Using Pattern Structures for Analyzing Ontology-Based Annotations of Biomedical Data
Identifieur interne : 001453 ( Main/Exploration ); précédent : 001452; suivant : 001454Using Pattern Structures for Analyzing Ontology-Based Annotations of Biomedical Data
Auteurs : Adrien Coulet [France] ; Florent Domenach [Chypre (pays)] ; Mehdi Kaytoue [France] ; Amedeo Napoli [France]Source :
- Lecture Notes in Computer Science [ 0302-9743 ]
Abstract
Abstract: Annotating data with concepts of an ontology is a common practice in the biomedical domain. Resulting annotations, i.e., data-concept relationships, are useful for data integration whereas the reference ontology can guide the analysis of integrated data. Then the analysis of annotations can provide relevant knowledge units to consider for extracting and understanding possible correlations between data. Formal Concept Analysis (FCA) which builds from a binary context a concept lattice can be used for such a knowledge discovery task. However annotated biomedical data are usually not binary and a scaling procedure for using FCA is required as a preprocessing, leading to problems of expressivity, ranging from loss of information to the generation of a large number of additional binary attributes. By contrast, pattern structures offer a general FCA-based framework for building a concept lattice from complex data, e.g., a set of objects with partially ordered descriptions. In this paper, we show how to instantiate this general framework when descriptions are ordered by an ontology. We illustrate our approach with the analysis of annotations of drug related documents, and we show the capabilities of the approach for knowledge discovery.
Url:
DOI: 10.1007/978-3-642-38317-5_5
Affiliations:
- Chypre (pays), France
- Auvergne-Rhône-Alpes, Grand Est, Lorraine (région), Rhône-Alpes
- Vandœuvre-lès-Nancy
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 000720
- to stream Istex, to step Curation: 000715
- to stream Istex, to step Checkpoint: 000079
- to stream Main, to step Merge: 001465
- to stream Main, to step Curation: 001453
Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Using Pattern Structures for Analyzing Ontology-Based Annotations of Biomedical Data</title><author><name sortKey="Coulet, Adrien" sort="Coulet, Adrien" uniqKey="Coulet A" first="Adrien" last="Coulet">Adrien Coulet</name></author><author><name sortKey="Domenach, Florent" sort="Domenach, Florent" uniqKey="Domenach F" first="Florent" last="Domenach">Florent Domenach</name></author><author><name sortKey="Kaytoue, Mehdi" sort="Kaytoue, Mehdi" uniqKey="Kaytoue M" first="Mehdi" last="Kaytoue">Mehdi Kaytoue</name></author><author><name sortKey="Napoli, Amedeo" sort="Napoli, Amedeo" uniqKey="Napoli A" first="Amedeo" last="Napoli">Amedeo Napoli</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:1FC97684FFA7FC390B598B4A5BA7C3AE9457A91D</idno><date when="2013" year="2013">2013</date><idno type="doi">10.1007/978-3-642-38317-5_5</idno><idno type="url">https://api.istex.fr/ark:/67375/HCB-3NMDLK6Z-H/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">000720</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000720</idno><idno type="wicri:Area/Istex/Curation">000715</idno><idno type="wicri:Area/Istex/Checkpoint">000079</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000079</idno><idno type="wicri:doubleKey">0302-9743:2013:Coulet A:using:pattern:structures</idno><idno type="wicri:Area/Main/Merge">001465</idno><idno type="wicri:Area/Main/Curation">001453</idno><idno type="wicri:Area/Main/Exploration">001453</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Using Pattern Structures for Analyzing Ontology-Based Annotations of Biomedical Data</title><author><name sortKey="Coulet, Adrien" sort="Coulet, Adrien" uniqKey="Coulet A" first="Adrien" last="Coulet">Adrien Coulet</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>LORIA (Université de Lorraine – CNRS – Inria Nancy Grand Est, UMR 7503), BP 239, F-54506, Vandoeuvre-lès-Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandœuvre-lès-Nancy</settlement></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">France</country></affiliation></author><author><name sortKey="Domenach, Florent" sort="Domenach, Florent" uniqKey="Domenach F" first="Florent" last="Domenach">Florent Domenach</name><affiliation wicri:level="1"><country xml:lang="fr">Chypre (pays)</country><wicri:regionArea>Computer Science Department, University of Nicosia, 46 Makedonitissas Av., P.O. Box 24005, 1700, Nicosia</wicri:regionArea><wicri:noRegion>Nicosia</wicri:noRegion></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Chypre (pays)</country></affiliation></author><author><name sortKey="Kaytoue, Mehdi" sort="Kaytoue, Mehdi" uniqKey="Kaytoue M" first="Mehdi" last="Kaytoue">Mehdi Kaytoue</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>CNRS, INSA-Lyon, LIRIS, UMR5205, Université de Lyon, F-69621</wicri:regionArea><placeName><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">France</country></affiliation></author><author><name sortKey="Napoli, Amedeo" sort="Napoli, Amedeo" uniqKey="Napoli A" first="Amedeo" last="Napoli">Amedeo Napoli</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>LORIA (Université de Lorraine – CNRS – Inria Nancy Grand Est, UMR 7503), BP 239, F-54506, Vandoeuvre-lès-Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandœuvre-lès-Nancy</settlement></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">France</country></affiliation></author></analytic><monogr></monogr><series><title level="s" type="main" xml:lang="en">Lecture Notes in Computer Science</title><idno type="ISSN">0302-9743</idno><idno type="eISSN">1611-3349</idno><idno type="ISSN">0302-9743</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0302-9743</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: Annotating data with concepts of an ontology is a common practice in the biomedical domain. Resulting annotations, i.e., data-concept relationships, are useful for data integration whereas the reference ontology can guide the analysis of integrated data. Then the analysis of annotations can provide relevant knowledge units to consider for extracting and understanding possible correlations between data. Formal Concept Analysis (FCA) which builds from a binary context a concept lattice can be used for such a knowledge discovery task. However annotated biomedical data are usually not binary and a scaling procedure for using FCA is required as a preprocessing, leading to problems of expressivity, ranging from loss of information to the generation of a large number of additional binary attributes. By contrast, pattern structures offer a general FCA-based framework for building a concept lattice from complex data, e.g., a set of objects with partially ordered descriptions. In this paper, we show how to instantiate this general framework when descriptions are ordered by an ontology. We illustrate our approach with the analysis of annotations of drug related documents, and we show the capabilities of the approach for knowledge discovery.</div></front></TEI><affiliations><list><country><li>Chypre (pays)</li><li>France</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Grand Est</li><li>Lorraine (région)</li><li>Rhône-Alpes</li></region><settlement><li>Vandœuvre-lès-Nancy</li></settlement></list><tree><country name="France"><region name="Grand Est"><name sortKey="Coulet, Adrien" sort="Coulet, Adrien" uniqKey="Coulet A" first="Adrien" last="Coulet">Adrien Coulet</name></region><name sortKey="Coulet, Adrien" sort="Coulet, Adrien" uniqKey="Coulet A" first="Adrien" last="Coulet">Adrien Coulet</name><name sortKey="Kaytoue, Mehdi" sort="Kaytoue, Mehdi" uniqKey="Kaytoue M" first="Mehdi" last="Kaytoue">Mehdi Kaytoue</name><name sortKey="Kaytoue, Mehdi" sort="Kaytoue, Mehdi" uniqKey="Kaytoue M" first="Mehdi" last="Kaytoue">Mehdi Kaytoue</name><name sortKey="Napoli, Amedeo" sort="Napoli, Amedeo" uniqKey="Napoli A" first="Amedeo" last="Napoli">Amedeo Napoli</name><name sortKey="Napoli, Amedeo" sort="Napoli, Amedeo" uniqKey="Napoli A" first="Amedeo" last="Napoli">Amedeo Napoli</name></country><country name="Chypre (pays)"><noRegion><name sortKey="Domenach, Florent" sort="Domenach, Florent" uniqKey="Domenach F" first="Florent" last="Domenach">Florent Domenach</name></noRegion><name sortKey="Domenach, Florent" sort="Domenach, Florent" uniqKey="Domenach F" first="Florent" last="Domenach">Florent Domenach</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Lorraine/explor/InforLorV4/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001453 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001453 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Lorraine
|area= InforLorV4
|flux= Main
|étape= Exploration
|type= RBID
|clé= ISTEX:1FC97684FFA7FC390B598B4A5BA7C3AE9457A91D
|texte= Using Pattern Structures for Analyzing Ontology-Based Annotations of Biomedical Data
}}
| This area was generated with Dilib version V0.6.33. |  |