The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo-and Bioinformatics
- C. Steinbeck, Yongquan Han, S. Kuhn, Oliver Horlacher, Edgar Luttmann, Egon Willighagen
- Computer Science, ChemistryJournal of chemical information and computer…
- 11 February 2003
The Chemistry Development Kit provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc.
ChEBI in 2016: Improved services and an expanding collection of metabolites
This update paper has substantially extended the collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast and added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery.
Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.
- C. Steinbeck, Christian Hoppe, S. Kuhn, M. Floris, R. Guha, Egon Willighagen
- Computer Science, ChemistryCurrent pharmaceutical design
- 31 May 2006
The Chemistry Development Kit's new QSAR capabilities and the recently introduced interface to statistical software are introduced.
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy
A comprehensive, flexible, and computable, purely structure-based chemical taxonomy (ChemOnt) is developed along with a computer program (ClassyFire) that uses only chemical structures and structural features to automatically assign all known chemical compounds to a taxonomy consisting of >4800 different categories.
MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data
The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique and will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments.
The Blue Obelisk—Interoperability in Chemical Informatics
- R. Guha, M. Howard, Egon Willighagen
- Computer ScienceJournal of Chemical Information and Modeling
- 22 February 2006
The Blue Obelisk Movement is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards.
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
This work has completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology, and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them.
Toward interoperable bioscience data
The prerequisites for data commoning are described and an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision are presented.
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
This paper highlights the continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library.
Chemical Entities of Biological Interest: an update
New features in ChEBI since the last NAR report in 2007 are reported, including substructure and similarity searching, a submission tool for authoring of ChE BI datasets by the community and a 30-fold increase in the number of chemical structures stored in Ch EBI.