We developed the Phenotype Assembly Method (PhenoAM), utilizing 13 feature and qualifier groups with controlled vocabularies to accurately describe multidimensional phenotypes from macro to micro scales. PhenoAM was applied to standardize Phenome Data Elements (PhenoDE) across all measurement platforms in the International Human Phenome Project (IHPP). As a result, these PhenoDEs aggregate 58,297 data elements with multidimensional descriptions from 80 detection items.