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  <front>
    <journal-meta>
      <journal-id journal-id-type="iso-abbrev">Pharmacophore</journal-id>
      <journal-id journal-id-type="publisher-id">pharmacophorejournal.com</journal-id>
      <journal-id journal-id-type="publisher-id">Pharmacophore</journal-id>
      <journal-title-group>
        <journal-title>Pharmacophore</journal-title>
      </journal-title-group>
      <issn pub-type="epub">2229-5402</issn>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="publisher-id">pharmacophorejournal.com-6919</article-id>
      <article-id pub-id-type="doi">10.51847/L0e6kRVTHx</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>Original research</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>A Common Provenance Language for Traceable Pharmaceutical Data, Reproducible Bioinformatics, and Auditable Computational Discovery</article-title>
      </title-group>
                    <contrib-group>
                      <contrib contrib-type="author">
              <name>
                <surname>Al-Jubouri</surname>
                <given-names>Ahmed</given-names>
              </name>
                              <xref rid="aff1" ref-type="aff">1</xref>
                                                            <xref rid="cor1" ref-type="corresp" />
                          </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Carter</surname>
                <given-names>Emma</given-names>
              </name>
                              <xref rid="aff2" ref-type="aff">2</xref>
                                        </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Hoffmann</surname>
                <given-names>Thomas</given-names>
              </name>
                              <xref rid="aff3" ref-type="aff">3</xref>
                                        </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Al-Hassan</surname>
                <given-names>Noor</given-names>
              </name>
                              <xref rid="aff1" ref-type="aff">1</xref>
                                        </contrib>
                  </contrib-group>
                  <aff id="aff1">
            <label>1</label>Department of Data Provenance and Computational Reproducibility, College of Pharmacy, University of Baghdad, Baghdad, Iraq.
          </aff>
                  <aff id="aff2">
            <label>2</label>Department of Bioinformatics Traceability and Auditable Workflows, Faculty of Pharmacy, University of London, London, United Kingdom.
          </aff>
                  <aff id="aff3">
            <label>3</label>Department of Computational Discovery and Data Governance, Faculty of Pharmaceutical Sciences, Heidelberg University, Heidelberg, Germany.
          </aff>
                          <author-notes>
            <corresp id="cor1">
              <bold>Address for correspondence:</bold> Prof. Wael Abu Dayyih, Department of
              Pharmaceutical Chemistry, Faculty of Pharmacy, Mutah University, Al-Karak 61710, Jordan.
                              E-mail: <email xlink:href="ahmed.aljubouri@uobaghdad.edu.iq">ahmed.aljubouri@uobaghdad.edu.iq</email>
                          </corresp>
          </author-notes>
                    <pub-date pub-type="epub">
        <day>28</day>
        <month>10</month>
        <year>2024</year>
      </pub-date>
      <volume>15</volume>
      <issue>5</issue>
      <fpage>69</fpage>
      <lpage>79</lpage>
      <permissions>
        <copyright-statement>
          Copyright: &#x000a9; 2026 Pharmacophore
        </copyright-statement>
        <copyright-year>2026</copyright-year>
        <license>
          <ali:license_ref xmlns:ali="http://www.niso.org/schemas/ali/1.0/"
            specific-use="textmining" content-type="ccbyncsalicense">
            https://creativecommons.org/licenses/by-nc-sa/4.0/</ali:license_ref>
          <license-p>This is an open access journal, and articles are distributed under the terms of
            the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows
            others to remix, tweak, and build upon the work non-commercially, as long as appropriate
            credit is given and the new creations are licensed under the identical terms.</license-p>
        </license>
      </permissions>
      <abstract>
        <title>A<sc>BSTRACT</sc></title>
        <p>Pharmaceutical computation increasingly depends on heterogeneous molecular, biological, experimental, clinical, and computational resources that are repeatedly transformed across data acquisition, preprocessing, modeling, interpretation, and decision-support activities. Although workflow systems, metadata standards, FAIR data practices, machine-learning reporting recommendations, and biomedical knowledge graphs address important parts of this landscape, they do not provide a shared language for describing how pharmaceutical evidence is produced, modified, interpreted, and reused. This article proposes a Common Pharmaceutical Provenance Language as an original ontological contribution for representing the entities, activities, agents, relationships, versions, decisions, and evidential boundaries that constitute computational pharmaceutical discovery. The proposed language distinguishes source observations from derived data, transformations from their outputs, computational predictions from interpretations, and evidence lineage from claims of mechanism, utility, or therapeutic validity. Its architecture organizes provenance across four linked analytical zones: acquisition, preprocessing, modeling, and interpretation. It further specifies minimum metadata requirements, typed relationships, version-aware transformation records, human-decision objects, and interfaces with FAIR data systems, executable workflows, and knowledge graphs. The contribution is conceptual rather than empirically validated. It does not establish that provenance completeness guarantees reproducibility, that transparent lineage ensures data suitability, or that auditable computation demonstrates biological mechanism, clinical value, or regulatory acceptability. Instead, it provides a structured vocabulary through which these distinctions can be recorded, evaluated, and communicated. Future research must test semantic coverage, cross-platform interoperability, annotation burden, governance processes, domain extensibility, and the relationship between provenance quality and reproducible pharmaceutical inference. A shared provenance language may thereby support more traceable computational research while preserving the limits of what computational records can establish.</p>
      </abstract>
      <kwd-group>
                <kwd>Pharmaceutical provenance</kwd>
                <kwd>Computational reproducibility</kwd>
                <kwd>Bioinformatics workflows</kwd>
                <kwd>Ontology engineering</kwd>
                <kwd>Evidence lineage</kwd>
                <kwd>FAIR data</kwd>
              </kwd-group>
    </article-meta>
  </front>
</article>