Debbie_img

About

The Database of Experimental Biomaterials and their Biological Effect (DEBBIE) is a new open access tool which will enable a more efficient and evidence-based selection of materials for medical applications. The database aims to curate exhaustive inventories of biomaterials and their associated data using text mining tools. It can be used to recreate or update reviews of the literature in a more rapid and repeatable manner as well as generate a comprehensive map of research activity and findings.


Pipeline

Ontology

The Devices, Experimental scaffolds and Biomaterials Ontology (DEB) is an open resource for organizing information about biomaterials, their design, manufacture and biological testing. It was developed using text analysis for identifying ontology terms from a biomaterials gold standard corpus, systematically curated to represent the domain’s lexicon. Topics covered by DEB were validated by members of the biomaterials research community. The ontology may be used for searching terms, performing annotations for machine learning applications, standardized meta-data indexing and other cross-disciplinary data exploitation. If you are a biomaterials scientist, we encourage and welcome your input to this effort! You can flag terms and errors through the 'issues' tab in DEB's GitHub repository.

In addition, below you can find the static and dynamic visualization of the ontology.


static

Static Visualization on OWLGrEd

dynamic

Dynamic Visualization on WebVOWL

Database

The Database of Experimental Biomaterials and their Biological Effect (DEBBIE) is a new open access tool which will enable a more efficient and evidence-based selection of materials for medical applications. The database aims to curate exhaustive inventories of biomaterials and their associated data using text mining tools. It can be used to recreate or update reviews of the literature in a more rapid and repeatable manner as well as generate a comprehensive map of research activity and findings.

The DEBBIE Database contains annotations of PubMed abstracts in field of biomaterials, including implants, medical devices, and exeprimental scaffolds. Each annotation is labelled by one or more of the following categories:




Research

Team

Osnat

Osnat Hakimi

Project Leader

Osnat is a Marie Curie Individual Fellow at the Universitat Politècnica de Catalunya and a visitor to the Barcelona Supercomputing Center

austin

Austin McKitrick

Research Assistant

Austin is a Masters Student in Bioinformatics for Health Sciences at Universitat Pompeu Fabra (UPF) in Barcelona

carla

Carla V. Fuenteslópez

Collaborator

Carla is a DPhil Student studying Engineering Science at the University of Oxford

javi

Javier Corvi

Collaborator

Javi is a Research Engineer at the Barcelona Supercomputing Center

Scientific Advisors

osnat

Maria-Pau Ginebra

Maria-Pau leads the Department of Materials Science and Engineering at the Universitat Politècnica de Catalunya

austin

Martin Krallinger

Martin leads the Text Mining Unit at the Barcelona Supercomputing Center

carla

Josep Gelpi

Josep leads the Computational Team for the National Institute of Bioinformatics at the Barcelona Supercomputing Center

javi

Alexandre Perera Lluna

Alexandre leads the Bioinformatics and Biomedical Signals Laboratory (B2S) at the Universitat Politècnica de Catalunya