Ambiguity of non-systematic chemical identifiers within and between small-molecule databases

“…Within the same database, the percentage of identifiers with multiplicity larger than one varies from 0% to 100%, whereas the ambiguity of names ranges from 0.07% to 29.4%. When mapping between databases, these ambiguities and multiplicities lead to larger inconsistencies, and this agree with previous observations regarding small molecules databases [ 31 , 35 ]. The inconsistencies when mapping using metabolite names range from 0% to 81.2%.…”

“…Finally, when desalted formulas were compared, which further eliminated discrepancies that could be attributed to salt-parent, stereo, and geometric isomer differences, 3% of the mismatches remained, indicating a significant remaining level of gross structural errors. These results are consistent with a recently published report quantifying the ambiguity of chemical identifiers in a selection of public databases, 35 but to our knowledge, the high degree of inconsistency of chemical supplier-provided information relative to manual curation results had not previously been reported. (Note: These results were based on an analysis of 90% of the current ToxCast sample inventory, as of March, 2014, using canonicalized SMILES strings for both sets of parent and desalted structures generated from the original SD files in ACD/ChemFolder, v2012, Toronto, Canada.…”

“…Within the same database, the percentage of identifiers with multiplicity larger than one varies from 0 % to 100 %, whereas the ambiguity of names ranges from 0.07 % to 29.4 %. When mapping between databases, these ambiguities and multiplicities lead to larger inconsistencies, and this agree with previous observations regarding small molecules databases [262,266]. The inconsistencies when mapping using metabolite names range from 0 % to 81.2 %.…”

“…In agreement with earlier studies [358,357], our observations in Chapter 2 also suggested that mapping without manual curation implies high risk of mismatch. Yet this is not the most efficient approach [357]. Detailed study has shown that manual curation has resolved only a small part of the inconsistency in ChemSpider [357].…”