Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
Open accessAbstract
BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. RESULTS: The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. CONCLUSION: The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
BioPAX follows the standard representation scheme of the Proteomics Standards Initiative Molecular Interaction (PSI-MI) format for molecular interactions.
“BioPAX follows the standard representation scheme of the Proteomics Standards Initiative Molecular Interaction (PSI-MI) format38.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [38]
BioPAX reuses standard controlled vocabularies, including Gene Ontology for cellular location, PSI-MI vocabularies for evidence codes and interaction types, and Sequence Ontology for sequence regions.
“BioPAX reuses a number of standard controlled vocabularies defined by other groups. For example, Gene Ontology40 is used to describe cellular location, PSI-MI vocabularies38 are used to define evidence codes, experimental forms, interaction types, relationship types and sequence modifications, and Sequence Ontology41 is used to define types of sequence regions, such as a promoter region on DNA in”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [38]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works
BioGRID: a general repository for interaction datasets
Stark, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj109 · Cited by 3,960 · see citing works
The Universal Protein Resource (UniProt)
Bairoch, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki070 · Cited by 3,774 · see citing works
The Database of Interacting Proteins: 2004 update
Salwinski, L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh086 · Cited by 2,271 · see citing works
Self-citationBindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
Liu, T., Lin, Y., Wen, X., Jorissen, R. N., & Gilson, M. K. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl999 · Cited by 2,145 · see citing works
Self-citationMINT: the Molecular INTeraction database
Chatr‐aryamontri, A., Ceol, A. G. M., Montecchi‐Palazzi, L., Nardelli, G., Schneider, M. V., Castagnoli, L., & Cesareni, G. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl950 · Cited by 1,027 · see citing works
Self-citationIntAct--open source resource for molecular interaction data
Kerrien, S., Alam-Faruque, Y., Aranda, B., Bancarz, I., Bridge, A. J., Derow, C., Dimmer, E. C., Feuermann, M., Friedrichsen, A., Huntley, R. P., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl958 · Cited by 800 · see citing works
Self-citationDatabase resources of the National Center for Biotechnology Information
Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl1031 · Cited by 734 · see citing works
Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt926 · Cited by 630 · see citing works
Self-citationThe Biomolecular Interaction Network Database and related tools 2005 update
Alfarano, C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki051 · Cited by 587 · see citing works
The Universal Protein Resource (UniProt)
The UniProt Consortium (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl929 · Cited by 572 · see citing works
MPact: the MIPS protein interaction resource on yeast
Güldener, U. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj003 · Cited by 353 · see citing works
Guidelines for the next 10 years of proteomics
Wilkins, M. R., Appel, R. D., Eyk, J. E. V., Chung, M. C. M., Görg, A., Hecker, M., Huber, L. A., Langen, H., Link, A. J., Paik, Y., et al. (2006) · PROTEOMICS · doi:10.1002/pmic.200500856 · Cited by 302 · see citing works
The minimum information required for reporting a molecular interaction experiment (MIMIx)
Orchard, S. E., Salwiński, Ł., Kerrien, S., Montecchi‐Palazzi, L., Oesterheld, M., Stümpflen, V., Ceol, A. G. M., Chatr‐aryamontri, A., Armstrong, J. T., Woollard, P. M., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1324 · Cited by 280 · see citing works
Self-citationThe Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
Côté, R. G., JONES, P. M., Apweiler, R., et al. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-97 · Cited by 224 · see citing works
Self-citationReporting Protein Identification Data
Bradshaw, R. A., Burlingame, A. L., Carr, S. A., et al. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.e600005-mcp200 · Cited by 222 · see citing works
The Proteomics Standards Initiative
Orchard, S. E., Hermjakob, H., & Apweiler, R. (2003) · PROTEOMICS · doi:10.1002/pmic.200300496 · Cited by 185 · see citing works
Self-citationOligomeric structures of poliovirus polymerase are important for function
Hobson, S. D., Rosenblum, E. S., Richards, O. C., Richmond, K., Kirkegaard, K., & Schultz, S. C. (2001) · The EMBO Journal · doi:10.1093/emboj/20.5.1153 · Cited by 137 · see citing works
FuGE: Functional Genomics Experiment Object Model
Jones, A. R., Pizarro, A., Spellman, P. T., et al. (2006) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2006.10.179 · Cited by 29 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
ChEMBL: a large-scale bioactivity database for drug discovery
Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr777 · Cited by 4,382 · see citing works
The BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745 · see citing works
“BioPAX follows the standard representation scheme of the Proteomics Standards Initiative Molecular Interaction (PSI-MI) format 38 .”
Self-citationConsensusPathDB: toward a more complete picture of cell biology
Kamburov, A., Pentchev, K., Galicka, H., Wierling, C., Lehrach, H., & Herwig, R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1156 · Cited by 671 · see citing works
The IntAct molecular interaction database in 2010
Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A. T., Kerrien, S., Khadake, J., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp878 · Cited by 620 · see citing works
Self-citationInteractome3D: adding structural details to protein networks
Mosca, R., Céol, A., & Aloy, P. (2013) · Nature Methods · doi:10.1038/nmeth.2289 · Cited by 479 · see citing works
The IntAct database: efficient access to fine-grained molecular interaction data
del Toro, N., Shrivastava, A., Ragueneau, E., Meldal, B., Combe, C., Barrera, E., Perfetto, L., How, K., Ratan, P., Shirodkar, G., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1006 · Cited by 405 · see citing works
Self-citationVirusMINT: a viral protein interaction database
Chatr-aryamontri, A., Ceol, A., Peluso, D., Nardozza, A., Panni, S., Sacco, F., Tinti, M., Smolyar, A., Castagnoli, L., Vidal, M., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn739 · Cited by 213 · see citing works
Self-citationMiteva, Y. V., Budayeva, H. G., & Cristea, I. M. (2013) · Analytical Chemistry · doi:10.1021/ac3033257 · Cited by 105 · see citing works
- Authors
- Kerrien, S., Orchard, S., Montecchi-Palazzi, L., Aranda, B., Quinn, A. F., Vinod, N., Bader, G. D., Xenarios, I., Wojcik, J., Sherman, D., Tyers, M., Salama, J. J., Moore, S., Ceol, A., Chatr-aryamontri, A., Oesterheld, M., Stümpflen, V., Salwinski, L., Nerothin, J., Cerami, E., Cusick, M. E., Vidal, M., Gilson, M., Armstrong, J., Woollard, P., Hogue, C., Eisenberg, D., Cesareni, G., Apweiler, R., & Hermjakob, H.
- Affiliations
- European Bioinformatics Institute (GB)
- Mount Sinai Hospital (CA)
- Merck Serono S.A. (Switzerland) (CH)
- Laboratoire Bordelais de Recherche en Informatique (FR)
- University of Rome Tor Vergata (IT)
- University of California, Los Angeles (US)
- Memorial Sloan Kettering Cancer Center (US)
- Harvard University (US)
- University of Maryland Biotechnology Institute (US)
- GlaxoSmithKline (United Kingdom) (GB)
- University of Toronto (CA)
- Corresponding author
- Kerrien, Samuel
- ORCID
- Venue
- BMC Biology
- Published
- 2007-10-09
- Volume
- 5
- Issue
- 1
- Pages
- 44-44
- ISSN
- 1741-7007 (ISSN-L)
- PMC
- PMC2189715
- OpenAlex
- W2158439765
- Cited by
- 266
- References
- 20
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 4 · 2023: 6 · 2022: 10 · 2021: 12 · 2020: 5 · 2019: 10 · 2018: 12 · 2017: 13 · 2016: 13 · 2015: 16 · 2014: 17 · 2013: 27 · 2012: 27
- FWCI
- 8.47
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- SERVAL (Université de Lausanne) (publishedVersion, other-oa)
- IRIS (submittedVersion, public-domain)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, public-domain)
- TSpace (University of Toronto) (submittedVersion, public-domain)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- National University of Singapore (submittedVersion)
- HAL (submittedVersion)
- Cineca Institutional Research Information System (Tor Vergata University) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Site cant be reached (submittedVersion)
- Funders
- U.S. Department of Energy (FC0302ER63421)
- Genome Canada
- Ontario Genomics
- Ontario Genomics Institute
- European Commission
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM071909, GM070064, R01GM070064)
- 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
- molecular interactions, protein-protein interaction, nucleic acid interactions, molecular complexes, interaction domains, data standardization
- MeSH terms
- Computer Graphics, Database Management Systems, Natural Language Processing, User-Computer Interface, Computational Biology, Protein Interaction Mapping, Databases, Protein, Proteomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
