Efficient tools for data management and integration are essential for many aspects of high-throughput
biology. In particular, annotations of genes and human genetic variants are …

Wikidata is a community-maintained knowledge base that has been assembled from repositories
in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds…

13 C NMR has many advantages for a metabolomics study, including a large spectral dispersion,
narrow singlets at natural abundance, and a direct measure of the backbone structures …

There are thousands of distinct disease entities and concepts, each of which are known by
different and sometimes contradictory names. The Monarch Initiative aims to integrate …

We discuss Shape Expressions (ShEx), a concise, formal, modeling and validation language
for RDF structures. For instance, a Shape Expression could prescribe that subjects in a …

Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is
exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We …

Compound identification is a major bottleneck in metabolomics studies. In nuclear magnetic
resonance (NMR) investigations, resonance overlap often hinders unambiguous database …

We demonstrate the global metabolic analysis of Caenorhabditis elegans stress responses
using a mass-spectrometry-based technique called isotopic ratio outlier analysis (IROA). In …

The gut microbiota plays an important yet incompletely understood role in the induction and
propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated …

Background Mass spectrometry-based shotgun proteomics experiments rely on accurate
matching of experimental spectra against a database of protein sequences. Existing …