Larisa Soldatova

Summary

larisa-soldatova
Dr Larisa Soldatova joined the Computer Science Department at Brunel University London as Lecturer in Computing in June 2012 after the end of her five-years Research Council UK Fellowship. She has previously worked at the University of Osaka, Japan and the Far Eastern State University, Russia. Dr Soldatova has over 50 research publications, including in such leading high impact journals as Science, Nature Biotechnology and Journal of the Royal Society Interface. Her work on ontology EXPO has been short-listed for the World Technology Award for Software 2006. Her work on an ontology LABORS constitutes an essential part of the work reported in Science and what was featured by Time Magazine as one of the most significant scientific discoveries of 2009. Soldatova is supervising several research projects, including “Learning how to learn to design drugs” funded by the Engineering Research Council UK, that aims to compare what machine learning algorithms work best for what drug targets, representations, and datasets.

Responsibilities

Dr Soldatova is
• A member of the Centre for Systems and Synthetic Biology at Brunel University London (http://www.brunel.ac.uk/research/centres/cssb)
• An organizer of ISMB/SIG bio-ontologies (http://www.bio-ontologies.org.uk/)
• An Editor of bio-ontologies special issues of the Journal of Biomedical Semantics (http://www.jbiomedsem.com/supplements/4/S1)
• A developer of SBOL (Synthetic Biology Open Language) (www.sbolstandard.org/‎) and SBOL visual (www.sbolstandard.org/visual‎).
• A developer of OBI (the Ontology for Biomedical Investigations) (obi-ontology.org/‎)

Research area(s)

Dr Soldatova is an expert in the semantic web technologies and its applications to life sciences. The primarily focus of her research is the development of formal methods for knowledge representation and their applications to the natural and social sciences.

Research

Research interests

During her scientific career she has contributed to ontology theory, developed EXPO (http://pubmedcentralcanada.ca/pmcc/articles/PMC1885356/) the first generic ontology of scientific experiments, applied EXPO to biology, physics, computer science, and to database design.


She has also proposed the language EXACT (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718634/) for the representation of biological protocols. Recently Dr Soldatova proposed the HELO (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632998/) framework for the representation of uncertain probabilistic knowledge. She is participating in the development of international standards for the reporting scientific investigations – the Ontology for Biomedical Investigations (OBI) (obi-ontology.org/‎).

Research project(s) and grant(s)

• Adaptive Automated Scientific Laboratory


• BRIEF (Brunel University London) (PI). Ontology of biomodelling.


• BBSRC BB/FOF/PF/13/09 (PI)  - Development of an Ontology Based Standard for the Reporting of Drug Discovery Investigations.


• JISC/Capital programme (PI) – ART an ontology based article preparation tool.


• BBSRC BB/E018025/1 (PDRA)  – an ontology of drug discovery. BBSRC JPA (Coordinator) – Advanced scientific discovery tools for bioinformatics.


• BBSRC 2/BEP17028 (PDRA) – An intelligent database for knowledge discovery in functional genomics.


• COE (Japan) (PDRA) - Towards Creating New Industries Based on Inter-Nanoscience.


• AR-MBA  (Russia) (Coordinator) – Investigation of commercial prospects for American-Russian MBA Program in Far East.



•EPSRC  EP/K030582/1 (PI) Learning how to learn to design drugs.
The research team is led by Professor Ross King (the University of Manchester, Manchester Institute of Biotechnology - the lead research organization of the project), and also includes a Co-Investigator Professor Andrew Hopkins (the University of Dundee, College of Life Sciences). The 24 month project is an ambitious one: its goal is to change the way drug-design research is done, and to make it more efficient and cost-effective. The most important deliverable of the project would be a knowledgebase about how to better apply quantitative structure activity (QSAR) methods for drug design.

 
•Representation of Biomedical protocols (PI). The project is partially supported by Occams Resources (occamsresources.com/‎)

The research team includes members of the Centre for Systems and Synthetic Biology at Brunel University London (http://www.brunel.ac.uk/research/centres/cssb), Manchester Institute of Biotechnology (www.mib.ac.uk/‎), Magdeburg Centre for Systems Biology, Germany (http://psb2.inqbus.de/hosts/pain-signaling.org/project-partners/modelling-group/magdeburg-centre-for-systems-biology), Laboratory of Molecular Biology of the Cell, CNRS, France (http://www.ens-lyon.eu/research/molecular-biology-of-the-cell-laboratory-lbmc-umr-5239-86513.kjsp?RH=ENS-LYON-ANG-LABS).

The project aims to define the minimum information required for the recording and information exchange about biomedical protocols in a machine processable form.  Our ontology EXACT defines explicit semantics of typical experimental actions and their descriptors, and can be integrated with the formalism of Petri nets to represent experimental workflows.

Research centre(s)

Teaching/Supervision

Teaching

Module leader for CS5513 semantic Integration Frameworks
The aim of the module is to develop a critical and practical understanding of concepts, standards and frameworks supporting systems integration with semantics in mind. The focus is primarily on semantic web technologies. Standards of conceptual and technological “tools” for supporting and realising integration play a significant part.

Module teaching contributor for CS5565 Service Oriented Architecture
The  use  of  heterogeneous  technologies  and  applications  in  business  and  organisations  is  a  reality  and  their  integration  can  be  achieved  from  multiple  perspectives.  Today many  of  these  are brought  together  in  the  form  of  Service Oriented  Architecture. 
Arguably, it  is  the  first  time  that  business  processes  and  their  technological  realisation  have  been  so  closely   brought   together.   In   this   context,  the   aim   of   the   module   is   to   develop   the  knowledge  and  skills  necessary  to  support  the  integration  of  intra  and  inter  organisational  information  systems  using  a  service -oriented  emphasis  and  to  critically  assess  their  impact.

Selected Publications

Journal articles

Klingstrom, T. , Soldatova, L. , Stevens, R. , Roos, TE. , et al.   (2013)   'Workshop on laboratory protocol standards for the molecular methods database'. NEW BIOTECHNOLOGY, 30 (2).  pp. 109 - 113. doi: 10.1016/j.nbt.2012.05.019 

King, RD. , Liakata, M. , Lu, C. , Soldatova, LN.  and Oliver, SG.   (2011)   'On the formalization and reuse of scientific research'. Journal of the Royal Society Interface, 8 (63).  pp. 1440 - 1448. doi: 10.1098/rsif.2011.0029 Download publication 

Soldatova, L.  and Rzhetsky, A.   (2011)   'Representation of research hypotheses'. Journal of Biomedical Semantics, 1 (1).  Download publication 

Lavrac, N. , Vavpetic, A. , Soldatova, L. , Trajkovski, I.  and Novak, PK.   (2011)   'Using Ontologies in Semantic Data Mining with SEGS and g-SEGS'. DISCOVERY SCIENCE, 6926 pp. 165 - +. 

Sparkes, A. , Aubrey, W. , Byrne, E. , Clare, A. , et al.   (2010)   'Towards Robot Scientists for autonomous scientific discovery'. Automated Experimentation, 2 (1).  doi: 10.1186/1759-4499-2-1 

Qi, D. , King, RD. , Hopkins, A. , Bickerton, GR.  and Soldatova, LN.   (2010)   'An ontology for description of drug discovery investigations.'. Journal of Integrative Bioinformatics, 25 pp. . doi: 10.2390/biecoll-jib-2010-126 

The OBI Consortium.   (2009)   'Modeling of biomedical experimental processes with OBI'. J. of Biomed. Semantics, 1 

King, RD. , Rowland, J. , Aubrey, W. , Liakata, M. , et al.   (2009)   'THE ROBOT SCIENTIST ADAM'. COMPUTER, 42 (8).  pp. 46 - 54. 

King, RD. , Rowland, J. , Oliver, SG. , Young, M. , et al.   (2009)   'The Automation of Science'. Science, 324 (5923).  pp. 85 - 89. doi: 10.1126/science.1165620 

Soldatova, L. , King, RD. , Aubrey, W.  and Clare, A.   (2008)   'The EXACT description of biomedical protocols'. Bioinformatics, 24 (13).  pp. i295 - i303. doi: 10.1093/bioinformatics/btn156 Download publication 

Schierz, AC. , Soldatova, LN.  and King, RD.   (2007)   'Overhauling the PDB'. NATURE BIOTECHNOLOGY, 25 (4).  pp. 437 - 442. doi: 10.1038/nbt0407-437 

Sansone, S-A. , Schober, D. , Atherton, HJ. , Fiehn, O. , et al.   (2007)   'Metabolomics standards initiative: ontology working group work in progress'. METABOLOMICS, 3 (3).  pp. 249 - 256. doi: 10.1007/s11306-007-0069-z 

Soldatova, LN.  and King, RD.   (2006)   'An ontology of scientific experiments'. JOURNAL OF THE ROYAL SOCIETY INTERFACE, 3 (11).  pp. 795 - 803. doi: 10.1098/rsif.2006.0134 

Soldatova, LN. , Clare, A. , Sparkes, A.  and King, RD.   (2006)   'An ontology for a Robot Scientist'. BIOINFORMATICS, 22 (14).  pp. E464 - E471. doi: 10.1093/bioinformatics/btl207 

Soldatova, LN.  and King, RD.   (2005)   'Are the current ontologies in biology good ontologies?'. Nature Biotechnology, 23 (9).  pp. 1095 - 1098. doi: 10.1038/nbt0905-1095 

Book chapters

Panov, P. , Soldatova, L.  and Dzeroski, S.  (2010)   'Representing Entities in the OntoDM Data Mining Ontology', in Džeroski, S. , Goethals, B.  and Panov, P. (eds.) Inductive Databases and Constraint-Based Data Mining.  Springer pp. . 

Soldatova, L.  (1999)   'Comparison of problem complexity', in Cumming, G. , Okamoto, T.  and Gomez, L. (eds.) Advanced Research in Computers and Communications in Education.  Ios Pr Incorporated pp. 169 - 172. 

Conference papers

Panov, P. , Soldatova, LN.  and Dzeroski, S.   (2009)   'Towards an Ontology of Data Mining Investigations' , 12th International Conference on Discovery Science. Porto, PORTUGAL. 1 - 5 October. SPRINGER-VERLAG BERLIN, pp. 257 - +. 

Soldatova, L. , Panov, P.  and Dzeroski, S.   (2008)   'OntoDM: An Ontology of Data Mining' , IEEE International Conference on Data Mining Workshops. [unpublished].  

Aroyo, L. , Inaba, A. , Soldatova, L.  and Mizoguchi, R.   (2004)   'EASE: Evolutional authoring support environment' , 7th International Conference on Intelligent Tutoring Systems. Maceio, BRAZIL. 30 - 3 September. SPRINGER-VERLAG BERLIN, pp. 140 - 149. 

Soldatova, L.  and Mizoguchi, R.   (2003)   'Test ontology' . 

Page last updated: Tuesday 21 June 2016