Tools and Resources

BridgeDb

BridgeDb is a framework to map identifiers between various biological databases and related resources. These mappings are provided for genes, proteins, metabolites, metabolic reactions, diseases, complexes and publications. BridgeDb includes a Java library that provides an API for programmatic access.

Collaboration: BridgeDb is maintained by the Department of Translational Genomics at Maastricht University, Gladstone Institutes, Heriot Watt University, University of Manchester.

Project architects: Egon Willighagen, Denise Slenter, Marvin Martens, Tooba Abbassi-Daloii (TGX)

Chemistry Development Kit (CDK)

The Chemistry Development Kit (CDK) is a open science cheminformatics toolkit founded in 2000 and written in the Java programming language. It provides cheminformatics functionality for 2D and 3D structure, various input/output formats like molfiles and SMILES, and can be used in multiple languages, including Python.

Collaboration: The CDK  is an international open science project with more than 100 contributors from academia and industry.

Project architects: Egon Willighagen

CyTargetLinker

CyTargetLinker  is a Cytoscape app that allows extending networks with additional nodes. In biomedical research context, these nodes can be transcription factors (Linkset: ENCODE), miRNA (Linksets from MirTarBase, TransMir, TargetScan or MirBase), chemical compounds (Linksets: DrugBank, CTD, ChEMBL), molecular pathways (Linksets: WikiPathways, REACTOME), or diseases (Linkset: Orphanet, OMIM)

TGX members involved:

- Susan Coort (architect)

- Friederike Ehrhart

- Egon Willighagen

WikiPathways

WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome, and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.

Collaboration: WikiPathways is maintained by Gladstone Institutes in San Francisco and the Department of Translational Genomics (TGX) at Maastricht University. 

Project architects: Alexander Pico (Gladstone Institutes) and Martina Summer-Kutmon (MACSBio)