Intelligence Ontology A Strategy for the Future Barry Smith University at Buffalo

ncor national center for ontological research

ncor national center for ontological research The goal of NCOR is to advance ontological research and applications by promoting the creation and use of high quality ontologies. It thus supports the development of metrics for ontology evaluation designed to bring about an evolutionary improvement in ontology quality. NCOR serves as a vehicle to coordinate, to enhance, to publicize, and to seek funding for ontology- related activities in fields such as scientific research, intelligence analysis and multisource information fusion, qualitative spatiotemporal reasoning, and terminological systems. It organizes conferences and research groups focusing on specific aspects of ontology development, facilitates the exchange of research personnel for short- and long-term visits, and participates in nationally and internationally funded research networks.

OIC-2007 Proceedings: Volume 299 OIC-2007 ONTOLOGY FOR THE INTELLIGENCE COMMUNITY towards effective exploitation and integration of intelligence resources NOVEMBER 28-29, 2007 · COLUMBIA, MD

ECOR – European Center for Ontological Research JCOR – Japanese Center for Ontological Research Inaugural meeting in Tokyo, February 26-27, 2008

NCOR Science-based ontology evaluation to create an evolutionary path towards ontology improvement Ontology interoperability Promotion of best practice

7 The problem we face in biology...

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9 where in the body? where in the cell? what kind of disease process? how was the data collected?

10 ontologies = high quality controlled structured vocabularies for the annotation (description) of data

11 annotating images

MouseEcotope GlyProt DiabetInGene GluChem sphingolipid transporter activity The OBO Foundry Idea

MouseEcotope GlyProt DiabetInGene GluChem Holliday junction helicase complex The OBO Foundry Idea

MouseEcotope GlyProt DiabetInGene GluChem sphingolipid transporter activity The OBO Foundry Idea

Broad-coverage semantic annotation systems which will enable intelligent integration of gigantic bodies of heterogeneous data need to be created also outside biology.

geospatial transport religion weather ethnicity chemicals politics law using common rules drawing on best practices for creating ontologies... and for linking ontologies In areas such as:

geospatial transport religion weather ethnicity chemicals politics law exploiting the division of labor relying on champions in dispersed communities to invest in public- domain resources

We will also need: ontology of documents ontology of provenance ontology of names ontology of numbers (IDs) ontology of signatures ontology of identity...

OntologyScopeURLCustodians Cell Ontology (CL) cell types from prokaryotes to mammals obo.sourceforge.net/cgi- bin/detail.cgi?cell Jonathan Bard, Michael Ashburner, Oliver Hofman Chemical Entities of Bio- logical Interest (ChEBI) molecular entitiesebi.ac.uk/chebi Paula Dematos, Rafael Alcantara Common Anatomy Refer- ence Ontology (CARO) anatomical structures in human and model organisms (under development) Melissa Haendel, Terry Hayamizu, Cornelius Rosse, David Sutherland, Foundational Model of Anatomy (FMA) structure of the human body fma.biostr.washington. edu JLV Mejino Jr., Cornelius Rosse Functional Genomics Investigation Ontology (FuGO) design, protocol, data instrumentation, and analysis fugo.sf.netFuGO Working Group Gene Ontology (GO) cellular components, molecular functions, biological processes Ontology Consortium Phenotypic Quality Ontology (PaTO) qualities of anatomical structures obo.sourceforge.net/cgi -bin/ detail.cgi? attribute_and_value Michael Ashburner, Suzanna Lewis, Georgios Gkoutos Protein Ontology (PrO) protein types and modifications (under development)Protein Ontology Consortium Relation Ontology (RO) relationsobo.sf.net/relationshipBarry Smith, Chris Mungall RNA Ontology (RnaO) three-dimensional RNA structures (under development)RNA Ontology Consortium Sequence Ontology (SO) properties and features of nucleic sequences song.sf.netKaren Eilbeck

20 CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Organism-Level Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Cellular Process (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) The OBO Foundry obofoundry.org GRANULARITY RELATION TO TIME

Ontologies facilitate grouping of annotations brain 20 hindbrain 15 rhombomere 10 Query brain without ontology 20 Query brain with ontology 45

All OBO Foundry ontologies work in the same way we have data (biosample, haplotype, clinical data, survey data,...) we need to make this data available for semantic search and algorithmic processing we create a consensus-based ontology for annotating the data

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to enhance alignment of data about instances (communities, places,...)

Community / Population Ontology family, clan ethnicity religion diet social networking education (literacy...) healthcare (economics...)... household forms demography public health

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Family, Community, Deme, Population Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO)

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT COMPLEX OF ORGANISMS Family, Community, Deme, Population Organ Function (FMP, CPRO) Population Phenotype Population Process ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO)

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT COMPLEX OF ORGANISMS Family, Community, Deme, Population Organ Function (FMP, CPRO) Population Phenotype Population Process ORGAN AND ORGANISM Organism (NCBI Taxonomy) (FMA, CARO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cell Com- ponent (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) E N V I R O N M E N T

OBO Foundry Genomic Standards Consortium National Environment Research Council (UK) Barcode of Life Project Encyclopedia of Life Project The Environment Ontology

Applications of EnvO in Biology  Support the annotation of meta-data related to:  Data about biological samples produced from various technologies Metagenomics, Metabolomics, Proteomics, Transcriptomics, Genomics...  Data Produced from remote sensing equipment  Images Web 2.0, tagging  Physical holdings Museum artifacts, (preserved) biological samples / organisms ...anything that has an environment

How EnvO currently works for information retrieval Retrieve all experiments on organisms obtained from: deep-sea thermal vents arctic ice cores rainforest canopy alpine melt zone Retrieve all data on organisms sampled from: hot and dry environments cold and wet environments a height above 5,000 meters Retrieve all the omic data from soil organisms subject to: moderate heavy metal contamination

Environment = totality of circumstances external to a living organism or group of organisms pH evapotranspiration turbidity available light predominant vegetation predatory pressure nutrient limitation …

extend EnvO to the clinical domain  neighborhood patterns built environment, living conditions climate social networking crime, transport education, religion, work health, hygiene  disease patterns bio-environment (bacteriological,...) patterns of disease transmission (links to IDO)

works in tandem with GAZ.obo: An Open Source Gazetteer Constructed on Ontological Principles The Environment Ontology