Cancer Nanotechnology Knowledge Base for Nanoparticle Analysis and Design

Dr. David Paik, Department of Radiology, Stanford University
Dr. Nathan Baker, Center for Computational Biology, Washington University School of Medicine

Nanotechnology has been applied to a wide spectrum of scientific research including very important life science applications. Nanoparticles are combinatorial and consist of a core constituent material, imaging/therapeutic payloads, and biological surface modifiers. This combinatorial nature creates a huge space of possible nanoparticle compositions. Informatics tools are a natural fit for addressing this need by providing decision support in the analysis and design of nanoparticles. As applied to cancer, nanotechnology is a new and promising approach to diagnostics and therapeutics with applications in imaging, early detection, reporting efficacy, and multifunctional therapeutics. Cancer nanotechnology presents a unique opportunity for informatics-driven approaches to accelerate discovery and translation.

The aims of this project are to integrate new sources of nanoparticle data into the NCBO Resource Index and develop a user friendly interface to search and browse nanoparticles. Data from caNanoLab, a curated repository of nanoparticle data, will be integrated into the NCBO Resource Index. This will provide detailed nanoparticle information needed by researchers in the cancer field. In addition, since caNanoLab is a node on caGrid this work will also lay the groundwork for incorporating a much wider range of biological information into the NCBO Resource Index from caBIG applications via queries of caGrid. To cover the need for chemical information needed for nanoparticles, data extracted from searches of PubChem will also be added to the NCBO Resource Index.

The second aim is to develop a graphically driven user interface to browse and search for semantically-related nanoparticle information stored in the NCBO Resource Index.  The browse mode will allow a user to interactively traverse the NCBO Resource Index data for semantically-related nanoparticle information. The search mode will allow users to specify nanoparticle components based on terms in the Nanoparticle Ontology.

PUBLICATIONS
Thomas DG, Pappu RV, Baker NA. NanoParticle Ontology for cancer nanotechnology research.
J Biomed Inform. 2010 Mar 6. [Epub ahead of print] PubMed PMID: 20211274.

Thomas DG, Pappu RV, Baker NA. Ontologies for cancer nanotechnology research.
Conf Proc IEEE Eng Med Biol Soc. 2009;2009:4158-61. PubMed PMID: 19964619.

CONFERENCE ABSTRACTS
Baker, NA, "Nanoparticle Ontology for Cancer Nanomedicine Research" Nanoinformatics 2010, October 2010

Kode KK, Shachaf C, Elchuri S, Nolan G, Paik DS, "Parametric Modeling of Raman Spectra of Nanoparticles for Quantitative Unmixing" World Molecular Imaging Congress 2009, September 2009.

Kode KK, Zavaleta C, Gambhir SS, Paik DS, "Quantitative Unmixing of Spectra for Raman Molecular Imaging of Living Subjects" World Molecular Imaging Congress 2009, September 2009.

Paik DS, Guccione S, Baker NA, Pan S, Gaheen S, Molnar L, Kode K, Thomas D, Pappu R, Jones P, Wang M, "An Informatics Perspective on the Experience of Developing and Populating a Database of Cancer-related Nanotechnology." Radiological Society of North America 94th Scientific Sessions, November 2008.

Paik DS, Kode K, Guccione S, Baker NA, Thomas D, Pappu R, Jones P, Wang M, Molnar L, Pan S, Gaheen S, "Experience Developing and Populating a Database of Cancer-related Nanotechnology." caBIG 2008 Annual Meeting, Washington, DC, June 2008.

Paik DS, "Role of the Bioinformatics and Biostatistics Resource Core in the Stanford CCNE", presented at NCI Nanotechnology Alliance Investigators Meeting, Chapel Hill, NC, October 2007.

WHITE PAPERS:
(in alphabetical order) Baker NA, Fritts M, Guccione S, Paik DS, Pappu RV, Patri A, Rubin D, Shaw SY, Thomas DG, "Nanotechnology Informatics White Paper," white paper commissioned by NCI caBIG, February 2009.

(in alphabetical order) Baker NA, Fritts M, Guccione S, Paik DS, Pappu RV, Rubin D, Shaw SY, Thomas DG, "The need for minimum information standards for development and advancement of nanomaterials as cancer diagnostics and therapeutics," white paper commissioned by NCI caBIG, February 2009.

(in alphabetical order) Baker NA, Fritts M, Guccione S, Paik DS, Pappu RV, Rubin D, Shaw SY, Thomas DG, "Ontologies in cancer nanotechnology research," white paper commissioned by NCI caBIG, January 2009.

INVITED PRESENTATIONS
Paik DS, "caBIG ICR Nanotechnology WG: Addressing the Emerging Discipline of Nano-bio-informatics." presented at caBIG 2008 Annual Meeting, Washington, DC, June 2008.

Paik DS, "Toward a Nanobioinformatics Infrastructure for Nanotechnology-based Prostate Cancer Therapeutic Response Tracking", presented at IEEE 7th International Symposium on Bioinformatics and Bioengineering, Boston, MA, October 2007.

Paik DS. "A Biomedical Informatics Perspective on Nanotechnology." presented to trans-NIH Task Force on Nanotechnology, May 2007.