Anyone for crystal mashups?

From the blogosphere through Bora:

Liz Allen posted this on the Wall of the PLoS Facebook group yesterday:

Here’s a fun Friday activity for all of you who like to track the stats of the inevitable rise and world domination of OA!


Another cool mash up site (great logo, takes a minute or so to load) is there you can see the number of OA repositories mapped across the globe, there were 808 as of earlier today.

PMR: This is fun. I’ve never done a mashup, but I’d love to try. Here’s my idea. Since CrystalEye is Open, anyone can do it or we can do it together:
CrystalEye contains > 100, 000 entries, all with author names and addresses. Here’s an example:
“College of Sciences Tianjin University of Science and Technology Tianjin 300457 P. R. China”
How easy it it to turn that into a Google coordinate? Of course not all addresses will have a consistent format, so we need a service that can guess formats.
Then how do we actually mash it with Google? I imagine it’s fairly easy.
Then we have a map of where every  crystal structure in CrystalEye has been done…
And of course this is only the start. We can add info on date, number of authors, field of study, etc. The only requirement is that you have to be prepared to work with Open Data. It’s not harmful. You don’t even have to let us know you are doing it. But you do have to acknowledge the source.

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7 Responses to Anyone for crystal mashups?

  1. Rich Apodaca says:

    I’d like to be able to mashup CrystalEye, but so far I’ve found no URL via Google, this blog, or WWMM. So…
    What’s the URL for the CrystalEye service?

  2. pm286 says:

    (1) Fantastic!
    [I am surprised you haven’t found it – it comes at number 1 in my Google search:
    CrystalEye: Homepage
    The aim of the CrystalEye project is to aggregate crystallography from web resources, and to provide methods to easily browse, search, and to keep up to … – 7k – Cached – Similar pages]
    We are fitting it with AtomPP feeds for efficient downloading. Jim Downing (ojd20 AT the normal place) will be able to help. Any idea what you want? The example I gave would be fun, but there are more serious mashups possible through InChIs. All the moieties should have InChIs and if you don’t find what you want contact me or Nick (ned24).

  3. Rich Apodaca says:

    Here’s the search I used:
    As of today there was no link to the service. Strange. Still, many thanks for the link to CrystalEye.

  4. What I would love to see is GoogleChemSpace… browse chemical space just like GoogleEarth… Using non-linear mapping techniques we can easily do that, such as (supervised) self-organizing maps… I only have not worked out yet the coordinate space… the downside of NLM and SOMs, is that the coordinate system changes each time you train the map.
    The UCC group in particular has recently written several reviews on this issue, and the closely related similarity (distance in the coordinate system) in particular…
    Four beers for the one who solves this problem. (Oh, and I throw in the Nobel price too…)

  5. Egon – I was talking recently about building some form of Chemical Map using the CHemSPider database as the training ground. It would be a significant undertaking and one that we might get to if we had time. usually we know HOW we would do something but don’t have the resources. In this case we have both challenges…not sure how AND not resourced. There are simply too many higher priorities in order for us to stay on mission of building community. That said, this does remain of interest but I’m not sure I’d watch us on this one. I prefer to under commit and over deliver rather than vice versa.

  6. Peter, as I mentioned to you earlier, I think many of us are looking for the open data in Crystal Eye, particularly fragments. Surely there’s an easier and more efficient way to get the data than AtomPP feeds. Will you have periodic dumps — say I get this quarter’s crystal structures and then can use the AtomPP feeds to just pull new entries?

  7. pm286 says:

    (3) Rich – your search works for me. Maybe this is locale-dependent

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