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We present an analytical study of the quality of metadata about samples used in biomedical experiments. The metadata under analysis are stored in two well-known databases: BioSample---a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples---a repository managed by the European Bioinformatics Institute (EBI). We tested whether 11.4M sample metadata records in the two repositories are populated with values that fulfill the stated requirements for such values. Our study revealed multiple anomalies in the metadata. Most metadata field names and their values are not standardized or controlled. Even simple binary or numeric fields are often populated with inadequate values of different data types. By clustering metadata field names, we discovered there are often many distinct ways to represent the same aspect of a sample. Overall, the metadata we analyzed reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements. The significant aberrancies that we found in the metadata are likely to impede search and secondary use of the associated datasets.
The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developed--the CEDAR Workbench--is a suite of Web-based tools and REST APIs
Across many scientific domains, there is a common need to automatically extract a simplified view or coarse-graining of how a complex systems components interact. This general task is called community detection in networks and is analogous to searchi
The metadata about scientific experiments published in online repositories have been shown to suffer from a high degree of representational heterogeneity---there are often many ways to represent the same type of information, such as a geographical lo
Most existing algorithms for dictionary learning assume that all entries of the (high-dimensional) input data are fully observed. However, in several practical applications (such as hyper-spectral imaging or blood glucose monitoring), only an incompl
Wireless sensor networks become integral part of our life. These networks can be used for monitoring the data in various domain due to their flexibility and functionality. Query processing and optimization in the WSN is a very challenging task becaus