The Human Proteome Organization (HUPO) includes in its over-arching goals: (1) completing the human protein “parts list” from known and predicted protein-coding genes as curated by GENCODE and UniProt, updated annually by the Human Proteome Project (HPP) led by the Chromosome-centric HPP (C-HPP); (2) integrating proteomics with genomics and other omics for use throughout the biomedical / life sciences community, led by the Biology and Disease-driven HPP (B/D-HPP); (3) Identifying and validating at least one function for every human protein in the HPP Grand Challenge.

In the past, integration of the various data sets for the HPP was performed by the SwissProt database, neXtProt. However, neXtProt is now deprecated and so commencing in 2025 the new human proteome project integration platform for the C-HPP and the Grand Challenge, is the Human Proteome Project Portal (HPP Portal). At its base GENCODE is used to establish the theoretical number of the protein encoding genes, with UniProt providing the identification of known and predicted human proteins. Integrating this information to a human only database of known and missing proteins, with their protein existence (PE) and functional evidence (FE) annotated and presented in the HPP Portal as a user-friendly online database.