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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 (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
more » ... tation and for the representation of molecular interactions and is a member of the IMEx consortium.
doi:10.1093/nar/gkr930 pmid:22096227 pmcid:PMC3244991 fatcat:73rcsyttxvbubdl436vmf2q4ma

Exploiting Publicly Available Biological and Biochemical Information for the Discovery of Novel Short Linear Motifs

Ahmed Sayadi, Leonardo Briganti, Anna Tramontano, Allegra Via, Christos A. Ouzounis
2011 PLoS ONE  
The function of proteins is often mediated by short linear segments of their amino acid sequence, called Short Linear Motifs or SLiMs, the identification of which can provide important information about a protein function. However, the short length of the motifs and their variable degree of conservation makes their identification hard since it is difficult to correctly estimate the statistical significance of their occurrence. Consequently, only a small fraction of them have been discovered so
more » ... ar. We describe here an approach for the discovery of SLiMs based on their occurrence in evolutionarily unrelated proteins belonging to the same biological, signalling or metabolic pathway and give specific examples of its effectiveness in both rediscovering known motifs and in discovering novel ones. An automatic implementation of the procedure, available for download, allows significant motifs to be identified, automatically annotated with functional, evolutionary and structural information and organized in a database that can be inspected and queried. An instance of the database populated with pre-computed data on seven organisms is accessible through a publicly available server and we believe it constitutes by itself a useful resource for the life sciences
doi:10.1371/journal.pone.0022270 pmid:21799808 pmcid:PMC3140502 fatcat:pm24jydc3bazxeoptoh52oqscy

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  
The vast amount of data published in the primary biomedical literature represents a challenge for the automated extraction and codification of individual data elements. Biological databases that rely solely on manual extraction by expert curators are unable to comprehensively annotate the information dispersed across the entire biomedical literature. The development of efficient tools based on natural language processing (NLP) systems is essential for the selection of relevant publications,
more » ... tification of data attributes and partially automated annotation. One of the tasks of the Biocreative 2010 Challenge III was devoted to the evaluation of NLP systems developed to identify articles for curation and extraction of protein-protein interaction (PPI) data. Results: The Biocreative 2010 competition addressed three tasks: gene normalization, article classification and interaction method identification. 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, and curated the test set for interaction method classification. These test datasets served as a gold standard for the evaluation of data extraction algorithms. Conclusion: The development of efficient tools for extraction of PPI data is a necessary step to achieve full curation of the biomedical literature. NLP systems can in the first instance facilitate expert curation by refining the list of candidate publications that contain PPI data; more ambitiously, NLP approaches may be able to directly extract relevant information from full-text articles for rapid inspection by expert curators. Close collaboration between biological databases and NLP systems developers will continue to facilitate the long-term objectives of both disciplines.
doi:10.1186/1471-2105-12-s8-s8 pmid:22151178 pmcid:PMC3269943 fatcat:qkhfjgydozhh5gwgz334hnlul4

SIGNOR: a database of causal relationships between biological entities

Livia Perfetto, Leonardo Briganti, Alberto Calderone, Andrea Cerquone Perpetuini, Marta Iannuccelli, Francesca Langone, Luana Licata, Milica Marinkovic, Anna Mattioni, Theodora Pavlidou, Daniele Peluso, Lucia Lisa Petrilli (+7 others)
2015 Nucleic Acids Research  
Assembly of large biochemical networks can be achieved by confronting new cell-specific experimental data with an interaction subspace constrained by prior literature evidence. The SIGnaling Network Open Resource, SIGNOR (available on line at http://signor.uniroma2.it), was developed to support such a strategy by providing a scaffold of prior experimental evidence of causal relationships between biological entities. The core of SIGNOR is a collection of approximately 12 000 manuallyannotated
more » ... sal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are complexes, chemicals, phenotypes and stimuli. The information captured in SIGNOR can be represented as a signed directed graph illustrating the activation/inactivation relationships between signalling entities. Each entry is associated to the post-translational modifications that cause the activation/inactivation of the target proteins. More than 4900 modified residues causing a change in protein concentration or activity have been curated and linked to the modifying enzymes (about 351 human kinases and 94 phosphatases). Additional modifications such as ubiquitinations, sumoylations, acetylations and their effect on the modified target proteins are also annotated. This wealth of structured information can support experimental approaches based on multi-parametric analysis of cell systems after physiological or pathological perturbations and to assemble large logic models.
doi:10.1093/nar/gkv1048 pmid:26467481 pmcid:PMC4702784 fatcat:z3v4zxzambacnixz6mxn3r33ea

Impact of Sex on Response to Neoadjuvant Chemotherapy in Patients with Upper-tract Urothelial Cancer

David D'Andrea, Beat Foerster, Surena F. Matin, Ja H. Ku, Tim Muilwijk, Leonardo L. Monteiro, Ross Liao, Firas G. Petros, Philippe E. Spiess, Trinity J. Bivalacqua, Kees Hendricksen, Bas W.G. van Rhijn (+8 others)
2020 European Urology Open Science  
Acquisition of data: Foerster, Matin, Ku, Muilwijk, Monteiro, Liao, Petros, Spiess, Bivalacqua, Hendricksen, van Rhijn, Shabsigh, Briganti, Joniau, Kassouf, Pierorazio, Margulis, Necchi.  ...  Critical revision of the manuscript for important intellectual content: Foerster, Matin, Ku, Muilwijk, Monteiro, Liao, Petros, Spiess, Bivalacqua, Hendricksen, van Rhijn, Shabsigh, Briganti, Joniau, Kassouf  ... 
doi:10.1016/j.euros.2020.04.001 fatcat:qb6ovl7jv5egzdzcunykqhw6uu

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  
perspective nature methods | VOL.9 NO.4 | APRIL 2012 | 345 the international molecular exchange (imex) consortium is an international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant set of protein interactions available in a single search interface on a common website (http://www.imexconsortium.org/). common curation rules have been developed, and a central registry is used to manage the selection of articles to enter
more » ... o the dataset. We discuss the advantages of such a service to the user, our quality-control measures and our data-distribution practices. Protein-protein interactions are a key element in our understanding of molecular biology. However, in contrast to areas of activity such as DNA sequencing or protein structural analysis, the systematic capture of published molecular interaction data into public domain repositories is still in its infancy. This is not due to lack of resources in this domain. As of December 2011, the PathGuide resource 1 listed more than 100 protein-protein interaction-related databases. Although many of these databases focus on predictions of potential interactions or on mapping interologs, rather than experimentally determined interactions, the extent of activity suggests ample resources. However, most of these resources are independently funded and pursue their goals in isolation. As a result, accessing all publicly available molecular interaction data, even on a specific biological or biomedical topic, is a challenging, time-consuming task that requires the user to query multiple resources, each with a different interface; additionally, many resources use different identifiers and often contain redundant data from overlapping sets of publications. Efforts to address this problem began ten years ago with the development of a common file format for representing protein-interaction data. The 'minimum information about a molecular interaction experiment' (MIMIX) guidelines had been published then 2 , defining a list of the information to be supplied when
doi:10.1038/nmeth.1931 pmid:22453911 pmcid:PMC3703241 fatcat:ev2rpzb3c5hkpo52af3rfglfou

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni (+22 others)
2011 BMC Bioinformatics  
BACKGROUND: Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human
more » ... n or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them.RESULTS:A total of 11 teams participated in at least one of the two PPI tasks (10 in ACT and 8 in the IMT) and a total of 62 persons were involved either as participants or in preparing data sets/evaluating these tasks. Per task, each team was allowed to submit five runs offline and another five online via the BioCreative Meta-Server. From the 52 runs submitted for the ACT, the highest Matthew's Correlation Coefficient (MCC) score measured was 0.55 at an accuracy of 89 and the best AUC iP/R was 68. Most ACT teams explored machine learning methods, some of them also used lexical resources like MeSH terms, PSI-MI concepts or particular lists of verbs and nouns, some integrated NER approaches. For the IMT, a total of 42 runs were evaluated by comparing systems against manually generated annotations done by curators from the BioGRID and MINT databases. The highest AUC iP/R achieved by any run was 53, the best MCC score 0.55. In case of competitive systems with an acceptable recall (above 35) the macro-averaged precision ranged between 50 and 80, with a maximum F-Score of 55. CONCLUSIONS: The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging. Nevertheless, text-mining tools that report ranked lists of relevant articles for manual selection can potentially reduce the time needed to identify half of the relevant articles to less than 1/4 of the time when compared to unranked results. Detecting associations between full text articles and interaction detection method PSI-MI terms (IMT) is more difficult than might be anticipated. This is due to the variability of method term mentions, errors resulting from pre-processing of articles provided as PDF files, and the heterogeneity and different granularity of method term concepts encountered in the ontology. However, combining the sophisticated techniques developed by the participants with supporting evidence strings derived from the articles for human interpretation could result in practical modules for biological annotation workflows.
doi:10.1186/1471-2105-12-s8-s3 pmid:22151929 pmcid:PMC3269938 fatcat:vireubnikbhgjg2y2fskgqvgse

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 (freely available at http://www.ebi.ac.uk/ intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMExand MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate
more » ... s of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. 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. Both IntAct and MINT are active contributors to the IMEx consortium
doi:10.1093/nar/gkt1115 pmid:24234451 pmcid:PMC3965093 fatcat:5qemzevwgzdjln3y4pxvgfz7aa

Page 477 of Nuova Antologia, Revista Di Lettere, Scienze Ed Arti Vol. 124, Issue [page]

1892 Nuova Antologia, Revista Di Lettere, Scienze Ed Arti  
Don Carmelo piantò una canna al luogo indicato; don Leonardo, appoggiato a un cipresso, segnò il nome su lo scartafaccio. — Undici, dodici, quindici, diciassette, venti!  ...  briganti! che non avete nè legge, nè fede! Fate ancora un passo qui dentro, e ve lo do io il primo maggio! Un mormorio si levò dalla folla.  ... 

Leonardo Sciascia, L'Adorabile Stendhal

Annalisa Bottacin
2004 Studi francesi  
L'Adorabile Stendhal che raccoglie quell'insieme di articoli, saggi, meditazioni e pensieri, tra storia e fiction, che nel corso dell'esistenza forse il maggior scrittore civile italiano della nostra epoca, Leonardo  ...  Ciò che si legge in questo volume è un interiorizzazione raffinatissima che spazia in vari campi: dai Napoleonidi ("Il principe Pietro", pp. 13-33, "Napoleone scrittore", pp. 149-159), ai briganti ("Les  ...  Ora, come ignorare una figura di critico così percettivo quale fu Leonardo Sciascia e non inserirla tra i maggiori studiosi del grenoblese degli ultimi anni?  ... 
doi:10.4000/studifrancesi.37907 fatcat:s3dtkwqtdvf3bbu545yhdpu23e

Malformação de Chiari e a sua correlação com transtornos orofaciais

Eugênia Leal de Figueiredo, Carolina Pereira da Silva, Maria Emanuella Letícia da Silva, Heitor Ferreira de Souza Neto, Henrique Lima Ferreira de Souza, Hanna Janyne Meira e Mello, Jair Carneiro Leão, Alessandra de Albuquerque Tavares Carvalho
2021 Research, Society and Development  
a depender da presença ou ausência de sintomatologia, dos achados neurológicos, do nível de ectopia tonsilar e se houver, ou não, comprometimento do estilo de vida (Poretti, 2016 , Langridge, 2017 , Briganti  ...  ser usados para tratar o MCI em pacientes sintomáticos, devendo ser ponderados em razão da possível, embora rara, ocorrência de uma diminuição espontânea ou resolução completa da herniação tonsilar (Briganti  ... 
doi:10.33448/rsd-v10i5.15151 fatcat:azoujz4ukjfy7mx4t7dcv5y6b4

Page 65 of The Journal of Art Vol. 4, Issue 7 [page]

1991 The Journal of Art  
., 1987; La pittura in Italia: Il Cinquecento ed. by Giuliano Briganti, 2 vol., 913 pp., 1000 illus., 1988; La pittura in Italia: Il Seicento ed. by Giuliano Briganti, 2 vol., 967 pp., 900 illus., 1989  ...  As accustomed as we are to turning up our noses at these “minor artists,” the truth is American museums are more likely to contain examples by Altobello Melone and Domenico Gargiulo than Leonardo da Vinci  ... 

Sobre Cervantes, Manzoni y Sciascia. Breve historia de un equívoco acerca del itinerario de la palabra "mafia"

Walter Ghia
2011 Ingenium Revista Electrónica de Pensamiento Moderno y Metodología en Historia de la Ideas  
RESUMEN En un artículo de 1986 Leonardo Sciascia propone la hipótesis de un origen español de la palabra "mafia", apoyándose en la lectura que Alessandro Manzoni hace de El Quijote.  ...  ABSTRACT In a 1986 article Leonardo Sciascia proposes the hypothesis of a Spanish origin of the word "mafia", as he reads the word in an Alessandro Manzoni's transcription of the Quixote.  ...  En 1985precisamente el año que precede al ensayo de Leonardo Sciascia-los Colloqui col Manzoni publicados bajo la dirección de Alessandra Briganti, en la sección de Borri consideran válida la lectura de  ... 
doi:10.5209/rev_inge.2011.n5.36225 fatcat:6hhm5wsp3nhabnvr3yr2hfw2dy

Roberto Saviano : la représentation des pouvoirs criminels mafieux et le conflit entre justice et littérature

Ketty Zanforlini
2019 TRANS-  
Leonardo Sciascia, Letteratura e mafia , in id. , Cruciverba , Turin, Einaudi, 1983, p. 145. Nous traduisons.  ...  Littérature italienne et mafia, ouvrages et articles : ALTOMONTE, Antonio, Mafia, briganti, camorra e letteratura , Milan, Pan Editrice, 1979 [1971].  ... 
doi:10.4000/trans.3044 fatcat:jsd33lfozvawfasnpev6gclula

Key Figures InPostwar Italian Architecture: The Mannerism of Leonardo Savioli (1950-1966)

Francesca Privitera
2015 Journal of Engineering and Architecture  
Architectural criticism has always analysed the theoretical and planning work of Leonardo Savioli , the master of twentieth-century Italian architecture, in two clearly different stages, one before and  ...  Leonardo Savioli: a hypothetical reading A fundamental role in the cultural education of the twentieth-century Florentine architect Leonardo Savioli was played by his study of the artistic culture of  ...  that Savioli, who was as interested in painting as he was in architecture and at the time was a friend of the art critic Carlo Ludovico Ragghianti, was aware of these publications, especially that of Briganti  ... 
doi:10.15640/jea.v3n2a17 fatcat:fkq4ypbxvrhzfnzf6k3lh47n44
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