Ask a Question
Use the ROBOKOP Question Builder to construct a new query, then use the visualization tool to explore relevant publications.
reasoning over biomedical objects linked in knowledge oriented pathways
ROBOKOP is an open-source, modular, biomedical knowledge graph–based system that includes the ROBOKOP biomedical knowledge graph, a user interface, and a variety of supporting resources, including tools and services to support deep exploration of the ROBOKOP KG and each of its underlying primary knowledge sources.
Additional Tools
ROBOKOP KG
ROBOKOP KG is an open-source biomedical knowledge graph containing ~10M nodes and ~250M edges drawn from ~30 biological data sources and bio-ontologies. Query the ROBOKOP KG directly in the Neo4j browser.
ExEmPLAR
The Extracting, Exploring and Embedding Pathways Leading to Actionable Research (ExEmPLAR) application is an experimental, generic Neo4j question-and-answer browser tool that supports queries of the ROBOKOP KG and other Neo4j databases.
ExEmPLAR is not a formal component of ROBOKOP but rather an experimental tool that supports queries of the ROBOKOP KG.
RoboDocumentation
A collection of notebooks and other documents to help users get the most out of ROBOKOP.
Citations
If you use ROBOKOP in your work, please cite the following papers:
- Bizon C, Cox S, Balhoff J, Kebede Y, Wang P, Morton K, Fecho K, Tropsha A. ROBOKOP KG and KGB: integrated knowledge graphs from federated sources. J Chem Inf Model 2019 Dec 23;59(12):4968–4973. doi: 10.1021/acs.jcim.9b00683. https://pubmed.ncbi.nlm.nih.gov/31769676/.
- Morton K, Wang P, Bizon C, Cox S, Balhoff J, Kebede Y, Fecho K, Tropsha A. ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering. Bioinformatics 2019;pii:btz604. doi: 10.1093/bioinformatics/btz604. https://pubmed.ncbi.nlm.nih.gov/31410449/.
Funding
ROBOKOP is a joint creation of the Renaissance Computing Institute (RENCI) at the University of North Carolina at Chapel Hill and CoVar LLC. The prototype was developed with funding from the National Center for Advancing Translational Sciences, National Institutes of Health (award #OT2TR002514). ROBOKOP's continued development is supported with joint funding from the National Institute of Environmental Health Sciences and the Office of Data Science Strategy within the National Institutes of Health (award #U24ES035214).
License
The ROBOKOP system and the ROBOKOP knowledge graph "KG" are governed under an open-source MIT License. Both resources make use of open-source primary data sources. While we make every effort to ensure that those sources can be freely ingested and redistributed, we encourage users to review and comply with the specific license terms applicable to each source. Furthermore, copyright remains with the respective originators, contributors, and maintainers of the primary data sources. This resource does not claim ownership of such intellectual property unless explicitly stated. The open-source ROBOKOP system, including the ROBOKOP KG, is provided "as is," without warranties or guarantees of any kind. The creators, maintainers, and distributors of the original primary data sources and derivative works disclaim any liability for errors, omissions, or misuse of the data. Users assume all responsibility for ensuring that the data sources are suitable for their specific applications and comply with all applicable legal and ethical guidelines.
Events
ROBOKOP has weekly office hours from 2-3pm EST. View details on our calendar or subscribe with the ICS file.