Natalia Villanueva-Rosales

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The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description of arbitrary (real, hypothesized, virtual, fictional) objects, processes and their attributes. SIO specifies simple design patterns to describe and(More)
Although pictorial renditions of statistical data are ubiquitous, few techniques and standards exist to exchange, search and query these graphical representations. We present several improvements to human-graph interaction including i) a new approach to manage statistical graph knowledge by semantic annotation of graphs that bridges the gap between Web 2.0(More)
Functional groups describe the semantics of chemical reactivity in terms of atoms and their connectivity, which exhibit characteristic chemical behavior when present in a compound. In this paper, we take a first step towards designing an OWL-DL ontology of functional groups for the classification of chemical compounds. We highlight the capabilities and(More)
Ontology reuse is often predicated on agreement to the semantics wholly defined within an ontology document. But when faced with overly constrained semantics that one might partially reject, might one instead prefer reduced ontological commitment? In this paper, we describe how three layered ontology design promotes maximal reuse of domain ontologies by(More)
Pharmacogenomics aims to understand pharmacological response with respect to genetic variation. Essential to the delivery of better health care is the use of pharmacogenomics knowledge to answer questions about therapeutic, pharmacological or genetic aspects. Several XML markup languages have been developed to capture pharmacogenomic and related information(More)
Knowledge management is an ongoing challenge for the biological community such that large, diverse and continuously growing information requires more sophisticated methods to store, integrate and query their knowledge. The semantic web initiative provides a new knowledge engineering framework to represent, share and discover information. In this paper, we(More)
The integration of data from heterogeneous sources is an ongoing challenge for the scientific community. The semantic web initiative provides a new knowledge engineering framework to represent, query and share information. In this paper, we describe our efforts towards the development of an ontology-driven knowledge base that allows semantic query answering(More)
SMART (Semantic web information Management with automated Reasoning Tool) is an open-source project, which aims to provide intuitive tools for life scientists for represent, integrate, manage and query heterogeneous and distributed biological knowledge. SMART was designed with interoperability and extensibility in mind and uses AJAX, SVG and JSF(More)
Statistical graphs are ubiquitous mechanisms for data visualization such that most, if not all, enterprises communicate information through them. However, many graphs are stored as unstructured images or proprietary binary objects, making them difficult to work with beyond the reports in which they are embedded. While graphs can be mapped to more common XML(More)