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Incorrect identifiers were identified and removed automatically (see Additional file 1: Section 2).
We identified 256 samples, which had incorrect identifiers as a result of manifest misreading, plate rotation and chip-related issues, and excluded 95 samples from unknown subjects (i.e. could not be assigned to identifiers).
Around half (65/124) of all incorrect identifiers were PubChem CID.
We further suggest implementing various quality checks, similar to those implemented in UniChem, to limit the number of incorrect identifiers returned for a metabolite.
When chemical name is included as an input identifier type (Figure 2a), the number of incorrect identifiers returned by CTS is much greater.
Valid identifiers point to valid but not preferred stereoisomers, invalid identifiers point to invalid stereoisomers or mixtures, incorrect identifiers point to different compounds, and nonexistent identifiers do not point to anything.
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If a metabolite is annotated with an incorrect identifier in a metabolic reconstruction it may not be mapped to the correct database or structure based identifier.
The number of incorrect output identifiers returned for names is also generally higher than for other input types, because names are more frequently associated with an incorrect structure [28].
Unfortunately, some of these parts are ignored by InChI conversion tools, resulting in generation of an incorrect InChI identifier.
Over half of the precision errors were due to mismatches against the gold standard hidden from annotator view (e.g. incorrect EntrezGene identifier or incorrect mutation position extracted), or incomplete task instructions (e.g. the need to exclude nonhuman mutations).
To allow for the possibility that the incorrect unique study identifier is recorded, the participant's initials will also be recorded on each case report form and questionnaire.
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