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On Matching Large Life Science Ontologies in Parallel

... Data Integration in the Life Sciences (DILS) URL:  ... for parallel matching on multiple compute nodes. In particular, we consider inter-matcher and intra-matcher parallelism as well ...

Publication - hartung - 07/26/2016 - 16:40 - 0 comments - 0 attachments

Alignment of biomedical ontologies using life science literature

... Workshop on Knowledge Discovery in Life Science Literature URL:  ... 483.55 KB In recent years many biomedical ontologies have been developed and many of ... able to use multiple ontologies they have to be aligned. In this paper we propose strategies for aligning ontologies based on life ...

Publication - cat - 04/17/2013 - 11:49 - 0 comments - 1 attachment

Challenges in precisely aligning models of human anatomy using generic schema matching

... solutions for them. (Journal, no paper type, OA in the Life Sciences) ...

Publication - hartung - 04/17/2013 - 03:16 - 0 comments - 1 attachment

GOMMA: A Component-based Infrastructure for managing and analyzing Life Science Ontologies and their Evolution

... describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a large set of ontology versions necessitates efficient management and ... (Compose, Diff, Journal, Mapping evolution, OA in the Life Sciences, Ontology evolution, Research paper, Versioning) ...

Publication - hartung - 04/16/2013 - 23:05 - 0 comments - 0 attachments

XML-based approaches for the integration of heterogeneous bio-molecular data

... 10 - 49 In this paper we survey the most interesting and novel approaches for the ... biological data represented through XML. (OA in the Life Sciences) ...

Publication - cat - 04/16/2013 - 10:16 - 0 comments - 0 attachments

Mapping the Gene Ontology into the Unified Medical Language System

... been developed for the purpose of annotating gene products in genome databases, and the UMLS has been developed as a framework for ... sources. The mapping of GO to UMLS highlighted issues in both terminology systems. After some initial explorations and discussions ...

Publication - hartung - 04/16/2013 - 09:05 - 0 comments - 0 attachments

Aligning representations of anatomy using lexical and structural methods

... inference is discussed. (Conference, no paper type, OA in the Life Sciences) ...

Publication - hartung - 04/16/2013 - 08:05 - 0 comments - 0 attachments

Mapping Composition for Matching Large Life Science Ontologies

... need to interrelate different life science ontologies in order to facilitate data integration or semantic data analysis. Ontology ... linguistic and structural similarity of their concepts. In this paper we investigate an indirect computation of ontology mappings that ...

Publication - hartung - 04/16/2013 - 02:05 - 0 comments - 0 attachments

Using annotations from controlled vocabularies to find meaningful associations

... the rich Web of interconnected and annotated objects in multiple repositories, and to identify meaningful associations. Consider a physical link between objects in two repositories, where each of the objects is annotated with controlled ...

Publication - hartung - 04/15/2013 - 23:05 - 0 comments - 0 attachments

Creating Mappings For Ontologies in Biomedicine: Simple Methods Work

... 211.45 KB Creating mappings between concepts in different ontologies is a critical step in facilitating data integration. In recent years, researchers have developed ...

Publication - cat - 04/15/2013 - 22:38 - 0 comments - 1 attachment

What Four Million Mappings Can Tell You About Two Hundred Ontologies

... ontologies. We analyzed ontologies and terminologies in BioPortal and the Unified Medical Language System (UMLS), creating more than 4 million mappings between concepts in these ontologies and terminologies based on the lexical similarity of ...

Publication - cat - 04/15/2013 - 22:05 - 0 comments - 1 attachment

An Evaluation of Hybrid Methods for Matching Biomedical Terminologies: Mapping the Gene Ontology to the UMLS

... Cantor, MN; Sarkar, IN; Gelman, R; F Hartel, O .. Author:  ... MN Sarkar, IN Gelman, R ...

Publication - cat - 04/15/2013 - 21:49 - 0 comments - 0 attachments

Collecting community-based mappings in an ontology repository

... collect ontologies automatically by crawling the Web; in other repositories, users submit ontologies themselves. In addition to providing search across multiple ontologies, the added value of ...

Publication - cat - 04/15/2013 - 21:38 - 0 comments - 0 attachments

Alignment of the UMLS semantic network with BioTop: methodology and assessment

... the categorization of terms from terminological resources in biomedicine. BioTop has recently been developed as an upper-level ontology for the biomedical domain. In contrast to the SN, it is founded upon strict ontological principles, using ...

Publication - cat - 04/15/2013 - 21:27 - 0 comments - 0 attachments