From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories

Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Michael Dannemann, Janet Kelso

Research output: Chapter in Book/Report/Conference proceedingConference Proceeding (Non-Journal item)

1 Citation (SciVal)

Abstract

The co-occurrence of terms in a text corpus may indicate the presence of a relation between the referents of these terms. We expect co-occurrence-based methods to identify association relations that cannot be found using static patterns. We developed a new method to identify associations between ontological categories in text using the co-occurrence of terms that designate these categories. We use the taxonomic structure of the ontologies to cumulate the number of co-occurrences of terms designating categories. Based on these cumulated values, we designed a novel family of statistical tests to identify associated categories. These tests take both co-occurrence specificity and relevance into consideration. We applied our method to a 2.2 GB text corpus containing fulltext articles and used Gene Ontology's biological process ontology and the Celltype Ontology. The software and results can be found at http: //bioonto.de/pmwiki.php/Main/ ExtractingBiologicalRelations.
Original languageEnglish
Title of host publicationProceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland
EditorsTapio Salakoski, Dietrich Rebholz-Schuhmann, Sampo Pyysalo
PublisherTurun tietotekniikan tutkimus- ja koulutuskeskus
Pages53-60
Number of pages8
Publication statusPublished - 01 Sept 2008
EventThird International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland - Turku, Finland
Duration: 01 Sept 200803 Sept 2008

Conference

ConferenceThird International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland
Country/TerritoryFinland
CityTurku
Period01 Sept 200803 Sept 2008

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