Rich Matlab client at BioinformaticStation.org

The recent development of a query language for automated interaction with S3DB, designated as S3QL, has enabled the development of client applications with rich graphic capabilities. Taking advantage of Matlab's new compiler toolbox, such a prototype is being developed at BioinformaticStation.org. A dedicated Blogger at BioinformaticStation.blogspot.com discusses this further and the S3DB related bits will be collected here.

RDF problem/solution

The Resource Description Framework is a tool to represent graphics by enabling description of triplets - two related concepts and the nature of their relatioship. It was due to this simplicity that it was chosen to represent S3DB statements. The permissiveness of vocabularies to describe particular pieces of level specific information by S3DB indexes and the graphical nature of RDF complement each other. Thus, we see in RDF the ideal platform where domain specific vocabularies, loosely coupled nomeclatures for emerging technologies and even lab jargon can be thrown in the same bucket of knowledge.

The challenge, thus, is developing a comprehensive representation of the slowly evolving, often shifting data models. Although this could be accomplished by representing the model in XML (and indeed there is a module in S3DB that enables this approach), we are seeking a more flexible approach, one which does not impose a hierarquical structure or even the determination of classes and subclasses. RDF, coupled with RDF Schema for description of the few controlled vocabularies and relashioships needed to make the model usefull and functional on S3DB seem to provide a good solution.

RDF export/import

A project in S3DB can be exported in the RDF/N3 format (w3c Notation 3 definition), the more "readable" version of RDF.

For an example of the nomenclature used for exporting ontologies, see N3 example or the RDF/XML convertion. #R, #V and #S refer to resources, rules and statements on S3DB. Similarly, #P refers to a project on S3DB (check out our paper for the definition of what each of these are).

How to read the RDF?
This RDF annotates data to the indexing schema, therefore each element can be backtracked to other elements in the document. In reality, this example carries only 6 statements, the first six lines. The rest of the document has information regarding the "metadata" needed to describe those 3 statement indexes.

The best way to understand this example is on the interface visualization of the "Example Project" in the demo.
Try adding a "House" and properties of that house, for example, adding a "Location" and an "Ocupant". If you export the RDF (Example Project/Export project in RDF), you can clearly see what changed in the statements.

S3DB paper comes out

The description of the indexing schema behind S3DB has been published on Nature Biotechnology this week. It describes the sources of inspiration and the ideas involded in the creation of S3DB: Data integration gets "Sloppy"

Interface

Some changes in the interface have been made, namely the project management page, which now includes several options.

Import from excel

The bugs on importing data from an excel spreadsheet have been fixed.

Debugging Status

The following modules of s3db are being updated:

- Sharing resources in different projects.
- Import from RDF
- Import from excel

Towards Data integration

A new feature has been created on the import module of S3DB. Import now validates UID and finds the appropriate information on it.
Try it at the demo.

Source code release

The source code that involves the project tree improvements has already been released in Sourceforge. A couple of bugs involving postgres compatibility ha also been resolved. Try our demo an report to us any bugs you might come into, comments from S3DB users are highly appreciated and in fact the best way to improve S3DB!

Demo relocation

The s3db demo has been relocated.
It now runs on a faster, more realiable linux machine! The link through s3db.org still works.

Improvements on project tree

It is now possible to create resources and rules directly on the project tree.
This is part of the interface improvement that will save at least 6 un-necessary clicks.

S3DB has been released

The first version of S3DB has been released at s3db.sourceforge.net
Is is also accessible through S3DB.org , where we currently have a demo version running.