A pragmatic approach to semantic repositories benchmarking

The aim of this paper is to benchmark various semantic repositories in order to evaluate their deployment in a commercial image retrieval and browsing application. We adopt a two-phase approach for evaluating the target semantic repositories: analytical parameters such as query language and reasoning support are used to select the pool of the target repositories, and practical parameters such as load and query response times are used to select the best match to application requirements. In addition to utilising a widely accepted benchmark for OWL repositories (UOBM), we also use a real-life dataset from the target application, which provides us with the opportunity of consolidating our findings. A distinctive advantage of this benchmarking study is that the essential requirements for the target system such as the semantic expressivity and data scalability are clearly defined, which allows us to claim contribution to the benchmarking methodology for this class of applications

Cross-concordances: terminology mapping and its effectiveness for information retrieval

The German Federal Ministry for Education and Research funded a major terminology mapping initiative, which found its conclusion in 2007. The task of this terminology mapping initiative was to organize, create and manage 'cross-concordances' between controlled vocabularies (thesauri, classification systems, subject heading lists) centred around the social sciences but quickly extending to other subject areas. 64 crosswalks with more than 500,000 relations were established. In the final phase of the project, a major evaluation effort to test and measure the effectiveness of the vocabulary mappings in an information system environment was conducted. The paper reports on the cross-concordance work and evaluation results.Comment: 19 pages, 4 figures, 11 tables, IFLA conference 200

An information retrieval approach to ontology mapping

In this paper, we present a heuristic mapping method and a prototype mapping system that support the process of semi-automatic ontology mapping for the purpose of improving semantic interoperability in heterogeneous systems. The approach is based on the idea of semantic enrichment, i.e., using instance information of the ontology to enrich the original ontology and calculate similarities between concepts in two ontologies. The functional settings for the mapping system are discussed and the evaluation of the prototype implementation of the approach is reported. \ud \u

Inferring gene ontologies from pairwise similarity data.

MotivationWhile the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms are needed that: analyze a full matrix of gene-gene pairwise similarities from -omics data; infer true hierarchical structure in these data rather than enforcing hierarchy as a computational artifact; and respect biological pleiotropy, by which a term in the hierarchy can relate to multiple higher level terms. Methods addressing these requirements are just beginning to emerge-none has been evaluated for GO inference.MethodsWe consider two algorithms [Clique Extracted Ontology (CliXO), LocalFitness] that uniquely satisfy these requirements, compared with methods including standard clustering. CliXO is a new approach that finds maximal cliques in a network induced by progressive thresholding of a similarity matrix. We evaluate each method's ability to reconstruct the GO biological process ontology from a similarity matrix based on (a) semantic similarities for GO itself or (b) three -omics datasets for yeast.ResultsFor task (a) using semantic similarity, CliXO accurately reconstructs GO (>99% precision, recall) and outperforms other approaches (<20% precision, <20% recall). For task (b) using -omics data, CliXO outperforms other methods using two -omics datasets and achieves ∼30% precision and recall using YeastNet v3, similar to an earlier approach (Network Extracted Ontology) and better than LocalFitness or standard clustering (20-25% precision, recall).ConclusionThis study provides algorithmic foundation for building gene ontologies by capturing hierarchical and pleiotropic structure embedded in biomolecular data