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Start Over Author "Del Toro N" Topic molecular interactions
5 results on '"Del Toro N"'

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

Author

Sivade (Dumousseau), M., Alonso-López, D., Ammari, M., Bradley, G., Campbell, N. H., Ceol, A., Cesareni, G., Combe, C., De Las Rivas, J., del-Toro, N., Heimbach, J., Hermjakob, H., Jurisica, I., Koch, M., Licata, L., Lovering, R. C., Lynn, D. J., Meldal, B. H. M., Micklem, G., Panni, S., Porras, P., Ricard-Blum, S., Roechert, B., Salwinski, L., Shrivastava, A., Sullivan, J., Thierry-Mieg, N., Yehudi, Y., Van Roey, K., and Orchard, S.

Published
2018
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3. The IMEx coronavirus interactome: an evolving map of Coronaviridae–host molecular interactions.

Author

Perfetto, L, Pastrello, C, del-Toro, N, Duesbury, M, Iannuccelli, M, Kotlyar, M, Licata, L, Meldal, B, Panneerselvam, K, Panni, S, Rahimzadeh, N, Ricard-Blum, S, Salwinski, L, Shrivastava, A, Cesareni, G, Pellegrini, M, Orchard, S, Jurisica, I, Hermjakob, H, and Porras, P

Subjects
COVID-19, MOLECULAR interactions, CORONAVIRUSES, PANDEMICS, HUMAN biology, SARS-CoV-2
Abstract

The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions can provide fine-grained resolution of the mechanisms behind the virus biology and the human organism response. We present a curated dataset of physical molecular interactions focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family that has been manually extracted by International Molecular Exchange (IMEx) Consortium curators. Currently, the dataset comprises over 4400 binarized interactions extracted from 151 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (https://www.ebi.ac.uk/intact) and will be continuously updated as research on COVID-19 progresses. [ABSTRACT FROM AUTHOR]

Published
2020
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4. Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

Author

Villaveces, J. M., Jiménez, R. C., Porras, P., del-Toro, N., Duesbury, M., Dumousseau, M., Orchard, S., Choi, H., Ping, P., Zong, N. C., Askenazi, M., Habermann, B. H., and Hermjakob, Henning

Subjects
MOLECULAR interactions, COMMUNITIES, STANDARDS, PROTEOMICS, ALGORITHMS
Abstract

The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. 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. 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 evidence. We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative-molecular interaction standards. In this manuscript, we introduce these two algorithms and provide community access to the tool suite, describe examples of how these tools are useful to selectively present molecular interaction data and demonstrate a case where the algorithms were successfully used to identify a systematic error in an existing dataset. [ABSTRACT FROM AUTHOR]

Published
2015
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5. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

Author

Sivade Dumousseau, M, Alonso-López, D, Ammari, M, Bradley, G, Campbell, NH, Ceol, A, Cesareni, G, Combe, C, De Las Rivas, J, Del-Toro, N, Heimbach, J, Hermjakob, H, Jurisica, I, Koch, M, Licata, L, Lovering, RC, Lynn, DJ, Meldal, BHM, Micklem, G, Panni, S, Porras, P, Ricard-Blum, S, Roechert, B, Salwinski, L, Shrivastava, A, Sullivan, J, Thierry-Mieg, N, Yehudi, Y, Van Roey, K, and Orchard, S

Subjects
Proteomics, PSI-MI, Proteome, HUPO-PSI, Systems Biology, Protein complexes, XML, 3. Good health, Protein-protein interaction, Data standards, Mutation, Molecular interactions, Humans, Protein Interaction Maps, Databases, Protein
Abstract

BACKGROUND: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. 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. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. 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 data types, following extensive community consultation. 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. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

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