SIGnaling Network Open Resource (Signor) Reference Ingest Guide
Source Information
InfoRes ID: infores:signor
Description: SIGNOR 3.0, https://signor.uniroma2.it, is a public repository that captures causal information and represents it according to an 'activity-flow' model. SIGNOR provides freely-accessible static maps of causal interactions that can be tailored, pruned and refined to build dynamic and predictive models. Each signaling relationship is annotated with an effect (up/down-regulation) and with the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing the regulation of the target entity. Since its latest release, SIGNOR has undergone a significant upgrade including: (i) a new website that offers an improved user experience and novel advanced search and graph tools; (ii) a significant content growth adding up to a total of approx. 33,000 manually-annotated causal relationships between more than 8900 biological entities; (iii) an increase in the number of manually annotated pathways, currently including pathways deregulated by SARS-CoV-2 infection or involved in neurodevelopment synaptic transmission and metabolism, among others; (iv) additional features such as new model to represent metabolic reactions and a new confidence score assigned to each interaction.
Citations: - Prisca Lo Surdo, Marta Iannuccelli, Silvia Contino, Luisa Castagnoli, Luana Licata, Gianni Cesareni, Livia Perfetto, SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D631–D637, https://doi.org/10.1093/nar/gkac883
Data Access Locations: - Signor 3.0 Downloads: https://signor.uniroma2.it/downloads.php (this page includes file sizes and simple data dictionaries for each download)
Data Provision Mechanisms: file_download
Data Formats: csv
Data Versioning and Releases: No consistent cadence for releases, but on average there are 1-2 releases each month. Versioning is based on the month and year of the release. Releases page / change log: https://signor.uniroma2.it/downloads.php
Ingest Information
Ingest Categories: primary_knowledge_provider
Utility: Signor is a rich source of manually curated genetic associations to other biological entities which are an important type of edge for Translator query and reasoning use cases, including treatment predictions, gene-gene regulation predictions, and pathfinder queries. It is one of the sources that focus on drug and genes.
Scope: This initial ingest of Signor covers curated Gene to Gene associations that report therapeutic and marker/mechanism relationships, and inferred statistical associations generated by Signor.
Relevant Files
| File Name | Location | Description |
|---|---|---|
| signor_genes.csv | https://signor.uniroma2.it/downloads.php | Associations generated by knowledge assertions between 'Gene' 'Complex' 'Chemical' 'Phenotype' 'Protein' 'Smallmolecule' 'Proteinfamily' 'Stimulus' 'Fusion Protein' 'Mirna' 'Antibody' and 'Ncrna' |
Included Content
| File Name | Included Records | Fields Used |
|---|---|---|
| signor_genes.csv | Associations generated by knowledge assertions with quality controlled edges between 'Gene' 'Complex' 'Chemical' 'Phenotype' 'Protein' 'Smallmolecule' 'Proteinfamily' 'Mirna' 'Antibody' and 'Ncrna' | subject_identifier, subject_name, subject_category, object_identifier, object_name, object_category, predicate, original_predicate, provided_by, Primary_Knowledge_Source, publications, knowledge_level |
Future Content Considerations
edge_content: While the current ingest includes only edges passing initial quality control of LLM & manual verification, future iterations will include additional edges fail initial quality control.
edge_content: Considering add new biolink categories: 'Fusion Protein': potential descendant to 'biolink:Protein', 'Stimulus': only partially overlap with 'biolink:EnvironmentalProcess'
Target Information
Target InfoRes ID: infores:catrax-pharmacogenomics
Edge Types
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:Gene | biolink:Gene | knowledge_assertion | manual_agent | Signor records indicate the gene to be 'regulate' another gene - which maps best to the Biolink predicate 'regulates' with additional directional qualifier. | |
| biolink:ChemicalEntity | biolink:Gene | knowledge_assertion | manual_agent | Signor records indicate the chemical to be 'regulate' another gene - which maps best to the Biolink predicate 'affects' with additional directional qualifier. | |
| biolink:Gene | biolink:Phenotype | knowledge_assertion | manual_agent | Signor records indicate the gene to be 'regulate' another phenotype - which maps best to the Biolink predicate 'affects' with additional directional qualifier. | |
| biolink:Complex | biolink:Gene | knowledge_assertion | manual_agent | Signor records indicate the complex to be 'regulate' another gene - which maps best to the Biolink predicate 'affects' with additional directional qualifier. | |
| biolink:Gene | biolink:SmallMolecule | knowledge_assertion | manual_agent | Signor records indicate the gene to be 'regulate' another smallmolecule - which maps best to the Biolink predicate 'affects' with additional directional qualifier. | |
| biolink:ProteinFamily | biolink:Gene | knowledge_assertion | manual_agent | Signor records indicate the proteinfamily to be 'regulate' another gene - which maps best to the Biolink predicate 'regulates' with additional directional qualifier. |
Provenance Information
Contributors: - Qi Wei: code author, data modeling - Yue Zhang: data modeling - Guangrong Qin: data modeling, domain expertise - Sierra Moxon: code support - Matthew Brush: data modeling, domain expertise
Artifacts: - Ingest Survey: https://docs.google.com/spreadsheets/d/1tqimhXxpWzQdfNxanpW-rAaLnmsP80YZUthY5O4mEc8/edit?gid=1223527032#gid=1223527032 - Ingest Ticket: https://github.com/NCATSTranslator/Data-Ingest-Coordination-Working-Group/issues/29