The National Cancer Institute (NCI) National Cancer Informatics Program (NCIP) Nanotechnology Working Group was established in 2008 for researchers with a specific interest in informatics and computational approaches to nanotechnology, with a particular emphasis on nanomedicine. The goal of this working group is to demonstrate the scientific potential of federating nanotechnology databases through pilot projects aimed at integrated semantic search and retrieval of nanomedicine and nanotoxicology datasets that are applicable across nanoscience. The NCIP Nanotechnology Working Group (NCIP Nano WG) comprises over 20 active participants from academia, government and industry with diverse interests.
This Working Group is motivated by two high-priority nanomedicine informatics applications:
These applications will be enabled by broad computational capability applied to nanotechnology research. The development of such capability has led to the following long-term objectives for the Nano WG:
To realize the long-term objectives outlined above, the NCIP Nano WG has established several short-term goals with 6-12 month timeframes.
We will work to identify datasets and develop statistical analytic models that help to identify the key features that describe the biological activity of selected nanomaterials. The main challenge is a lack of large high quality datasets to support predictive modeling. Datasets that are incomplete, lack validation, or are low quality are considered to be in the ‘incubator phase’ to ensure that we do not dilute the quality of data for informatics. However, the data currently available in such incubators can be used to discover interesting trends (generate hypotheses) to guide development of new approaches for both the characterization of nanomaterials and the modeling. We recognize that diverse nanoparticles with different cores and surface modifiers tested for specific biological activity can be characterized by experimental physical, geometrical, and electronic properties to enable modeling; alternatively, nanoparticles with the same core but different surface modifiers can be characterized by computed chemical descriptors of these modifiers. The goals of this activity will be to (1) collect and standardize experimental properties of nanoparticles (which will also fuel ontology development under Aim 2, vide infra), (2) develop approaches to identifying descriptors of chemical, physical, geometrical, and electronic properties of nanoparticles, and (3) develop predictive models of nanoparticles’ biological activity that can be interpreted to elucidate activity-defining features and obtain mechanistic insight into nanomaterial biological activity. Specific tasks will include:
Where sufficient data is available, we will identify priorities and next steps for predictive modeling of nanomaterial biological activity.
Proposed Data Sharing “Ground Rules” for Data Analyzed by the Nano WG: NanoWG_DataSharing.pptx
Data generated from nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. The Nano WG supports the continuing development and application of the NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. Nano WG will work closely with data repositories and data curation efforts to capture requirements and incorporate new terminology in NPO. See http://nano-ontology.org for more information. Work on this aim will consist of the following tasks:
ISA-TAB-Nano was developed to facilitate the import and export of data on nanomaterials and their characterizations among nanotechnology resources. Nano WG will continue to update the specification based on the feedback from the community. Nano WG will also continue to work with the ISA-team to extend the ISA-TAB validator to support ISA-TAB-Nano extensions, and to explore the use of ISA OntoMaton that allows users to search for ontology terms while annotating their experiments. The ISA-TAB-Nano project is under development as an ASTM standard (WK28974 at http://is.gd/foSKV) See the ISA-TAB-Nano Specification for more information. Work on this Aim will be focused on the following tasks:
In the course of these activities, we also plan to survey and identify issues in nanotechnology data curation and search that should be standardized across data resources.
See Nanocharacterization Library
Standardizing nanomaterial characterization protocols. Several Working Group members have noted that standard characterizations discussed above are only useful if the protocols for these characterizations are themselves standardized and reproducible. Furthermore, evidence from inter-laboratory studies by ASTM and IANH suggests that there is significant variability in results from existing "standard" protocols, suggesting that current mechanisms for protocol communication are ineffective. This nanotechnology problem is currently under investigation by ASTM and ISO groups. The Working Group assists in this effort by:
Defining standards for nanomedicine data sharing and exchange. Currently, access to relevant data is a major barrier to the realization of the nanomedical goals of rational nanomaterial design and toxicity prediction. While a few detailed datasets exist for nanomaterial toxicity (ONAMI), and nanomaterial-cellular interactions (Shaw and others) most of the necessary data is dispersed across a wide array of nanotechnology data resources. Therefore, it is essential to implement an infrastructure to ensure that these data can be shared among researchers and data resources. To develop this (federated) data sharing infrastructure, the Working Group has undertaken development of the ISA-TAB-Nano spreadsheet form, based on the ISA-TAB framework, to facilitate submission of data by experimental researchers. The ISA-TAB-Nano effort is translating the great success of MAGE-TAB microarray and similar formats for enabling data sharing in other communities. Ongoing development is based on community requirements and feedack: See ISA-TAB-Nano Specification
Providing vocabulary and semantic support to the nanomedicine community. Data generated from nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. The NCIP Nano WG supports the continuing development and application the of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. The NPO was developed to represent knowledge underlying the preparation, chemical composition and characterization of nanomaterials involved in research.
More information can be found at http://nano-ontology.org