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Nucleic acids research
01 08, 2020;48 (D1): D504-D510.

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
Author Information
  1. Luana Licata: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
  2. Prisca Lo Surdo: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
  3. Marta Iannuccelli: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
  4. Alessandro Palma: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
  5. Elisa Micarelli: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
  6. Livia Perfetto: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
  7. Daniele Peluso: IRCSS Fondazione Santa Lucia, 00142 Rome, Italy.
  8. Alberto Calderone: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
  9. Luisa Castagnoli: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
  10. Gianni Cesareni: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
PMID: 31665520 DOI: 10.1093/nar/gkz949

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/.

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MeSH Term

Animals
Databases, Factual
Humans
Protein Interaction Maps
Signal Transduction
Software
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

Database Commons: DBC001757 (SIGNOR)
Article has an altmetric score of 1

Word Cloud

Created with Highcharts 10.0.02SIGNOR0causaldataSIGnalingNetworkOpenResourcestoressignalinginformationrelationshipsup/down-regulationetcsignificantalmostdownloadablepublicrepositorybinarybiologicalentitiescapturedrepresentedgraphicallysigneddirectedgraphrelationshipassociatedeffectmechanismegbindingphosphorylationtranscriptionalactivationcausingtargetentitySincefirstreleaseundergonecontentincreasenumberannotatedinteractionsdoublednow23000manually-annotatedproteinsbiologicallyrelevantentities:chemicalsphenotypescomplexesdescribechangescurationpolicynewconfidencescoreassignedinteractionalsoimprovedcomplianceFAIRprinciplesprovidingstableidentifiersiiprogrammaticaccessRESTAPIsiiibioschemasivstandard-compliantformatsPSI-MICausalTABGMTfreelyaccessiblehttps://signoruniroma2it/0:2019update

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