Nanoinformatics for environmental health and biomedicine

• Rong Liu and
• Yoram Cohen

Beilstein J. Nanotechnol. 2015, 6, 2449–2451, doi:10.3762/bjnano.6.253

• , a data collection framework was developed [10] through ISA-TAB-Nano (a set of standardized specifications for nano-data representation). Advances in automating nano-data discovery and extraction is the subject of two other contributions that report on using advanced literature/text mining techniques

An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology

• Richard L. Marchese Robinson,
• Mark T. D. Cronin,
• Andrea-Nicole Richarz and
• Robert Rallo

Beilstein J. Nanotechnol. 2015, 6, 1978–1999, doi:10.3762/bjnano.6.202

• Rovira i Virgili, Av. Paisos Catalans 26, 43007 Tarragona, Catalunya, Spain 10.3762/bjnano.6.202 Abstract Analysis of trends in nanotoxicology data and the development of data driven models for nanotoxicity is facilitated by the reporting of data using a standardised electronic format. ISA-TAB-Nano has

• associated with the use of ISA-TAB-Nano and presents a set of resources designed to facilitate the manual creation of ISA-TAB-Nano datasets from the nanotoxicology literature. These resources were developed within the context of the NanoPUZZLES EU project and include data collection templates, corresponding

• business rules that extend the generic ISA-TAB-Nano specification as well as Python code to facilitate parsing and integration of these datasets within other nanoinformatics resources. The use of these resources is illustrated by a “Toy Dataset” presented in the Supporting Information. The strengths and

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

• Christina M. Powers,
• Karmann A. Mills,
• Stephanie A. Morris,
• Fred Klaessig,
• Sharon Gaheen,
• Nastassja Lewinski and
• Christine Ogilvie Hendren

Beilstein J. Nanotechnol. 2015, 6, 1860–1871, doi:10.3762/bjnano.6.189

• nanocuration is nascent, with few individuals formally trained in data curation or utilizing available nanocuration resources (e.g., ISA-TAB-Nano). Additional emphasis on the potential benefits of cultivating nanomaterial data via nanocuration processes (e.g., capability to analyze data from across research

• common data format in their respective workflows. An example data format is ISA-TAB-Nano, which is a file transfer protocol for querying among federated data repositories that are independently maintained by organizations with related, but not necessarily overlapping objectives [8]. Communication among

• a curator; Figure 3). In most cases, there was no process for non-curators to submit data to the repository (Figure 3). One example of a process for others to submit data consisted of researchers sending data in a standardized format (ISA-TAB-Nano) to a single person designated as responsible for

The Nanomaterial Data Curation Initiative: A collaborative approach to assessing, evaluating, and advancing the state of the field

• Christine Ogilvie Hendren,
• Christina M. Powers,
• Mark D. Hoover and
• Stacey L. Harper

Beilstein J. Nanotechnol. 2015, 6, 1752–1762, doi:10.3762/bjnano.6.179

• 2011 and periodically updated. In addition, the group recently developed and published data-exchange standards along with tools to enable the use of these standards (ISA-TAB-Nano; ASTM International E2909-13) [6]. To build on these efforts, the NCIP NanoWG is now developing a shared vision for curation

• ) Opportunities to leverage existing nanoinformatics resources (e.g. ISA-TAB-nano) in addressing integration for this sub-topic, or reasons not to do so? (ii) Practical next steps for individual stakeholders or the community as a whole? Results and Discussion For each sub-topic paper, information relevant to the

The eNanoMapper database for nanomaterial safety information

• Nina Jeliazkova,
• Charalampos Chomenidis,
• Philip Doganis,
• Bengt Fadeel,
• Roland Grafström,
• Barry Hardy,
• Janna Hastings,
• Markus Hegi,
• Vedrin Jeliazkov,
• Nikolay Kochev,
• Pekka Kohonen,
• Cristian R. Munteanu,
• Haralambos Sarimveis,
• Bart Smeets,
• Pantelis Sopasakis,
• Georgia Tsiliki,
• David Vorgrimmler and
• Egon Willighagen

Beilstein J. Nanotechnol. 2015, 6, 1609–1634, doi:10.3762/bjnano.6.165

• -Nano [16]. The latest ISA-Tab-Nano 1.2 specification recommends using the material file only for material composition and nominal characteristics, and to describe the experimentally determined characteristics in regular ISA-Tab assay files. The definitions of the terms “substance” and “material” are

• particular property is measured. ISA-Tab-Nano also allows for defining the qualities measured and detailed protocol conditions and instruments. The level of detail in the OHT, CODATA UDS, ISA-Tab-Nano and available ontologies differ, which is due to their different focus. Mapping between terms defined in the

• different sources is an ongoing effort supported by the eNanoMapper ontology team and the EU NanoSafety Cluster database working group. In Supporting Information File 1, we provide a table of OECD WPMN recommended endpoints and their potential correspondence to UDS and ISA-Tab-Nano concepts. To summarise

Experiences in supporting the structured collection of cancer nanotechnology data using caNanoLab

• Stephanie A. Morris,
• Sharon Gaheen,
• Michal Lijowski,
• Mervi Heiskanen and
• Juli Klemm

Beilstein J. Nanotechnol. 2015, 6, 1580–1593, doi:10.3762/bjnano.6.161

• (http://isatab.sourceforge.net/) and nanotechnology communities to develop a specification that provides descriptive information applicable to nanotechnology using spreadsheet-based file formats – ISA-TAB-Nano [14]. Curated caNanoLab data are annotated by terms from Bioportal (http

• ://bioportal.bioontology.org) and entered into ISA-TAB-Nano files that are available for download at https://wiki.nci.nih.gov/x/lgFwBg by individual users or other databases to enable data exchange. In addition to the development and utilization of data exchange standards, another challenge to data sharing, as viewed by

• area have included development and enhancement of the NPO and ISA-TAB-Nano. ISA-TAB-Nano is currently used by NCI, the NBI Knowledgebase (http://nbi.oregonstate.edu/), and the EU NanoSafety Cluster (http://www.nanosafetycluster.eu/) to enable interoperability between databases. Most recently, the Nano

Using natural language processing techniques to inform research on nanotechnology

• Nastassja A. Lewinski and
• Bridget T. McInnes

Beilstein J. Nanotechnol. 2015, 6, 1439–1449, doi:10.3762/bjnano.6.149

• , Nanomaterial Registry), domain ontologies (e.g., NanoParticle Ontology), terminologies and standards (e.g., ISA-TAB-Nano), data and text mining (e.g., NEIminer, TechPerceptor), and modeling/simulation (e.g., HDAT). Extracting information usually comes from two different sources: (1) literature to which natural