organic chemistry

InChIKey Web Services Facilitates Indexing of Molecules

Jean-Claude Bradley — Mon, 05 May 2008 03:59:44 -0700

Description

ChemSpider (1) now provides free web services to inter-convert molecular formats, including a look-up for InChIKeys. These are available either with a manual (2) or API interface (3).

Wikipedia describes the InChIKey (4):

The condensed, 25 character InChIKey is a hashed version of the full InChI (using the SHA-256 algorithm), designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, which are not searchable for chemical content. The full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed.

Essentially InChIKeys are a way of representing organic molecules with a unique text string, no matter how large. Search engines like Google have no trouble indexing InChIKeys. Other text representations have been problematic. Molecules may be represented by multiple SMILES (5) and InChIs (6) can become too long for proper indexing.

In order for InChIKeys to be usable, it is necessary to be able to inter-convert them with other formats. These new web services make this process much easier.

If InChIKeys are systematically used as tags (7) on the open web, it will make it much easier to track the chemistry being reported using automated means.

Future of chemistry

Source

1) http://www.chemspider.com
2) http://www.chemspider.com/WebServices/WSInChIDemo.aspx
3) http://www.chemspider.com/InChI.asmx
4) http://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey
5) http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
6) http://en.wikipedia.org/wiki/International_Chemical_Identifier
7) http://usefulchem.blogspot.com/2008/01/tracking-results-with-workflow-tables.html

Robot Scientist Creates and Evaluates Microbiology Hypotheses

Jean-Claude Bradley — Sun, 04 May 2008 12:09:59 -0700

Description

From Ross King's Robot Scientist web site (1):

The Robot Scientist is perhaps the first physical implementation of the task of Scientific Discovery in a microbiology laboratory. It represents the merging of increasingly automated and remotely controllable laboratory equipment and knowledge discovery techniques from Artificial Intelligence.

Automation of laboratory equipment (the "Robot" of Robot Scientist) has revolutionised laboratory practice by removing the "drudgery" of constructing many wet lab experiments by hand, allowing an increase in both the scope and scale of potential experiments. Most lab robots only require a simple description of the various chemical/ biological entities to be used in the experiments, along with their required volumes and where these entities are stored. Automation has also given rise to significantly increased productivity and a concomitant increase in the production of results and data requiring interpretation, giving rise to an "interpretation bottleneck" where the process of understanding the results is lagging behind the production of results.

The research fields of Computational Scientific Discovery and Bioinformatics have emerged in part as a response to this bottleneck. Both disciplines use computational approaches from Statistics and Machine Learning to provide an "automated understanding" of the experimental results.

This is a strong signal foreshadowing the near automation of the entire scientific process. This robot is able to function within the framework of molecular biology. However, each field has its own set of opportunities and challenges. The difficulty in extending this concept to other fields, such as organic (2) or inorganic chemistry will depend upon the conceptual models used. Providing the system with fewer human-based rules about how chemistry works would make it more difficult but ultimately could be more interesting.

Coupled with the practice of Open Data (3) and Crowdsourcing (4), a new form of distributed scientific intelligence could emerge that would "understand" reality in the sense that it is predictive and able to control phenomena but not in a way that is necessarily intuitive to humans.

This may be a pathway to the technological singularity.(5)

Future of chemistry

Source

1) http://www.aber.ac.uk/compsci/Research/bio/robotsci/intro/
2) http://sciencex2.org/en/node/16263
3) http://sciencex2.org/en/node/15726
4) http://precedings.nature.com/documents/1505/version/1
5) http://en.wikipedia.org/wiki/Technological_singularity

Methane Discovered in Exoplanet Atmosphere

Matt Daniels — Thu, 20 Mar 2008 15:11:31 -0700

Description

Researchers report in tomorrow's issue of Nature that a 40-minute gaze with the Hubble Space Telescope last May [2007] has revealed methane in the atmosphere of HD 189733b, a Jupiter-size planet orbiting close to its very bright parent star located 63 light-years away. The observation also confirmed last year's discovery by the Spitzer Space Telescope of water vapor in the planet's atmosphere (see: ScienceNOW, 11 July 2007).

ESA calls this a breakthrough [that] is an important step in eventually identifying signs of life on a planet outside our Solar System.

Science/AAAS News:

Astronomers have detected the organic molecule methane in the atmosphere of an extrasolar planet for the first time and have confirmed earlier observations of water vapor. Alas, the findings don't come close to suggesting that life has emerged on this other world, but they do contribute to a growing body of data about planetary evolution outside our own solar system.

Co-author Mark Swain of NASA's Jet Propulsion Laboratory in Pasadena, California, emphasized that HD 189733b is far too hot--average atmospheric temperature about 1000°C--to support life as we know it. But the presence of methane raises intriguing questions, he said, because the high temperature should have sequestered all of the carbon in the planet's atmosphere in the form of carbon monoxide (CO), not methane (CH4). That suggests a currently unknown chemical process is at work, he said.

Physics & Space Science

Source

http://sciencenow.sciencemag.org/cgi/content/full/2008/319/2

http://www.esa.int/esaSC/SEMTZ1N5NDF_index_0.html