Pages

Tuesday, November 06, 2012

What online services support InChI and REST?

The adoption if InChI is increasing, despite its limitations. But one thing I find greatly missing, is chemical databases supporting access of entries via the appropriate InChI. I know there are resolvers around, but that is different. They do a search, and give me multiple links to individual structures that may match to a certain extend. I am not interested in that in this context.

What I want instead is to be able to deep link to a particular entry in ChemSpider, PubChem, HMDB, or whatever databases using the InChI instead. The only service currently supporting this that I am aware of, is rdf.openmolecules.net. It uses a URI pattern like http://rdf.openmolecules.net/?$INCHI. For example, the entry for methane is http://rdf.openmolecules.net/?InChI=1/CH4/h1H4 and this URI deep links to the entry of methane, rather than a search result list.

So, the core requirement is that the database URI tells me, either: "yes, this is the one and only entry matching 100% this InChI", or "no, I do not have data for this structure".

What other databases support deep linking using the InChI? And what would the URI look like?

8 comments:

  1. I am not quite following you in this post - both ChemSpider and PubChem do provide direct access by InChI, for example ChemSpider:

    http://www.chemspider.com/Search.aspx?q=[urlencoded inchi]

    For PubChem, look at their official REST API documentation.

    ReplyDelete
    Replies
    1. Wolf, yes, that is 'resolver' functionality: it allows you to do a search. What I want is to end up at a single structure, which has that particular InChI. So, 'deep linking'.

      Delete
  2. Everything working on a database would be a search and doing this kind of thing without a database would be as a library without index. Would a resolver on a database without duplicates would be the thing your looking for?

    ReplyDelete
    Replies
    1. Yes, sort of. What I want is to be able to do the same thing as with database IDs. For example, I can use the PubChem ID to deep link to, e.g. elongacornane (cid=60140829) [0]:

      http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=60140829

      But, I also want to be able to use the InChI for that, like this one for methane:

      http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?InChI=1S/CH4/h1H4

      So, it still would not really be a search, because the InChI would be used for an index, just like the Compound ID.

      0.https://plus.google.com/u/0/104186710895049917005/posts/AnTthZiqbJs

      Delete
  3. Would a search engine search -

    /inchikey=AAADCJYVFVJSLT-LOXKKDEGNA-N

    which gives accurate answers be what you want?

    ReplyDelete
    Replies
    1. It would if I would only get one exact hit.

      Delete
    2. Egon-

      How can you expect only one hit when there is so much information and data on the web?

      Steve

      Delete
    3. One the web, sure... in a single database, I expect one entry for one InChI...

      Delete