Ontology-based retrieval of bio-medical information based on microarray text corpora

Kim Allan Hansen, Sine Zambach, Christian Theil Have

Research output: Contribution to conferencePaperResearchpeer-review

Abstract

Microarray technology is often used in gene expression exper-
iments. Information retrieval in the context of microarrays has mainly
been concerned with the analysis of the numeric data produced; how-
ever, the experiments are often annotated with textual metadata. Al-
though biomedical resources are exponentially growing, the text corpora
are sparse and inconsistent in spite of attempts to standardize the format.
Ordinary keyword search may in some cases be insucient to nd rele-
vant information and the potential benet of using a semantic approach
in this context has only been investigated to a limited degree. We explore
the possibilities of retrieving biomedical information from microarrays in
Gene Expression Omnibus (GEO), of which we have indexed a sample
semantically, as a rst step towards ontology based searches. Through an
example we argue that it is possible to improve the retrieval of biological
information.
Original languageEnglish
Publication date2010
Publication statusPublished - 2010
Event15th ESSLLI Student session - København, Denmark
Duration: 9 Aug 201020 Aug 2010
Conference number: 15

Seminar

Seminar15th ESSLLI Student session
Number15
CountryDenmark
CityKøbenhavn
Period09/08/201020/08/2010

Keywords

    Cite this

    Hansen, K. A., Zambach, S., & Have, C. T. (2010). Ontology-based retrieval of bio-medical information based on microarray text corpora. Paper presented at 15th ESSLLI Student session , København, Denmark.
    Hansen, Kim Allan ; Zambach, Sine ; Have, Christian Theil. / Ontology-based retrieval of bio-medical information based on microarray text corpora. Paper presented at 15th ESSLLI Student session , København, Denmark.
    @conference{9c8ca593e13c4b56b761e6ba7253e039,
    title = "Ontology-based retrieval of bio-medical information based on microarray text corpora",
    abstract = "Microarray technology is often used in gene expression exper-iments. Information retrieval in the context of microarrays has mainlybeen concerned with the analysis of the numeric data produced; how-ever, the experiments are often annotated with textual metadata. Al-though biomedical resources are exponentially growing, the text corporaare sparse and inconsistent in spite of attempts to standardize the format.Ordinary keyword search may in some cases be insucient to nd rele-vant information and the potential benet of using a semantic approachin this context has only been investigated to a limited degree. We explorethe possibilities of retrieving biomedical information from microarrays inGene Expression Omnibus (GEO), of which we have indexed a samplesemantically, as a rst step towards ontology based searches. Through anexample we argue that it is possible to improve the retrieval of biologicalinformation.",
    keywords = "semantic search, Semantic annotation, ontologies, domain analysis",
    author = "Hansen, {Kim Allan} and Sine Zambach and Have, {Christian Theil}",
    note = "Recieved {"}Best Poster Award{"} by Springer; null ; Conference date: 09-08-2010 Through 20-08-2010",
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    Hansen, KA, Zambach, S & Have, CT 2010, 'Ontology-based retrieval of bio-medical information based on microarray text corpora' Paper presented at, København, Denmark, 09/08/2010 - 20/08/2010, .

    Ontology-based retrieval of bio-medical information based on microarray text corpora. / Hansen, Kim Allan ; Zambach, Sine; Have, Christian Theil.

    2010. Paper presented at 15th ESSLLI Student session , København, Denmark.

    Research output: Contribution to conferencePaperResearchpeer-review

    TY - CONF

    T1 - Ontology-based retrieval of bio-medical information based on microarray text corpora

    AU - Hansen, Kim Allan

    AU - Zambach, Sine

    AU - Have, Christian Theil

    N1 - Recieved "Best Poster Award" by Springer

    PY - 2010

    Y1 - 2010

    N2 - Microarray technology is often used in gene expression exper-iments. Information retrieval in the context of microarrays has mainlybeen concerned with the analysis of the numeric data produced; how-ever, the experiments are often annotated with textual metadata. Al-though biomedical resources are exponentially growing, the text corporaare sparse and inconsistent in spite of attempts to standardize the format.Ordinary keyword search may in some cases be insucient to nd rele-vant information and the potential benet of using a semantic approachin this context has only been investigated to a limited degree. We explorethe possibilities of retrieving biomedical information from microarrays inGene Expression Omnibus (GEO), of which we have indexed a samplesemantically, as a rst step towards ontology based searches. Through anexample we argue that it is possible to improve the retrieval of biologicalinformation.

    AB - Microarray technology is often used in gene expression exper-iments. Information retrieval in the context of microarrays has mainlybeen concerned with the analysis of the numeric data produced; how-ever, the experiments are often annotated with textual metadata. Al-though biomedical resources are exponentially growing, the text corporaare sparse and inconsistent in spite of attempts to standardize the format.Ordinary keyword search may in some cases be insucient to nd rele-vant information and the potential benet of using a semantic approachin this context has only been investigated to a limited degree. We explorethe possibilities of retrieving biomedical information from microarrays inGene Expression Omnibus (GEO), of which we have indexed a samplesemantically, as a rst step towards ontology based searches. Through anexample we argue that it is possible to improve the retrieval of biologicalinformation.

    KW - semantic search

    KW - Semantic annotation

    KW - ontologies

    KW - domain analysis

    M3 - Paper

    ER -

    Hansen KA, Zambach S, Have CT. Ontology-based retrieval of bio-medical information based on microarray text corpora. 2010. Paper presented at 15th ESSLLI Student session , København, Denmark.