The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data
Abstract
A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).
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Detailed information about experimental evidence supporting a pathway map is only included in BioPAX for molecular interactions because it was already defined by PSI-MI and reused.
“This information is only included in BioPAX for molecular interactions, because that was already defined by the Proteomics Standards Initiative Molecular Interactions (PSI-MI) language58 and it was reused.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [58]
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- Authors
- Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S. G. N., Sander, C., Bork, P., Zhu, W., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, I., Eisenberg, D., Steipe, B., Hogue, C., & Apweiler, R.
- Affiliations
- European Bioinformatics Institute (GB)
- Memorial Sloan Kettering Cancer Center (US)
- Hybrigenics (France) (FR)
- University of Rome Tor Vergata (IT)
- Lunenfeld-Tanenbaum Research Institute (CA)
- SIB Swiss Institute of Bioinformatics (CH)
- Chinese Academy of Sciences (CN)
- Centre National de la Recherche Scientifique (FR)
- University of Edinburgh (GB)
- Johns Hopkins University (US)
- Harvard University (US)
- Howard Hughes Medical Institute (US)
- University of Toronto (CA)
- Corresponding author
- Hermjakob, Henning
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2004-01-30
- Volume
- 22
- Issue
- 2
- Pages
- 177-183
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2006933206
- Cited by
- 630
- References
- 33
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 7 · 2023: 9 · 2022: 13 · 2021: 14 · 2020: 11 · 2019: 13 · 2018: 18 · 2017: 16 · 2016: 23 · 2015: 26 · 2014: 24 · 2013: 34 · 2012: 32
- FWCI
- 25.99
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- HAL AMU (submittedVersion)
- HAL (submittedVersion)
- Cineca Institutional Research Information System (Tor Vergata University) (submittedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Keywords
- protein-protein interaction, data exchange standards, Proteomics Standards Initiative, interaction networks, data integration, interaction databases
- MeSH terms
- Database Management Systems, Natural Language Processing, Protein Binding, Proteins, Reference Standards, Software, User-Computer Interface, Information Storage and Retrieval, Guidelines as Topic, Protein Interaction Mapping, Databases, Protein, Internationality, Proteomics
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