Integration of data: the Nanomaterial Registry project and data curation

Guzan, Kimberly; Mills, Karmann; Gupta, Vijay; Murry, Damaris; Scheier, CN; Willis, D. R.; Ostraat, Michele L.

doi:10.1088/1749-4699/6/1/014007

Cited by 10 publications

(6 citation statements)

References 4 publications

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“…Because it is costly to conduct new experiments to obtain new experimental data in nanotechnology, several approaches tried to share such information [16], [17], [18]. The extraction of experimental information is supposed to be applied as a preprocessing step for such shared data construction in nanoinformatics.…”

Section: Discussionmentioning

confidence: 99%

“…Other researchers are working on developing databases and repositories for nanomaterials and their related applications. For example, the Nanomaterial Registry [16] uses information about nanomaterials to support a robust data curation process that promotes integration across a diverse data set. Another example is the DaNa project [17], which provides information about products and applications related to nanomaterials, aiming to illuminate their health and environmental aspects.…”

Section: Related Workmentioning

confidence: 99%

See 1 more Smart Citation

NaDev: An Annotated Corpus to Support Information Extraction from Research Papers on Nanocrystal Devices

Dieb¹,

Yoshioka²,

Hara

2016

Journal of Information Processing

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The process of nanocrystal device development is not well systematized. To support this process, analysis of the information produced by developmental experiments is required. In this study, we constructed an annotated corpus to support the extraction of experimental information from relevant publications. We designed the corpus-construction guidelines by cooperating with a domain expert. We evaluated these guidelines through corpusconstruction experiments with graduate students from this domain, and then evaluated the corpus with the domain expert. In the corpus construction experiments, we achieved a sufficient level of Inter-Annotator Agreement by using a loose agreement measure that ignored the term-boundary mismatch problem, and made an agreement corpus that excluded annotations based on misunderstanding the guidelines. The domain expert evaluated this agreement corpus and modified the guidelines based on real examples. Using these guidelines, we finalized the corpus called "NaDev" (Nanocrystal Device development corpus). The NaDev corpus and its construction guidelines will be released via our website, http://nanoinfo.ist.hokudai.ac.jp/. The NaDev corpus aims to support automatic information extraction from publications relevant to nanocrystal device development. This information can be used to solve problems in the nanotechnology domain using the massive availability of fresh information. To the best of our knowledge, this is the first corpus constructed for the development of nanocrystal devices.

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Section: Discussionmentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%

NaDev: An Annotated Corpus to Support Information Extraction from Research Papers on Nanocrystal Devices

Dieb¹,

Yoshioka²,

Hara

2016

Journal of Information Processing

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“…In contrast, the following schemes assign numeric quality scores and were specifically designed to evaluate nanomaterial data curated into a specific data resource. The Nanomaterial Registry, 109,110 assigns normalised, numeric “compliance” scores to each nanomaterial record in the database based upon its associated measurements, corresponding to the physicochemical characteristics specified in the “minimal information about nanomaterials (MIAN)”, which are designed to capture the “quality and quantity” of the physicochemical characterisation performed for that nanomaterial. 39,86,87 The MOD-ENP-TOX and ModNanoTox curated nanomaterial data resources also developed quality scoring schemes which assign numeric scores (see Electronic Supplementary Information).…”

Section: Existing Proposals For Evaluating Nanomaterials Data Complmentioning

confidence: 99%

How should the completeness and quality of curated nanomaterial data be evaluated?

et al. 2016

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Nanotechnology is of increasing significance. Curation of nanomaterial data into electronic databases offers opportunities to better understand and predict nanomaterials’ behaviour. This supports innovation in, and regulation of, nanotechnology. It is commonly understood that curated data need to be sufficiently complete and of sufficient quality to serve their intended purpose. However, assessing data completeness and quality is non-trivial in general and is arguably especially difficult in the nanoscience area, given its highly multidisciplinary nature. The current article, part of the Nanomaterial Data Curation Initiative series, addresses how to assess the completeness and quality of (curated) nanomaterial data. In order to address this key challenge, a variety of related issues are discussed: the meaning and importance of data completeness and quality, existing approaches to their assessment and the key challenges associated with evaluating the completeness and quality of curated nanomaterial data. Considerations which are specific to the nanoscience area and lessons which can be learned from other relevant scientific disciplines are considered. Hence, the scope of this discussion ranges from physicochemical characterisation requirements for nanomaterials and interference of nanomaterials with nanotoxicology assays to broader issues such as minimum information checklists, toxicology data quality schemes and computational approaches that facilitate evaluation of the completeness and quality of (curated) data. This discussion is informed by a literature review and a survey of key nanomaterial data curation stakeholders. Finally, drawing upon this discussion, recommendations are presented concerning the central question: how should the completeness and quality of curated nanomaterial data be evaluated?

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“…18 Images should be linked to assay measurements using a new "ImageLink" file type, if the generic ISA-TAB-Nano approach cannot be applied. 19 Any nanomaterial structure representation files, which are not associated with specific Assay file "Measurement Value […]" entries, should be linked to the corresponding Material file using ZIP archives specified in the appropriate "Material Data File" column entry. 20 Empty "Factor Value […]", "Parameter Value […]" or "Measurement Value […]" columns in Study or Assay files can be deleted without having to update the corresponding Investigation file "Study Protocol Parameters Name", "Study Factor Name", or "Study Assay Measurement Name" fields.…”

Section: Business Rule Nomentioning

confidence: 99%

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

Robinson¹,

Cronin²,

Richarz³

et al. 2016

Nano Online

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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 been proposed as such a format. However, in order to build useful datasets according to this format, a variety of issues has to be addressed.These issues include questions regarding exactly which (meta)data to report and how to report them. The current article discusses some of the challenges 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 weaknesses of the resources are discussed along with possible future developments.

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Integration of data: the Nanomaterial Registry project and data curation

Cited by 10 publications

References 4 publications

NaDev: An Annotated Corpus to Support Information Extraction from Research Papers on Nanocrystal Devices

NaDev: An Annotated Corpus to Support Information Extraction from Research Papers on Nanocrystal Devices

How should the completeness and quality of curated nanomaterial data be evaluated?

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

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