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

national center for ontological research

OIC 2007: Ontology for the Intelligence Community Volume 299 3

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

Science-based ontology evaluation to create an evoluationary path towards ontology improvement Ontology interoperability 5

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MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDR KRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPIPSKYLIPKKINLMVYTLFQVHTLKFNRKDYDTL SLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYM FLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRA CALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCAC TARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTR RIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDP NQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGS RFETDLYESATSELMANHSVQTGRNIYGVDSFSLTSVSGTTATLLQERASERWIQWLGLESDYHCS FSSTRNAEDVVAGEAASSNHHQKISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDLHQLRLCYEI YMADTPSVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGCLNVAPV RNFIEEGYDGVTDLYVGIYDDLASTNFTDRIAAWENIVECTFRTNNVKLGYLIVDEFHNFETEVYRQS QFGGITNLDFDAFEKAIFLSGTAPEAVADAALQRIGLTGLAKKSMDINELKRSEDLSRGLSSYPTRMF NLIKEKSEVPLGHVHKIRKKVESQPEEALKLLLALFESEPESKAIVVASTTNEVEELACSWRKYFRVV WIHGKLGAAEKVSRTKEFVTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLRDGG LCYLLSRKNSWAARNRKGELPPKEGCITEQVREFYGLESKKGKKGQHVGCCGSRTDLSADTVELIE RMDRLAEKQATASMSIVALPSSFQESNSSDRYRKYCSSDEDSNTCIHGSANASTNASTNAITTAST NVRTNATTNASTNATTNASTNASTNATTNASTNATTNSSTNATTTASTNVRTSATTTASINVRTSATT TESTNSSTNATTTESTNSSTNATTTESTNSNTSATTTASINVRTSATTTESTNSSTSATTTASINVRTS ATTTKSINSSTNATTTESTNSNTNATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSAATTESTN SNTSATTTESTNASAKEDANKDGNAEDNRFHPVTDINKESYKRKGSQMVLLERKKLKAQFPNTSEN MNVLQFLGFRSDEIKHLFLYGIDIYFCPEGVFTQYGLCKGCQKMFELCVCWAGQKVSYRRIAWEAL AVERMLRNDEEYKEYLEDIEPYHGDPVGYLKYFSVKRREIYSQIQRNYAWYLAITRRRETISVLDSTR GKQGSQVFRMSGRQIKELYFKVWSNLRESKTEVLQYFLNWDEKKCQEEWEAKDDTVVVEALEKG GVFQRLRSMTSAGLQGPQYVKLQFSRHHRQLRSRYELSLGMHLRDQIALGVTPSKVPHWTAFLSM LIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDG RFDILLCRDSSREVGE 7

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

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

10 annotating images

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12 The OBO Foundry Idea MouseEcotope GlyProt DiabetInGene GluChem sphingolipid transporter activity

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

14 how create broad-coverage semantic annotation systems which will enable intelligent integration of gigantic bodies of heterogeneous data?

15 for science geospatial transport religion weather bacteria chemicals politics law use common rules drawing on best practices for creating ontologies... and for linking ontologies

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

17 ontology of documents ontology of provenance ontology of names ontology of numbers (IDs) ontology of signatures ontology of identity...

18 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

19 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 20

21 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,...) 26

Community / Population Ontology 27 − family, clan − ethnicity − religion − diet − social networking − education (literacy...) − healthcare (economics...) − household forms − demography − public health −...

28 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)

29 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)

30 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

The Environment Ontology 31 OBO Foundry Genomic Standards Consortium National Environment Research Council (UK) Barcode of Life Project Encyclopedia of Life Project

32 Applications of EnvO in biology

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 33

Environment = totality of circumstances external to a living organism or group of organisms –pH –evapotranspiration –turbidity –available light –predominant vegetation –predatory pressure –nutrient limitation … 34

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) 35

EnvO GAZ.obo: An Open Source Gazetteer Constructed on Ontological Principles oxford.ac.uk/gc_wiki/index.php/EnvO_Project 36