ontology:OntologyNotes

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Ontology Notes

NITRC indexes Tools and Resources. We need to define what a tool and resource is; i.e. we need working definitions of these terms. We then need to define the characteristics of tools and resouces that are important for indexing the tools and resrouces in NITRC.

I guess for simplicity, until we define it better, a tool' is a type of resource, and restating the NITRC goal is to index fMRI Resources. Resources can be software (tools), websites, databases, etc. Some resources' may be of more than one type. But, to take this any further, we really need proper definitions of these terms, so that we know what we're talking about.

Definitions

Resource

A resource is "a source of supply, support, or aid, esp. one that can be readily drawn upon when needed." (from dictionary.com)

Wikipedia defines computer science resource as: http://en.wikipedia.org/wiki/Resource_%28computer_science%29

Software

Software is an executable entity of computer programing. Also, "The programs, routines, and symbolic languages that control the functioning of the hardware and direct its operation." And "The programs and instructions that run a computer, as opposed to the actual physical machinery and devices that compose the hardware." (dictionary.com)

This is contrasted with the hardware upon which software runs.

A software tool' is synonomous with software in my opinion.

Wikipedia says: http://en.wikipedia.org/wiki/Software

Other Resources

The non-software resources can be of many types.

Data Resources

A repository of data. Data can be raw data, images, processed data. fMRIDC and IBVD are examples of data resources.

Models

Specifically, computational modesl, or even more specifically, neurocomputational models are under the purview of NITRC. A model is a symbolic representation of the behaviour of a system (taken vaguely from http://en.wikipedia.org/wiki/Mathematical_model). The system of interest to us is the brain. ModelDB (http://senselab.med.yale.edu/senselab/ModelDB/) is an example database of computational neuroscience models that describe a number of neuroscience phenomena, such as neurons, receptors, transmitters, networks, synapses, junctions, axons and channels, etc. Models may, or may not, be actual software executables; they can be symbolic and/or descriptive parametric instructions for use in other software systems.

Web-based Resources

In contrast (or addition) to an executable software resource, some fMRI resources operate as websites or web-services. These are not tools that are run on the clients own computer, but rather some sort of URI that manages user input and provides information back (in either human or machine readable format).

Atlas

Wikipedia says: "An atlas is a collection of maps or manifolds, traditionally bound into book form, but also found in multimedia formats. (http://en.wikipedia.org/wiki/Atlas) Neuroimaging has latched upon this later concept, to provide various types of multimedia (2D, 3D, 4D images) of specific neural properties, such as structures, receptors, neuro anatomic, population probabilities, function, etc. properties of the brain. This is intimately connected to the specific space' that the atlas is created in. Human and other animals have numerous atlases available.

Database

Again, according to Wikipedia, "a database is a structured collection of records or data which is stored in a computer so that a program can consult it to answer queries. (http://en.wikipedia.org/wiki/Database)" For the purposes here, there are databases that are resources for the fMRI community; but these databases have various User Interfaces (UI), which may be web-based (website or webservice), or part of a software tool which mediates the interaction with the database.

Resource Characteristics

For each resource, the following set of characteristics can be defined:

User Interface (UI): can be command line, web-based, custom graphical, etc.

Operating System: The resource runs on a particular computer operating system; this is important for software tools, but less so for web-resources or other situations where the execution of the resources does not hppen locally.

Prefered Name (and acceptable synomyms):

Intended Users: this can be end users, other software developers, etc.

Supported Functionallity: this resources is intended to do the following things...

I/O expectations: The resources expects the following input and output options to be set by the user:

Supported file formats: when images are utilized as input or output, the following formats are supported...

Single/Multi Function: This resource is specific for a single (or limited) set of functions, or is multi-functional, supporting many diverse classes of operations.

Dependancies: web/internet access, matlab, etc.

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