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I have found a need for a standardization for storage and recording of data relating to diabetes information (I don't think there's any, but I may have missed it).

To that end I made this github project because I want to create one.. but I don't really know how to go about it, or even for sure what I want to create is called.

Do I need to pick a language (xml, json) or a database type (mongo, sqlite, mysql), or how 'unspecific' is possible with something like this.

Is a data format as I describe here a thing? Are there other names for what I want to try to do? It's a bit of a strange task to accomplish compared to what I'm used to.

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Pick JSON; create a data schema (this could be changed) and push to MongoDB. My preferred choice is MongoEngine for Python. Else, you can use HDF5 (its a self-explanatory data model) but you must represent your data in hierarchical arrays. – Ubermensch Aug 24 '12 at 5:19
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What kind of data do you want to manage? Have you looked at at HL7(v3)? Might be quite overkill but it's an "e-healthcare" standard. – ysdx Aug 24 '12 at 19:48
I want to get pretty nitty gritty covering the stuff recorded by glucometers, insulin pumps, as well as continuous blood monitoring systems, which at root is generally insulin application and glucose reading, but it needs to be tied to a device as well, and it ought to track settings on the device and settings changes. I'll look into HL7, though.. I'm very much on the outside as far as ehealthcare, bc not sure where the inside is.. – Damon Aug 24 '12 at 23:09

3 Answers

up vote 3 down vote

Have you found a need for a standardized format, or just a format?

The need for a standardized format really only arises when you want to make data available to multiple clients, and want to enable other providers to provide data as well. In that case, you need to discuss this with all the interested organizations and mutually come up with a good, all-covering data specification.

Any data format sufficiently specified can be called a 'standard'. However, it's only when it becomes widely adopted that it is truly a standard.

Anyway, the data specification will need to be unambiguous, easy to implement, robust, possibly versioned, and probably more.

Then you need to lobby to have major organizations or lots of people use your format, forcing the rest of the world to also use the format.

Congratulations, you've introduced a standard!

Obligatory:

http://xkcd.com/927/

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up vote 1 down vote

Don't use XML or Mr. Atwood will find and destroy you. All kidding aside, JSON could be used, and can be loaded, manipulated, and saved out from a variety of tech these days, such as with Javascript (JQuery) on web pages. JQuery can load a file hosted on a remote URL, the result from a web service API URI, parse it into Javascript objects, save it back out to disk or send results off to other places. Ubermensch mentions above that MongoDB can load from JSON, but you could just as easily create your own web service (REST or SOAP) that takes JSON via HTTP POST and then stores it in any database system you want. He also mentions that you can create a data schema, but I'm not sure if there exists something as easy to validate with as an XML Schema Definition (XSD) and the various more robust tools around that older tech. So one advantage to using XML would be to create an XSD and publish it, and various editing tools could load that and understand how to give you "code-completion" (Visual Studio's IntelliSense, for example) and in-line validation. Another technology to consider to making accessing the data standardized would be OData, so if you did have a web service in front of your data warehouse you could expose it to people for querying in a secure fashion.

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Mr. Atwood isn't the God Of Programming. Not everything he says is correct. XML is a tool like any other, it can be used well or abused. Use it if it's appropriate. – GordonM Aug 24 '12 at 6:40
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Yes, that's why I said, "All kidding aside.." Did you finish reading what I wrote? I suggested XML... – Matt Kerr Aug 24 '12 at 6:46
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In this case Atwood's argument is basically what I just said, it's a tool that can be used or abused. It looks like you misunderstood the article's intent and just used it as an argument to not use XML at all. And in answer to your question, I found your reply hard to read because it's just one long paragraph. You might want to break it down into paragraphs. And if you're not against XML you might not want to put a blanket "don't use XML" remark at the top and then say that actually it's OK near the bottom, put those two statements closer together. – GordonM Aug 24 '12 at 6:49
up vote 0 down vote

At first, you need to define an ontology: what are the "things" that need representation in your problem domain, what are their properties, how do they link together? If you're trying to define a general standard for sharing data, then your ontology needs to cover any of the cases that could come up in a rather broad collection of scenarios.

Once you've got that semantic bit out of the way, the next part is comparatively simple: just define a data format that can express all of the above :-). Seriously, choosing the technology to represent the problem domain is going to be much less problematic than unambiguously expressing the problem in the first place.

This is definitely "the hard bit" with medical data, where multiple existing practices and techniques already exist: where someone has recorded that treatment was started, have they given you the calendar date, or the number of days after diagnosis, or the number of days after symptoms were first presented? Which of those is important? Can you "standardise" that into a single representation in all cases?

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