Standards and Reference Implementation (SRI) Team
The SRI Team is tasked with developing and implementing the standards and references necessary to support R&D of the Translator system.
PIs - Chris Bizon, Chris Mungall, Matt Brush
Max Wang, Abrar Mesbah, Carrie Pasfield, Gaurav Vaidya, Kenny Morton, Yaphet Kebede, Tim Putman, Kevin Schaper, Nomi Harris, Sierra Moxon, Tursynay Issabekova, Richard Bruskiewich, Jim Balhoff, Kara Fecho.
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Node normalization takes a CURIE, and returns, the preferred CURIE for this entity, all other known equivalent identifiers for the entity, and semantic types for the entity as defined by the Biolink Model
- Node Normalizer wiki page
- Open API: https://nodenormalization-sri.renci.org/docs
- NodeNormalization Jupyter Notebook for documentation
This service takes lexical strings and attempts to map them to identifiers (curies) from a vocabulary or ontology. The lookup is not exact, but includes partial matches.
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- Name Resolution Service wiki page
- Open API: https://name-resolution-sri.renci.org/docs
- NameResolution Jupyter Notebook for documentation
The purpose of the Biolink Model is to provide a high-level data model of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc), their properties, and relationships, as well as to enumerate ways in which they can be associated. The specification of the Biolink Model is a single YAML file built using linkml.
- Documentation: Biolink Model
Biolink Model Toolkit (BMT): A Python API for working with the Biolink Model. BMT provides utility functions to look up Biolink Model for classes, relations, and properties based on Biolink CURIEs or external CURIEs that have been mapped to Biolink Model.
- Documentation: Biolink Model Toolkit
KGX is a utility library and set of command-line tools for exchanging data in Knowledge Graphs (KGs). The tooling here is partly generic but intended primarily for building the translator-knowledge-graph, and thus expects KGs to be Biolink Model compliant.
- Documentation: KGX
- KG Hub for Shared Knowledge Graphs
Suppose you have constructed a biolink-compliant knowledge graph, and want to deploy it as a TRAPI endpoint with limited fuss. Plater is a web server that automatically exposes a Neo4j instance through TRAPI compliant endpoints.
Monarch Initiative provides a reference knowledge graph that transforms human and non-human data sources to a Biolink Model compliant knowledge graph.