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For: Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L. CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinformatics 2020;35:3779-3785. [PMID: 30793173 DOI: 10.1093/bioinformatics/btz132] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/01/2019] [Accepted: 02/19/2019] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Touré V, Unni D, Krauss P, Abdelwahed A, Buchhorn J, Hinderling L, Geiger TR, Österle S. The SPHN Schema Forge - transform healthcare semantics from human-readable to machine-readable by leveraging semantic web technologies. J Biomed Semantics 2025;16:9. [PMID: 40341005 PMCID: PMC12063216 DOI: 10.1186/s13326-025-00330-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Accepted: 04/30/2025] [Indexed: 05/10/2025]  Open
2
Orchard SE. What have Data Standards ever done for us? Mol Cell Proteomics 2025:100933. [PMID: 40024375 DOI: 10.1016/j.mcpro.2025.100933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 03/04/2025]  Open
3
Hoyt CT, Gyori BM. The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources. Sci Data 2024;11:547. [PMID: 38811583 PMCID: PMC11136952 DOI: 10.1038/s41597-024-03406-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]  Open
4
Attrill H, Antonazzo G, Goodman JL, Thurmond J, Strelets VB, Brown NH, the FlyBase Consortium. A new experimental evidence-weighted signaling pathway resource in FlyBase. Development 2024;151:dev202255. [PMID: 38230566 PMCID: PMC10911275 DOI: 10.1242/dev.202255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/09/2024] [Indexed: 01/18/2024]
5
Csabai L, Bohár B, Türei D, Prabhu S, Földvári-Nagy L, Madgwick M, Fazekas D, Módos D, Ölbei M, Halka T, Poletti M, Kornilova P, Kadlecsik T, Demeter A, Szalay-Bekő M, Kapuy O, Lenti K, Vellai T, Gul L, Korcsmáros T. AutophagyNet: high-resolution data source for the analysis of autophagy and its regulation. Autophagy 2024;20:188-201. [PMID: 37589496 PMCID: PMC10761021 DOI: 10.1080/15548627.2023.2247737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/18/2023]  Open
6
Li H, Ma T, Hao M, Guo W, Gu J, Zhang X, Wei L. Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics. Brief Bioinform 2023;24:bbad359. [PMID: 37824741 DOI: 10.1093/bib/bbad359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/25/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023]  Open
7
Attrill H, Antonazzo G, Goodman JL, Thurmond J, Strelets VB, Brown NH. A new experimental evidence-weighted signaling pathway resource in FlyBase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552786. [PMID: 37645956 PMCID: PMC10461922 DOI: 10.1101/2023.08.10.552786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
8
Giuseppe A, Chiara P, Yun N, Igor J. Pathway integration and annotation: building a puzzle with non-matching pieces and no reference picture. Brief Bioinform 2022;23:6691914. [PMID: 36063560 DOI: 10.1093/bib/bbac368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/25/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022]  Open
9
Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level. mSystems 2022;7:e0149321. [PMID: 35913188 PMCID: PMC9426430 DOI: 10.1128/msystems.01493-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
10
Milano M, Agapito G, Cannataro M. Challenges and Limitations of Biological Network Analysis. BIOTECH 2022;11:24. [PMID: 35892929 PMCID: PMC9326688 DOI: 10.3390/biotech11030024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]  Open
11
Kalman ZE, Dudola D, Mészáros B, Gáspári Z, Dobson L. PSINDB: the postsynaptic protein-protein interaction database. Database (Oxford) 2022;2022:baac007. [PMID: 35234850 PMCID: PMC9216581 DOI: 10.1093/database/baac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/21/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
12
Porras P, Orchard S, Licata L. IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. Methods Mol Biol 2022;2449:27-42. [PMID: 35507258 DOI: 10.1007/978-1-0716-2095-3_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
13
Kuiper M, Bonello J, Fernández-Breis JT, Bucher P, Futschik ME, Gaudet P, Kulakovskiy IV, Licata L, Logie C, Lovering RC, Makeev VJ, Orchard S, Panni S, Perfetto L, Sant D, Schulz S, Zerbino DR, Lægreid A. The Gene Regulation Knowledge Commons: The action area of GREEKC. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021;1865:194768. [PMID: 34757206 DOI: 10.1016/j.bbagrm.2021.194768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 02/08/2023]
14
Csabai L, Fazekas D, Kadlecsik T, Szalay-Bekő M, Bohár B, Madgwick M, Módos D, Ölbei M, Gul L, Sudhakar P, Kubisch J, Oyeyemi OJ, Liska O, Ari E, Hotzi B, Billes VA, Molnár E, Földvári-Nagy L, Csályi K, Demeter A, Pápai N, Koltai M, Varga M, Lenti K, Farkas IJ, Türei D, Csermely P, Vellai T, Korcsmáros T. SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. Nucleic Acids Res 2021;50:D701-D709. [PMID: 34634810 PMCID: PMC8728204 DOI: 10.1093/nar/gkab909] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022]  Open
15
Touré V, Flobak Å, Niarakis A, Vercruysse S, Kuiper M. The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Brief Bioinform 2021;22:bbaa390. [PMID: 33378765 PMCID: PMC8294520 DOI: 10.1093/bib/bbaa390] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022]  Open
16
Cesareni G, Sacco F, Perfetto L. Assembling Disease Networks From Causal Interaction Resources. Front Genet 2021;12:694468. [PMID: 34178043 PMCID: PMC8226215 DOI: 10.3389/fgene.2021.694468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022]  Open
17
Meldal BHM, Pons C, Perfetto L, Del-Toro N, Wong E, Aloy P, Hermjakob H, Orchard S, Porras P. Analysing the yeast complexome-the Complex Portal rising to the challenge. Nucleic Acids Res 2021;49:3156-3167. [PMID: 33677561 PMCID: PMC8034636 DOI: 10.1093/nar/gkab077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]  Open
18
Touré V, Vercruysse S, Acencio ML, Lovering RC, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, Del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Hoyt CT, Licata L, Lægreid A, Mungall CJ, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Saez-Rodriguez J, Thieffry D, Thomas PD, Türei D, Kuiper M. The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinformatics 2021;36:5712-5718. [PMID: 32637990 PMCID: PMC8023674 DOI: 10.1093/bioinformatics/btaa622] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/06/2020] [Accepted: 06/30/2020] [Indexed: 12/30/2022]  Open
19
Touré V, Zobolas J, Kuiper M, Vercruysse S. CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021;2021:6129748. [PMID: 33547799 PMCID: PMC7904049 DOI: 10.1093/database/baaa107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/16/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022]
20
Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S. Towards a unified open access dataset of molecular interactions. Nat Commun 2020;11:6144. [PMID: 33262342 PMCID: PMC7708836 DOI: 10.1038/s41467-020-19942-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022]  Open
21
Licata L, Lo Surdo P, Iannuccelli M, Palma A, Micarelli E, Perfetto L, Peluso D, Calderone A, Castagnoli L, Cesareni G. SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. Nucleic Acids Res 2020;48:D504-D510. [PMID: 31665520 PMCID: PMC7145695 DOI: 10.1093/nar/gkz949] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 09/30/2019] [Accepted: 10/09/2019] [Indexed: 01/11/2023]  Open
22
Iannuccelli M, Micarelli E, Surdo PL, Palma A, Perfetto L, Rozzo I, Castagnoli L, Licata L, Cesareni G. CancerGeneNet: linking driver genes to cancer hallmarks. Nucleic Acids Res 2020;48:D416-D421. [PMID: 31598703 PMCID: PMC6943052 DOI: 10.1093/nar/gkz871] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/12/2019] [Accepted: 09/30/2019] [Indexed: 12/28/2022]  Open
23
Kovács D, Sigmond T, Hotzi B, Bohár B, Fazekas D, Deák V, Vellai T, Barna J. HSF1Base: A Comprehensive Database of HSF1 (Heat Shock Factor 1) Target Genes. Int J Mol Sci 2019;20:ijms20225815. [PMID: 31752429 PMCID: PMC6888953 DOI: 10.3390/ijms20225815] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/11/2019] [Accepted: 11/15/2019] [Indexed: 12/28/2022]  Open
24
Palma A, Cerquone Perpetuini A, Ferrentino F, Fuoco C, Gargioli C, Giuliani G, Iannuccelli M, Licata L, Micarelli E, Paoluzi S, Perfetto L, Petrilli LL, Reggio A, Rosina M, Sacco F, Vumbaca S, Zuccotti A, Castagnoli L, Cesareni G. Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. Front Physiol 2019;10:1216. [PMID: 31611808 PMCID: PMC6776608 DOI: 10.3389/fphys.2019.01216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/06/2019] [Indexed: 12/12/2022]  Open
25
Caufield JH, Ping P. New advances in extracting and learning from protein-protein interactions within unstructured biomedical text data. Emerg Top Life Sci 2019;3:357-369. [PMID: 33523203 DOI: 10.1042/etls20190003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/11/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022]
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