<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.0 20120330//EN" "JATS-archivearticle1.dtd">
<article xmlns:xlink="http://www.w3.org/1999/xlink">
  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Ontology Alignments?⋆</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Cassia Trojahn</string-name>
          <email>cassia.trojahn@irit.fr</email>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Nicolas Matentzoglu</string-name>
          <email>nicolas.matentzoglu@gmail.com</email>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Institut de Recherche en Informatique de Toulouse</institution>
          ,
          <addr-line>Université de Toulouse 2, Toulouse</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>Semanticly</institution>
          ,
          <country country="UK">United Kingdom</country>
        </aff>
      </contrib-group>
      <pub-date>
        <year>2022</year>
      </pub-date>
      <abstract>
        <p>The FAIR (Findable, Accessible, Interoperable, Reusable) principles [1] have become increasingly important in data management. A number of recommendations has been proposed for making FAIR data1, such as the “FAIR Data Maturity Model” [2]. Best practices for implementing FAIR vocabularies and ontologies on the Web [3, 4] have been also proposed and the evaluation of their degree of FAIRness addressed [5, 6]. Despite this wave of eforts, few attention has been given to producing FAIR ontology alignments. Recently, the EOSC has addressed the problem of “semantic mapping sharing”, reporting on the requirements for creating, documenting, and publishing alignments and crosswalks [7]. A complementary efort is the Simple Standard for Sharing Ontological Mappings (SSSOM) [8] that proposes a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in correspondences explicit.</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>-</title>
      <p>1. Introduction
CEUR
Workshop
Proceedings</p>
      <p>Alignment API format and EDOAL [9], they lack on providing rich metadata on the alignments.
Alignments have at least to be described with metadata on their provenance (who, when, tool,
tool version, etc.), usage license, version (as ontologies evolve),and so on.</p>
      <p>Requirement 2: correspondences have to be described with rich metadata A fine-grained
metadata is required at correspondence level, in terms of relation interpretation, confidence
interpretation, explanation, justification (how the correspondence has been found). In fact, it is
hard to interpret the truth relation expressed between the involved ontologies entities within a
correspondence, without clear statements.</p>
      <p>Requirement 3: alignments have to be published For being reusable, alignments have
to the accessible. They have to be at least exposed and stored, in dedicated repositories (e.g.,
github), and ideally indexed in alignment (searchable) catalogs. They have to be published with
standard formats. It is evident that the field lacks searchable services (Linked Open Alignment
service, LOA), as LOV for ontologies.</p>
      <p>Requirement 4: alignments have to be exposed with content negotiation
This set of minimum requirements has not been defined from questionnaires and deeper
discussion in the community, but rather from observations on the FAIR recommendations in
general.</p>
      <p>
        As a future work, an alignment of recommendations ([
        <xref ref-type="bibr" rid="ref4">10, 4</xref>
        ], for citing a very few) is required to
provide further concrete guidelines; together with an extensive involvement of the community in
order to refine the requirements presented here and/or define necessary and suficient conditions
for making FAIR alignments.
P. Wittenburg, C. M. Zwolf, SEMAF: A Proposal for a Flexible Semantic Mapping
Framework, 2021. URL: https://doi.org/10.5281/zenodo.4651421. doi:10.5281/zenodo.4651421.
[8] N. Matentzoglu, J. P. Balhof, S. M. e. a. Bello, A Simple
Standard for Sharing Ontological Mappings (SSSOM), Database 2022
(2022). URL: https://doi.org/10.1093/database/baac035. doi:10.1093/
database/baac035.
arXiv:https://academic.oup.com/database/articlepdf/doi/10.1093/database/baac035/43832024/baac035.pdf, baac035.
[9] J. David, J. Euzenat, F. Scharfe, C. Trojahn, The alignment API 4.0, Semantic Web 2 (2011)
3–10. URL: https://doi.org/10.3233/SW-2011-0028. doi:10.3233/SW-2011-0028.
[10] Y. Le Franc, J. Parland-von Essen, L. Bonino, H. Lehväslaiho, G. Coen, C. Staiger, D2.2
fair semantics: First recommendations, 2020. URL: https://doi.org/10.5281/zenodo.3707985.
doi:10.5281/zenodo.3707985.
      </p>
    </sec>
  </body>
  <back>
    <ref-list>
      <ref id="ref1">
        <mixed-citation>
          [1]
          <string-name>
            <given-names>M.</given-names>
            <surname>Wilkinson</surname>
          </string-name>
          ,
          <string-name>
            <given-names>M.</given-names>
            <surname>Dumontier</surname>
          </string-name>
          , et al.,
          <article-title>The FAIR Guiding Principles for scientific data management and stewardship</article-title>
          ,
          <source>Scientific data 3</source>
          (
          <year>2016</year>
          )
          <fpage>1</fpage>
          -
          <lpage>9</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref2">
        <mixed-citation>
          [2]
          <string-name>
            <given-names>FAIR</given-names>
            <surname>Data Maturity Model Working Group</surname>
          </string-name>
          <string-name>
            <surname>RDA</surname>
          </string-name>
          ,
          <source>FAIR Data Maturity Model. Specification and Guidelines</source>
          ,
          <year>2020</year>
          . URL: https://doi.org/10.15497/rda00050. doi:
          <volume>10</volume>
          .15497/rda00050, https://doi.org/10.15497/rda00050 Accessed 6 May
          <year>2022</year>
          .
        </mixed-citation>
      </ref>
      <ref id="ref3">
        <mixed-citation>
          [3]
          <string-name>
            <given-names>D.</given-names>
            <surname>Garijo</surname>
          </string-name>
          ,
          <string-name>
            <given-names>M.</given-names>
            <surname>Poveda-Villalón</surname>
          </string-name>
          ,
          <article-title>Best practices for implementing FAIR vocabularies and ontologies on the web</article-title>
          , CoRR abs/
          <year>2003</year>
          .13084 (
          <year>2020</year>
          ). URL: https://arxiv.org/abs/
          <year>2003</year>
          .13084. arXiv:
          <year>2003</year>
          .13084.
        </mixed-citation>
      </ref>
      <ref id="ref4">
        <mixed-citation>
          [4]
          <string-name>
            <given-names>S. J. D.</given-names>
            <surname>Cox</surname>
          </string-name>
          ,
          <string-name>
            <given-names>A. N.</given-names>
            <surname>Gonzalez-Beltran</surname>
          </string-name>
          ,
          <string-name>
            <given-names>B.</given-names>
            <surname>Magagna</surname>
          </string-name>
          ,
          <string-name>
            <surname>M.-C. Marinescu</surname>
          </string-name>
          ,
          <article-title>Ten simple rules for making a vocabulary fair</article-title>
          ,
          <source>PLOS Computational Biology</source>
          <volume>17</volume>
          (
          <year>2021</year>
          )
          <fpage>1</fpage>
          -
          <lpage>15</lpage>
          . URL: https: //doi.org/10.1371/journal.pcbi.1009041. doi:
          <volume>10</volume>
          .1371/journal.pcbi.
          <volume>1009041</volume>
          .
        </mixed-citation>
      </ref>
      <ref id="ref5">
        <mixed-citation>
          [5]
          <string-name>
            <given-names>D.</given-names>
            <surname>Garijo</surname>
          </string-name>
          , Ó. Corcho,
          <string-name>
            <surname>M.</surname>
          </string-name>
          <article-title>Poveda-Villalón, FOOPS!: An Ontology Pitfall Scanner for the FAIR principles</article-title>
          ,
          <source>in: Proc. of the ISWC 2021 Posters, Demos and Industry Tracks</source>
          ,
          <year>2021</year>
          . URL: http://ceur-ws.
          <source>org/</source>
          Vol-
          <volume>2980</volume>
          /paper321.pdf.
        </mixed-citation>
      </ref>
      <ref id="ref6">
        <mixed-citation>
          [6]
          <string-name>
            <given-names>E.</given-names>
            <surname>Amdouni</surname>
          </string-name>
          ,
          <string-name>
            <given-names>S.</given-names>
            <surname>Bouazzouni</surname>
          </string-name>
          ,
          <string-name>
            <given-names>C.</given-names>
            <surname>Jonquet</surname>
          </string-name>
          ,
          <string-name>
            <surname>O'</surname>
          </string-name>
          <article-title>FAIRe: Ontology FAIRness Evaluator in the AgroPortal semantic resource repository, in: ESWC 2022 Poster and demos</article-title>
          , Greece,
          <year>2022</year>
          . URL: https://hal-lirmm.ccsd.cnrs.fr/lirmm-03630543.
        </mixed-citation>
      </ref>
      <ref id="ref7">
        <mixed-citation>
          [7]
          <string-name>
            <given-names>D.</given-names>
            <surname>Broeder</surname>
          </string-name>
          ,
          <string-name>
            <given-names>P.</given-names>
            <surname>Budroni</surname>
          </string-name>
          ,
          <string-name>
            <given-names>E.</given-names>
            <surname>Degl'Innocenti</surname>
          </string-name>
          ,
          <string-name>
            <given-names>Y.</given-names>
            <surname>Le Franc</surname>
          </string-name>
          ,
          <string-name>
            <given-names>W.</given-names>
            <surname>Hugo</surname>
          </string-name>
          ,
          <string-name>
            <given-names>K.</given-names>
            <surname>Jefery</surname>
          </string-name>
          , C. Weiland,
        </mixed-citation>
      </ref>
    </ref-list>
  </back>
</article>