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Posted to user@couchdb.apache.org by "Kevin R. Coombes" <ke...@gmail.com> on 2012/04/09 16:34:32 UTC
formal database schema?
Hi,
We just had a manuscript that describes three applications of CouchDB in
bioinformatics accepted with minor revisions. (I think this will be
the first paper describing a CouchDB application in the area of
bioinformatics.)
One of the requested minor changes is for "schematics, data models,
etc". I'm sure that the reviewer is thinking about the kinds of schema
diagrams that can easily be supplied for a relational database. Other
than a table or a screenshot showing the reviewer what a typical
document looks like in these databases, does anyone know of equivalent
tools or diagrams to describe a document-oriented database? Are there
any (formal) design or document conventions that have evolved or are
evolving for describing databases built using Couch?
Kevin
In case anyone wants to take a look at the applications, here are the URLs:
geneSmash
http://app1.bioinformatics.mdanderson.org/genesmash/_design/basic/index.html
drugBase
http://app1.bioinformatics.mdanderson.org/drugbase/_design/basic/index.html
HapMap-CN
http://app1.bioinformatics.mdanderson.org/hapmap/_design/basic/index.html
Re: formal database schema?
Posted by "Kevin R. Coombes" <ke...@gmail.com>.
That was the sort of table I had in mind in my initial question. I've
thought about adding an extra column that indicates which fields are
used as keys for which views.
On 4/9/2012 12:43 PM, Paul Davis wrote:
> There's really not much in the way of a formal definition/diagram for
> JSON documents. If I were going to try and mollify a reviewer I'd
> probably generate a three column table with a key/path column, type,
> and intent.
>
> Also, in a pinch, UML isn't necessarily a bad way to try and show such
> things as long as you have explanatory text describes some of the
> assumptions that change since its non-relational.
>
> On Mon, Apr 9, 2012 at 1:34 PM, Kevin R. Coombes
> <ke...@gmail.com> wrote:
>> Hmm. This _might_ be what I want, even though my immediate reaction is that
>> it may be too self-referential to send back to the reviewer. (Is JSON
>> really the write language/format in which to describe JSON documents?) But
>> it's a start; thanks.
>> Kevin
>>
>>
>> On 4/9/2012 9:41 AM, Jeroen Janssen wrote:
>>> Hi,
>>>
>>> Not sure if this is what you are looking for, but there is a draft
>>> JSON schema specification at http://json-schema.org/ which is "a JSON
>>> based format for defining the structure of JSON data".
>>>
>>> Best regards,
>>>
>>> Jeroen
>>>
>>> On Mon, Apr 9, 2012 at 4:34 PM, Kevin R. Coombes
>>> <ke...@gmail.com> wrote:
>>>> Hi,
>>>>
>>>> We just had a manuscript that describes three applications of CouchDB in
>>>> bioinformatics accepted with minor revisions. (I think this will be the
>>>> first paper describing a CouchDB application in the area of
>>>> bioinformatics.)
>>>>
>>>> One of the requested minor changes is for "schematics, data models, etc".
>>>> I'm sure that the reviewer is thinking about the kinds of schema
>>>> diagrams
>>>> that can easily be supplied for a relational database. Other than a
>>>> table
>>>> or a screenshot showing the reviewer what a typical document looks like
>>>> in
>>>> these databases, does anyone know of equivalent tools or diagrams to
>>>> describe a document-oriented database? Are there any (formal) design or
>>>> document conventions that have evolved or are evolving for describing
>>>> databases built using Couch?
>>>>
>>>> Kevin
>>>>
>>>> In case anyone wants to take a look at the applications, here are the
>>>> URLs:
>>>>
>>>> geneSmash
>>>>
>>>>
>>>> http://app1.bioinformatics.mdanderson.org/genesmash/_design/basic/index.html
>>>> drugBase
>>>>
>>>>
>>>> http://app1.bioinformatics.mdanderson.org/drugbase/_design/basic/index.html
>>>> HapMap-CN
>>>>
>>>> http://app1.bioinformatics.mdanderson.org/hapmap/_design/basic/index.html
>>>>
Re: formal database schema?
Posted by Paul Davis <pa...@gmail.com>.
There's really not much in the way of a formal definition/diagram for
JSON documents. If I were going to try and mollify a reviewer I'd
probably generate a three column table with a key/path column, type,
and intent.
Also, in a pinch, UML isn't necessarily a bad way to try and show such
things as long as you have explanatory text describes some of the
assumptions that change since its non-relational.
On Mon, Apr 9, 2012 at 1:34 PM, Kevin R. Coombes
<ke...@gmail.com> wrote:
> Hmm. This _might_ be what I want, even though my immediate reaction is that
> it may be too self-referential to send back to the reviewer. (Is JSON
> really the write language/format in which to describe JSON documents?) But
> it's a start; thanks.
> Kevin
>
>
> On 4/9/2012 9:41 AM, Jeroen Janssen wrote:
>>
>> Hi,
>>
>> Not sure if this is what you are looking for, but there is a draft
>> JSON schema specification at http://json-schema.org/ which is "a JSON
>> based format for defining the structure of JSON data".
>>
>> Best regards,
>>
>> Jeroen
>>
>> On Mon, Apr 9, 2012 at 4:34 PM, Kevin R. Coombes
>> <ke...@gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> We just had a manuscript that describes three applications of CouchDB in
>>> bioinformatics accepted with minor revisions. (I think this will be the
>>> first paper describing a CouchDB application in the area of
>>> bioinformatics.)
>>>
>>> One of the requested minor changes is for "schematics, data models, etc".
>>> I'm sure that the reviewer is thinking about the kinds of schema
>>> diagrams
>>> that can easily be supplied for a relational database. Other than a
>>> table
>>> or a screenshot showing the reviewer what a typical document looks like
>>> in
>>> these databases, does anyone know of equivalent tools or diagrams to
>>> describe a document-oriented database? Are there any (formal) design or
>>> document conventions that have evolved or are evolving for describing
>>> databases built using Couch?
>>>
>>> Kevin
>>>
>>> In case anyone wants to take a look at the applications, here are the
>>> URLs:
>>>
>>> geneSmash
>>>
>>>
>>> http://app1.bioinformatics.mdanderson.org/genesmash/_design/basic/index.html
>>> drugBase
>>>
>>>
>>> http://app1.bioinformatics.mdanderson.org/drugbase/_design/basic/index.html
>>> HapMap-CN
>>>
>>> http://app1.bioinformatics.mdanderson.org/hapmap/_design/basic/index.html
>>>
>
Re: formal database schema?
Posted by "Kevin R. Coombes" <ke...@gmail.com>.
Hmm. This _might_ be what I want, even though my immediate reaction is
that it may be too self-referential to send back to the reviewer. (Is
JSON really the write language/format in which to describe JSON
documents?) But it's a start; thanks.
Kevin
On 4/9/2012 9:41 AM, Jeroen Janssen wrote:
> Hi,
>
> Not sure if this is what you are looking for, but there is a draft
> JSON schema specification at http://json-schema.org/ which is "a JSON
> based format for defining the structure of JSON data".
>
> Best regards,
>
> Jeroen
>
> On Mon, Apr 9, 2012 at 4:34 PM, Kevin R. Coombes
> <ke...@gmail.com> wrote:
>> Hi,
>>
>> We just had a manuscript that describes three applications of CouchDB in
>> bioinformatics accepted with minor revisions. (I think this will be the
>> first paper describing a CouchDB application in the area of bioinformatics.)
>>
>> One of the requested minor changes is for "schematics, data models, etc".
>> I'm sure that the reviewer is thinking about the kinds of schema diagrams
>> that can easily be supplied for a relational database. Other than a table
>> or a screenshot showing the reviewer what a typical document looks like in
>> these databases, does anyone know of equivalent tools or diagrams to
>> describe a document-oriented database? Are there any (formal) design or
>> document conventions that have evolved or are evolving for describing
>> databases built using Couch?
>>
>> Kevin
>>
>> In case anyone wants to take a look at the applications, here are the URLs:
>>
>> geneSmash
>>
>> http://app1.bioinformatics.mdanderson.org/genesmash/_design/basic/index.html
>> drugBase
>>
>> http://app1.bioinformatics.mdanderson.org/drugbase/_design/basic/index.html
>> HapMap-CN
>> http://app1.bioinformatics.mdanderson.org/hapmap/_design/basic/index.html
>>
Re: formal database schema?
Posted by Jeroen Janssen <je...@gmail.com>.
Hi,
Not sure if this is what you are looking for, but there is a draft
JSON schema specification at http://json-schema.org/ which is "a JSON
based format for defining the structure of JSON data".
Best regards,
Jeroen
On Mon, Apr 9, 2012 at 4:34 PM, Kevin R. Coombes
<ke...@gmail.com> wrote:
> Hi,
>
> We just had a manuscript that describes three applications of CouchDB in
> bioinformatics accepted with minor revisions. (I think this will be the
> first paper describing a CouchDB application in the area of bioinformatics.)
>
> One of the requested minor changes is for "schematics, data models, etc".
> I'm sure that the reviewer is thinking about the kinds of schema diagrams
> that can easily be supplied for a relational database. Other than a table
> or a screenshot showing the reviewer what a typical document looks like in
> these databases, does anyone know of equivalent tools or diagrams to
> describe a document-oriented database? Are there any (formal) design or
> document conventions that have evolved or are evolving for describing
> databases built using Couch?
>
> Kevin
>
> In case anyone wants to take a look at the applications, here are the URLs:
>
> geneSmash
>
> http://app1.bioinformatics.mdanderson.org/genesmash/_design/basic/index.html
> drugBase
>
> http://app1.bioinformatics.mdanderson.org/drugbase/_design/basic/index.html
> HapMap-CN
> http://app1.bioinformatics.mdanderson.org/hapmap/_design/basic/index.html
>