Knowledge discovery via an informatics resource is constrained by the completeness of the resource, both in terms of the amount of data it contains and in terms of the metadata that exists to describe the data. Increasing completeness in one of these...
BACKGROUND: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association stu...
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Jan 1, 2019
Phylogeography research involving virus spread and tree reconstruction relies on accurate geographic locations of infected hosts. Insufficient level of geographic information in nucleotide sequence repositories such as GenBank motivates the use of na...
International journal of medical informatics
Jan 1, 2019
OBJECTIVE: Reproducibility of research studies is key to advancing biomedical science by building on sound results and reducing inconsistencies between published results and study data. We propose that the available data from research studies combine...
While convolutional neural networks (CNNs) have successfully been applied for skin lesion classification, previous studies have generally considered only a single clinical/macroscopic image and output a binary decision. In this work, we have presente...
BACKGROUND: Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associated repositories, leading to a ...
MOTIVATION: The ever-increasing number of biomedical datasets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide conte...
Studies in health technology and informatics
Jan 1, 2018
Metadata management is an important task in medical informatics and highly affects the gain out of existing health information data. Data Warehouse solutions like Informatics for Integrating Biology and the Bedside (i2b2) are common tools for identif...
Database : the journal of biological databases and curation
Jan 1, 2018
Many life science datasets are now available via Linked Data technologies, meaning that they are represented in a common format (the Resource Description Framework), and are accessible via standard APIs (SPARQL endpoints). While this is an important ...
Studies in health technology and informatics
Jan 1, 2018
Performing image feature extraction in radiation oncology is often dependent on the organ and tumor delineations provided by clinical staff. These delineation names are free text DICOM metadata fields resulting in undefined information, which require...