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

Autor: M. Sivade (Dumousseau), 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, I. Jurisica, M. Koch, L. Licata, R. C. Lovering, D. J. Lynn, B. H. M. Meldal, G. Micklem, S. Panni, P. Porras, S. Ricard-Blum, B. Roechert, L. Salwinski, A. Shrivastava, J. Sullivan, N. Thierry-Mieg, Y. Yehudi, K. Van Roey, S. Orchard

Publikováno v: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-8 (2018)

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

Externí odkaz: https://doaj.org/article/9fd01102da0f43b2a9c9ea2fd780c54c

The IntAct database: efficient access to fine-grained molecular interaction data

Autor: Marta Iannuccelli, Juri Rappsilber, Matteo Pellegrini, Gautam Shirodkar, Colin W. Combe, Pablo Porras, Maria Jesus Martin, Eliot Ragueneau, Anjali Shrivastava, Livia Perfetto, Margaret Duesbury, Sangya Pundir, Xavier Watkins, Lukasz Salwinski, Sandra Orchard, Sylvain D. Vallet, Bálint Mészáros, Luana Licata, Simona Panni, Karyn How, Prashansa Ratan, Gianni Cesareni, Kalpana Panneerselvam, Odilia Lu, Henning Hermjakob, Sylvie Ricard-Blum, Elisabet Barrera, Noemi del Toro, Birgit H M Meldal

Publikováno v: del Toro, N, Shrivastava, A, Ragueneau, E, Meldal, B, Combe, C, Barrera, E, Perfetto, L, How, K, Ratan, P, Shirodkar, G, Lu, O, Mészáros, B, Watkins, X, Pundir, S, Licata, L, Iannuccelli, M, Pellegrini, M, Martin, M J, Panni, S, Duesbury, M, Vallet, S D, Rappsilber, J, Ricard-Blum, S, Cesareni, G, Salwinski, L, Orchard, S, Porras, P, Panneerselvam, K & Hermjakob, H 2021, ' The IntAct database : Efficient access to fine-grained molecular interaction data ', Nucleic Acids Research, vol. 50, no. D1, pp. D648-D653 . https://doi.org/10.1093/nar/gkab1006
Nucleic Acids Research
Nucleic Acids Research, vol 50, iss D1

The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one millio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bf456c7abad01c6b8254885ffe621e6f
https://doi.org/10.1093/nar/gkab1006

Analysing the yeast complexome—the Complex Portal rising to the challenge

Autor: Henning Hermjakob, Livia Perfetto, Pablo Porras, Edith D. Wong, Sandra Orchard, Noemi del-Toro, Carles Pons, Birgit H M Meldal, Patrick Aloy

Publikováno v: Nucleic Acids Research

The EMBL-EBI Complex Portal is a knowledgebase of macromolecular complexes providing persistent stable identifiers. Entries are linked to literature evidence and provide details of complex membership, function, structure and complex-specific Gene Ont

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1bb4b7fab935350f6f9949c52fd53e65
https://doi.org/10.1093/nar/gkab077

Mondo: Unifying diseases for the world, by the world

Autor: Nicole A Vasilevsky, Nicolas A Matentzoglu, Sabrina Toro, Joseph E Flack, Harshad Hegde, Deepak R Unni, Gioconda F Alyea, Joanna S Amberger, Larry Babb, James P Balhoff, Taylor I Bingaman, Gully A Burns, Orion J Buske, Tiffany J Callahan, Leigh C Carmody, Paula Carrio Cordo, Lauren E Chan, George S Chang, Sean L Christiaens, Michel Dumontier, Laura E Failla, May J Flowers, H. Alpha Garrett, Jennifer L Goldstein, Dylan Gration, Tudor Groza, Marc Hanauer, Nomi L Harris, Jason A Hilton, Daniel S Himmelstein, Charles Tapley Hoyt, Megan S Kane, Sebastian Köhler, David Lagorce, Abbe Lai, Martin Larralde, Antonia Lock, Irene López Santiago, Donna R Maglott, Adriana J Malheiro, Birgit H M Meldal, Monica C Munoz-Torres, Tristan H Nelson, Frank W Nicholas, David Ochoa, Daniel P Olson, Tudor I Oprea, David Osumi-Sutherland, Helen Parkinson, Zoë May Pendlington, Ana Rath, Heidi L Rehm, Lyubov Remennik, Erin R Riggs, Paola Roncaglia, Justyne E Ross, Marion F Shadbolt, Kent A Shefchek, Morgan N Similuk, Nicholas Sioutos, Damian Smedley, Rachel Sparks, Ray Stefancsik, Ralf Stephan, Andrea L Storm, Doron Stupp, Gregory S Stupp, Jagadish Chandrabose Sundaramurthi, Imke Tammen, Darin Tay, Courtney L Thaxton, Eloise Valasek, Jordi Valls-Margarit, Alex H Wagner, Danielle Welter, Patricia L Whetzel, Lori L Whiteman, Valerie Wood, Colleen H Xu, Andreas Zankl, Xingmin Aaron Zhang, Christopher G Chute, Peter N Robinson, Christopher J Mungall, Ada Hamosh, Melissa A Haendel

There are thousands of distinct disease entities and concepts, each of which are known by different and sometimes contradictory names. The lack of a unified system for managing these entities poses a major challenge for both machines and humans that

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::eb95e9f275c4c5ac6590aa22f6896dbb
https://doi.org/10.1101/2022.04.13.22273750

Complex Portal 2022: new curation frontiers

Autor: Anjali Shrivastava, Noemi del-Toro, Tiago Lubiana, Pablo Porras, Andra Waagmeester, Elisabeth Barrera, Egon Willighagen, Sandra Orchard, Bernhard Mlecnik, Juri Rappsilber, Birgit H M Meldal, João Vitor Ferreira Cavalcante, Kalpana Panneerselvam, Gabriela Bindea, Livia Perfetto, Henning Hermjakob, Colin W. Combe, Edith D. Wong, Hema Bye-A-Jee

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, In press, ⟨10.1093/nar/gkab991⟩
Nucleic Acids Research, 50(D1), D578-D586. Oxford University Press
Meldal, B H M, Perfetto, L, Combe, C, Lubiana, T, Cavalcante, J V F, Bye-A-Jee, H, Waagmeester, A, del-Toro, N, Shrivastava, A, Barrera, E, Wong, E, Mlecnik, B, Bindea, G, Panneerselvam, K, Willighagen, E, Rappsilber, J, Porras, P, Hermjakob, H & Orchard, S 2021, ' Complex Portal 2022 : New curation frontiers ', Nucleic Acids Research, vol. 50, no. D1, pp. D578-D586 . https://doi.org/10.1093/nar/gkab991

The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from a range of model organisms. It summarizes complex composition, topology and function along with links

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::53b9dff31ee0f84c010761cc808caebb
https://hal.sorbonne-universite.fr/hal-03421220/file/gkab991.pdf