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Capturing cooperative interactions with the PSI-MI format

Kim Van Roey, Sandra Orchard, Samuel Kerrien, Marine Dumousseau, Sylvie Ricard-Blum, Henning Hermjakob, Toby J. Gibson
2013 Database: The Journal of Biological Databases and Curation  
As a result, we are able to capture cooperative interaction data in a structured format that is backward compatible with PSI-MI-based data and applications.  ...  To tackle this shortcoming, we added functionality to the widely used PSI-MI interchange format for molecular interaction data by defining new controlled vocabulary terms that allow annotation of different  ...  Weatheritt for critical evaluation of this manuscript and members of the PSI consortium for fruitful discussions on this topic. Conflict of interest. None declared.  ... 
doi:10.1093/database/bat066 pmid:24067240 pmcid:PMC3782717 fatcat:whkmaq6mmnhwvh3jvpdanjvwby

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

M. Sivade, D. Alonso-López, M. Ammari, G. Bradley, N. H. Campbell, A. Ceol, G. Cesareni, C. Combe, J. De Las Rivas, N. del-Toro, J. Heimbach, H. Hermjakob (+18 others)
2018 BMC Bioinformatics  
PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format.  ...  Results: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new  ...  Acknowledgements Not applicable Funding MD, MK, AS, JS, JH and YY were funded by BBSRC MIDAS grant (BB/L024179/1), this grant provided the funds for the design of PSI-MI XML3.0 and its implementation  ... 
doi:10.1186/s12859-018-2118-1 pmid:29642841 pmcid:PMC5896046 fatcat:mbt2a7laf5bttpq7z4tbnjp3oq

JAMI: a Java library for molecular interactions and data interoperability

M. Sivade, M. Koch, A. Shrivastava, D. Alonso-López, J. De Las Rivas, N. del-Toro, C. W. Combe, B. H. M. Meldal, J. Heimbach, J. Rappsilber, J. Sullivan, Y. Yehudi (+1 others)
2018 BMC Bioinformatics  
Results: A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB.  ...  These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, usespecific downloads produced by other resources  ...  All software is available from https:// github.com/MICommunity/psi-jami  ... 
doi:10.1186/s12859-018-2119-0 pmid:29642846 pmcid:PMC5896107 fatcat:oocgaynr25e2zjt4vtritibrse

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

Samuel Kerrien, Sandra Orchard, Luisa Montecchi-Palazzi, Bruno Aranda, Antony F Quinn, Nisha Vinod, Gary D Bader, Ioannis Xenarios, Jérôme Wojcik, David Sherman, Mike Tyers, John J Salama (+18 others)
2007 BMC Biology  
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  ...  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  ...  Acknowledgements This is a community effort with voluntary contributions from many organisations not directly funded for this work. In addition, this work has been supported by the  ... 
doi:10.1186/1741-7007-5-44 pmid:17925023 pmcid:PMC2189715 fatcat:mihxus5nn5asfll7hsugdsqw4m

Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop

Sandra Orchard, Pierre-Alain Binz, Christoph Borchers, Michael K. Gilson, Andrew R. Jones, George Nicola, Juan Antonio Vizcaino, Eric W. Deutsch, Henning Hermjakob
2012 Proteomics  
The 2012 meeting further advanced this work, with the mass spectrometry groups finalising approaches to capturing the output from recent developments in the field, such as quantitative proteomics and SRM  ...  The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was established in 2002 with the aim of defining community standards for data representation in proteomics and facilitating data  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.  ... 
doi:10.1002/pmic.201270126 pmid:22969026 pmcid:PMC3895333 fatcat:frbdlpwee5hlzjga3ym3aohqkm

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth C Lovering, Sandra Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi del-Toro, Åsmund Flobak, Pascale Gaudet, Henning Hermjakob (+15 others)
2020 Bioinformatics  
These causal interactions and the biological processes they enable (e.g., gene regulation) need to be described with a careful appreciation of the underlying molecular reactions.  ...  Availability The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST Supplementary information Supplementary data are available at Bioinformatics online.  ...  Acknowledgements The authors would like to acknowledge the MI group from the HUPO-PSI consortium, the IMEx consortium and the GREEKC consortium for fruitful discussions.  ... 
doi:10.1093/bioinformatics/btaa622 pmid:32637990 pmcid:PMC8023674 fatcat:sh7w5xjnmrfntl3ik5jtgmyx4i

THE USE OF COMMON ONTOLOGIES AND CONTROLLED VOCABULARIES TO ENABLE DATA EXCHANGE AND DEPOSITION FOR COMPLEX PROTEOMIC EXPERIMENTS

SANDRA ORCHARD, LUISA MONTECCHI-PALAZZI, HENNING HERMJAKOB, ROLF APWEILER
2004 Biocomputing 2005  
The PSI-MI format is designed for data exchange by many data providers.  ...  The interaction detection method controlled vocabulary lists Fig. 1 Controlled vocabularies to describe experimental methodologies developed for use with the PSI-MI XML interchange format technologies  ... 
doi:10.1142/9789812702456_0018 fatcat:cpmf3gzbvzgjxgftqt6d2g5pbm

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany

Sandra Orchard, Juan Pablo Albar, Eric W. Deutsch, Martin Eisenacher, Juan A. Vizcaíno, Henning Hermjakob
2011 Proteomics  
EWD is also funded by NIH/NIGMS grant number R01 GM087221, NIH/NIGMS grant number PM50 GMO76547/Center for Systems Biology, and the Systems Biology initiative from the Grand Duchy of Luxembourg.  ...  Acknowledgements Much of this work has been funded by the European Commission under PSIMEx, contract number FP7-HEALTH-2007-223411 and ProteomeXchange, grant number 260558.  ...  Work is currently ongoing to determine whether the current PSI-MI XML format is flexible enough to capture such a sequential series of biological events.  ... 
doi:10.1002/pmic.201190117 pmid:22045680 pmcid:PMC4362542 fatcat:6hlzsx3tbrbydctwm4phfty66u

An Evaluation of the Use of XML for Representation, Querying, and Analysis of Molecular Interactions [chapter]

Lena Strömbäck, David Hall
2006 Lecture Notes in Computer Science  
The paper ends with a discussion regarding the usability of XQuery in this domain.  ...  In particular we point out the need for more efficient graph handling and that XQuery also requires the user to understand the exact XML format of each dataset.  ...  We are also grateful to Liu Ke for performing some of the tests.  ... 
doi:10.1007/11896548_20 fatcat:hej5jvbyx5dqrlwp4dg2rmiwae

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data

Sandra Orchard, Paul Kersey, Henning Hermjakob, Rolf Apweiler
2003 Comparative and Functional Genomics  
Initially the fields of protein–protein interactions (PPI) and mass spectroscopy have been targeted and the inaugural meeting of the PSI addressed the questions of data storage and exchange in both of  ...  The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification.  ...  Major progress was made in the field of protein-protein interactions, with a draft exchange format being produced and work on an XML version in progress.  ... 
doi:10.1002/cfg.232 pmid:18629102 pmcid:PMC2447389 fatcat:65d4ypum2fdkdbmr6j7uad23em

Towards a unified open access dataset of molecular interactions

Pablo Porras, Elisabet Barrera, Alan Bridge, Noemi Del-Toro, Gianni Cesareni, Margaret Duesbury, Henning Hermjakob, Marta Iannuccelli, Igor Jurisica, Max Kotlyar, Luana Licata, Ruth C Lovering (+15 others)
2020 Nature Communications  
The International Molecular Exchange (IMEx) Consortium provides scientists with a single body of experimentally verified protein interactions curated in rich contextual detail to an internationally agreed  ...  through the introduction of new interactor types and data formats.  ...  Acknowledgements The IntAct team at EMBL-EBI received funding from EMBL core funding, Open Targets (grant agreements OTAR-044 and OTAR02-048) and the Wellcome Trust  ... 
doi:10.1038/s41467-020-19942-z pmid:33262342 pmcid:PMC7708836 fatcat:soyrqsypencbrkmqwxzjz6crp4

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience

M. Krallinger, F. Leitner, M. Vazquez, D. Salgado, C. Marcelle, M. Tyers, A. Valencia, A. Chatr-aryamontri
2012 Database: The Journal of Biological Databases and Curation  
Special emphasis is given to protein-protein interaction data and PSI-MI terms referring to interaction detection methods.  ...  annotating an ontology term, e.g. from the PSI-MI or GO controlled vocabularies.  ...  Acknowledgements We would like to thank Lynette Hirschman and Christian Blaschke for their active feedback in the BioCreative tasks described in this article.  ... 
doi:10.1093/database/bas017 pmid:22438567 pmcid:PMC3309177 fatcat:3q2zwcobxfaebl4rw4hsnddid4

Linking entries in protein interaction database to structured text: The FEBS Letters experiment

Arnaud Ceol, Andrew Chatr-Aryamontri, Luana Licata, Gianni Cesareni
2008 FEBS Letters  
Databases are striving to capture this valuable information and to organize it in a structured format ready for automatic analysis.  ...  controlled vocabularies, the protein interactions reported in the manuscript.  ...  Krallinger for critically reading the manuscript. This work is supported by a European Union grant within the NOE ''ENFIN'' and by a FEBS fellowship to A.C.  ... 
doi:10.1016/j.febslet.2008.02.071 pmid:18328820 fatcat:vhvh2v2bnrfulkgsyqzaeir3uq

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers
2011 BMC Bioinformatics  
, and curated the test set for interaction method classification.  ...  The BioGRID and MINT protein interaction databases both participated in the generation of the test publication set for gene normalization, annotated the development and test sets for article classification  ...  Both databases curated proteinprotein interactions in accordance with the PSI-MI controlled vocabulary, choosing the deepest possible child term of PSI-MI controlled vocabulary root term 'interaction detection  ... 
doi:10.1186/1471-2105-12-s8-s8 pmid:22151178 pmcid:PMC3269943 fatcat:qkhfjgydozhh5gwgz334hnlul4

HUPO Initiatives Relevant to Clinical Proteomics

Sam Hanash
2004 Molecular & Cellular Proteomics  
or more pertinently when contrasted with the tremendous untapped potential of clinical proteomics.  ...  However, much of the effort undertaken in clinical proteomics to date represents either demonstrations of principles or relatively small-scale studies when compared with genomics effort and accomplishments  ...  PSI-MS data formats and MIAPE data model B. Molecular interactions 1. PSI MI XML schema 2. Controlled vocabularies a. Procedure for maintenance of controlled vocabularies b.  ... 
doi:10.1074/mcp.r400004-mcp200 pmid:14747694 fatcat:sjrgggvh4bdb5mdxw327cuw6q4
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