Wednesday, July 28, 2010

ChemSpider

“When spider webs unite, they can tie up a lion” -- Ethiopian Proverb

ChemSpider (http://www.chemspider.com/), a Royal Society of Chemistry resource, is a tool that desulfurization researchers will find useful. The ChemSpider Web describes itself so well that I will just quote from it …
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“ChemSpider links together compound information across the web, providing free text and structure search access of millions of chemical structures. With an abundance of additional property information, tools to upload, curate and use the data, and integration to a multitude of other online services, ChemSpider is the richest single source of structure-based chemistry information. It is provided to the community by the Royal Society of Chemistry.”
source:
http://www.chemspider.com/
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What is ChemSpider?
“ChemSpider is a free-to-access collection of compound data from across the web, provided for the benefit of the community by the Royal Society of Chemistry (RSC). It aggregates chemical structures and their associated information into a single searchable repository and makes it available to everybody.

“ChemSpider builds on the collected sources by adding additional properties, related information and links back to original data sources. ChemSpider offers text and structure searching to find compounds of interest and provides unique services to improve this data by curation and annotation and to integrate it with users’ applications.

“ChemSpider SyntheticPages, CSSP, extends this model to cover reactions, providing quick publication, peer review and semantic enhancement of repeatable reactions

“The ChemSpider mission is to:
•Bring together compound data on the web
◦Nearly 25M compounds from almost 400 data sources, deduplicated with the original source links provided
◦Provide easy and powerful search options
◦Structure and substructure search
◦Validated synonyms improve accurate text search expansion
•Improve the quality of public chemistry data sources
◦Automated chemistry checking of structures on loading
◦Manual comment and correction tools offer crowdsourced curation with expert review
•Provide a publishing platform for the addition and preservation of data
◦Registered users can upload their own structure sets online and have their own home page
◦Registered users can add spectra, additional data, links, videos, audio to compound records
◦ChemSpider SyntheticPages allows publishing of reactions
•Make this data accessible and reusable
◦Mobile ChemSpider – accessed through mobile phone browsers, iPhones and iPads
◦Downloadable compound sets from search results
◦Web services to query and deliver data
◦Tools to embed linked structure images and spectra into web pages and blogs
•Integrate with publications
◦Direct links to an expanding collection of structures in RSC journals
◦Searching of PubMed and RSC books, journals and databases via validated chemical name dictionaries expands accurate compound name searching
ChemSpider grows daily with more depositions, more links. You are invited to help build this community for chemists by contributing your structures, spectra, syntheses. You can also actively participate in the curation of the data; registration enables you to become a depositor or curator.”

source: http://www.chemspider.com/About.aspx
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A couple of related resources are …

How to Search ChemSpider - Quick Search Guide
daviesje Posted: Friday, June 25, 2010 1:30:57 PM
021020 - ChemSpider Quick Card Name Search.pdf (282kb) downloaded 2 time(s).
source: http://forum.chemspider.com/Default.aspx?g=posts&t=233
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ChemSpider Blog: Archive for the Community Building Category
source: http://www.chemspider.com/blog/category/community-building
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The article below, while not directly related, definitely is worth reading …

Chemical - Text Hybrid Search Engines
zhou@gnf.org
Yingyao Zhou,*,†Bin Zhou,†Shumei Jiang,†and Frederick J. King†,‡
Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, and, Developmental and Molecular Pathways, Novartis Institutes for BioMedical
Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139
J. Chem. Inf. Model. 2010, 50, 47–54
Abstract
As the amount of chemical literature increases, it is critical that researchers be enabled to accurately locate documents related to a particular aspect of a given compound. Existing solutions, based on text and chemical search engines alone, suffer from the inclusion of “false negative” and “false positive” results, and cannot accommodate diverse repertoire of formats currently available for chemical documents. To address these concerns, we developed an approach called Entity-Canonical Keyword Indexing (ECKI), which converts a chemical entity embedded in a data source into its canonical keyword representation prior to being indexed by text search engines. We implemented ECKI using Microsoft Office SharePoint Server Search, and the resultant hybrid search engine not only supported complex mixed chemical and keyword queries but also was applied to both intranet and Internet environments. We envision that the adoption of ECKI will empower researchers to pose more complex search questions that were not readily attainable previously and to obtain answers at much improved speed and accuracy.
Document Source: http://pubs.acs.org/doi/abs/10.1021/ci900380s
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