Introduction to Ontologies for Environmental Biology
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Introduction to Ontologies for Environmental Biology

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Oxford, August 2007

Oxford, August 2007

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  • dir.niehs.nih.gov/ microarray/datamining/
  • dir.niehs.nih.gov/ microarray/datamining/
  • http://www.ags.gov.ab.ca/GRAPHICS/uranium/athabasca_group_map_with_legend.jpg
  • http://www.ags.gov.ab.ca/GRAPHICS/uranium/athabasca_group_map_with_legend.jpg
  • dir.niehs.nih.gov/ microarray/datamining/
  • dir.niehs.nih.gov/ microarray/datamining/
  • dir.niehs.nih.gov/ microarray/datamining/
  • http://www.pnas.org/misc/archive011904.html
  • http://www.pnas.org/misc/archive011904.html
  • http://www.pnas.org/misc/archive011904.html
  • Rome, Piazza Navona
  • Florence
  • Rome, Piazza Navona
  • http://www.sacsplash.org/cimages/Solitarybee.jpg
  • http://www.geobabble.org/~hnw/esri99/
  • http://www.geobabble.org/~hnw/esri99/
  • http://www.stankievech.net/projectsFrame.html
  • http://library.thinkquest.org/25896/images/blood/ingestion.jpg
  • www.biomedcentral.com/1471-230x/5/6/figure/F6

Introduction to Ontologies for Environmental Biology Introduction to Ontologies for Environmental Biology Presentation Transcript

  • Introduction to Ontologiesfor Environmental BiologyBarry Smithhttp://ontology.buffalo.edu/smith
  • 2Finnegans Webconcepttypeclassinstancemodelrepresentationdataprocessproperty
  • Disciplines here involvedGISEcologyEnvironmental biologyVarious -omics disciplinesBioinformaticsMedical InformaticsDatabase scienceSemantic webists...
  • 4Part 1: What is an Ontology?
  • 5what cellular component?what molecular function?what biological process?
  • 6natural language labelsdesigned for use in annotationsto make the data cognitivelyaccessible to human beingsand algorithmically tractableto computers
  • 7compare: legends for mapscompare: legends for maps
  • 8compare: legends for mapscommon legends allow (cross-border) integration
  • 9ontologies are legends for data
  • 10compare: legends for diagrams
  • Ramirez et al.Linking of Digital Images to Phylogenetic Data Matrices Using aMorphological OntologySyst. Biol. 56(2):283–294, 2007
  • 12computationally tractable legendshelp integrate complex representationsof realityhelp human beings find things incomplex representations of realityhelp computers reason with complexrepresentations of reality
  • ontologies are used to annotate data
  • but there are two kinds of annotations
  • 16names of types
  • 17names of instances
  • 18A basic distinctiontype vs. instancescience text vs. diaryhuman being vs. Michael Ashburner
  • 19A 515287 DC3300 Dust Collector FanB 521683 Gilmer BeltC 521682 Motor Drive BeltCatalog vs. inventory
  • 20Ontology types Instances
  • 21An ontology is a collection ofstandardized names for typesWe learn about types in reality from lookingat the results of scientific experimentscaptured in the form of scientific theoriesOntologies provide the terminologicalscaffolding of scientific theoriesexperiments relate to what is particularscience describes what is general
  • siamesemammalcatorganismthingtypesanimalinstancesfrog22
  • 23types vs. their extensionstypec,...} class of instances= a collectionsof particulars
  • 24Extension =defThe extension of a type A is the class ofinstances of A(the class of all entities to which the term ‘A’applies)
  • 25types vs. classestypes{c,d,e,...} classes
  • 26types vs. classestypesextensions ~ defined classes
  • 27Defined class =defmember of Abba aged > 50 yearspizza with > 4 different toppingsred wine to serve with fish
  • 28Part 2: The OBO Foundry
  • 29what cellular component?what molecular function?what biological process?
  • The Gene Ontology
  • The Gene Ontology
  • 32Five bangs for your GO buck1. based in biological science2. cross-species data comparability (human,mouse, yeast, fly ...)3. cross-granularity data integration(molecule, cell, organ, organism)4. cumulation of scientific knowledge inalgorithmically tractable form5. links people to software6. part of Open Biomedical Ontologies (OBO)The Gene Ontology
  • 33Entry point for creation of web-accessible biomedical dataGO initially low-tech to encourage usersSimple (web-service-based) toolscreated to support the work of biologistsin creating annotations (data entry)OBO  OWL DL converters nowmaking OBO Foundry annotated dataimmediately accessible to SemanticWeb data integration projects
  • The OBO FoundryA suite of high quality interoperablereference ontologies to serve theannotation of biomedical dataproviding guidelines for those who need tocreate new ontology resourceshttp://obofoundry.org
  • 35RELATIONTO TIMEGRANULARITYCONTINUANT OCCURRENTINDEPENDENT DEPENDENTORGAN ANDORGANISMOrganism(NCBITaxonomy)AnatomicalEntity(FMA, CARO)OrganFunction(FMP, CPRO) PhenotypicQuality(PaTO)Biological Process(GO)CELL ANDCELLULARCOMPONENTCell(CL)CellularComponent(FMA, GO)CellularFunction(GO)MOLECULEMolecule(ChEBI, SO,RnaO, PrO)Molecular Function(GO)Molecular Process(GO)The OBO Foundry building out from the original GO
  • Simple guidelines• use singular nouns• distinguish continuants from occurrents• distinguish things from their qualities• distinguish types from their instances• do not use the weasel word ‘concept’
  • 37 OPENNESS: The ontology is open and available to beused by all. FORMAL LANGUAGE: The ontology is in, or can beinstantiated in, a common formal language. ORTHOGONALITY: The developers of the ontologyagree in advance to collaborate with developers of otherOBO Foundry ontology where domains overlap. CONVERGENCE: The developers agree to worktorwards a single ontology for each domain.http://obofoundry.org/http://obofoundry.org/CRITERIA
  • 38 UPDATE: The developers of each ontology commit to itsmaintenance in light of scientific advance, and tosoliciting community feedback for its improvement. IDENTIFIERS: The ontology possesses a uniqueidentifier space within OBO. VERSIONING: The ontology provider has procedures foridentifying distinct successive versions. DEFINITIONS: The ontology includes textual definitionsfor all terms.CRITERIAhttp://obofoundry.org/http://obofoundry.org/
  • 39 CLEARLY BOUNDED: The ontology has a clearlyspecified and clearly delineated content. DOCUMENTATION: The ontology is well-documented. USERS: The ontology has a plurality of independentusers. COMMON ARCHITECTURE: The ontology uses relationswhich are unambiguously defined following the pattern ofdefinitions laid down in the OBO Relation Ontology.CRITERIAhttp://obofoundry.org/http://obofoundry.org/
  • 40Foundry ontologies all work in thesame wayall are built to represent the types existing in a pre-existing domain and the relations between thesetypes in a way which can support reasoning– we have data– we need to make this data available for semanticsearch and algorithmic processing– we create a consensus-based ontology for annotatingthe data– and ensure that it can interoperate with Foundryontologies for neighboring domains
  • 41Formal-Ontological Relationsis_apart_oflocated_atdepends_onis_boundary_ofadjacent_to
  • 42To support integration of ontologiesrelational expressions such asis_apart_of...should be used in the same way in allontologies involved
  • 43to define these relations properlywe need to take account of both typesand instances in reality
  • 44Kinds of relations<instance, type>: Toronto instance_ofcity<instance, instance>: Toronto part_ofOntario<type, type>: waterfall part_of river
  • 45is_ahuman is_a mammalall instances of the type human are as amatter of necessity instances of the typemammal
  • 46Karen Eilbecksong.sf.netproperties and features ofnucleic sequencesSequence Ontology(SO)RNA Ontology Consortium(under development)three-dimensional RNAstructuresRNA Ontology(RnaO)Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)Protein Ontology Consortium(under development)protein types andmodificationsProtein Ontology(PrO)Michael Ashburner, SuzannaLewis, Georgios Gkoutosobo.sourceforge.net/cgi-bin/ detail.cgi?attribute_and_valuequalities of biomedical entitiesPhenotypic QualityOntology(PaTO)Gene Ontology Consortiumwww.geneontology.orgcellular components,molecular functions,biological processesGene Ontology(GO)FuGO Working Groupfugo.sf.netdesign, protocol, datainstrumentation, and analysisFunctional GenomicsInvestigation Ontology(FuGO)JLV Mejino Jr.,Cornelius Rossefma.biostr.washington.edustructure of the human bodyFoundational Model ofAnatomy (FMA)Melissa Haendel, TerryHayamizu, Cornelius Rosse,David Sutherland,(under development)anatomical structures inhuman and model organismsCommon Anatomy Refer-ence Ontology (CARO)Paula Dematos,Rafael Alcantaraebi.ac.uk/chebimolecular entitiesChemical Entities of Bio-logical Interest (ChEBI)Jonathan Bard, MichaelAshburner, Oliver Hofmanobo.sourceforge.net/cgi-bin/detail.cgi?cellcell types from prokaryotesto mammalsCell Ontology(CL)CustodiansURLScopeOntology
  • 47Karen Eilbecksong.sf.netproperties and features ofnucleic sequencesSequence Ontology(SO)RNA Ontology Consortium(under development)three-dimensional RNAstructuresRNA Ontology(RnaO)Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)Protein Ontology Consortium(under development)protein types andmodificationsProtein Ontology(PrO)Michael Ashburner, SuzannaLewis, Georgios Gkoutosobo.sourceforge.net/cgi-bin/ detail.cgi?attribute_and_valuequalities of biomedical entitiesPhenotypic QualityOntology(PaTO)Gene Ontology Consortiumwww.geneontology.orgcellular components,molecular functions,biological processesGene Ontology(GO)FuGO Working Groupfugo.sf.netdesign, protocol, datainstrumentation, and analysisFunctional GenomicsInvestigation Ontology(FuGO)JLV Mejino Jr.,Cornelius Rossefma.biostr.washington.edustructure of the human bodyFoundational Model ofAnatomy (FMA)Melissa Haendel, TerryHayamizu, Cornelius Rosse,David Sutherland,(under development)anatomical structures inhuman and model organismsCommon Anatomy Refer-ence Ontology (CARO)Paula Dematos,Rafael Alcantaraebi.ac.uk/chebimolecular entitiesChemical Entities of Bio-logical Interest (ChEBI)Jonathan Bard, MichaelAshburner, Oliver Hofmanobo.sourceforge.net/cgi-bin/detail.cgi?cellcell types from prokaryotesto mammalsCell Ontology(CL)CustodiansURLScopeOntology
  • PleuralCavityPleuralCavityInterlobarrecessInterlobarrecessMesotheliumof PleuraMesotheliumof PleuraPleura(Wallof Sac)Pleura(Wallof Sac)VisceralPleuraVisceralPleuraPleural SacPleural SacParietalPleuraParietalPleuraAnatomical SpaceAnatomical SpaceOrganCavityOrganCavitySerous SacCavitySerous SacCavityAnatomicalStructureAnatomicalStructureOrganOrganSerous SacSerous SacMediastinalPleuraMediastinalPleuraTissueTissueOrgan PartOrgan PartOrganSubdivisionOrganSubdivisionOrganComponentOrganComponentOrgan CavitySubdivisionOrgan CavitySubdivisionSerous SacCavitySubdivisionSerous SacCavitySubdivisionFoundational Model of Anatomy
  • PleuralCavityPleuralCavityInterlobarrecessInterlobarrecessMesotheliumof PleuraMesotheliumof PleuraPleura(Wallof Sac)Pleura(Wallof Sac)VisceralPleuraVisceralPleuraPleural SacPleural SacParietalPleuraParietalPleuraAnatomical SpaceAnatomical SpaceOrganCavityOrganCavitySerous SacCavitySerous SacCavityAnatomicalStructureAnatomicalStructureOrganOrganSerous SacSerous SacMediastinalPleuraMediastinalPleuraTissueTissueOrgan PartOrgan PartOrganSubdivisionOrganSubdivisionOrganComponentOrganComponentOrgan CavitySubdivisionOrgan CavitySubdivisionSerous SacCavitySubdivisionSerous SacCavitySubdivisionpart_ofis_a
  • 50Mature OBO Foundry ontologiesnow undergoing reformCell Ontology (CL)Chemical Entities of Biological Interest (ChEBI)Foundational Model of Anatomy (FMA)Gene Ontology (GO)Phenotypic Quality Ontology (PaTO)Relation Ontology (RO)Sequence Ontology (SO)
  • 51Ontologies being built to satisfy Foundryprinciples ab initioOntology for Clinical Investigations (OCI)Common Anatomy Reference Ontology(CARO)Ontology for Biomedical Investigations (OBI)Protein Ontology (PRO)RNA Ontology (RnaO)Subcellular Anatomy Ontology (SAO)
  • 52Ontologies in planning phaseBiobank/Biorepository Ontology (BrO, part of OBI)Environment Ontology (EnvO)Immunology Ontology (ImmunO)Infectious Disease Ontology (IDO)Mouse Adult Neurogenesis Ontology (MANGO)
  • OBO Foundry Success StoryModel organism research seeks results valuable forthe understanding of human disease.This requires the ability to make reliable cross-species comparisons, and for this anatomy is crucial.But different MOD communities have developed theiranatomy ontologies in uncoordinated fashion.53
  • Ontologies facilitate grouping of annotationsbrain 20hindbrain 15rhombomere 10Query brain without ontology 20Query brain with ontology 4554
  • CARO – Common AnatomyReference Ontologyfor the first time provides guidelines for modelorganism researchers who wish to achievecomparability of annotationsfor the first time provides guidelines for thosenew to ontology workSee Haendel et al., “CARO: The Common Anatomy Reference Ontology”,in: Burger (ed.), Anatomy Ontologies for Bioinformatics: Springer, in press.55
  • 56CARO-conformant ontologiesalready in development:Fish Multi-Species Anatomy Ontology (NSF fundingreceived)Ixodidae and Argasidae (Tick) Anatomy OntologyMosquito Anatomy Ontology (MAO)Spider Anatomy OntologyXenopus Anatomy Ontology (XAO)undergoing reform: Drosophila and ZebrafishAnatomy Ontologies
  • Part 3The Hole Story
  • The Ontology of Environments
  • Initial hypothesis:Environments are holes
  • environmentplacesitenichehabitatsettingholespatial regioninteriorlocation
  • Places are holes
  • 66RELATIONTO TIMEGRANULARITYCONTINUANT OCCURRENTINDEPENDENT DEPENDENTORGAN ANDORGANISMOrganism(NCBITaxonomy)AnatomicalEntity(FMA, CARO)OrganFunction(FMP, CPRO) PhenotypicQuality(PaTO)Biological Process(GO)CELL ANDCELLULARCOMPONENTCell(CL)CellularComponent(FMA, GO)CellularFunction(GO)MOLECULEMolecule(ChEBI, SO,RnaO, PrO)Molecular Function(GO)Molecular Process(GO)No place for environments
  • A Neglected Major Category inOntologies thus farThings (e.g. organisms)Qualities / FeaturesFunctionsProcessesEnvironments = that into whichorganisms (etc.) fit
  • 68RELATIONTO TIMEGRANULARITYCONTINUANT OCCURRENTINDEPENDENT DEPENDENTORGAN ANDORGANISMOrganism(NCBITaxonomy)AnatomicalEntity(FMA,CARO)OrganFunction(FMP, CPRO) PhenotypicQuality(PaTO)BiologicalProcess(GO)CELL ANDCELLULARCOMPONENTCell(CL)CellularComponent(FMA, GO)CellularFunction(GO)MOLECULEMolecule(ChEBI, SO,RnaO, PrO)Molecular Function(GO)Molecular Process(GO)Environments are holes in whichorganisms, cells, molecules ... can liveenvironmentsarehere
  • Environments are holes
  • Double Hole Structure of theOccupied NicheMedium(filling the environing hole)Tenant(occupying the central hole)Retainer(a boundary ofsomesurrounding structure)
  • Tenant, medium and retainerthe medium of the bear’s niche is acircumscribed body of airmedium might be body of water, cytosol,nasal mucosa, epithelium, endocardium,synovial tissue ...
  • The Empty NicheFiat boundary Physical boundary
  • Two Types of BoundaryFiat boundary Physical boundary
  • Positive and negative partspositivepartnegativepartor hole(made of matter)(not madeof matter)
  • Four Basic Niche Types(Niche as generalized hole)1 2 3 41: a womb; an egg; a house (better: the interior thereof)2: a snail’s shell;3: the niche of a pasturing cow;4: the niche around a circling buzzard (fiat boundary)
  • Types of relations for EnvOinon (surface of)surroundslives_inattaches torealizesoccupies (spatial region)...
  • Lexical Semanticsthe fruit is in the bowlthe bird is in the nestthe lion is in the cagethe pencil is in the cupthe fish is in the riverthe river is in the valleythe water is in the lakethe car is in the garagethe fetus is in the cavity in the uterine liningthe colony of whooping crane is in its breeding grounds
  • Double Hole StructureMedium(filling the environing hole)Tenant(occupying the central hole)Retainer(a boundary ofsomesurrounding structure)when a tenant leaves its niche the gapleft by the tenant is filled immediatelyby the surrounding medium
  • A hole in the groundSolid physical boundaries at the floorand wallsbut with a fiat lid:hole
  • Part 4: Not every hole is anenvironment
  • An environment is a special kindof (generalized) holebut what kind?
  • Elton – niche as rolethe ‘niche’ of an animal meansits place in the biotic environment, itsrelations to food and enemies. [...]When an ecologist says ‘there goes abadger’ he should include in his thoughtssome definite idea of the animal’s place inthe community to which it belongs,just as if he had said ‘there goes the vicar’(Elton 1927, pp. 63f.)
  • G.E. Hutchinson: niche as volumein a functionally defined spacethe niche = an n-dimensional hyper-volume whose dimensions correspond toresource gradients over which species aredistributed
  • G.E. Hutchinson (1957, 1965)
  • Hypervolume niche = a locationin an attribute spacedefined by a specific constellation ofenvironmental variables such as degree ofslope, exposure to sunlight, soil fertility,foliage density, salinity...
  • Niche ConstructionLewontin: niches normally arise in symbiosiswith the activities of organisms or groups oforganisms (“ecosystem engineering”);they are not already there, like vacant rooms ina gigantic evolutionary hotel, awaiting organismswho would evolve into them. (The Triple Helix,Gene Organism, Environment)
  • Part Last: Bringing Together theSpatial and Functional Approachesto Environment OntologyThe environment is not a location in anattribute space, but it must have featureshave such location
  • Every environment must havesome spatial locationThe functional niche presupposes thespatial-structural nicheOntology of environment + ontology ofassociated environmental features
  • J. J. Gibson’s EcologicalPsychologyThe terrestrial environment is [best]described in terms of a medium,substances, and the surfaces thatseparate them. (Gibson 1979, p. 16)
  • Gibson’s theory of surface layout‘a sort of applied geometry that isappropriate for the study of perception andbehavior’ (1979, p. 33)ground, open environment, enclosure,detached object, attached object, hollowobject, place, sheet, fissure, stick, fiber,dihedral, etc.
  • Gibson’s theory of surface layoutas an anatomy of environments• systems of barriers, doors, pathways towhich the behavior of organisms isspecifically attuned,• temperature gradients, patterns ofmovement of air or water molecules• water holes, food sources (features)• apertures (mouths, sphincters ...)
  • Two sets of issuesEnvironments, as spatial structures, andtheir partsEnvironmental attributes (qualities,functions), determining multidimensionalloci à la Hutchinson
  • AimTo define structural properties such as:open, closed,connected, compact,spatial coincidence,integrity,aggregate,boundaryRCC (Region Connection Calculus) plusextensions
  • Ecological Niche Conceptsniche as particular place or subdivision of anenvironment that an organism orpopulation occupiesvs.niche as function of an organism orpopulation within an ecologicalcommunity
  • Next stepsOur data needs are to link niche featureswith geo-locations
  • Scale: From geographic tomicrobiologicalFrom locations of organisms/samples,sources of museum artifacts ...to organism interactions, e.g. on bacterialinfection – how the interior of oneorganism or organism part serves asenvironment for another organism
  • Hosts for bacterial infection(interior of) lungblood (bacteremia)erythrocyte - plasmodium inhabits red bloodcellshepatocyte – plasmodium infects liver cellsmacrophagegut and oral mucosa, nasal mucosa, vaginalmucosakidneybladderportion of epithelial tissue
  • C: bacteria (arrows) adhering to andpenetrating the epithelial cells (×3,000)D: abscess (Ab) formation in subepithelialregion with a colony of bacteria (arrows)and a red blood cell (RBC) in it (×2,000)
  • 106RELATIONTO TIMEGRANULARITYCONTINUANT OCCURRENTINDEPENDENT DEPENDENTORGAN ANDORGANISMOrganism(NCBITaxonomy)AnatomicalEntity(FMA, CARO)OrganFunction(FMP, CPRO) PhenotypicQuality(PaTO)Biological Process(GO)CELL ANDCELLULARCOMPONENTCell(CL)CellularComponent(FMA, GO)CellularFunction(GO)MOLECULEMolecule(ChEBI, SO,RnaO, PrO)Molecular Function(GO)Molecular Process(GO)Environments, environment parts (features),environment qualities
  • Ontologies neededEnvironment -- Taxonomyplace, habitat, city, farm, building (interior), oral cavity,uterine cavity, gut ...Environment part – Anatomy ofenvironments (Surface, conduit, entry ...)city wall, uterine wall, water source, ...Environment functionprotection, supply of food,...Environment quality – (Phenotypes)ambient temperature, salinity, ...