The Human Protein Atlas background and history

The Human Protein Atlas (HPA) journey started in 2000, the same year as the announcement of the completion of the Human Genome Project. In 2003, the program received generous support from the Knut and Alice Wallenberg Foundation (KAW), and the program was changed to an exclusively academic endeavor. The aim of the program has been to map the human proteins in cells, tissues, organs and blood, using integration of various 'omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, proximity extension assay (PEA)-based protein profiling and systems biology.

Primarily based in Sweden, the Human Protein Atlas project involves the joint efforts of the Royal Institute of Technology in Stockholm, Uppsala University, Uppsala Akademiska University Hospital, and more recently also Science for Life Laboratory based in both Uppsala and Stockholm. Formal collaborations are with groups in India, South Korea, Japan, China, Germany, France, Switzerland, USA, Canada, Denmark, Finland, The Netherlands, Spain, and Italy.

The first version of the Human Protein Atlas website was launched in 2005 and consisted of protein expression data based on approximately 700 antibodies. Since then, each new release has included more data and new functionalities and features to the website.

Important additions include:

Version	Year released	Feature
1	2005	The launch of the Human Protein Atlas. 700 antibodies.
2	2006	Inclusion of cell-line data and confocal images showing subcellular localizations.
3	2007	A new search function that allowed advanced query based searches was included.
4	2008	The overall database structure was shifted from a previously antibody-centric structure, to a gene-centric structure in order to include information on all genes predicted by Ensembl.
7	2010	A major restructure accompanying the introduction of the concept of annotated protein expression for paired antibodies (two independent antibodies directed against different, non-overlapping epitopes on the same protein).
12	2013	The protein atlas database was complemented with transcriptomics profiles from 27 normal tissues, and the format with four sub-atlases was introduced.
13	2014	An analysis of all major organ and tissues in the human body using transcriptomics and antibody-based profiling was included. The results were summarized on interactive knowledge-pages divided into 7 human proteomes and 27 tissues and organs.
14	2015	A new mouse brain atlas was introduced.
15	2016	Inclusion of RNA-seq data from the Genotype-Tissue Expression (GTEx) consortium.
16	2016	A new Cell Atlas was launched with subcellular localization corresponding to over 12,000 protein-coding genes, together with a new approach for visualization of antibody validation and the inclusion of transcriptomics data from the FANTOM5 program.
17	2017	The Pathology Atlas was launched, where a systems-level approach based on genome-wide transcriptomics data and clinical meta data of almost 8000 patients was used in order to analyze the proteome of 17 major cancer types.
19	2019	Three new Atlases were introduced; a Blood Atlas, a Brain Atlas and a Metabolic Atlas.
21	2021	The resource now includes 10 separate sections including the new additions Single Cell Type, Tissue Cell Type and Cell line.
22	2022	Two new sections were introduced; the Structure section and the Disease Blood Atlas section
23	2023	The Interaction section was introduced. It was built on the former Metabolic section and includes protein-protein interaction networks as well as metabolic networks

A 20-year journey into the body

In an expansive supplement published by Science, a journey is taken through the 20 years since the establishment of the Human Protein Atlas (HPA) consortium, to underscore milestones reached and to celebrate releases of updates and additions to the atlas. For the reader’s convenience, reprints of the relevant journal articles associated with the most important of these milestones are provided. You can download the pdf version here.

Together with Science, the microsite hpajourney.proteinatlas.org has been produced to show some of HPA's hightlighs.

Below, the 39 most significant milestones in the history of the HPA consortium are outlined. Click on any milestone and read about key facts and publications related to each milestone.

Scientific Milestones
Year	No	Title	Year	No	Title
1985	1	Affinity tags for protein purification	2015	21	The Tissue Atlas
1989	2	Solid phase sequencing	2016	22	Correlation of RNA and protein levels
1993	3	Next generation sequencing	2016	23	Human secretome resource
1996	4	First concept of antibody-based proteomics	2016	24	Antibody validation
2000	5	The Human Genome Project	2017	25	The Subcellular Atlas
2000	6	Chromosome 21 pilot	2017	26	The Pathology Atlas
2003	7	Start of the Human Protein Atlas program	2017	27	Systems medicine
2004	8	Tissue microarrays	2018	28	Wellness profiling and precision medicine
2004	9	The HPA data management system	2018	29	Deep learning and citizen science
2005	10	Launch of the Human Protein Atlas portal	2019	30	Human secretome annotation
2006	11	Creation of an antibody resource	2019	31	The Blood Atlas
2007	12	Protein arrays	2019	32	The HPA Kaggle Challenge
2008	13	Web-based pathology annotation	2020	33	The Brain Atlas
2008	14	Epitope mapping of antibodies	2020	34	The Metabolic Atlas
2008	15	Antibodypedia antibody portal	2020	35	The fight against the novel coronavirus
2009	16	Antibody-based biomarker discovery	2021	36	The Single Cell Type Atlas
2010	17	Knowledge-based portal	2022	37	The Disease Blood Atlas
2011	18	Therapeutic antibodies and Affibodies	2022	38	Protein 3D structures
2012	19	Targeted proteomics	2023	39	Interaction section
2014	20	Integration of RNA and protein profiles