Stealthy annotation of experimental biology by spreadsheets

Abstract

SUMMARYThe increase in volume and complexity of biological data has led to increased requirements to reuse that data. Consistent and accurate metadata is essential for this task, creating new challenges in semantic data annotation and in the constriction of terminologies and ontologies used for annotation. The BioSharing community are developing standards and terminologies for annotation, which have been adopted across bioinformatics, but the real challenge is to make these standards accessible to laboratory scientists. Widespread adoption requires the provision of tools to assist scientists whilst reducing the complexities of working with semantics. This paper describes unobtrusive 'stealthy' methods for collecting standards compliant, semantically annotated data and for contributing to ontologies used for those annotations. Spreadsheets are ubiquitous in laboratory data management. Our spreadsheet-based RightField tool enables scientists to structure information and select ontology terms for annotation within spreadsheets, producing high quality, consistent data without changing common working practices. Furthermore, our Populous spreadsheet tool proves effective for gathering domain knowledge in the form of Web Ontology Language (OWL) ontologies. Such a corpus of structured and semantically enriched knowledge can be extracted in Resource Description Framework (RDF), providing further means for searching across the content and contributing to Open Linked Data (http://linkeddata.org/).

Editorial

“…Wolstencroft et al . describe new methods for building a better bridge between the semantic data annotation and the laboratory scientist. Using unobtrusive ‘stealthy’ methods for collecting standards compliant, semantically annotated data, and for contributing ontologies used for those annotations, the authors have built upon the ubiquitous spreadsheet to enable scientist to structure information and select ontology terms without changing common workplace practices.…”

Excel–SBOL Converter: Creating SBOL from Excel Templates and Vice Versa

“…Associated with this interdisciplinary movement is the need for tools that support reusability and supplement the current understanding of genetic sequences. To satisfy this need, synthetic biology communities across the world have developed tools and ontologies to help describe their unique semantic annotations. − Shared representations for data and metadata, grounded in well-defined ontology terms, can help reduce confusion when researchers share materials . The Synthetic Biology Open Language (SBOL) has been developed to address this challenge.…”

“…2−15 Shared representations for data and metadata, grounded in well-defined ontology terms, can help reduce confusion when researchers share materials. 16 The Synthetic Biology Open Language (SBOL) 6 has been developed to address this challenge. SBOL provides a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs, supporting the use of engineering principles such as abstraction, modularity, and standardization for synthetic biology.…”

Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa

“…[2][3][4][5][6][7][8][9][10][11][12][13][14][15] Shared representations for data and metadata, grounded in well-defined ontology terms, can help reduce confusion when sharing materials between researchers. 16 The Synthetic Biology Open Language (SBOL) 6 has been developed to address this challenge. SBOL provides a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs, supporting the use of engineering principles such as abstraction, modularity, and standardization for synthetic biology.…”