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Background: Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different research teams have adopted Javascript Object Notation (JSON) as their primary data format. While usage of a common data format offers significant advantages, that alone is not sufficient for rich integrative queries across APIs. Results: Here, we have implemented JSON for Linking Data (JSON-LD) technology on the BioThings APIs that we have developed, MyGene.info, MyVariant.info and MyChem.info. JSON-LD provides a standard way to add semantic context to the existing JSON data structure, for the purpose of enhancing the interoperability between APIs. We demonstrated several use cases that were facilitated by semantic annotations using JSON-LD, including simpler and more precise query capabilities as well as API cross-linking. Conclusions: We believe that this pattern offers a generalizable solution for interoperability of APIs in the life sciences. [ABSTRACT FROM AUTHOR]

Background: This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering. Results: The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed anetwork analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they subdivide into functional groups that may control cellular gastrointestinal development. Conclusions: As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites http://biogps.org and http://www.macrophages.com/pig-atlas. [ABSTRACT FROM AUTHOR]

Background: Elevated serum ferritin levels have been reported to contribute to metabolic syndrome (MetS). We examined the association of serum ferritin levels with the development of MetS in a representative sample of Chinese male adult population., Method: The data came from the 2009-2013 Fangchenggang Area Males Health and Examination Survey (FAMHES). We combined a cross-sectional study of 2417 males and a longitudinal study of 857 males who participated in the FAMHES., Result: The serum ferritin level of MetS was higher than that of nonMetS (median and percentiles 25-75: 447.4 (294.1-612.4) vs. 302.4 (215.0-435.8) ng/ml, p < 0.01). A positive correlation between ferritin concentrations and blood pressure (Systolic BP: R = 0.110, Diastolic BP: R = 0.158), waist circumference (R = 0.333), fasting glucose (R = 0.089), triglyceride (R = 0.315) and low high-density lipoprotein cholesterol (R = 0.130) was significant (all p < 0.001). Compared with the level of ferritin in the group with no MetS component, the group with all five MetS components had a higher ferritin level (554.7 (340.1-606.4) vs. 274.2 (198.2-384.4) ng/ml). The odd radio (OR) was higher for MetS in the highest ferritin quartile (OR = 2.29, 95% CI = 1.47-3.54) compared with the lowest ferritin quartile after adjustment for multi-factors. After 4-year follow up, 79 subjects newly diagnosed with MetS in 857 cohort male participants in 2013. Compared with the lowest ferritin quartile, the RR of the highest ferritin quartile was 2.55 (95% CI = 1.30-5.00) after multiple adjustments (p < 0.01)., Conclusion: Our findings confirm that the serum ferritin level is associated with the independent components of MetS, and elevated ferritin level is an independent risk factor for MetS development in the Chinese male population during the 4-year follow-up period.