Table 2 Field definitions and controlled vocabulary used across the sample component details pages.
From: Scalable cyberinfrastructure for experimental NMR data
Details Page | Fields and controlled lists |
|---|---|
protein | name, role, quantity/unit, molecular weight (MW), purity, UniProt ID, # subunits, conformational state (globular, membrane, fibril, disordered), monomer/homo-oligomer (symmetric/asymmetric), AA sequence, modifications (linkage, post-translational modifications [phosphorylation, acetylation, glycosylation, lipidation, nitrosylation, ubiquitination], non-standard AA, paramagnetic tags, purification tags [N-His6, C-His6, N-Strep, C-Strep, N-GST, C-GST, N-thioredoxin, C-thioredoxin]) |
nucleic acid (DNA/RNA) | name, role, quantity/unit, MW, purity, GenBank ID, sequence, non-standard description, covalent linkage description, modifications (linkage, post-translational modifications [phosphorylation, acetylation, glycosylation, lipidation, nitrosylation, ubiquitination], non-standard AA, paramagnetic tags, purification tags [N-His6, C-His6, N-Strep, C-Strep, N-GST, C-GST, N-thioredoxin, C-thioredoxin]) |
carbohydrate | name, role, quantity/unit, MW, purity, classification (oligosaccharide/polysaccharide), IUPAC-condensed string, tags, modifications (glycopeptide, glycolipid, glycosides) |
polymer | name, role, quantity/unit, purity, tacticity (atactic, eutectic, isotactic, syntactic, indeterminate), branching (linear, branched), source (synthetic, biological [biological source]), weight average MW, # average MW, dispersity, # of subunits, degree of substitution, length of repeated sequence, total # of repeats, sequence order, define polymer subunit(s) |
biological material | name, quantity/unit, source organism (human, mouse, E. coli), biological type (serum, urine, whole blood, cell extract, tissue), sample category (study sample, buffer blank, extraction blank, internal QC, external QC), local sample ID, extraction method (none, methanol:water, methanol, water, isopropanol, DMSO, chloroform:methanol, other), description |
environmental sample | name, quantity/unit, source location, source class/material, geo location, sample category, local sample ID, extraction type, description |
chemical formula | name, role, quantity/unit, MW, purity, CHEBI ID, CAS ID, PubChem ID, chemical formula, InChi String, class (small molecule, polycrystalline, amorphous, zeolite, single crystal, heterostructure, glass) |
component | name, role, quantity/unit, MW purity |
