Simple Rules for a Tool and Data Ontology

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

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. 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. Three kinds of relations <instance, instance> Mary’s heart part_of Mary <instance, type> Mary’s heart instance_of heart <type, type> human heart part_of human

5. Data • Clinical Information • Aggregate Human Data • Individual Human Data • Nonhuman Data • Experimental Data • Gene-Phenotype Association DB • Medical Images DB • Molecular Interaction DB • Ontologies

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

7. Dissemination • Interactive Web-Based Tools • Publication • Training Courses • Web Postings • publication is_a dissemination • interactive web-based tools is_a dissemination

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

9. Tools • Analysis and Modeling • Data Management • Ontology Development and Management

10. Tools • Analysis and Modeling • EDA • Feature Analysis • Genomic & Phenotypic Data Analysis • 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) • User and developer documentation • Visualization

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

12. Analysis and Modeling • EDA • Feature Analysis • Shape Analysis • Pattern Recognition • Genomic & Phenotypic Data Analysis • Image Processing(2 instances) • Atlas Generation • Cortical Modeling • Registration • Segmentation • Network characterization • Pre-Processing • Data Transforms • Spectral Transforms • Fourier Transform • Wavelet Transform • Filtering • Skull Stripping • Inhomogeneity Correction

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

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

15. Analysis and Modeling • Statistical Analysis • E.g., R • Structure-based protein classification • Toolkits(4 instances) • User and developer documentation • Visualization • Clinical Charts e.g., Demographics • Graph Viewers • Hyperbolic Graphs • Hierarchical Trees • Imaging • Cross-Sectional Viewers • Manifold Viewers 2D, 3D, 4D, ND • Sequences

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

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