SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update

Luana Licata, Prisca Lo Surdo, Marta Iannuccelli, Alessandro Palma, Elisa Micarelli, Livia Perfetto, Daniele Peluso, Alberto Calderone, Luisa Castagnoli, Gianni Cesareni

Research output: Contribution to journalArticle

Abstract

The SIGnaling Network Open Resource 2.0 (SIGNOR 2.0) is a public repository that stores signaling information as binary causal relationships between biological entities. The captured information is represented graphically as a signed directed graph. Each signaling relationship is associated to an effect (up/down-regulation) and to the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing the up/down-regulation of the target entity. Since its first release, SIGNOR has undergone a significant content increase and the number of annotated causal interactions have almost doubled. SIGNOR 2.0 now stores almost 23 000 manually-annotated causal relationships between proteins and other biologically relevant entities: chemicals, phenotypes, complexes, etc. We describe here significant changes in curation policy and a new confidence score, which is assigned to each interaction. We have also improved the compliance to the FAIR data principles by providing (i) SIGNOR stable identifiers, (ii) programmatic access through REST APIs, (iii) bioschemas and (iv) downloadable data in standard-compliant formats, such as PSI-MI CausalTAB and GMT. The data are freely accessible and downloadable at https://signor.uniroma2.it/.

Original languageEnglish
Pages (from-to)D504-D510
JournalNucleic Acids Research
Volume48
Issue numberD1
DOIs
Publication statusE-pub ahead of print - Oct 9 2019

ASJC Scopus subject areas

  • Genetics

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    Licata, L., Lo Surdo, P., Iannuccelli, M., Palma, A., Micarelli, E., Perfetto, L., Peluso, D., Calderone, A., Castagnoli, L., & Cesareni, G. (2019). SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. Nucleic Acids Research, 48(D1), D504-D510. https://doi.org/10.1093/nar/gkz949