Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies

TitleMetadata in the BioSample Online Repository are Impaired by Numerous Anomalies
Publication TypeConference Paper
Year of Publication2017
AuthorsGonçalves RS, O’Connor MJ, Martínez-Romero M, Graybeal J, Musen MA
Conference Name1st International Workshop SemSci: Enabling Open Semantic Science
Date PublishedOctober, 2017
PublisherSemantic Science
Conference LocationVienna, Austria

The metadata about scientific experiments are crucial for finding, re-producing, and reusing the data that the metadata describe. We present a study of the quality of the metadata stored in BioSample—a repository of metadata about samples used in biomedical experiments managed by the U.S. National Center for Biomedical Technology Information (NCBI). We tested whether 6.6 million BioSample metadata records are populated with values that fulfill the stated re-quirements for such values. Our study revealed multiple anomalies in the ana-lyzed metadata. The BioSample metadata field names and their values are not standardized or controlled—15% of the metadata fields use field names not spec-ified in the BioSample data dictionary. Only 9 out of 452 BioSample-specified fields ordinarily require ontology terms as values, and the quality of these con-trolled fields is better than that of uncontrolled ones, as even simple binary or numeric fields are often populated with inadequate values of different data types (e.g., only 27% of Boolean values are valid). Overall, the metadata in BioSample reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements. The aberrancies in the metadata are likely to impede search and secondary use of the associated datasets.

Last Updated: 
Dec 11 2017 - 2:21pm