Internet Analysis Tools Registry (IATR)

A Public Resource for Image Analysis ToolsAND

An Instance of an Ontology Problem

Center for Morphometric Analysis, MGH/HMS

Athinoula A. Martinos Center for Biomedical Imaging, HST/MGH/MIT

David N. Kennedy

Overview

IATR Website Review

Existing Tool ‘Proto-Ontology’ (i.e. keywords)

Proposed Expanded Tool Ontology

Now what???

See also: Kennedy & Haselgrove, The Internet Analysis Tools Registry: A Public Resource for Image Analysis, Neuroinformatics, In Press, 2006.

See Preprint at:http://na-mic.org/Wiki/index.php/SDIWG:NCBC_Software_Classification#IATR

IATR Homehttp://www.cma.mgh.harvard.edu/iatr

IATR

Example Tool Description

Issues:Keeping up to date Application List Contact URLs Platforms etc.

Completeness

IATR Schema

Tool DescriptionFramework

Information Category Description

Name Name of the tool.

Byline Short institutional or laboratory attribution for tool source (i.e. the tool NIH Image is attributed to the Research Service Branch, NIMH).

Description Brief description of the tool functions and purpose.

NIfTI-1 Support A description of how the NIfTI-1 image data format is supported, if applicable.

Creator Name of person, group or institution claiming credit for the creation of the tool.

Contact Email contact information to o btain information about the tool.

URL Tool website.

Availability Indication regarding the availability of the tool to the public.

How to get Instructions regarding how to obtain the tool.

Current Vers ion Current software release version of the tool (i.e. the tool NIH Image is in version 1.63 at the time of this writing).

Current Vers ion Release Date Release date for the current software version (i.e. the current version of the tool NIH Image was released on November 19, 2002).

Open Source? Indication of whether the tool is open source.

License Indication of what license the tool and/or source code is distributed under, if any.

Available Free of Charge? Indication of whether there is a cost to obtaining the tool.

Requirements Requirements for tool use. Includes special hardware or software dependencies.

Technical Publications Listing of publications regarding the technological background of the tool.

Application Publications Listing of publications indicative of applications of the tool.

Other Information Free text field to provide any additional information the tool developer deems appropriate.

Keywords A selection of system supplied keywords to categ orize the types of functions that the tool is designed to perform. User-supplied keywords are permitted to cover functions not included in the system-supplied keyword list.

Platforms System supplied check list of the platform(s) that the tool will run under.

Current System-Supplied Tool Function Keywords

• Atlas: Delivers an atlas or supports atlas-based

interpretation of images.• Functional: Supports functional image analysis.

• Microscopy: Supports analysis of microscopy images.• Registration: Supports image registration.• Surface analysis: Supports surface-based analysis• Statistical: Supports statistical inference and analysis.

• Segmentation: Supports segmentation analysis.• Visualization: Provides a significant visualization capability.

• Volume: A tool that provides volumetric analysis.

• Warping: Supports warping spatial transformations.

Tool Function Keywords

Keyword Count Source

visualization 92 Primary volume 59 Primary functional 46 Primary statistical 43 Primary segmentation 42 Primary registration 37 Primary HBP supported 32 Primary surface analysis 23 Primary atlas 21 Primary warping 18 Primary microscopy 15 Primary API 4 User DICOM 3 User reconstruction 3 User alignment 2 User Daemon 2 User deconvolution 2 User diffusion 2 User fiber tracking 2 User perfusion 2 User region of interest 2 User resampling 2 User ROI 2 User stereology 2 User Talairach 2 User

Towards a Software Tool Ontology

• Image is_a type• DerivedImage instance_of Image• DerivedImage created_from Image• DerivedImage created_by SoftwareTool

• SoftwareTool has_a tool_creator• has_a tool_function• has_a operating_system• has_a funding_source• etc.

Towards a Software Tool Ontology

• ImageEntity (ImageFeature) is_a type• ImageEntity created_from Image• ImageEntity created_by AnalysisProcess

• Observation (or Finding) created by AnalysisProcess

• SoftwareTool instance_of AnalysisProcess

• RadiologicalRead instance_of AnalysisProcess

Towards a Software Tool Ontology

• 3DSlicer instance_of SoftwareTool• BWH instance_of tool_creator• Visualization instance_of tool_function

• NCBC_NA-MIC instance_of funding_source

• Linux instance_of operating_system

• 3DSlicer has_function Visualization• has_creator BWH• has_funding NCBC_NA-MIC• has_operating_system Linux

ProposedToolDescriptionHierarchy

ProposedToolDescriptionHierarchy

ProposedToolDescriptionHierarchy

ProposedToolDescriptionHierarchy

ProposedToolDescriptionHierarchy

Now What???

• Community Vetting• Integration w/ Other Efforts• Compliance/Usability Issues• Other Issues

DraftOntologyFrom Rubin, Musen, Dinov, et al.of the SDIWG