  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.
