The RInChI Project The aim of the RInChI Project is to create a unique, canonical, text string to describe a reaction. Different researchers working on the same reaction should be able to generate the same RInChI without needing to confer with each other https://www-rinchi.ch.cam.ac.uk/ International chemical identifier for chemical reactions 8th German […]
InChI Tag: Toolkits
8 posts
PubChem chemical structure standardization Volker D. Hähnke, Sunghwan Kim & Evan E. Bolton Journal of Cheminformatics volume 10, Article number: 36 (2018) Background: PubChem is a chemical information repository, consisting of three primary databases: Substance, Compound, and BioAssay. When individual data contributors submit chemical substance descriptions to Substance, the unique […]
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on Journal of Cheminformatics volume 3, Article number: 37 (2011) Noel M O’Boyle, Rajarshi Guha, Egon L Willighagen, Samuel E Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor V Filippov, Robert M Hanson, Marcus D Hanwell, Geoffrey R […]
Consistency of systematic chemical identifiers within and between small-molecule databases Saber A Akhondi, Jan A Kors & Sorel Muresan Journal of Cheminformatics volume 4, Article number: 35 (2012) Abstract Background: Correctness of structures and associated metadata within public and commercial chemical databases greatly impacts drug discovery research activities such as […]
Detection of IUPAC and IUPAC-like chemical names Roman Klinger, Corinna Kolá?ik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich Bioinformatics, Volume 24, Issue 13, July 2008, Pages i268–i276, https://doi.org/10.1093/bioinformatics/btn181 Motivation: Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. Several representations and nomenclatures […]
Webinar: Solving the issues in standardisation of stereochemical representations from Chemistry World on Vimeo. Sponsored by Bio-Rad Laboratories Abstract: Learn about technology that solves the issue of interpreting 3D stereochemical information implied in 2D structure representations.
This RDKit InChI Calculation with Jupyter Notebook tutorial is useful to teach the basics of how to interact with InChI using a cheminformatics toolkit in a Jupyter Notebook. The notebook has the following learning objectives: Setup RDKit with a Jupyter Notebook Construct a molecule (RDKit molecular object) from a SMILES […]
The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports Gert Wohlgemuth, Pradeep Kumar Haldiya, Egon Willighagen, Tobias Kind, Oliver Fiehn Author Notes Bioinformatics, Volume 26, Issue 20, October 2010, Pages 2647–2648, https://doi.org/10.1093/bioinformatics/btq476 Summary: Metabolomic publications and databases use different database identifiers or even trivial names which disable queries […]