Biomedical subjects

John Ingraham

Publications and source records attributed to John Ingraham.

3 recordsLinked to original sources

PubMed2006

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

MetaCyc is a database of metabolic pathways and enzymes located at http://MetaCyc.org/. Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. Most of the pathways in MetaCyc occur in microorganisms and plants, although animal pathways are also represented. MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments. Enzyme information includes substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements and links to sequence and structure databases. Data are curated from the primary literature by curators with expertise in biochemistry and molecular biology. MetaCyc serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. Querying, visualization and curation of the database is supported by SRI's Pathway Tools software. The PathoLogic component of Pathway Tools is used in conjunction with MetaCyc to predict the metabolic network of an organism from its annotated genome. SRI and the European Bioinformatics Institute employed this tool to create pathway/genome databases (PGDBs) for 165 organisms, available at the BioCyc.org website. These PGDBs also include predicted operons and pathway hole fillers.

Animals↗

PubMed2005

EcoCyc: a comprehensive database resource for Escherichia coli.

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein-ligand interactions.

Computational Biology↗

PubMed2002

Contrast enhanced duplex ultrasound imaging of the mesenteric arteries.

Duplex ultrasound of the visceral arteries is a technically challenging procedure. We examined the clinical usefulness of perflutren intravenous ultrasound contrast to improve the diagnostic accuracy of such studies. Seventeen patients were prospectively studied. A color duplex imaging study of the visceral vasculature was performed with and without the contrast agent. Vessels were imaged and peak systolic velocity and Doppler waveforms of the aorta, celiac artery, superior mesenteric artery, and the inferior mesenteric artery were examined. These results were independently compared to those of contrast angiography. From this analysis we concluded contrast-enhanced duplex imaging of the mesenteric arteries is safe but not routinely required when performed by an experienced sonographer. Ultrasound contrast may be helpful in difficult patients when the vessels are not initially successfully visualized.

Aged↗