenGate Imagine:</b> <a href="https://tb.plazi.org/GgServer/Downloads/GgImagine-Default.imagine.zip">Download <img src="/img/zip.svg" width="30"></a> • <a href="https://drive.google.com/file/d/0B_yrQwn4yBySbzFhS2JqeU1TeUk/view?usp=sharing">Manual <img src="/img/pdf.svg" width="30"></a> <br><br> <p><a href="https://tb.plazi.org/GgServer/search">TreatmentBank (TB)</a> is a service provided by the Swiss Plazi GmbH to liberate data from scholarly publications, and convert, enhance, link, store, and disseminate it as <a href="https://www.force11.org/group/fairgroup/fairprinciples">Findable, Accessible, Interoperable and Reusable (FAIR)</a> data. These data include <a href="what-treatment/">taxonomic treatments</a>, treatment citations, figures, tables, material citations and bibliographic reference. The data extraction processes can be highly automated to process entire journal back-issues as well as current publications. A quality control (QC) process as well as manual checks produce data fit to become reference deposits of treatments in <a href="http://biolitrepo.org/">Biodiversity Literature Repository (BLR)</a>, as well as daily uploads of treatment articles data sets to the <a href="https://www.gbif.org/">Global Biodiversity Information Facility (GBIF)</a>, with persistent identifiers minted in BLR. Input formats can be printed to born-digital publications. All data are openly accessible in various formats and are searchable. Currently, BLR contains more than 650,000 treatments extracted from 66,000 articles, 400,000 figures and 1,040,000 material citations.</p> <p><strong>Role in <a href="https://bicikl-project.eu/">BiCIKL</a></strong>: TB is providing a service for Transnational Access, developing and improving conversion of PDF publications, and serving as the access point for bidirectional linking to data liberated from literature. TB will provide a search portal to find specimens cited in literature as well as a service to link material citations to other research infrastructures (RIs) covering taxonomic names, genomics and specimen data.</p> <div class='featured'> <a href="https://tb.plazi.org/GgServer/search">Fulltext Search</a> <p class="summary"><a href="https://tb.plazi.org/GgServer/search">The TreatmentBank can be searched using a fulltext search. </a></p> </div> <div class='featured'> <a href="https://tb.plazi.org/GgServer/search">Extended Search</a> <p class="summary"><a href="https://tb.plazi.org/GgServer/search">The extended search allows more precise searches related to taxonomic names, bibliographic records or observation records. </a></p> </div> <div class='featured'> <a href="desktop-data-mining">Desktop data mining and extraction</a> <p class="summary"><a href="desktop-data-mining">The GoldenGATE Document Editor is a visual editor for marking up documents in XML. It is designed to do most of the markup automatically. </a></p> </div> <div class='featured'> <a href="data-and-statistics">Data and Statistics</a> <p class="summary"><a href="data-and-statistics">Treatment Stats, Article Stats, RefBank</a></p> </div> <div class='featured'> <a href="treatment-data-access">Treatment Data Access</a> <p class="summary"><a href="treatment-data-access">API, RSS-Feed</a></p> </div> <div class='featured'> <a href="schemas-and-ontologies">Schemas and ontologies</a> <p class="summary"><a href="schemas-and-ontologies">TaxPub, TaxonX, Treatment Ontology</a></p> </div> <div class='featured'> <a href="/source-code/">Source Code</a> <p class="summary"><a href="/source-code/">Source code for all our programs</a></p> </div> <div class='featured'> <a href="/data-apis-tools/visualization-tools/">Visualization Tools</a> <p class="summary"><a href="/data-apis-tools/visualization-tools/">Plazi offers tools for visualizing the data extracted from the taxonomic literature.</a></p> </div> <div class='featured'> <a href="https://github.com/plazi/community/blob/master/learningModules.md" target="_blank">Learning modules</a> <p class="summary"><a href="https://github.com/plazi/community/blob/master/learningModules.md" target="_blank">Explanations and courses to learn about and contribute to and use TreatmentBank.</a></p> </div> </div>  <article class="list__item post"> <header class="list__header"> <h2 class="list__title post__title"> <a href="/treatmentbank/data-and-statistics/" rel="bookmark">Data and Statistics</a> </h2> <div class="meta__item-datetime"> <svg class="meta__icon icon icon-time" width="16" height="14" viewBox="0 0 30 28"><path d="M15 0C7 0 1 6 1 14s6 14 14 14 14-6 14-14S23 0 15 0zm0 25C9 25 4 20 4 14S9 3 15 3s11 5 11 11-5 11-11 11zm1-18h-2v8.4l6.8 4.4L22 18l-6-3.8V7z"/></svg><time class="meta__text" datetime="2021-06-13T19:17:05+02:00">Jun 13, 2021</time> </div> </header> <div class="content list__excerpt post__content clearfix"> Tools to analyze and mine data in TreatmentBank at article and treatment level. <a href="/treatmentbank/data-and-statistics/" rel="bookmark">more</a> </div> </article>   <article class="list__item post"> <header class="list__header"> <h2 class="list__title post__title"> <a href="/treatmentbank/desktop-data-mining/" rel="bookmark">Desktop data mining and extraction</a> </h2> <div class="meta__item-datetime"> <svg class="meta__icon icon icon-time" width="16" height="14" viewBox="0 0 30 28"><path d="M15 0C7 0 1 6 1 14s6 14 14 14 14-6 14-14S23 0 15 0zm0 25C9 25 4 20 4 14S9 3 15 3s11 5 11 11-5 11-11 11zm1-18h-2v8.4l6.8 4.4L22 18l-6-3.8V7z"/></svg><time class="meta__text" datetime="2021-06-13T19:17:05+02:00">Jun 13, 2021</time> </div> </header> <div class="content list__excerpt post__content clearfix"> The GoldenGATE Document Editor is a visual editor for marking up documents in XML. It is designed to do most of the markup automatically. <a href="/treatmentbank/desktop-data-mining/" rel="bookmark">more</a> </div> </article>   <article class="list__item post"> <header class="list__header"> <h2 class="list__title post__title"> <a href="/treatmentbank/schemas-and-ontologies/" rel="bookmark">Schemas and Ontologies</a> </h2> <div class="meta__item-datetime"> <svg class="meta__icon icon icon-time" width="16" height="14" viewBox="0 0 30 28"><path d="M15 0C7 0 1 6 1 14s6 14 14 14 14-6 14-14S23 0 15 0zm0 25C9 25 4 20 4 14S9 3 15 3s11 5 11 11-5 11-11 11zm1-18h-2v8.4l6.8 4.4L22 18l-6-3.8V7z"/></svg><time class="meta__text" datetime="2021-06-13T19:17:05+02:00">Jun 13, 2021</time> </div> </header> <div class="content list__excerpt post__content clearfix"> Schemas and ontologies used in TreatmentBank and Biodiversity Literature Repository. <a href="/treatmentbank/schemas-and-ontologies/" rel="bookmark">more</a> </div> </article>   <article class="list__item post"> <header class="list__header"> <h2 class="list__title post__title"> <a href="/treatmentbank/what-treatment/" rel="bookmark">What is a Treatment?</a> </h2> <div class="meta__item-datetime"> <svg class="meta__icon icon icon-time" width="16" height="14" viewBox="0 0 30 28"><path d="M15 0C7 0 1 6 1 14s6 14 14 14 14-6 14-14S23 0 15 0zm0 25C9 25 4 20 4 14S9 3 15 3s11 5 11 11-5 11-11 11zm1-18h-2v8.4l6.8 4.4L22 18l-6-3.8V7z"/></svg><time class="meta__text" datetime="2021-06-13T19:17:05+02:00">Jun 13, 2021</time> </div> </header> <div class="content list__excerpt post__content clearfix"> A taxonomic treatment is a well-defined part of an article describing a scientific name by an author at the time of the publication. <a href="/treatmentbank/what-treatment/" rel="bookmark">more</a> </div> </article>   <article class="list__item post"> <header class="list__header"> <h2 class="list__title post__title"> <a href="/treatmentbank/treatment-data-access/" rel="bookmark">Treatment Data Access</a> </h2> <div class="meta__item-datetime"> <svg class="meta__icon icon icon-time" width="16" height="14" viewBox="0 0 30 28"><path d="M15 0C7 0 1 6 1 14s6 14 14 14 14-6 14-14S23 0 15 0zm0 25C9 25 4 20 4 14S9 3 15 3s11 5 11 11-5 11-11 11zm1-18h-2v8.4l6.8 4.4L22 18l-6-3.8V7z"/></svg><time class="meta__text" datetime="2021-06-13T19:16:15+02:00">Jun 13, 2021</time> </div> </header> <div class="content list__excerpt post__content clearfix"> Machine-actionable access to TreatmentBank data <a href="/treatmentbank/treatment-data-access/" rel="bookmark">more</a> </div> </article>   <article class="list__item post"> <header class="list__header"> <h2 class="list__title post__title"> <a href="/treatmentbank/visualization-tools/" rel="bookmark">Visualization Tools</a> </h2> <div class="meta__item-datetime"> <svg class="meta__icon icon icon-time" width="16" height="14" viewBox="0 0 30 28"><path d="M15 0C7 0 1 6 1 14s6 14 14 14 14-6 14-14S23 0 15 0zm0 25C9 25 4 20 4 14S9 3 15 3s11 5 11 11-5 11-11 11zm1-18h-2v8.4l6.8 4.4L22 18l-6-3.8V7z"/></svg><time class="meta__text" datetime="2021-04-26T19:17:05+02:00">Apr 26, 2021</time> </div> </header> <div class="content list__excerpt post__content clearfix"> A taxonomic treatment is a well-defined part of an article describing a scientific name by an author at the time of the publication. <a href="/treatmentbank/visualization-tools/" rel="bookmark">more</a> </div> </article>  </main>  </div> <aside class="sidebar sidebar--left">  <div class="widget-stats widget"> <h4 class="widget__title">Stats</h4> <div class="widget__content"> <ul> <li><b>Articles:</b> <span id="DocArticleUuid"></span></li> <li><b>Treatments:</b> <span id="DocUuid"></span></li> <li><b>Treatments with Mat. Citations:</b> <span id="DocCount"></span></li> <li><b>Material Citations:</b> <span id="MatCitId"></span></li> <li><b>Georeferenced Mat. Citations:</b> <span id="MatCitIdGeoRef"></span></li> </ul> </div> </div> <script> const tbstats = [ { src: 'pubAndTreatmentCounts', tgt: [ 'DocArticleUuid' ] }, { src: 'pubAndTreatmentCountsWithStubs', tgt: [ 'DocUuid' ] }, { src: 'materialsCitationCount', tgt: [ 'DocCount', 'MatCitId' ] }, { src: 'materialsCitationGeoRefCount', tgt: [ 'MatCitIdGeoRef' ] } ] const tburl = 'https://tb.plazi.org/GgServer/srsStaticStats' tbstats.forEach(t => { fetch(`${tburl}/${t.src}.json`, {mode: 'cors'}) .then(function(response) { if (!response.ok) { throw new Error('HTTP error, status = ' + response.status); } return response.json(); }) .then(function(response) { t.tgt.forEach(tgt => { let resTgt = tgt if (tgt === 'MatCitIdGeoRef') { resTgt = 'MatCitId' } document.getElementById(tgt).innerHTML = response[resTgt] }) }) }) </script>   <div class="widget-events widget"> <h4 class="widget__title">Events</h4> <div class="widget__content"> <ul class="widget__list"> <li class="widget__item"> <a class='widget__link currentEvent' href="/posts/2024/12/biodiversity-knowledge-in-digital-era/">Mar 10, 2025. Free Access and Reuse of Scientific Data (Course), Universidad Nacional de Colombia (UNC) – Bogota - Colombia</a> </li> </ul> </div> </div>  <div class="widget-taglist widget"> <h4 class="widget__title">Tags</h4> <div class="widget__content"> <a class="widget-taglist__link widget__link btn tags" href="/tags/about/" title="About">About (8)</a> <a class="widget-taglist__link widget__link btn tags" href="/tags/batlit/" title="Batlit">Batlit (1)</a> <a class="widget-taglist__link widget__link btn tags" href="/tags/bhl-sibils/" title="BHL Sibils">BHL Sibils (1)</a> <a class="widget-taglist__link widget__link btn tags" href="/tags/bicikl/" title="BiCIKL">BiCIKL (3)</a> <a class="widget-taglist__link widget__link btn tags" href="/tags/blr/" title="BLR">BLR (2)</a> <a class="widget-taglist__link widget__link btn tags" href="/tags/blue-list/" title="Blue List">Blue List (1)</a> <a class="widget-taglist__link widget__link btn tags" href="/tags/dak/" title="DAK">DAK (1)</a> <a 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TreatmentBank - Plazi