Christoph Steinbeck

Venkata Chandrasekhar Nainala

J. Cheminformatics, December, 2023

MORTAR: a rich client application for in silico molecule fragmentation.

[BibT_eX]

[DOI]

J. Cheminformatics, 2023

Harmonising, Harvesting, and Searching Metadata Across a Repository Federation.

[BibT_eX]

[DOI]

Noura Rayya

Oliver Koepler

Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

Digitalizing the Chemical Landscape: A Comprehensive Overview and Progress Report of NFDI4Chem.

[BibT_eX]

[DOI]

Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

2022

Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK).

[BibT_eX]

[DOI]

J. Cheminformatics, 2022

Surge: a fast open-source chemical graph generator.

[BibT_eX]

[DOI]

Brendan D. McKay

Mehmet Aziz Yirik

J. Cheminformatics, 2022

An algorithm to classify homologous series within compound datasets.

[BibT_eX]

[DOI]

J. Cheminformatics, 2022

DECIMER - hand-drawn molecule images dataset.

[BibT_eX]

[DOI]

J. Cheminformatics, 2022

RanDepict: Random chemical structure depiction generator.

[BibT_eX]

[DOI]

J. Cheminformatics, 2022

Toward a Framework for Integrative, FAIR, and Reproducible Management of Data on the Dynamic Balance of Microbial Communities.

[BibT_eX]

[DOI]

Luiz M. R. Gadelha Jr.

Proceedings of the 18th IEEE International Conference on e-Science, 2022

2021

Chemical graph generators.

[BibT_eX]

[DOI]

Mehmet Aziz Yirik

PLoS Comput. Biol., 2021

MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle.

[BibT_eX]

[DOI]

Mehmet Aziz Yirik

J. Cheminformatics, 2021

COCONUT online: Collection of Open Natural Products database.

[BibT_eX]

[DOI]

J. Cheminformatics, 2021

DECIMER 1.0: deep learning for chemical image recognition using transformers.

[BibT_eX]

[DOI]

J. Cheminformatics, 2021

STOUT: SMILES to IUPAC names using neural machine translation.

[BibT_eX]

[DOI]

J. Cheminformatics, 2021

Molecule Set Comparator (MSC): a CDK-based open rich-client tool for molecule set similarity evaluations.

[BibT_eX]

[DOI]

J. Cheminformatics, 2021

DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature.

[BibT_eX]

[DOI]

J. Cheminformatics, 2021

2020

Review on natural products databases: where to find data in 2020.

[BibT_eX]

[DOI]

J. Cheminformatics, 2020

Too sweet: cheminformatics for deglycosylation in natural products.

[BibT_eX]

[DOI]

J. Cheminformatics, 2020

DECIMER: towards deep learning for chemical image recognition.

[BibT_eX]

[DOI]

J. Cheminformatics, 2020

A review of optical chemical structure recognition tools.

[BibT_eX]

[DOI]

J. Cheminformatics, 2020

2019

NaPLeS: a natural products likeness scorer - web application and database.

[BibT_eX]

[DOI]

J. Cheminformatics, 2019

ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK).

[BibT_eX]

[DOI]

J. Cheminformatics, 2019

Interoperable and scalable data analysis with microservices: applications in metabolomics.

[BibT_eX]

[DOI]

Bioinform., 2019

2017

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

[BibT_eX]

[DOI]

J. Cheminformatics, 2017

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

[BibT_eX]

[DOI]

J. Cheminformatics, 2017

The future of metabolomics in ELIXIR.

[BibT_eX]

[DOI]

F1000Research, 2017

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

[BibT_eX]

[DOI]

Bioinform., 2017

2016

ChEBI in 2016: Improved services and an expanding collection of metabolites.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2016

libChEBI: an API for accessing the ChEBI database.

[BibT_eX]

[DOI]

Neil Swainston

Adriano Dekker

John W. May

Pedro Mendes

J. Cheminformatics, 2016

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.

[BibT_eX]

[DOI]

J. Cheminformatics, 2016

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

[BibT_eX]

[DOI]

Syed Asad Rahman

Gilliean Torrance

Lorenzo Baldacci

Sergio Martínez Cuesta

Bioinform., 2016

2015

Updates in Rhea - a manually curated resource of biochemical reactions.

[BibT_eX]

[DOI]

Nevila Hyka-Nouspikel

Nucleic Acids Res., 2015

SpeckTackle: JavaScript charts for spectroscopy.

[BibT_eX]

[DOI]

J. Cheminformatics, 2015

BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology.

[BibT_eX]

[DOI]

Stephan Beisken

Bhavana Harsha

BMC Bioinform., 2015

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.

[BibT_eX]

[DOI]

J. Biomed. Semant., 2015

ChEBI for systems biology and metabolic modelling.

[BibT_eX]

[DOI]

Neil Swainston

Proceedings of the International Conference on Biomedical Ontology, 2015

2014

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

[BibT_eX]

[DOI]

J. Cheminformatics, 2014

Efficient ring perception for the Chemistry Development Kit.

[BibT_eX]

[DOI]

John W. May

J. Cheminformatics, 2014

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking.

[BibT_eX]

[DOI]

Alejandra N. González-Beltrán

BMC Bioinform., 2014

2013

MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data.

[BibT_eX]

[DOI]

Susanna-Assunta Sansone

Julian L. Griffin

Nucleic Acids Res., 2013

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2013

The EBI enzyme portal.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2013

Review of "Contemporary computer-assisted approaches to molecular structure elucidation (new developments in NMR)" by Mikhail E Elyashberg, Antony Williams and Kirill Blinov.

[BibT_eX]

[DOI]

J. Cheminformatics, 2013

Expanding natural product chemistry resources at the EBI.

[BibT_eX]

[DOI]

Namrata Kale

Tejasvi Mahendraker

J. Cheminformatics, 2013

The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

KNIME-CDK: Workflow-driven Cheminformatics.

[BibT_eX]

[DOI]

Stephan Beisken

Thorsten Meinl

Bernd Wiswedel

Luis F. de Figueiredo

Michael R. Berthold

BMC Bioinform., 2013

OntoQuery: easy-to-use web-based OWL querying.

[BibT_eX]

[DOI]

Ilinca Tudose

Bioinform., 2013

Metingear: a development environment for annotating genome-scale metabolic models.

[BibT_eX]

[DOI]

John W. May

A. Gordon James

Alejandra N. González-Beltrán

Bioinform., 2013

The MetaboLights repository: curation challenges in metabolomics.

[BibT_eX]

[DOI]

Philippe Rocca-Serra

Susanna-Assunta Sansone

Database J. Biol. Databases Curation, 2013

An Ontology for Drug-drug Interactions.

[BibT_eX]

[DOI]

Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2013

2012

Bioinformatics Meets User-Centred Design: A Perspective.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2012

Rhea - a manually curated resource of biochemical reactions.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2012

Structure-based classification and ontology in chemistry.

[BibT_eX]

[DOI]

J. Cheminformatics, 2012

Structured chemical class definitions and automated matching for chemical ontology evolution.

[BibT_eX]

[DOI]

J. Cheminformatics, 2012

Natural product-likeness score revisited: an open-source, open-data implementation.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

Self-organizing ontology of biochemically relevant small molecules.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

Modular Extensions to the ChEBI Ontology.

[BibT_eX]

[DOI]

Steve Turner

Gareth I. Owen

Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

2011

CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution.

[BibT_eX]

[DOI]

J. Cheminformatics, 2011

New developments on the cheminformatics open workflow environment CDK-Taverna.

[BibT_eX]

[DOI]

Andreas Truszkowski

J. Cheminformatics, 2011

Computational metabolomics - a field at the boundaries of cheminformatics and bioinformatics.

[BibT_eX]

[DOI]

Stefan Kuhn

J. Cheminformatics, 2011

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.

[BibT_eX]

[DOI]

J. Cheminformatics, 2011

Towards automated metabolome assembly: application of text mining to correlate small molecules, targets and tissues.

[BibT_eX]

[DOI]

Dietrich Rebholz-Schuhmann

J. Cheminformatics, 2011

Chemical ontologies: what are they, what are they for and what are the challenges.

[BibT_eX]

[DOI]

J. Cheminformatics, 2011

Modularization Requirements in Bio-Ontologies: A Case Study of ChEbi.

[BibT_eX]

[DOI]

Proceedings of the Modular Ontologies - Proceedings of the Fifth International Workshop, 2011

Modelling Threshold Phenomena in OWL: Metabolite Concentrations as Evidence For Disorders.

[BibT_eX]

[DOI]

Proceedings of the 8th International Workshop on OWL: Experiences and Directions (OWLED 2011), 2011

Use of Multiple Ontologies to Characterize the Bioactivity of Small Molecules.

[BibT_eX]

[DOI]

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Recent Developments in the ChEBI Ontology.

[BibT_eX]

[DOI]

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

What's in an 'is about' Link? Chemical Diagrams and the Information Artifact Ontology.

[BibT_eX]

[DOI]

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2010

Chemical Entities of Biological Interest: an update.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2010

OrChem: an open source chemistry search engine for Oracle.

[BibT_eX]

[DOI]

Mark Rijnbeek

J. Cheminformatics, 2010

ChEBI: a chemistry ontology and database.

[BibT_eX]

[DOI]

J. Cheminformatics, 2010

Progress on an open source computer-assisted structure elucidation suite (SENECA).

[BibT_eX]

[DOI]

Stefan Kuhn

J. Cheminformatics, 2010

Molecular fragments chemoinformatics.

[BibT_eX]

[DOI]

J. Cheminformatics, 2010

CDK-Taverna: an open workflow environment for cheminformatics.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

Representing Chemicals Using OWL, Description Graphs and Rules.

[BibT_eX]

[DOI]

Proceedings of the 7th International Workshop on OWL: Experiences and Directions (OWLED 2010), 2010

What are chemical structures and their relations?

[BibT_eX]

[DOI]

Proceedings of the Formal Ontology in Information Systems, 2010

Ontological dependence, dispositions and institutional reality in chemistry.

[BibT_eX]

[DOI]

Colin R. Batchelor

Proceedings of the Formal Ontology in Information Systems, 2010

2009

OrChem - An open source chemistry search engine for Oracle®.

[BibT_eX]

[DOI]

Mark Rijnbeek

J. Cheminformatics, 2009

Bioclipse 2: A scriptable integration platform for the life sciences.

[BibT_eX]

[DOI]

BMC Bioinform., 2009

Semantic access to chemistry data with the ChEBI ontology and web services.

[BibT_eX]

[DOI]

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, 2009

2008

Performance Validation of Neural Network Based 13C NMR Prediction Using a Publicly Available Data Source.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2008

Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction.

[BibT_eX]

[DOI]

BMC Bioinform., 2008

The ChEBI Ontology: An Ontology for Chemistry within a Biological Context.

[BibT_eX]

[DOI]

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

2007

Chemical Markup, XML, and the World Wide Web, 7. CMLSpect, an XML Vocabulary for Spectral Data.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2007

Userscripts for the Life Sciences.

[BibT_eX]

[DOI]

Egon L. Willighagen

Noel M. O'Boyle

Harini Gopalakrishnan

BMC Bioinform., 2007

Bioclipse: an open source workbench for chemo- and bioinformatics.

[BibT_eX]

[DOI]

BMC Bioinform., 2007

2006

The Blue Obelisk-Interoperability in Chemical Informatics.

[BibT_eX]

[DOI]

Rajarshi Guha

Michael T. Howard

Geoffrey R. Hutchison

J. Chem. Inf. Model., 2006

2004

Evolutionary-Algorithm-Based Strategy for Computer-Assisted Structure Elucidation.

[BibT_eX]

[DOI]

Yongquan Han

J. Chem. Inf. Model., 2004

2003

NMRShiftDB-Constructing a Free Chemical Information System with Open-Source Components.

[BibT_eX]

[DOI]

Stefan Krause

Stefan Kuhn

J. Chem. Inf. Comput. Sci., 2003

The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics.

[BibT_eX]

[DOI]

J. Chem. Inf. Comput. Sci., 2003

2001

SENECA: A Platform-Independent, Distributed, and Parallel System for Computer-Assisted Structure Elucidation in Organic Chemistry.

[BibT_eX]

[DOI]

J. Chem. Inf. Comput. Sci., 2001

1997

MASP-A Program Predicting Mass Spectra of Combinatorial Libraries.

[BibT_eX]

[DOI]

Kurt Berlin

Clemens Richert

J. Chem. Inf. Comput. Sci., 1997

1995

LUCY, ein Programm zur Konstitutionsbestimmung aus Korrelations-NMR-Experimenten sowie Beispiele zur Identifizierung von Naturstoffen durch NMR-Spektroskopie.

[BibT_eX]

[DOI]