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Category Archives: ChemSpider Services

ChemSpider provides a series of services. These will expand with time and we will post here about changes, enhancements and struggles with the services.

The Mass Spectrometry Web Services Interface to ChemSpider

We have previously rolled out a number of web services integrating to ChemSpider (1,2,3). This was recently extended by unveiling the MassSpec API. Details are below.

  • GetCompoundDetails
    Return specified compound details.
  • GetDatabases
    Get the list of datasources in ChemSpider.
  • SearchByFormula
    Search ChemSpider compounds by molecular formula. Search within specified datasources (if given).
  • SearchByFormula2
    Search ChemSpider compounds by molecular formula.
  • SearchByMass
    Search ChemSpider compounds by mass +/- range. Search within specified datasources (if given).
  • SearchByMass2
    Search ChemSpider compounds by mass +/- range.
  • With these web services it is now feasible for mass spectrometrists to integrate their own software systems directly to ChemSpider for their own purposes. If anyone is interested in integrating via the MassSpecAPI please contact us at info|AT|chemspider.com

     
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    Posted by on November 26, 2007 in ChemSpider Services, Community Building

     

    Uploads, Downloads and Managing Activity Data on ChemSpider – Open Notebook Science Support for JC Bradley at Drexel University

    As part of a collaborative project with Jean-Claude Bradley from Drexel University (and member of our Advisory Group) we are in the process of delivering new capabilities for the upload of “activity data” associated with one or more structures, the display of these data with the associated structures on ChemSpider and the download of these data to the desktop. Our efforts are part of JC’s overall workflow outlined here.

    So far we have enabled the ability to upload CSV files containing SMILES strings and associated data, converting the CSV files on the fly to SDF files for deposition onto ChemSpider. We have also enabled a general capability for the download of collections of data using checkbox selection and download as an SDF file with associated properties. Rather than insert images into this blog posting please click here to see the PDF of the Powerpoint overview.

    While we have the deposition process and downloading process essentially completed (except for testing) we now need to resolve the process for deduplicating the submitted data onto the database (or generating new structure records) as well as defining the format for display on the site. Watch this space.

     

    Something New and Exciting Coming Soon…

    I think the image below will tell the story of what’s coming soon to ChemSpider. As part of a collaboration with a member of our advisory group we will be unveiling this new capability for beta testing in the very near future. I’m sure some of you will see where we are going next…watch this space.

     
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    Posted by on November 16, 2007 in ChemSpider Services, Vision

     

    Focused Libraries – Intention to Publish on ChemSpider

    This is a declaration of intent that ChemSpider will shortly start hosting so-called “Focused Libraries” on ChemSpider in the very near future. The focused libraries will contain a set of compounds with in silico predicted affinities for specific protein targets. The availability of focused libraries can dramatically reduce how many compounds might require experimental examination for activity. The first sets of Focused Libraries have been supplied to us by Otava Chemicals.

    This is part of our path to offering new services via ChemSpider. Discussions are underway to integrate to online docking, to the possibility of offering synthetic feasibility analysis  and to expand the growing list of services integrated to ChemSpider due to the kindness and support of our collaborators.

     
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    Posted by on November 14, 2007 in ChemSpider Chemistry, ChemSpider Services

     

    Improved Integrations to the SureChem Patent Database – Searchable by Chemical Structure

    Previously I reported on the integration between ChemSpider and the SureChem Online Patent Portal. I also put together a technical note here describing how to perform the searches. For those of you new to SureChem the system provides online access to patents and enables searching via chemical structures, substructures and similarity of structures as well as searching by text. We’ve now enhanced the integration so that you don’t have to go through the Data Sources in order to find your way to the patents directly.

    Nicko Goncharoff recently gave a talk at the ICIC conference in Barcelona and I’ve linked to it here (with his permission) if you are interested in an overview of the technology. I’ve been using the system of late for some searches I’ve been doing. It’s fast, easy to use and found hits for every search I did. You can sign up online at the SureChem website and, according to what I’ve been hearing from them. their intention is to provide the service as Free Access for the foreseeable future and maybe indefinitely with their business coming from in-house licensing to either the data or to the portal itself.

     
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    Posted by on November 5, 2007 in ChemSpider Services

     

    Spectral Data Can Now Be Declared Open Data

    In his ongoing comments regarding our efforts here at ChemSpider Peter Murray-Rust has provided “interesting feedback”. This is one of MANY commentaries (1,2,3,….). Despite repeated requests to direct his comments directly to us/me, and suggestions to use the feedback form or participate on our blogs he prefers to comment on his blog.

    For those of you who read our blogs and watch our service I hope that you see we are responsive to requests and feedback. I have chosen to take all comments, however directed, as opportunities for improvement so, in less than 24 hours, and because of the commitment of our development team to help preserve our reputation, here’s what we have done…

    We looked at the CrystalEye system as a model of Open Data. CrystalEye is hosted by Peter’s Lab. We took this as an appropriate model and now when a user submits spectral data to ChemSpider they have a CHOICE to make the data Open or not. Their choice, not ours. This is a simple checkbox as shown below.

    Open Data Spectra
    The Open Data policies are those listed here. When a user allows us to host their data as Open Data then we allow others to download it and use it. When a spectrum is submitted as Open Data then those data can be downloadable. Simply click on the DOWNLOAD SPECTRUM button as shown in the image below (an example spectrum here) and you can download the JCAMP spectrum to your desktop.

    Download Spectrum

    Welcome to the world of Open Data on ChemSpider.

     
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    Posted by on October 14, 2007 in ChemSpider Chemistry, ChemSpider Services

     

    Open Chemistry Web is Will Griffiths’ Blog – Text and Structure Mining on ChemSpider

    Will Griffiths has opened up a new blog he has entitled the Open Chemistry Web. It went online today. I recommend keeping your eye on Will’s comments as he has great expertise in the domain of text mining and has a passion for facilitating searching of the Open Access Chemistry literature. In Will’s own words…”At a time when there is a great deal of openly available literature and data in this arena, it is time there was an openly available service with the cheminformatics and text indexing capabilities to search this effectively. We want to play a role in making that happen. ” Will is the gentleman responsible for innovating ChemRefer!

     
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    Posted by on October 11, 2007 in ChemSpider Services

     

    Simpler URLS For Better Indexing and Easier Searching

    We have noticed that despite the millions of InChIStrings and InChIKeys on ChemSpider they are not being indexed very well. Thanks to some constructive feedback from an interested party from Google (Thanks Simon!) we have revamped our URLs and improved the nature of how structures can be identified by various identifiers as shown below. These are now all valid URLs to identify a molecule and, as people mbed such links in their sites, indexing is more likely to be catalyzed.

    http://www.chemspider.com/InChIKey=DEIYFTQMQPDXOT-RERXVCSDCZ

    http://www.chemspider.com/Molecular-Formula=C28H38N6O11S

    http://www.chemspider.com/Substance-Suppliers.10482071.html

    http://www.chemspider.com/1234

    http://www.chemspider.com/q=benzene

    http://www.chemspider.com/InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H

     

    We will also submit an updated version of our SiteMap to Google and see if we can catalyze the indexing of the InChIKeys and InChIStrings at least. This will definitely help in making the web more structure searchable.

     
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    Posted by on September 29, 2007 in ChemSpider Services

     

    Structure Images on ChemSpider Tagged for InChI Searching. Web Service Enabled.

    If you’ve been frequenting our blog(s) you will have seen our passion for InChI adoption (1,2). A few months ago I started a discussion with Martin Walker (Walkerma), a very active member of the Chemistry community on Wikipedia. We were chatting about how to make chemical structure images searchable and while I was managing ChemSketch at ACD/Labs we embedded information into PNG images to facilitate this.

    it just made sense to facilitate this via ChemSpider also so now all structure images on ChemSpider are also tagged in the image with BOTH InChI Strings and InChI keys and the ChemSpider ID.

    There is a fairly standard way to embed tags into the PNG format. An effort to standardize the approach is described at: http://pmt.sourceforge.net/exif/drafts/d020.html. We have used the following fields to enclose information:

    1. DocumentName – contains http://www.chemspider.com/RecordView.aspx?id=#
    2. Software – contains ChemSpider (http://www.chemspider.com/)
    3. Artist – ChemSpider
    4. ImageTitle – InChI
    5. ImageDescription – InChIKey

    If there are other tages you would like included in the image please let us know. The format for the time being is PNG. I assume there will be requests for SVG but let’s see…

    18,630,699 structures are on the database right now. Not all of them have structure images generated yet but they will be done shortly after we have updated the database to over 20 million compounds (we are presently updating the structures associated with the Surechem Patent Database.

    A new web service has been published online, GetRecordImage, allowing you to get the record image based on a search by systematic name, synonym, trade name, InChI etc. As an example of this in action visit the test page at http://www.chemspider.com/WSSearch.aspx . Simply type in a compound name or some text string and hit return. For Xanax for example, there is one image returned.

    Image Retrieval Web Service

    In some cases you will see MULTIPLE structures…if the text string you search on is in the DB. For example, diazonamide A has SIX hits.

    We hope you find value in this service to access structure images directly from ChemSpider. You will notice our ChemSpider logo on the image and our URL. We acknowledge they can be removed. Our request is respect our efforts and leave them there.

     
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    Posted by on September 24, 2007 in ChemSpider Services

     

    InChIKey Generation Now Available via the Services Page on ChemSpider

    Over the weekend I had a couple of email exchanges with Paul Doherty (from TotallySynthetic.com) and Peter Murray-Rust. We were espousing the value of InChIStrings and Keys for indexing the TotallySynthetic.com pages (a great site for synthetic chemists) and specifically I was urging the move to InChIKeys for their compact nature and providing exposure for the new InChIKey. Paul’s already started to expose the InChIkeys on his postings, for an example see the Diazonamide A posting.

    TotallySynthetic

    With the keys published it is possible to check the structures inside ChemSpider, validate them an, if not present, submit the structures to ChemSpider and link back to the original blog posting to help link the blogosphere together until there’s an alternative solution. We will be figuring out how to scrape these InChIs in a a more automated fashion in the near future.

    This exchange encouraged us to put an InChIKey generation capability onto the services page. On this page you can draw a structure using the applet, upload a molfile, translate a SMILES or InChI string, whatever is necessary to submit the structure…then the InChIKey is generated using “Generate Properties”.

    InChIKey Generation

    There are many new capabilities accessible from the Services page as shown below…go visit.

    Services page

     
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    Posted by on September 23, 2007 in ChemSpider Services

     
     
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