MINT, the molecular interaction database: 2009 update.
Arnaud Ceol,Andrew Chatr Aryamontri,Luana Licata,Daniele Peluso,Leonardo Briganti,Livia Perfetto,Luisa Castagnoli,Gianni Cesareni +7 more
TLDR
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.Abstract:
MINT (http://mint.bio.uniroma2.it/mint) is a public repository for molecular interactions reported in peer-reviewed journals. Since its last report, MINT has grown considerably in size and evolved in scope to meet the requirements of its users. 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 has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium.read more
Citations
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The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk,Andrea Franceschini,Michael Kuhn,Milan Simonovic,Alexander Roth,Pablo Minguez,Tobias Doerks,Manuel Stark,Jean Muller,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: An update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING), which provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information.
Journal ArticleDOI
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
David Warde-Farley,Sylva L. Donaldson,Ovi Comes,Khalid Zuberi,Rashad Badrawi,Pauline Chao,Max Franz,Chris Grouios,Farzana Kazi,Christian Lopes,Anson Maitland,Sara Mostafavi,Jason Montojo,Quentin Shao,George Wright,Gary D. Bader,Quaid Morris +16 more
TL;DR: The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make Gene MANIA a useful tool for any biologist.
Journal ArticleDOI
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Sandra Orchard,Mais G. Ammari,Bruno Aranda,Lionel Breuza,Leonardo Briganti,Fiona Broackes-Carter,Nancy H. Campbell,Gayatri Chavali,Carol Chen,Noemi del-Toro,Margaret Duesbury,Marine Dumousseau,Eugenia Galeota,Ursula Hinz,Marta Iannuccelli,Sruthi Jagannathan,Rafael C. Jimenez,Jyoti Khadake,Astrid Lagreid,Luana Licata,Ruth C. Lovering,Birgit H M Meldal,Anna N. Melidoni,Mila Milagros,Daniele Peluso,Livia Perfetto,Pablo Porras,Arathi Raghunath,Sylvie Ricard-Blum,Bernd Roechert,Andre Stutz,Michael Tognolli,Kim Van Roey,Gianni Cesareni,Henning Hermjakob +34 more
TL;DR: All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset.
Journal ArticleDOI
Reactome: a database of reactions, pathways and biological processes
David Croft,Gavin O'Kelly,Guanming Wu,Robin Haw,Marc Gillespie,Lisa Matthews,Michael Caudy,Phani V. Garapati,Gopal R. Gopinath,Bijay Jassal,S Jupe,Irina Kalatskaya,Shahana S. Mahajan,Shahana S. Mahajan,Bruce May,Nelson Ndegwa,Esther Schmidt,Veronica Shamovsky,Christina K. Yung,Ewan Birney,Henning Hermjakob,Peter D'Eustachio,Lincoln Stein,Lincoln Stein,Lincoln Stein +24 more
TL;DR: A new web site with improved tools for pathway browsing and data analysis is developed, and orthology-based inferences of pathways in non-human species are made, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species.
Journal ArticleDOI
The IntAct molecular interaction database in 2012
Samuel Kerrien,Bruno Aranda,Lionel Breuza,Alan Bridge,Fiona Broackes-Carter,Carol Chen,Margaret Duesbury,Marine Dumousseau,M Feuermann,Ursula Hinz,Christine Jandrasits,Rafael C. Jimenez,Jyoti Khadake,Usha Mahadevan,Patrick Masson,Ivo Pedruzzi,Eric Pfeiffenberger,Pablo Porras,Arathi Raghunath,Bernd Roechert,Sandra Orchard,Henning Hermjakob +21 more
TL;DR: Two levels of curation are now available within the IntAct database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported.
References
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MINT: the Molecular INTeraction database
Andrew Chatr-aryamontri,Arnaud Ceol,Luisa Montecchi Palazzi,Giuliano Nardelli,Maria Victoria Schneider,Luisa Castagnoli,Gianni Cesareni +6 more
TL;DR: MINT, a database designed to store data on functional interactions between proteins, consists of entries extracted from the scientific literature by expert curators assisted by 'MINT Assistant', a software that targets abstracts containing interaction information and presents them to the curator in a user-friendly format.
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Reactome knowledgebase of human biological pathways and processes.
Lisa Matthews,Gopal Gopinath,Marc Gillespie,Michael Caudy,David B. Croft,Bernard de Bono,Phani V. Garapati,Jill Hemish,Henning Hermjakob,Bijay Jassal,Alexander Kanapin,Suzanna E. Lewis,Shahana S. Mahajan,Bruce May,Esther Schmidt,Imre Vastrik,Guanming Wu,Ewan Birney,Lincoln Stein,Peter D'Eustachio +19 more
TL;DR: Improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa, Drosophila and Gallus gallus.
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