1. 1 Simple Rules for a Tool and Data Ontology Barry Smith

2. 2 is_a (sensu MeSH) (?) MeSH Descriptors Index Medicus Descriptor Anthropology, Education, Sociology and Social Phenomena (MeSH Category) Social Sciences Political Systems National Socialism National Socialism is_a Political Systems National Socialism is_a Anthropology National Socialism is_a MeSH Descriptors

3. 3 is_a (sensu OBO-RO) A is_a B =Def every instance of A is an instance of B instances are real-world examples, e.g. actual software tools, actual bodies of data,...

4. 4 Three kinds of relations Mary’s heart part_of Mary Mary’s heart instance_of heart human heart part_of human

5. 5 Data –Clinical InformationClinical Information Aggregate Human Data Individual Human Data Nonhuman Data –Experimental DataExperimental Data Gene-Phenotype Association DB Medical Images DB Molecular Interaction DB –OntologiesOntologies

6. 6 Rules on terms Terms should be in the singular ontologies is_a data

7. 7 Dissemination –Interactive Web-Based ToolsInteractive Web-Based Tools –PublicationPublication –Training CoursesTraining Courses –Web PostingsWeb Postings –publication is_a dissemination –interactive web-based tools is_a dissemination

8. 8 Dissemination Terms should be count nouns interactive web-based tools is_a dissemination

9. 9 Tools –Analysis and ModelingAnalysis and Modeling –Data ManagementData Management –Ontology Development and ManagementOntology Development and Management

10. 10 Tools –Analysis and ModelingAnalysis and Modeling EDA Feature Analysis Genomic & Phenotypic Data Analysis Image Processing (2 instances)Image Processing(2 instances) Network characterization Pre-Processing Regulatory/Signaling network reconstruction Sequence Annotation Simulation Software Engineering and Development Tools Statistical Analysis Structure-based protein classification Toolkits (4 instances)Toolkits(4 instances) User and developer documentation Visualization

11. 11 Analysis and Modeling avoid terms with ‘and’ or ‘or’ or ‘and/or’

12. 12 Analysis and Modeling EDA Feature Analysis –Shape AnalysisShape Analysis »Pattern RecognitionPattern Recognition Genomic & Phenotypic Data Analysis Image Processing (2 instances)Image Processing(2 instances) –Atlas GenerationAtlas Generation –Cortical ModelingCortical Modeling –RegistrationRegistration –SegmentationSegmentation Network characterization Pre-Processing –Data TransformsData Transforms »Spectral TransformsSpectral Transforms »Fourier TransformFourier Transform »Wavelet TransformWavelet Transform –FilteringFiltering »Skull StrippingSkull Stripping »Inhomogeneity CorrectionInhomogeneity Correction

13. 13 Analysis and Modeling Regulatory/Signaling network reconstruction Sequence Annotation Simulation Software Engineering and Development Tools –Cross-LanguageWrapping (1 instance)Cross-LanguageWrapping(1 instance) –Cross-Platform Tools (2 instances)Cross-Platform Tools(2 instances) –IntegrationIntegration »Graphical e.g., HIVE PipelineGraphical e.g., HIVE Pipeline »Grid Computing ResourcesGrid Computing Resources »Mappers e.g., BrainGraph BrainMapperMappers e.g., BrainGraph BrainMapper »PortalsPortals »Resource Integration ComponentsResource Integration Components –Testing Tools (2 instances)Testing Tools(2 instances)

14. 14 Analysis and Modeling Integration is_a Software Engineering and Development Tools

15. 15 Analysis and Modeling Statistical Analysis –E.g., RE.g., R Structure-based protein classification Toolkits (4 instances)Toolkits(4 instances) User and developer documentation Visualization –Clinical Charts e.g., DemographicsClinical Charts e.g., Demographics –Graph ViewersGraph Viewers »Hyperbolic GraphsHyperbolic Graphs »Hierarchical TreesHierarchical Trees –ImagingImaging »Cross-Sectional ViewersCross-Sectional Viewers »Manifold Viewers 2D, 3D, 4D, NDManifold Viewers 2D, 3D, 4D, ND –SequencesSequences

16. 16 Tools –Data ManagementData Management Data Storage Data Transfer Information retrieval, traversal and querying –Ontology Development and ManagementOntology Development and Management Data Annotation Ontology Development Ontology Diff and Alignment Ontology Visualization Programmatic Access Web Access

17. 17 Don’t be afraid to write down what seems trivial data management is_a tools data management tool is_a tool