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Dr. Larisa Soldatova

RCUK Fellow
Aberystwyth University
Computer science Department, Penglais

Brief Biography:

I have an international research reputation in Ontology development and its application to the Semantic Web, Data Mining, and the Life Science. I am currently a RCUK Fellow in the Computational Biology group, Computer Science Department, Aberystwyth University. The primarily focus of my research is the development of formal methods for knowledge representation, and their applications to the natural and social sciences. During my scientific career I have contributed to ontology theory[13,36], developed EXPO the first generic ontology of scientific experiments[12], applied EXPO to biology and physics[12], computer science[11], to database design[9], and developed an ontology of tests (exams)[25-27]. I have also proposed the language EXACT for the representation of biology experiment protocols[8]. My work has been published in Science [6] and other high impact journals, and short-listed for the World Technology Award for Software 2006.  My work on the ontology LABORS constitutes an essential part of the work reported in [6] - named by Time Magazine as one of the most significant scientific discoveries of 2009.

My research over the last seven years has established Aberystwyth as one of the leading centers of ontology research for science. After I moved to Aberystwyth from Osaka University (one of the top three Universities in Japan, and the top one in ontology engineering), I started a research focused on biological applications of ontologies. I examined the state-of-the-art ontologies in describing scientific experiments in biology. This investigation led to a highly cited paper in Nature Biotechnology (57 citations, impact factor 22.7) in which I criticised the current state of ontologies in biology and suggested remedies[13]. This generated a debate within the biology ontology community, and many of my suggestions have now been generally adopted [34]. My colleagues and I then used an ontology engineering methodology to analyse the problems that affect the quality of information stored in the PDB (Protein Data Bank). Our paper in Nature Biotechnology also elicited a lively debate on the structure of this key database[9]; a summary of the discussion also was published in Nature Biotechnology[33]. I then developed a generic ontology of scientific experiments EXPO (within BBSRC grant 2/BEP17028). This ontology is designed to structure the formal annotation of general scientific experiments[12]. EXPO provides a clear structured framework for a consistent and shareable description of experiments for both humans and computer systems. EXPO has received a lot of publicity, with articles describing it in the New Scientist, and the US Chronicle of Higher Education; and it was short-listed for the World Technology Award for Software 2006. I also proposed the EXACT (Experiment ACTions) ontology as a method of representing biological laboratory protocols[8]. EXACT provides a model for the description of experiment actions, and it can be used to fully formalise the representation of protocols. It can also be combined with other formalisms for the description of biological investigations. EXACT is also valuable as a language for the initial specification of an automated system.

My colleagues and I have proposed an ontology for data mining OntoDM[23, 24 (25 citations)] and Expose [20]. These ontologies provide the description of computational investigations and support a general framework for data mining. OntoDM allows representation of complex entities in data mining and supports knowledge sharing and connections with other domains.

I am one of co-ordinators of the ontology for biomedical investigations (OBI)[4]. This is a large international project that currently involves 19 biomedical research communities. The aim is to develop an integrated ontology for the description of life-science and clinical investigations. I am also a member of the ontology working group of the metabolomics standard initiative[10, 16 citations]. This seeks to develop an ontology to facilitate the consistent annotation of metabolomics experiments. This will enable the consistent semantic annotation of metabolomic data from disparate sources.

I was the principal investigator on the ART (an ontology based ARticle preparation Tool) project sponsored by the JISC (Joint Information Systems Committee, UK).  The aim of ART was to develop an ontology based tool to assist in: translating scientific papers into a format with an explicit content semantics; the explicit linking of papers in repositories to data and metadata; and creating a proof-of-concept intelligent digital repository [22].

I am leading the development of an ontology for the description of drug discovery investigations (proposed within BBSRC grant BB/E018025/1)[3].

I am also leading the work on LABORS, an ontology which formalises automatic investigations run by a Robot Scientist. A Robot Scientist is a physically implemented robotic system that applies techniques from Artificial Intelligence to carry out cycles of scientific investigations. LABORS defines the associated metadata (design, goals, hypotheses, results, conclusions, etc.) of the various research units [1,6]. Applying LABORS to our current investigations resulted in a formalisation involving over 10,000 different research units. This formalism has a nested tree-like structure, eleven levels deep, that logically connects the experimental observations to the experimental metadata: hypotheses, goals, results, etc. LABORS constitutes an essential part of the work which has been published in Science [6]. This work has captured public imagination with > 500 articles in press around the world, reports on radio 1,2,4, on BBC World News, etc. 


Academic positions:

RCUK Fellow


Research interests:

Knowledge engineering, Ontologies, Data mining


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