A number of new data sources have been added/updated to the ChemSpider database. A separate posting on the ChemSpider News blog outlines HOW to search only specific data sources rather than the entire dataset. This should be of interest to you.

Newly added databases are listed below:

1) A set of “synthesized peptides”. Over 168,000 peptide structures generated from all amino acids – from the individual amino acids up to and including all tetrapeptides. This database will likely be of value to mass spectrometrists examining biofluids.

2) The Human Metabolome Database – a database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. An example is shown for phenylephrine which is linked through to the HMDB here.

3) The DrugBank database is a cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4300 drug entries including >1,000 FDA-approved small molecule drugs, 113 FDA-approved biotech (protein/peptide) drugs, 62 nutraceuticals and >3,000 experimental drugs. The link through from ChemSpider to DrugBank is not yet enabled but will come shortly.

4) The CombiUgi set – Jean-Claude Bradley‘s team, in collaboration with others are working together on the CombiUgi project as described on their wiki. The basis of the work is explained in Nature Precedings in the article “The CombiUgi Project and Closing the Open Science Loop” by Jean-Claude Bradley, Rikesh Parikh, Dan Zaharevitz and Rajarshi Guha. ChemSpider has added and indexed the 68,000 structures to the database, together with the predicted properties. We will be adding additional data to these structure records as the data become available.

We have additional data to deposit onto the database and will keep you informed on new additions.

Stumble it!

3 Responses to “New Data Sources Added to ChemSpider”

  1. Jean-Claude Bradley says:

    Thanks for working with us on the CombiUgi project – this should help with some of our processing.

  2. Egon Willighagen says:

    Hi Tony, the addition of the first three databases is indeed rather interesting to life sciences and metabolomics in particular. Might you give an overview on the state of mass values, with respect to giving them for salts? Has then been addressed throughout the database now? (The problem was that several molecular properties were calculated for just one of the fragments for multicomponent entries.)

  3. Antony Williams says:

    Hi Egon. This was all resolved in early May and posted on the ChemSpider News site at http://www.chemspider.com/news/?p=4. I know it’s confusing to have the two sites but a blog is simply an easier way to keep people informed of new functionality. Please test it out and let us know your thoughts.

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