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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  ...  Availability of data and materials Data sharing is not applicable to this article as no datasets were generated or analysed during the current study.  ... 
doi:10.1186/s12859-018-2119-0 pmid:29642846 pmcid:PMC5896107 fatcat:oocgaynr25e2zjt4vtritibrse

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination

2019 Bioinformatics  
Here, we present a common standard for the representation and dissemination of signalling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI  ...  We define the new term 'causal interaction', and related child terms, which are children of the PSI-MI 'molecular interaction' term.  ...  Acknowledgements We thank Birgit Meldal for critically reading and reviewing the manuscript. Funding  ... 
doi:10.1093/bioinformatics/btz132 pmid:30793173 pmcid:PMC6896241 fatcat:jgsbahpzwvcatdk2cn4usdyjyi

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

Bruno Aranda, Hagen Blankenburg, Samuel Kerrien, Fiona S L Brinkman, Arnaud Ceol, Emilie Chautard, Jose M Dana, Javier De Las Rivas, Marine Dumousseau, Eugenia Galeota, Anna Gaulton, Johannes Goll (+28 others)
2011 Nature Methods  
A plethora of resources now exist to capture molecular interaction data from the many laboratories generating such information, but whereas such databases are rich in information, the sheer number and  ...  To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood.  ...  MI) XML format, a community standard for the representation of molecular-interaction data.  ... 
doi:10.1038/nmeth.1637 pmid:21716279 pmcid:PMC3246345 fatcat:zxstbcqmfjcdtng4i62netmtfq

CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination [article]

Livia Perfetto, Marcio Luis Acencio, Glyn Bradley, Gianni Cesareni, Noemi del Toro, David Fazekas, Henning Hermjakob, Tamas Korcsmaros, Martin Kuiper, Astrid laegreid, Prisca Lo Surdo, Ruth C. Lovering (+6 others)
2018 bioRxiv   pre-print
Here, we present a common standard for the representation and dissemination of signaling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI  ...  We define the new term causal interaction, and related child terms, which are children of the PSI-MI molecular interaction term.  ...  Implementation of these standards by all the leading molecular interaction databases has considerably contributed to data exchange, representation and comparison and encouraged the development of specific  ... 
doi:10.1101/385773 fatcat:h3yxmo6hd5c3ppuk2yo6zqxtv4

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  
The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data.  ...  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

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  
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  ...  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  ...  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

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  
This work evaluates the usage of the XML Query language XQuery for molecular interactions, as it would be of great benefit to the user to work directly on data represented in the new standards.  ...  As one step in this direction, new standards for describing molecular interactions have been defined based on XML.  ...  Acknowledgements Thanks to Patrick Lambrix for valuable comments on this work. We are also grateful to Liu Ke for performing some of the tests.  ... 
doi:10.1007/11896548_20 fatcat:hej5jvbyx5dqrlwp4dg2rmiwae

A Method for Comparison of Standardized Information Within Systems Biology

Lena Stromback
2006 Proceedings of the 2006 Winter Simulation Conference  
In this paper we present a method for comparison of standards. We illustrate how the method works by providing an analysis of the three standards SBML, PSI MI and BioPAX.  ...  As the number of available standards within systems biology is large, tools for comparison and translation of standards are of high interest.  ...  ACKNOWLEDGMENTS We acknowledge the financial support from the Center for Industrial Information Technology. I am also grateful to  ... 
doi:10.1109/wsc.2006.322933 dblp:conf/wsc/Stromback06 fatcat:b2pr6eqnejbg5npnassmky2xsy

Identification of clustering artifacts in photoactivated localization microscopy

Paolo Annibale, Stefano Vanni, Marco Scarselli, Ursula Rothlisberger, Aleksandra Radenovic
2011 Nature Methods  
MI) XML format, a community standard for the representation of molecular-interaction data.  ...  This challenge has led to the development of the PSI common query interface (PSICQUIC), a community standard for computational access to molecular-interaction data resources.  ...  competInG FInancIaL Interests The authors declare no competing financial interests. paolo annibale 1,3 , stefano Vanni 2,3 , marco scarselli 1,3 , ursula rothlisberger 2 & aleksandra radenovic 1  ... 
doi:10.1038/nmeth.1627 pmid:21666669 fatcat:qnfmyot74jatpbowjro7flmt3a

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

Eric W. Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert, Yasset Perez-Riverol, Reza M. Salek (+5 others)
2017 Journal of Proteome Research  
The molecular interactions formats use the PSI-MI CV.  ...  The work of the PSI-MI is described at groups/molecular-interactions.  ... 
doi:10.1021/acs.jproteome.7b00370 pmid:28849660 pmcid:PMC5715286 fatcat:7oigf27kencedhbhmvtrbuv5a4

ComplexViewer: visualization of curated macromolecular complexes

Colin W Combe, Marine (Dumousseau) Sivade, Henning Hermjakob, Joshua Heimbach, Birgit H M Meldal, Gos Micklem, Sandra Orchard, Juri Rappsilber, Jonathan Wren
2017 Bioinformatics  
ComplexViewer visualizes interactions with more than two participants and thereby avoids the need to first expand these into multiple binary interactions.  ...  Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary interactions.  ...  Implementation PSI-MI data standards come in two distinct formats-XML based and tab-delimited.  ... 
doi:10.1093/bioinformatics/btx497 pmid:29036573 pmcid:PMC5870653 fatcat:kpee5g2y4zcy5c5vpcjjuz6doq

The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

Henning Hermjakob, Luisa Montecchi-Palazzi, Gary Bader, Jérôme Wojcik, Lukasz Salwinski, Arnaud Ceol, Susan Moore, Sandra Orchard, Ugis Sarkans, Christian von Mering, Bernd Roechert, Sylvain Poux (+27 others)
2004 Nature Biotechnology  
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  ...  A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology.  ...  COMPETING INTERESTS STATEMENT The authors declare that they have no competing financial interests. Published online at  ... 
doi:10.1038/nbt926 pmid:14755292 fatcat:45igrs4skjf75ckj5xfyosfj5u

Representing, storing and accessing molecular interaction data: a review of models and tools

L. Stromback, V. Jakoniene, H. Tan, P. Lambrix
2006 Briefings in Bioinformatics  
In this paper we put focus on the recent developments within the field. We compare the recent updates for the three standard representations for exchange of data SBML, PSI MI and BioPAX.  ...  This makes standards for representation of data and technology for exchange and integration of data important key points for the developments within the area.  ...  SBML, PSI MI and BioPAX This section presents the recent developments of the three different standards, SBML, PSI MI and BioPAX.  ... 
doi:10.1093/bib/bbl039 pmid:17132622 fatcat:b4idm26hnvgwbn76avuxkq3ghi

A new reference implementation of the PSICQUIC web service

Noemi del-Toro, Marine Dumousseau, Sandra Orchard, Rafael C. Jimenez, Eugenia Galeota, Guillaume Launay, Johannes Goll, Karin Breuer, Keiichiro Ono, Lukasz Salwinski, Henning Hermjakob
2013 Nucleic Acids Research  
to molecular-interaction data resources by means of a standard Web Service and query language.  ...  Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions.  ...  ACKNOWLEDGEMENTS The authors would like to thank and congratulate the organisers of the PSIMEX Hackathon 2012, without whose efforts, this work would not have been possible. FUNDING  ... 
doi:10.1093/nar/gkt392 pmid:23671334 pmcid:PMC3977660 fatcat:7ti5gy6sxvaotbwn2pcqbham4e

APID database: redefining protein–protein interaction experimental evidences and binary interactomes

Diego Alonso-López, Francisco J Campos-Laborie, Miguel A Gutiérrez, Luke Lambourne, Michael A Calderwood, Marc Vidal, Javier De Las Rivas
2019 Database: The Journal of Biological Databases and Curation  
the 'ontology and controlled vocabulary':; developed by 'HUPO PSI-MI').  ...  This includes the unification of all the PPIs from five primary databases of molecular interactions (BioGRID, DIP, HPRD, IntAct and MINT), plus the information from two original systematic sources of human  ...  Conflict of interest. None declared.  ... 
doi:10.1093/database/baz005 pmid:30715274 pmcid:PMC6354026 fatcat:jjpl4nnc2retpcta2syx6mamjq
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