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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  
The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience.  ...  The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers.  ...  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

mentha: the interactome browser

A Calderone, G Cesareni
2012 EMBnet journal  
Users can search the database using a web search engine that returns interaction information for any protein of interest displaying it in the context of the "global interactome".  ...  We have developed mentha, a new resource that addresses this problem. mentha archives evidence about PPI in the human proteome evidence collected from different PPI sources -and offers a series of tools  ...  PSICQUIC defines a list of common fields for each database, and specifies a standard web service with a well-defined list of methods.  ... 
doi:10.14806/ej.18.a.455 fatcat:zxuzlnospjadxeufxczbjfj2ay

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

Karin Breuer, Amir K. Foroushani, Matthew R. Laird, Carol Chen, Anastasia Sribnaia, Raymond Lo, Geoffrey L. Winsor, Robert E. W. Hancock, Fiona S. L. Brinkman, David J. Lynn
2012 Nucleic Acids Research  
Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface  ...  , enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools.  ...  Grateful thanks also go to the many researchers who have taken the time to respond to our queries regarding curation of their publications. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gks1147 pmid:23180781 pmcid:PMC3531080 fatcat:jmmbldnvuzgg7fm4vjbqnoknrm

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  
Over the last 10 years significant advances have been made, with common data standards now published and implemented in the field of both mass spectrometry and molecular interactions.  ...  The molecular interaction group focused on improving the integration of data from multiple resources.  ...  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 disease and gene annotations (DGA): an annotation resource for human disease

Kai Peng, Wei Xu, Jianyong Zheng, Kegui Huang, Huisong Wang, Jiansong Tong, Zhifeng Lin, Jun Liu, Wenqing Cheng, Dong Fu, Pan Du, Warren A. Kibbe (+2 others)
2012 Nucleic Acids Research  
Through the flexible PSICQUIC web service, the DGA can easily integrate new MINs, for instance, transcription factor information that can be used to target gene regulation, microRNA regulation and pathway-level  ...  OVERVIEW OF THE DGA SYSTEM ARCHITECTURE The DGA system is implemented using PHP, MySQL, JavaScript and Cytoscape Web (12) .  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gks1244 pmid:23197658 pmcid:PMC3531051 fatcat:4mo2woafejdb5gxdxzovy232le

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study

J. M. Villaveces, R. C. Jimenez, P. Porras, N. del-Toro, M. Duesbury, M. Dumousseau, S. Orchard, H. Choi, P. Ping, N. C. Zong, M. Askenazi, B. H. Habermann (+1 others)
2015 Database: The Journal of Biological Databases and Curation  
Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental  ...  Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in a cellular environment.  ...  Web interface To enable human access to the web service and as an example of a use case for the web service, a web interface has been built ( mimergeclient/).  ... 
doi:10.1093/database/bau131 pmid:25652942 pmcid:PMC4316181 fatcat:n2oauiczgjgqtlgpkv6tuopexm

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

Thibaut Guirimand, Stéphane Delmotte, Vincent Navratil
2014 Nucleic Acids Research  
This resource is shared publicly, in PSI-MI TAB 2.5 format, using a PSICQUIC web service.  ...  The new interface of VirHostNet 2.0 is based on Cytoscape web library and provides a user-friendly access to the most complete and accurate resource of virus-virus and virus-host protein-protein interactions  ...  We want to thank the EBI PSIC-QUIC team for registering our PSICQUIC web service, but also Marie Primout for her contribution to the biocuration and Sidoine, Justine, Charli and Marius Navratil for their  ... 
doi:10.1093/nar/gku1121 pmid:25392406 pmcid:PMC4383936 fatcat:hhyashqdsjdylbghnmvdtqbvxi

MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities

G. Launay, R. Salza, D. Multedo, N. Thierry-Mieg, S. Ricard-Blum
2014 Nucleic Acids Research  
Other major changes include the creation of a new website and the development of a novel graphical navigator, iNavigator, to build and expand interaction networks.  ...  Any molecule of the network may be selected and its partners added to the network at any time.  ...  Vallet for his contribution to the curation process, Marine Dumousseau (European Bioinformatics Institute, Hinxton, UK) for her help regarding data exchange and Sandra Orchard (European Bioinformatics  ... 
doi:10.1093/nar/gku1091 pmid:25378329 pmcid:PMC4383919 fatcat:wimm6cnnwvgftphrtggemgddka

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

Sandra Orchard, Mais Ammari, Bruno Aranda, Lionel Breuza, Leonardo Briganti, Fiona Broackes-Carter, Nancy H. Campbell, Gayatri Chavali, Carol Chen, Noemi del-Toro, Margaret Duesbury, Marine Dumousseau (+23 others)
2013 Nucleic Acids Research  
IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMExand MIMIx-level curation.  ...  Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance.  ...  This also included the development of curation standards and CV terms in addition to tools and services such as the PSICQUIC Web service.  ... 
doi:10.1093/nar/gkt1115 pmid:24234451 pmcid:PMC3965093 fatcat:5qemzevwgzdjln3y4pxvgfz7aa

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

Frank Kramer, Michaela Bayerlová, Tim Beißbarth
2014 Biology  
Putting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results.  ...  A total of 12 packages integrating pathway data are reviewed in this manuscript.  ...  a web service.  ... 
doi:10.3390/biology3010085 pmid:24833336 pmcid:PMC4009765 fatcat:op62z6xt7jgwnkmdbabf4veaiq

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

2019 Bioinformatics  
PSI-MITAB 2.8 format and the new reference implementation of PSICQUIC are available online ( and  ...  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

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows

Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Load Hendrix Barboza (+45 others)
2010 Journal of Biomedical Semantics  
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient  ...  To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard  ...  Acknowledgements BioHackathon 2008 is financially supported by the Integrated Database Project, Ministry of Education, Culture, Sports, Science and Technology of Japan and the Computational Biology Research  ... 
doi:10.1186/2041-1480-1-8 pmid:20727200 pmcid:PMC2939597 fatcat:ytcct7auwbexdf4qwcvhl4ac4a

From Proteomics Data Representation to Public Data Flow: A Report on the HUPO-PSI Workshop September 2011, Geneva, Switzerland

Sandra Orchard, Juan-Pablo Albar, Eric W. Deutsch, Martin Eisenacher, Pierre-Alain Binz, Salvador Martinez-Bartolomé, Juan Antonio Vizcaíno, Henning Hermjakob
2012 Proteomics  
including the release of the Minimum Information About a Proteomics Experiment (MIAPE) standards, exchange formats and the accompanying controlled vocabularies (CVs) for several aspects of a mass spectrometry  ...  The PSI Workshop at the Tenth Annual HUPO World Congress in Geneva was opened by Pierre-Alain Binz (SIB) who welcomed delegates and briefly summarised the work of the initiative over the last 10 years,  ...  The shared usage of a common format has enabled the creation of the Proteomics Standards Initiative Common QUery interface (PSICQUIC) web service.  ... 
doi:10.1002/pmic.201290016 pmid:22290802 fatcat:xdlfmptbzbd43jckx7b3sizcki

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

Sandra Orchard, Samuel Kerrien, Sara Abbani, Bruno Aranda, Jignesh Bhate, Shelby Bidwell, Alan Bridge, Leonardo Briganti, Fiona S L Brinkman, Gianni Cesareni, Andrew Chatr-aryamontri, Emilie Chautard (+19 others)
2012 Nature Methods  
We discuss the advantages of such a service to the user, our quality-control measures and our data-distribution practices.  ...  been developed, and a central registry is used to manage the selection of articles to enter into the dataset.  ...  However, in 2010 we released IMExCentral, a web service that enables IMEx consortium partners to reserve any publication for curation, either manually through a web interface or through a web service directly  ... 
doi:10.1038/nmeth.1931 pmid:22453911 pmcid:PMC3703241 fatcat:ev2rpzb3c5hkpo52af3rfglfou

MINT, the molecular interaction database: 2012 update

Luana Licata, Leonardo Briganti, Daniele Peluso, Livia Perfetto, Marta Iannuccelli, Eugenia Galeota, Francesca Sacco, Anita Palma, Aurelio Pio Nardozza, Elena Santonico, Luisa Castagnoli, Gianni Cesareni
2011 Nucleic Acids Research  
MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium.  ...  The main changes include a more precise definition of the curation policy and the development of an enhanced and user-friendly interface to facilitate the analysis of the ever-growing interaction dataset  ...  MINT uses the PSICQUIC reference implementation, implemented at the European Bioinformatics Institute.  ... 
doi:10.1093/nar/gkr930 pmid:22096227 pmcid:PMC3244991 fatcat:73rcsyttxvbubdl436vmf2q4ma
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