Towards self-describing and FAIR bulk formats for biomedical data.

We introduce a self-describing serialized format for bulk biomedical data called the Portable Format for Biomedical (PFB) data. The Portable Format for Biomedical data is based upon Avro and encapsulates a data model, a data dictionary, the data itself, and pointers to third party controlled vocabularies. In general, each data element in the data dictionary is associated with a third party controlled vocabulary to make it easier for applications to harmonize two or more PFB files. We also introduce an open source software development kit (SDK) called PyPFB for creating, exploring and modifying PFB files. We describe experimental studies showing the performance improvements when importing and exporting bulk biomedical data in the PFB format versus using JSON and SQL formats.

Comparing nutrient intake from food to the estimated average requirements shows middle- to upper-income pregnant women lack iron and possibly magnesium.

OBJECTIVE: To determine whether nutrient intake from food alone was adequate across trimesters for middle- to upper-income pregnant women when compared with estimated average requirements (EAR), and to determine whether food intake exceeded the tolerable upper intake level (UL) for any nutrient. DESIGN: Observational study in which pregnant women completed 3-day diet records each month during their pregnancy. Records were analyzed for nutrient content, and usual intake distributions were determined. SUBJECTS/SETTING: Subjects were low-risk women in their first trimester of pregnancy (living in middle- to upper-income households). Ninety-four women were recruited, and sixty-three participated. STATISTICAL ANALYSIS PERFORMED: Nutrient intake data were adjusted to achieve normality by using a power transformation. A mixed model method was used to assess trends in intake over time, and to estimate mean intake and within-subjects and between-subjects variance. The usual intake distribution for each nutrient was determined and compared with the EAR and UL. RESULTS: The probabilities of usual nutrient intake from food being less than the EAR were highest for iron (.91), magnesium (.53), zinc (.31), vitamin B6 (.21), selenium (.20), and vitamin C (.12). Women were not at risk of exceeding the UL from food intake for any nutrient studied. APPLICATIONS/CONCLUSIONS: Study participants did not consume adequate amounts of iron from food to meet the needs of pregnancy, and therefore iron supplementation is warranted in this population. Intake of magnesium was suboptimal using the EAR as a cut-point for adequacy.