title: Annotating the structure and components of a nanoparticle formulation using computable string expressions.
abstract: Nanoparticle formulations that are being developed and tested for various medical applications are typically multi-component systems that vary in their structure, chemical composition, and function. It is difficult to compare and understand the differences between the structural and chemical descriptions of hundreds and thousands of nanoparticle formulations found in text documents. We have developed a string nomenclature to create computable string expressions that identify and enumerate the different high-level types of material parts of a nanoparticle formulation and represent the spatial order of their connectivity to each other. The string expressions are intended to be used as IDs, along with terms that describe a nanoparticle formulation and its material parts, in data sharing documents and nanomaterial research databases. The strings can be parsed and represented as a directed acyclic graph. The nodes of the graph can be used to display the string ID, name and other text descriptions of the nanoparticle formulation or its material part, while the edges represent the connectivity between the material parts with respect to the whole nanoparticle formulation. The different patterns in the string expressions can be searched for and used to compare the structure and chemical components of different nanoparticle formulations. The proposed string nomenclature is extensible and can be applied along with ontology terms to annotate the complete description of nanoparticles formulations.
authors.affiliation: Pacific Northwest National Laboratory Richland, WA, USA.
authors.forename: Dennis G
authors.initials: DG
authors.lastname: Thomas
authors.affiliation: Pacific Northwest National Laboratory Richland, WA, USA.
authors.forename: Satish
authors.initials: S
authors.lastname: Chikkagoudar
authors.affiliation: Pacific Northwest National Laboratory Richland, WA, USA.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Chappell
authors.affiliation: Pacific Northwest National Laboratory Richland, WA, USA.
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Baker
keywords: informatics; nanoparticle; ontology; string nomenclature