<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article PUBLIC "-//TaxonX//DTD Taxonomic Treatment Publishing DTD v0 20100105//EN" "../../nlm/tax-treatment-NS0.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:tp="http://www.plazi.org/taxpub" article-type="research-article">
  <front>
    <journal-meta>
      <journal-id journal-id-type="publisher-id">63</journal-id>
      <journal-id journal-id-type="index">urn:lsid:arphahub.com:pub:0E0032F4-55AE-5263-8B3C-F4DD637C30C2</journal-id>
      <journal-title-group>
        <journal-title xml:lang="en">Biodiversity Information Science and Standards</journal-title>
        <abbrev-journal-title xml:lang="en">BISS</abbrev-journal-title>
      </journal-title-group>
      <issn pub-type="epub">2535-0897</issn>
      <publisher>
        <publisher-name>Pensoft Publishers</publisher-name>
      </publisher>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.3897/tdwgproceedings.1.20379</article-id>
      <article-id pub-id-type="publisher-id">20379</article-id>
      <article-id pub-id-type="manuscript">7736</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>Conference Abstract</subject>
        </subj-group>
        <subj-group subj-group-type="conference-part">
          <subject>Symposium: Biodiversity Data Quality – concepts, methods and tools</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>Fitness-for-Use-Framework-aware Data Quality workflows in Kurator</article-title>
      </title-group>
      <contrib-group content-type="authors">
        <contrib contrib-type="author" corresp="yes">
          <name name-style="western">
            <surname>Morris</surname>
            <given-names>Paul J.</given-names>
          </name>
          <email xlink:type="simple">mole@morris.net</email>
          <xref ref-type="aff" rid="A1">1</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Hanken</surname>
            <given-names>James</given-names>
          </name>
          <xref ref-type="aff" rid="A1">1</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Lowery</surname>
            <given-names>David B.</given-names>
          </name>
          <xref ref-type="aff" rid="A1">1</xref>
          <xref ref-type="aff" rid="A2">2</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Ludäscher</surname>
            <given-names>Bertram</given-names>
          </name>
          <xref ref-type="aff" rid="A3">3</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Macklin</surname>
            <given-names>James</given-names>
          </name>
          <xref ref-type="aff" rid="A4">4</xref>
          <xref ref-type="aff" rid="A4">4</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>McPhillips</surname>
            <given-names>Timothy</given-names>
          </name>
          <xref ref-type="aff" rid="A3">3</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Morris</surname>
            <given-names>Robert A.</given-names>
          </name>
          <xref ref-type="aff" rid="A2">2</xref>
          <xref ref-type="aff" rid="A1">1</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Wieczorek</surname>
            <given-names>John</given-names>
          </name>
          <xref ref-type="aff" rid="A1">1</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Zhang</surname>
            <given-names>Qian</given-names>
          </name>
          <xref ref-type="aff" rid="A3">3</xref>
        </contrib>
      </contrib-group>
      <aff id="A1">
        <label>1</label>
        <addr-line content-type="verbatim">Museum of Comparative Zoology, Harvard University, Cambridge, United States of America</addr-line>
        <institution>Museum of Comparative Zoology, Harvard University</institution>
        <addr-line content-type="city">Cambridge</addr-line>
        <country>United States of America</country>
      </aff>
      <aff id="A2">
        <label>2</label>
        <addr-line content-type="verbatim">University of Massachusetts, Boston, Boston, United States of America</addr-line>
        <institution>University of Massachusetts, Boston</institution>
        <addr-line content-type="city">Boston</addr-line>
        <country>United States of America</country>
      </aff>
      <aff id="A3">
        <label>3</label>
        <addr-line content-type="verbatim">University of Illinois Urbana-Champaign, Champaign, United States of America</addr-line>
        <institution>University of Illinois Urbana-Champaign</institution>
        <addr-line content-type="city">Champaign</addr-line>
        <country>United States of America</country>
      </aff>
      <aff id="A4">
        <label>4</label>
        <addr-line content-type="verbatim">Agriculture and Agri-Food Canada, Ottawa, Canada</addr-line>
        <institution>Agriculture and Agri-Food Canada</institution>
        <addr-line content-type="city">Ottawa</addr-line>
        <country>Canada</country>
      </aff>
      <author-notes>
        <fn fn-type="corresp">
          <p>Corresponding author: Paul J. Morris (<email xlink:type="simple">mole@morris.net</email>).</p>
        </fn>
        <fn fn-type="edited-by">
          <p>Academic editor: </p>
        </fn>
      </author-notes>
      <pub-date pub-type="collection">
        <year>2017</year>
      </pub-date>
      <pub-date pub-type="epub">
        <day>16</day>
        <month>08</month>
        <year>2017</year>
      </pub-date>
      <volume>1</volume>
      <elocation-id>e20379</elocation-id>
      <uri content-type="arpha" xlink:href="http://openbiodiv.net/637030E7-7481-5662-94C0-A78483AE3611">637030E7-7481-5662-94C0-A78483AE3611</uri>
      <uri content-type="zenodo_dep_id" xlink:href="https://zenodo.org/record/1140601">1140601</uri>
      <history>
        <date date-type="received">
          <day>16</day>
          <month>08</month>
          <year>2017</year>
        </date>
      </history>
      <permissions>
        <copyright-statement>Paul J. Morris, James Hanken, David B. Lowery, Bertram Ludäscher, James Macklin, Timothy McPhillips, Robert A. Morris, John Wieczorek, Qian Zhang</copyright-statement>
        <license license-type="creative-commons-attribution" xlink:href="http://creativecommons.org/licenses/by/4.0" xlink:type="simple">
          <license-p>This is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
        </license>
      </permissions>
      <abstract>
        <label>Abstract</label>
        <p>In the Kurator project, we are developing libraries of small modules, each designed to address a particular data quality test. These libraries, which can be run on single computers or scalable architecture, can be incorporated into data management processes in the form of customizable data quality scripts. A script composed of these modules can be incorporated into other software, run as command-line programs, or provided as a suite of “canned” workflows through a web interface.</p>
        <p>In some of these modules, we have implemented a subset of the standard tests under development by Task Group 2 (TG2) of the Data Quality Interest Group. We have also been exploring use of the fitness-for-use-framework (<xref ref-type="bibr" rid="B3710252">Veiga et al. 2017</xref>) produced by Task Group 1 (TG1) of the Data Quality Interest Group. Our goals have been to explore use of the framework to describe capabilities of atomic modules of code, how we can use concepts in the framework to produce data quality reports, and what lessons can be learned from implementing data quality control code in the context of the framework.  We have focused on the Data Quality Reports level of the framework; in particular, the representation of Data Quality Measures (measurements on some data quality dimension), Validations (tests for compliance with quality needs), and Amendments (proposals to improve data quality).</p>
        <p>At the implementation level, we have developed a set of Java annotations to mark methods as providing specific tests from the test suite. In terms of the framework, the annotations can also be used to mark methods as providing Measures, Validations, or Amendments and to associate method parameters with Information Elements by linking them to the Darwin Core terms that were either "acted upon" or "consulted" (<xref ref-type="bibr" rid="B3710332">Lowery et al. 2016</xref>).</p>
        <p>These annotations can be used by a consumer to identify and run Measures and Validations in two phases: a Pre-Amendment phase, before the Amendments are run; and a Post-Amendment phase, after the changes proposed by the Amendments have been applied. Capturing the test results across both stages allows us to report on how much accepting the amendments would improve the quality of the dataset as a whole, data in some quality dimension, or data for some specific purpose.</p>
        <p>We have found it important to be able to render data quality reports that identify which Darwin Core terms are the Valuable Information elements involved in a specific test, and, further, to identify which terms are acted upon and which are consulted. Identifying this information allows us, for example, to render tabular reports highlighting cells where amendments have proposed a change.</p>
        <p>We have also found reporting of error and failure conditions to be important, and have been working on implementing the TG1 suggestion that report elements consist of a result (containing only appropriate values), status (containing a controlled vocabulary term such as completed, or data_prerequisites_not_met), and a human readable message (metadata about why the conclusion that was drawn was drawn, or error messages).</p>
        <p>We have developed a stake-in-the-ground vocabulary for status values to describe failure conditions including the following concepts: Ambiguous (there was a result, but it has ambiguity, e.g., an event date inferred from the verbatim event date 04/05/1954), Internal Prerequisites Not Met (not able to run the test on the data provided, e.g., day was not an integer), and External Prerequisites Not Met (some external resource that this test consults was unavailable at runtime).</p>
        <p>In implementing tests in the context of the framework, we have seen the value of identifying Measures, Validations, and Amendments in forcing us to develop small, focused tests, and in allowing us group assertions within data quality reports based on data quality needs.</p>
      </abstract>
      <kwd-group>
        <label>Keywords</label>
        <kwd>Biodiversity Informatics</kwd>
        <kwd>Workflows</kwd>
        <kwd>Data Quality</kwd>
      </kwd-group>
      <funding-group>
        <award-group>
          <funding-source>
            <named-content content-type="funder_name">National Science Foundation</named-content>
            <named-content content-type="funder_identifier">100000001</named-content>
            <named-content content-type="funder_doi">http://doi.org/10.13039/100000001</named-content>
          </funding-source>
        </award-group>
      </funding-group>
      <conference>
        <conf-date>1-6 October 2017</conf-date>
        <conf-name>TDWG 2017 Annual Conference</conf-name>
        <conf-acronym>TDWG 2017</conf-acronym>
        <conf-loc>Ottawa, Canada</conf-loc>
        <conf-theme>Data Integration in a Big Data Universe: Associating Occurrences with Genes, Phenotypes, and Environments</conf-theme>
      </conference>
      <counts>
        <fig-count count="0"/>
        <table-count count="0"/>
        <ref-count count="2"/>
      </counts>
    </article-meta>
    <notes>
      <sec sec-type="Presenting author">
        <title>Presenting author</title>
        <p>Paul J. Morris</p>
      </sec>
      <sec sec-type="Funding program">
        <title>Funding program</title>
        <p>NSF DBI <ext-link ext-link-type="uri" xlink:href="http://nsf.gov/awardsearch/showAward?AWD_ID=1356438">1356438</ext-link> and <ext-link ext-link-type="uri" xlink:href="http://www.nsf.gov/awardsearch/showAward?AWD_ID=1356751">1356751</ext-link></p>
      </sec>
    </notes>
  </front>
  <back>
    <ref-list>
      <title>References</title>
      <ref id="B3710332">
        <element-citation publication-type="article">
          <person-group person-group-type="author">
            <name name-style="western">
              <surname>Lowery</surname>
              <given-names>David</given-names>
            </name>
            <name name-style="western">
              <surname>Morris</surname>
              <given-names>Paul J.</given-names>
            </name>
            <name name-style="western">
              <surname>Veiga</surname>
              <given-names>Allan Koch</given-names>
            </name>
          </person-group>
          <year>2016</year>
          <article-title>Kurator-Org/Kurator-Ffdq: Initial Release Of Kurator-Ffdq Library Version 1.0.0.</article-title>
          <source>Zenodo</source>
          <uri>http://dx.doi.org/10.5281/ZENODO.192186</uri>
          <pub-id pub-id-type="doi">10.5281/ZENODO.192186</pub-id>
        </element-citation>
      </ref>
      <ref id="B3710252">
        <element-citation publication-type="article">
          <person-group person-group-type="author">
            <name name-style="western">
              <surname>Veiga</surname>
              <given-names>Allan Koch</given-names>
            </name>
            <name name-style="western">
              <surname>Saraiva</surname>
              <given-names>Antonio Mauro</given-names>
            </name>
            <name name-style="western">
              <surname>Chapman</surname>
              <given-names>Arthur David</given-names>
            </name>
            <name name-style="western">
              <surname>Morris</surname>
              <given-names>Paul John</given-names>
            </name>
            <name name-style="western">
              <surname>Gendreau</surname>
              <given-names>Christian</given-names>
            </name>
            <name name-style="western">
              <surname>Schigel</surname>
              <given-names>Dmitry</given-names>
            </name>
            <name name-style="western">
              <surname>Robertson</surname>
              <given-names>Tim James</given-names>
            </name>
          </person-group>
          <year>2017</year>
          <article-title>A conceptual framework for quality assessment and management of biodiversity data</article-title>
          <source>PLOS ONE</source>
          <volume>12</volume>
          <issue>6</issue>
          <fpage>e0178731</fpage>
          <uri>http://dx.doi.org/10.1371/journal.pone.0178731</uri>
          <pub-id pub-id-type="doi">10.1371/journal.pone.0178731</pub-id>
        </element-citation>
      </ref>
    </ref-list>
  </back>
</article>
