Herbie - The Semantic Laboratory Notebook & Research Database

Herbie is the electronic laboratory notebook (ELN) and research database developed at the Helmholtz-Zentrum Hereon to facilitate the digitalization efforts within several institutes. Herbie builds upon semantic technologies like OWL and SHACL to offer a user-friendly interface to the RDF ecosystem.

Herbie is a platform to collaboratively work on a shared knowledge graph. At its core it is a wrapper around an RDF triple store, offering additional features like versioning, user handling, and management of access rights.

Users can upload any RDF graph to Herbie in one of the standard formats like Turtle or JSON-LD. This includes, in particular vocabularies and ontologies, as well as documents containing SHACL shapes.

Moreover, Herbie offers an advanced form generation feature which turns all SHACL documents into user-friendly web forms. By filling out and submitting these forms, end users can contribute to a fully semantically annotated knowledge graph without having to deal with the intricacies of RDF.

To eventually extract the entered knowledge as tabular data (CSV), JSON, or in graph form, Herbie offers a default SPARQL endpoint as well as a simple user interface to interactively create advanced queries which are run against the (virtual) knowledge graph belonging to the requesting user.

Herbie provides the means to offer structured, well-adapted protocols to capture standardized processes and offering an easy and flexible documentation platform. It can be flexibly adapted to the needs of any (scientific) domain (e.g. material science, biology, medicine) making it a perfect choice for interdisciplinary groups who want to create a rich and connected data pool.