Abstract— The paper presents several solutions for improving access to data in biomedical ontologies, considering a particular dataspace which contain highly heterogeneous data or has an unknown or unreliable structure. The main goal is to provide means for explorative querying, which can be performed without any prior in-depth knowledge of the queried data. After presenting the features and the advantages in using Web services technologies, two new achievements are discussed: 1) an architecture for multiple sources data integration using interfaces harmonized by a wrapper component which is accessed by a mediator for implementing the required functionalities and 2) the prototype of a portable question- answering system named MQAS (Medical Question Answering System) which takes queries expressed in natural language and an ontology as input, and returns answers drawn from one or more knowledge bases. Conclusions on the results of preliminary tests performed in Clinical Institute in Bucharest and purposes for further work are also presented. Keywords— biomedical ontology, query interface, semantic web technologies, web services. I. INTRODUCTION T is challenging for biomedical researchers to stay current with the literature in their field. At the other hand, to ensure best practice and treatment for patients, clinicians must access medical information, acquire new knowledge, and achieve information mastery in their field. Information retrieval systems are widely used; however, they return documents that have to be read by the user to extract relevant information. Inspired by the work of Cimino and Ayres [1] which developed a self-service query interface for re-use in clinical and translational research of the data captured in the course of routine patient available in the Biomedical This work was supported in part by doctoral program POSDRU/107/1.5/S/76813. Eng Ioana Branescu-Raspop is PhD. student, Faculty of Automatic Control and Computers, University POLITEHNICA of Bucharest, Romania, e-mail: ioana.branescu@gmail.com Prof. Victor Lorin Purcarea, Ph.D., is with Department of Healthcare Marketing, Technology and Medical Devices, Medical Informatics and Biostatistics, “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania, e-mail: victor.purcarea@gmail.com. Prof. Radu Dobrescu, Ph.D, is with Faculty of Automatic Control and Computers, University POLITEHNICA of Bucharest, Romania, e-mail: rd_dobrescu@yahoo.com Translational Research Information System (BTRIS) at the US National Institutes of Health (NIH), we have developed an ontology-driven Question Answering system to interface the Semantic Web to provide answers for a wide array of questions that arise in clinical work and biomedical research.. While semantic information can be used in several different ways to improve question answering, an important consequence of the availability of semantic markup on the web is that this can indeed be queried directly. In other words, we can exploit the availability of semantic statements to provide precise answers to complex queries, allowing the use of inference and object manipulation. Moreover, as semantic markup becomes ubiquitous, it will become important to be able to ask queries and obtain answers, using natural language (NL) expressions, rather than the keyword-based retrieval mechanisms used by the current search engines. More of that, our methodology for question answering was implemented in a prototype tool which returns answers (known facts) first, and only later the documents from which the facts are extracted. The proposed prototype titled MQAS (Medical Question Answering System) is a natural language based front-end for the semantic web which takes queries expressed in natural language and an ontology as input, and returns answers drawn from one or more knowledge bases (KBs), which instantiate the input ontology with domain-specific information. Also, MQAS is coupled with a portable and contextualized learning mechanism to obtain domain-dependent knowledge by creating a lexicon. The learning component ensures that the performance of the system improves over time, in response to the particular community jargon of the end users. II. SEMANTIC WEB TECHNOLOGIES The goal of the Semantic Web is to solve the current limitations of the Web by augmenting Web information with a formal representation of its meaning. A direct benefit of this machine processable semantics would be the enhancement and automation of several information management tasks, such as search or data integration. The current focus of Semantic Web research is more and more directed towards supporting intelligent data exchange. In this case the information that is being annotated is not unstructured text but rather semi- structured information available from databases or exchanged between Web services. Improving Query Mechanisms for Biomedical Ontologies Ioana Branescu-Raspop, Victor Lorin Purcarea and Radu Dobrescu I INTERNATIONAL JOURNAL OF BIOLOGY AND BIOMEDICAL ENGINEERING Volume 9, 2015 ISSN: 1998-4510 56