Mashups and CB2

Posted on September 7, 2006 by pm286

There’s a regular monthly meeting in Cambridge on Thursdays in the Internet cafe called CB2. Organised with enormous energy by Rufus Pollock – see the Open Knowledge Foundation link. Mostly geeks, we have a common theme of wanting to liberate knowledge. Typical domains are legal, where access to reports in the public domain is effectively controlled by commercial suppliers, maps which are controlled (in the UK) by the Ordnance Survey and my own interest in chemistry. So we talk about bottom up approaches to liberation – what can we get going that has dynamism but is built on modern lightweight software engineering approaches?
A key approach is the mash-up – a fairly new term for me. A mashup is the linking of information from two or more accessible data resources. An excellent example is Placeopedia. This is a really simple, brilliant mashup. It links Google maps to Wikipedia articles. Have a look before you read on.
So any place in Wikipedia in Wikipedia can be linked to its place on Google Maps. Anyone can add a new place just by browsing the map and clicking a link to the Wikipedia entry.
Tonight I learned how lightweigfht it is… It’s simply a link to the Google Maps API and to the Wikipedia API. All Placeopedia is is a table of locations against WP entries. Stunningly clever. And it emphaiszes the power of mashups – link between two separate data sources and you get a completely new information resource.
The Placeopedia mashup came from the MySociety folks – a group of developers committed to
“mySociety builds websites which give people simple, tangible benefits in the civic and community aspects of their lives.” For example in the UK it’s difficult to get hold of some government data – including the formal proceedings. They effectively liberated government proceedings in TheyWorkForYou.
The UK government has actually funded some activities in mashups – see Rufus’ OKF blog.
Unfortunately we have to have access to data sources before we can create mashups. In chemistry there were virtually no data sources before PubChem. Now that PubChem has survived the troubles of last year we can start to create mashups – and we’ll be showing some quite soon – based on InChIs. As we liberate more data sources in chemistry, expect some really exciting things to happen.

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3 Responses to Mashups and CB2

  1. Joerg Kurt Wegner says:
    September 7, 2006 at 11:56 pm

    Sounds like a kind server based (centralized) type of meta knowledge tagging, ontology and mind-map.
    If you just think about mashing-up biologial function, drug information, interaction networks and so on … that would be a killer application.
    A brilliant idea would be to collect indeed PubChem, NCBI-PDB, EMBL-PDB, Swissprot, etc. … of course everything must be extractable and minable 😉 Wow, stunning idea, especially in combination with user data, user notes, keywords, literature references, and so on.
    In fact, just a kind of extended CiteULike, but of course with chemical meaning and CML support, ShiftNMR support, etc.
    Joerg
    P.S.: You have a couple of duplicated words and typos in this entry.

    Reply
  2. pm286 says:
    September 8, 2006 at 7:26 am

    It is mindboggling exciting and incredibly simple. A mashup can consist of simply two APIs, a list of links between them, and some AJAX to manage the clicks. The Placeopedia doesn’t even retrieve the maps, it simply gives a link to the GoogleApi with some coordinates. Google does the rest! I gather the protoctype was written in 3 days!
    Peter Corbett has a wonderful mashup in OSCAR3 onto PubChem. I didn’t know it was called a mashup then. He recosgnises chemical names in papers. These are either (a) known connection tables (b) can be translated on the fly using his software into connection tables or (c) mashed up onto PubChem. As you know the quality in PubChem varies from the wonderful to the less wonderful – see:
    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pccompound&term=etcetera
    for a bit of chemical nomenclature amusement. So we do have to check that a name in PubChem is what it says it is.
    The exciting thing is that this needs only to be done once – with a world wide chemical name mashup and social computing then once a reliable chemist has OKed a PubChem entry it never needs to be done again. And a mashup can be layered on top of PubChem.
    Yes we can and will transform the world. The difficult is getting good connection tables. At present we have the strategies:
    (a) use deposited ones. Good places are PubChem, ChEBI, MSD, KEGG. Does anyone see a connection? Yes, they’re all done by bioscientists.
    (b) read CIFs. We have done this with very high success and now have ca. 50,000 CIFs – all legal. They are on our CMLRSS Bioclipse feed. All will be revealed on Sunday
    (c) read names and use OSCAR3. Runs at ca 50%
    (d) read InChIs. There are a few out there besides (a)
    But the main strategy is to get the publishers to add (a) InChI and then (b) connection tables to their publications. Then all the robots have to do is get legal permission to read the papers!
    Sorry about the typos – I rely heavily on spell checkes and I haven’t yet found one on WordPress

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  3. Pingback: Unilever Centre for Molecular Informatics, Cambridge - petermr’s blog » Blog Archive » Open Map Data?

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