Tools and Resources
Tools and Resources
Chemistry Development Kit (CDK)
Description:
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:
Links:
CyTargetLinker
Description:
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:
- Dr Susan Steinbusch - Coort (S.L.M.) (architect)
- Dr Friederike Ehrhart (F.)
- Dr Egon Willighagen (E.L.)
Links:
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 MaCSBio and the Department of Translational Genomics (TGX), both at Maastricht University, and in collaboration with ELIXIR-NL and many research communities around the world.
Project architects:
TGX Members:
- Dr Egon Willighagen (E.L.)
- Dr Susan Steinbusch - Coort (S.L.M.)
- Dr Denise Slenter, MSc
- Marvin Martens, MSc (M.T.L.J.)
- Dr Friederike Ehrhart (F.)
- Dr Lars Eijssen (L.M.T.)
Links:
Scholia
Description:
Scholia is a service that creates visual scholarly profiles for topics, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.
TGX Members:
Collaboration:
- Danmarks Tekniske Universitet
- FIZ Karlruhe - Leibniz Institute for Information Infrastructure
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB)
- Albert-Ludwigs-Universität Freiburg
- BITPlan GmbH
Links: