<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-01847326</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-24T22:54:17+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Reproducibility in Biomedical Natural Language Processing</title>
            <author role="aut">
              <persName>
                <forename type="first">Kevin</forename>
                <surname>Cohen</surname>
              </persName>
              <email type="md5">5ca9028730bda7e5440d3c935be20457</email>
              <email type="domain">limsi.fr</email>
              <idno type="idhal" notation="numeric">1034704</idno>
              <idno type="halauthorid" notation="string">1400680-1034704</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-1749-8290</idno>
              <idno type="IDREF">https://www.idref.fr/110356608</idno>
              <affiliation ref="#struct-466298"/>
              <affiliation ref="#struct-229493"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Aurélie</forename>
                <surname>Névéol</surname>
              </persName>
              <email type="md5">e940b30e4efdd83272c0245ca6255b44</email>
              <email type="domain">limsi.fr</email>
              <idno type="idhal" notation="string">aurelie-neveol</idno>
              <idno type="idhal" notation="numeric">20620</idno>
              <idno type="halauthorid" notation="string">6298-20620</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-1846-9144</idno>
              <idno type="IDREF">https://www.idref.fr/094239428</idno>
              <affiliation ref="#struct-466298"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Jingbo</forename>
                <surname>Xia</surname>
              </persName>
              <idno type="idhal" notation="numeric">792187</idno>
              <idno type="halauthorid" notation="string">1400681-792187</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-7285-588X</idno>
              <affiliation ref="#struct-462316"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Negacy</forename>
                <surname>Hailu</surname>
              </persName>
              <idno type="halauthorid">1405851-0</idno>
              <affiliation ref="#struct-229493"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Lawrence</forename>
                <surname>Hunter</surname>
              </persName>
              <idno type="halauthorid">479845-0</idno>
              <affiliation ref="#struct-229493"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Pierre</forename>
                <surname>Zweigenbaum</surname>
              </persName>
              <email type="md5">875a8768fc7f867a01a904fe839de31d</email>
              <email type="domain">limsi.fr</email>
              <idno type="idhal" notation="string">pierre-zweigenbaum</idno>
              <idno type="idhal" notation="numeric">14995</idno>
              <idno type="halauthorid" notation="string">1218-14995</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-8410-4808</idno>
              <idno type="IDREF">https://www.idref.fr/06664268X</idno>
              <affiliation ref="#struct-466298"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Limsi</forename>
                <surname>Publications</surname>
              </persName>
              <email type="md5">8e5605f65b0cc7a415570f9c535b6d01</email>
              <email type="domain">limsi.fr</email>
            </editor>
            <funder ref="#projeurop-650213"/>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2018-07-23 14:59:31</date>
              <date type="whenWritten">2017</date>
              <date type="whenModified">2025-08-22 09:04:02</date>
              <date type="whenReleased">2018-07-27 13:55:50</date>
              <date type="whenProduced">2017-11-01</date>
              <date type="whenEndEmbargoed">2018-07-23</date>
              <ref type="file" target="https://hal.science/hal-01847326v1/document">
                <date notBefore="2018-07-23"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://hal.science/hal-01847326v1/file/Reproducibility_AMIA2017_poster_final.pdf" id="file-1847355-1875944">
                <date notBefore="2018-07-23"/>
              </ref>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="560720">
                <persName>
                  <forename>Limsi</forename>
                  <surname>Publications</surname>
                </persName>
                <email type="md5">8e5605f65b0cc7a415570f9c535b6d01</email>
                <email type="domain">limsi.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-01847326</idno>
            <idno type="halUri">https://hal.science/hal-01847326</idno>
            <idno type="halBibtex">cohen:hal-01847326</idno>
            <idno type="halRefHtml">&lt;i&gt;AMIA Annual Symposium&lt;/i&gt;, Nov 2017, Washington, DC, United States</idno>
            <idno type="halRef">AMIA Annual Symposium, Nov 2017, Washington, DC, United States</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-1847355-1875944"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="UNIV-PSUD">Université Paris Sud - Paris XI</idno>
            <idno type="stamp" n="OPENAIRE">OpenAIRE</idno>
            <idno type="stamp" n="LIMSI">Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur</idno>
            <idno type="stamp" n="UNIV-PARIS-SACLAY">Université Paris-Saclay</idno>
            <idno type="stamp" n="UNIV-PSUD-SACLAY" corresp="UNIV-PARIS-SACLAY">Université Paris Sud pour Paris Saclay</idno>
            <idno type="stamp" n="SORBONNE-UNIVERSITE">Sorbonne Université</idno>
            <idno type="stamp" n="SU-INF-2018" corresp="SORBONNE-UNIVERSITE">SORBONNE université &lt;2018</idno>
            <idno type="stamp" n="TEST-HALCNRS">Collection test HAL CNRS</idno>
            <idno type="stamp" n="SU-TI">Sorbonne Université - Texte Intégral</idno>
            <idno type="stamp" n="LISN">Laboratoire Interdisciplinaire des Sciences du Numérique</idno>
            <idno type="stamp" n="GS-ENGINEERING">Graduate School Sciences de l'Ingénierie et des Systèmes</idno>
            <idno type="stamp" n="GS-COMPUTER-SCIENCE">Graduate School Computer Science</idno>
            <idno type="stamp" n="GS-SPORT-HUMAN-MOVEMENT">Graduate School Sport, Mouvement, Facteurs Humains</idno>
            <idno type="stamp" n="LISN-ILES" corresp="LISN">Information, Langue Ecrite et Signée </idno>
            <idno type="stamp" n="COMUE-UPSACLAY" corresp="UNIV-PARIS-SACLAY">Comue Univeristé Paris-Saclay</idno>
            <idno type="stamp" n="ALLIANCE-SU"> Alliance Sorbonne Université</idno>
            <idno type="stamp" n="LISN-STL">Sciences et Technologies des Langues</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="invited" n="0">No</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
            <note type="proceedings" n="0">No</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Reproducibility in Biomedical Natural Language Processing</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Kevin</forename>
                    <surname>Cohen</surname>
                  </persName>
                  <email type="md5">5ca9028730bda7e5440d3c935be20457</email>
                  <email type="domain">limsi.fr</email>
                  <idno type="idhal" notation="numeric">1034704</idno>
                  <idno type="halauthorid" notation="string">1400680-1034704</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-1749-8290</idno>
                  <idno type="IDREF">https://www.idref.fr/110356608</idno>
                  <affiliation ref="#struct-466298"/>
                  <affiliation ref="#struct-229493"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Aurélie</forename>
                    <surname>Névéol</surname>
                  </persName>
                  <email type="md5">e940b30e4efdd83272c0245ca6255b44</email>
                  <email type="domain">limsi.fr</email>
                  <idno type="idhal" notation="string">aurelie-neveol</idno>
                  <idno type="idhal" notation="numeric">20620</idno>
                  <idno type="halauthorid" notation="string">6298-20620</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-1846-9144</idno>
                  <idno type="IDREF">https://www.idref.fr/094239428</idno>
                  <affiliation ref="#struct-466298"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Jingbo</forename>
                    <surname>Xia</surname>
                  </persName>
                  <idno type="idhal" notation="numeric">792187</idno>
                  <idno type="halauthorid" notation="string">1400681-792187</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-7285-588X</idno>
                  <affiliation ref="#struct-462316"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Negacy</forename>
                    <surname>Hailu</surname>
                  </persName>
                  <idno type="halauthorid">1405851-0</idno>
                  <affiliation ref="#struct-229493"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Lawrence</forename>
                    <surname>Hunter</surname>
                  </persName>
                  <idno type="halauthorid">479845-0</idno>
                  <affiliation ref="#struct-229493"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Pierre</forename>
                    <surname>Zweigenbaum</surname>
                  </persName>
                  <email type="md5">875a8768fc7f867a01a904fe839de31d</email>
                  <email type="domain">limsi.fr</email>
                  <idno type="idhal" notation="string">pierre-zweigenbaum</idno>
                  <idno type="idhal" notation="numeric">14995</idno>
                  <idno type="halauthorid" notation="string">1218-14995</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-8410-4808</idno>
                  <idno type="IDREF">https://www.idref.fr/06664268X</idno>
                  <affiliation ref="#struct-466298"/>
                </author>
              </analytic>
              <monogr>
                <meeting>
                  <title>AMIA Annual Symposium</title>
                  <date type="start">2017-11-01</date>
                  <date type="end">2017-11-08</date>
                  <settlement>Washington, DC</settlement>
                  <country key="US">United States</country>
                </meeting>
                <imprint/>
              </monogr>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <classCode scheme="halDomain" n="info">Computer Science [cs]</classCode>
              <classCode scheme="halDomain" n="info.info-cl">Computer Science [cs]/Computation and Language [cs.CL]</classCode>
              <classCode scheme="halTypology" n="COMM">Conference papers</classCode>
              <classCode scheme="halOldTypology" n="COMM">Conference papers</classCode>
              <classCode scheme="halTreeTypology" n="COMM">Conference papers</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>To assess the state of reproducibility in biomedical Natural Language Processing, we analyze the proceedings of the 2016 BioNLP workshop to check for code and data availability. We find that only 21% of papers report experiments where both data and code are available, with moderate to substantial inter-annotator agreement. This suggests that reproducibility in biomedical NLP would benefit from increased attention and understanding.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="researchteam" xml:id="struct-466298" status="OLD">
          <orgName>Information, Langue Ecrite et Signée</orgName>
          <orgName type="acronym">ILES</orgName>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <addrLine>LimsiCampus Universitaire bât 50891405 Orsay cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.limsi.fr/fr/recherche/iles</ref>
          </desc>
          <listRelation>
            <relation active="#struct-247329" type="direct"/>
            <relation active="#struct-92966" type="indirect"/>
            <relation active="#struct-408837" type="indirect"/>
            <relation active="#struct-413221" type="indirect"/>
            <relation active="#struct-419361" type="indirect"/>
            <relation name="UPR3251" active="#struct-441569" type="indirect"/>
            <relation active="#struct-562112" type="indirect"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-229493" status="VALID">
          <orgName>Computational Bioscience Program. University of Colorado Denver</orgName>
          <desc>
            <address>
              <addrLine>School of Medicine Aurora, CO 80045, USA</addrLine>
              <country key="US"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-302215" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-462316" status="VALID">
          <idno type="IdRef">177575859</idno>
          <idno type="ISNI">0000000417904137</idno>
          <idno type="ROR">https://ror.org/023b72294</idno>
          <idno type="Wikidata">Q3429270</idno>
          <orgName>Huazhong Agricultural University [Wuhan]</orgName>
          <orgName type="acronym">HZAU</orgName>
          <date type="start">2016-07-29</date>
          <desc>
            <address>
              <addrLine>No.1,Shizishan Street, Hongshan District, Wuhan, Hubei Province, 430070, P.R.China</addrLine>
              <country key="CN"/>
            </address>
            <ref type="url">https://www.hzau.edu.cn/en/HOME.htm</ref>
          </desc>
        </org>
        <org type="laboratory" xml:id="struct-247329" status="OLD">
          <orgName>Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur</orgName>
          <orgName type="acronym">LIMSI</orgName>
          <date type="start">1962-01-01</date>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <addrLine>Université Paris-Sud Bât. 507 - Rue du Belvédère -91405 ORSAY CEDEX</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.limsi.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-92966" type="direct"/>
            <relation active="#struct-408837" type="direct"/>
            <relation active="#struct-413221" type="indirect"/>
            <relation active="#struct-419361" type="direct"/>
            <relation name="UPR3251" active="#struct-441569" type="direct"/>
            <relation active="#struct-562112" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-92966" status="OLD">
          <idno type="ROR">https://ror.org/028rypz17</idno>
          <orgName>Université Paris-Sud - Paris 11</orgName>
          <orgName type="acronym">UP11</orgName>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <addrLine>Bâtiment 300 - 91405 Orsay cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.u-psud.fr/</ref>
          </desc>
        </org>
        <org type="regrouplaboratory" xml:id="struct-408837" status="VALID">
          <orgName>Sorbonne Université - UFR d'Ingénierie</orgName>
          <orgName type="acronym">UFR 919</orgName>
          <desc>
            <address>
              <addrLine>SORBONNE UNIVERSITEFACULTE DES SCIENCES ET INGENIERIEUFR D'INGENIERIETour 55/65 - 2e étage4 place Jussieu75252 Paris cedex 05</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://ingenierie.sorbonne-universite.fr/fr/index.html</ref>
          </desc>
          <listRelation>
            <relation active="#struct-413221" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-413221" status="VALID">
          <idno type="IdRef">221333754</idno>
          <idno type="ROR">https://ror.org/02en5vm52</idno>
          <orgName>Sorbonne Université</orgName>
          <orgName type="acronym">SU</orgName>
          <date type="start">2018-01-01</date>
          <desc>
            <address>
              <addrLine>21 rue de l’École de médecine - 75006 Paris</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.sorbonne-universite.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-419361" status="VALID">
          <idno type="IdRef">241345251</idno>
          <idno type="ROR">https://ror.org/03xjwb503</idno>
          <orgName>Université Paris-Saclay</orgName>
          <desc>
            <address>
              <addrLine>Bâtiment Bréguet, 3 Rue Joliot Curie 2e ét, 91190 Gif-sur-Yvette</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.universite-paris-saclay.fr/fr</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-562112" status="OLD">
          <orgName>Université Paris Saclay (COmUE)</orgName>
          <desc>
            <address>
              <addrLine>Espace Technologique, Bât. Discovery - RD 128 - 2è ététage, 91190 Saint-Aubin</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.universite-paris-saclay.fr/fr</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-302215" status="VALID">
          <idno type="ROR">https://ror.org/02ttsq026</idno>
          <orgName>University of Colorado [Boulder]</orgName>
          <desc>
            <address>
              <addrLine>Boulder, Colorado 80309</addrLine>
              <country key="US"/>
            </address>
            <ref type="url">http://www.colorado.edu/</ref>
          </desc>
        </org>
      </listOrg>
      <listOrg type="projects">
        <org type="europeanProject" xml:id="projeurop-650213" status="VALID">
          <idno type="number">676207</idno>
          <idno type="program">H2020-MSCA-ITN-2015</idno>
          <idno type="call">H2020-MSCA-ITN-2015</idno>
          <orgName>MIROR</orgName>
          <desc>Methods in Research on Research</desc>
          <date type="start">2016-03-01</date>
          <date type="end">2020-02-29</date>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>