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About ontologies Melissa Haendel

About ontologies Melissa Haendel. And who am I that I am giving you this talk? Melissa Haendel Anatomist, developmental neuroscientist, molecular biologist, curator, ontologist. Most ontologists become ontologists because they have a need to classify and compute on a specific domain.

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About ontologies Melissa Haendel

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  1. About ontologies Melissa Haendel

  2. And who am I that I am giving you this talk? Melissa Haendel Anatomist, developmental neuroscientist, molecular biologist, curator, ontologist Most ontologists become ontologists because they have a need to classify and compute on a specific domain

  3. Information retrieval from text-based resources is hard:

  4. Common vocabularies allow grouping of disparate data GlyProt MouseEcotope sphingolipid transporter activity DiabetInGene GluChem Use of the same defined term indicates the same meaning under different annotation circumstances

  5. The controlled vocabulary spectrum OBO http://www.mkbergman.com/?m=20070516 Bottom line: you get what you pay for. Ontologies are expensive but powerful.

  6. Why build an ontology? A simple example Number of genes annotated to each of the following brain parts in an ontology: brain 20 part_of hindbrain 15 part_of rhombomere 10 Query brain without ontology 20 Query brain with ontology 45 Ontologies can facilitate grouping and retrieval of data

  7. An ontologyis a classification vocabulary Philosophers: Ontology = The study of being as a branch of philosophy Bioinformaticists: Domain ontology = representing a specific knowledge base • Features of ontologies: • Terms are defined • Terms are arranged in a hierarchy • Relationships between the terms are defined • Expressed in a knowledge representation language Some well known ontologies are: SnoMED, Foundational Model of Anatomy, Gene Ontology, Linnean Taxonomy of species

  8. Defining ontology classes, a beginner’s guide An X =Y that has one or more differentiating characteristics. where Y is the is_a parent of X. Definition: cylinder = Surface formed by the set of lines perpendicular to a plane, which pass through a given circle in that plane. Y is_a is_a X Definition: Blue cylinder = Cylinder that is blue. Definition: Red cylinder = Cylinder that is red. These types are Disjoint: A cylinder can be either blue or red by definition, but not both. Definitions specify necessary and sufficient conditions.

  9. Subsumption reasoning:The simplest ontology reasoning entity organism is_a is_a animal is_a mammal is_a is_a cat human instance_of instance_of Peanut Chris Shaffer

  10. Hierarchy types Simple taxonomy Directed acyclic graph

  11. Ontology classes, instances, and relations are stored as sentences Subject —— Property —— Object brain (class) has_part neuron (class) PloS 2009 (instance) has_author Melissa (instance) Chris (instance) owns red tie (instance)

  12. The True Path Rule The pathway from a child term all the way up to its top level parent(s) must be universally true. GO Before: GO After: cuticle synthesis --[i] chitin metabolism cell wall biosynthesis --[i] chitin metabolism ----[i] chitin biosynthesis ----[i] chitin catabolism chitin metabolism --[i] chitin biosynthesis --[i] chitin catabolism --[i] cuticle chitin metabolism ----[i] cuticle chitin biosynthesis ----[i] cuticle chitin catabolism --[i] cell wall chitin metabolism ----[i] cell wall chitin biosynthesis ----[i] cell wall chitin catabolism BUT: A fly chitin synthase could be annotated to chitin biosynthesis, and appear in a query for genes annotated to cell wall biosynthesis (and its children), which makes no sense because flies don't have cell walls. NOW: all the child terms can be followed up to chitin metabolism, but cuticle chitin metabolism terms do not trace back to cell wall terms, so all the paths are true.

  13. Where does the True Path Rule come from? • Transitivity. • Some relations are transitive, and apply across all levels of the hierarchy. • For example, a cat is_a mammal, and a mammal is_a vertebrate • SO • a cat is_a vertebrate • => This is the true path rule and is because the is_a relation is transitive. • Some properties are not transitive. • For example, head has_quality round. • and, • head part_of organism. • So is the organism round? Of course not! • BUT, eyes are part_of head, and head part_of organism, SO eye part_of organism is true, because part_of is a tranistive relation. • Relations are logically defined in a common relation ontology or within each ontology that uses them. ≠ >

  14. Domain ontologies are organized according to upper ontologies that specify the general types of things that exist => Classification according to these higher level types helps ensure the True Path Rule holds

  15. More about using ontology classes and relations Univocity Terms should have the same meanings on every occasion of use. (= They should refer to the same universal types) Basic ontological relations such as is_a and part_of should be used in the same way by all ontologies Universality Often, the order of the terms in an assertion will matter: We can assert adult transformation_of child but not child transformation_of adult

  16. Common ontology languages OBO simple, more easily readable, used by many biologists, restricted expressivity OWL is a recognized standard, more tools available, less restricted expressivity [Term] id: OBI:0000626 name: DNA sequencing def:"DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument." [OBI:sourced "OBI Branch derived"] is_a: OBI:0600047 ! sequencing assay </owl:Class> <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000626"><!-- DNA sequencing --> <owl:disjointWith> <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000705"/><!-- Edman degradation --> </owl:disjointWith> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >DNA sequencing</rdfs:label> <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >DNA sequencing</obo:IAO_0000111> <obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >OBI Branch derived</obo:IAO_0000119> <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.</obo:IAO_0000115> <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/> <rdfs:subClassOf> <owl:Restriction> <owl:onProperty> <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000293"/><!-- has_specified_input --> </owl:onProperty> <owl:someValuesFrom> <owl:Class> <owl:intersectionOf rdf:parseType="Collection"> <owl:Class rdf:about="http://purl.org/obo/owl/CHEBI#CHEBI_16991"/> <owl:Restriction> <owl:someValuesFrom> <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000067"/><!-- evaluant role --> </owl:someValuesFrom> <owl:onProperty> <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000316"/><!-- has_role --> </owl:onProperty> </owl:Restriction> </owl:intersectionOf> </owl:Class> </owl:someValuesFrom> </owl:Restriction> </rdfs:subClassOf> <rdfs:subClassOf> <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600047"/><!-- sequencing assay --> </rdfs:subClassOf> <rdfs:subClassOf> <owl:Restriction> <owl:someValuesFrom> <owl:Class> <owl:intersectionOf rdf:parseType="Collection"> <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030"/> <owl:Restriction> <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000811"/><!-- primary structure of DNA macromolecule --> <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/> </owl:Restriction> </owl:intersectionOf> </owl:Class> </owl:someValuesFrom> <owl:onProperty> <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000299"/><!-- has_specified_output --> </owl:onProperty> </owl:Restriction> </rdfs:subClassOf> <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Philippe Rocca-Serra</obo:IAO_0000117> <rdfs:subClassOf> <owl:Restriction> <owl:onProperty> <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000417"/><!-- achieves_planned_objective --> </owl:onProperty> <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000441"/><!-- assay objective --> </owl:Restriction> </rdfs:subClassOf> <obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858</obo:IAO_0000112> </owl:Class> <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000743"><!-- immune response assay --> <owl:equivalentClass> <owl:Class> <owl:intersectionOf rdf:parseType="Collection"> <owl:Restriction> <owl:someValuesFrom> <owl:Class> <owl:intersectionOf rdf:parseType="Collection"> <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/> <owl:Restriction> <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/> <owl:someValuesFrom rdf:resource="http://purl.org/obo/owl/GO#GO_0006955"/> </owl:Restriction> </owl:intersectionOf> </owl:Class> </owl:someValuesFrom> <owl:onProperty> <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000299"/><!-- has_specified_output --> </owl:onProperty> </owl:Restriction> <owl:Restriction> <owl:onProperty> <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000417"/><!-- achieves_planned_objective --> </owl:onProperty> <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000441"/><!-- assay objective --> </owl:Restriction> </owl:intersectionOf> </owl:Class> </owl:equivalentClass> <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000124"/> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >immune response assay</rdfs:label> <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >immune response assay</obo:IAO_0000111> <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Is an assay with the objective to determine information about an immune response</obo:IAO_0000115> <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/><!-- assay -->

  17. Ontology Lookup Service at EBI http://www.ebi.ac.uk/ontology-lookup/

  18. Bioportal at the NCBO http://bioportal.bioontology.org/

  19. Ontology Editors (and viewers) OBOEdit- OBO ontology editor and viewer http://oboedit.org/ Protégé - OWL ontology editor and viewer http://protege.stanford.edu/

  20. Ontologies can help reconcile annotation inconsistencies

  21. Using ontologies for error checking only_in_taxon UBERON: bone Vertebrata NOT is_a is_a is_a Drosophila melanogaster Homo sapiens UBERON: tibia is_a is_a part_of part_of Fruit fly ‘tibia’ Human ‘tibia’ Text match mapping Developmental Biology, Scott Gilbert, 6th ed.

  22. Using ontologies for alignment of similar vocabularies

  23. Using ontologies for computation Information Content (IC) is based on depth within the ontology and annotation frequency

  24. Why do we need all these rules and standards for ontology use and construction? Ontologies must be intelligible to both: Humans Machines • Automatic reasoning to infer related classes • Annotation consistency • Error checking • Alignment with other ontologies • Computation

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