AIMC Topic: Metadata
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Automation With Intelligence in Drug Research.
Clinical therapeutics
Oct 1, 2019
The industry has adopted Clinical Data Interchange Standards Consortium standards for clinical trial data and the Food and Drug Administration electronic common technical document standard for documents for many years but still faces many challenges....
Phenotype annotation with the ontology of microbial phenotypes (OMP).
Journal of biomedical semantics
Jul 15, 2019
BACKGROUND: Microbial genetics has formed a foundation for understanding many aspects of biology. Systematic annotation that supports computational data mining should reveal further insights for microbes, microbiomes, and conserved functions beyond m...
OMeta: an ontology-based, data-driven metadata tracking system.
BMC bioinformatics
Jan 7, 2019
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...
ProvCaRe: Characterizing scientific reproducibility of biomedical research studies using semantic provenance metadata.
International journal of medical informatics
Nov 3, 2018
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...
Multimodal skin lesion classification using deep learning.
Experimental dermatology
Sep 27, 2018
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...
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata.
BMC bioinformatics
Jul 16, 2018
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 ...
ProvCaRe Semantic Provenance Knowledgebase: Evaluating Scientific Reproducibility of Research Studies.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Apr 16, 2018
Scientific reproducibility is critical for biomedical research as it enables us to advance science by building on previous results, helps ensure the success of increasingly expensive drug trials, and allows funding agencies to make informed decisions...
ALE: automated label extraction from GEO metadata.
BMC bioinformatics
Dec 28, 2017
BACKGROUND: NCBI's Gene Expression Omnibus (GEO) is a rich community resource containing millions of gene expression experiments from human, mouse, rat, and other model organisms. However, information about each experiment (metadata) is in the format...
Automatic identification of high impact articles in PubMed to support clinical decision making.
Journal of biomedical informatics
Jul 26, 2017
OBJECTIVES: The practice of evidence-based medicine involves integrating the latest best available evidence into patient care decisions. Yet, critical barriers exist for clinicians' retrieval of evidence that is relevant for a particular patient from...
Scientific Reproducibility in Biomedical Research: Provenance Metadata Ontology for Semantic Annotation of Study Description.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Feb 10, 2017
Scientific reproducibility is key to scientific progress as it allows the research community to build on validated results, protect patients from potentially harmful trial drugs derived from incorrect results, and reduce wastage of valuable resources...
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