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Towards a Top-Level Ontology for Molecular Biology

Towards a Top-Level Ontology for Molecular Biology. Stefan Schulz 1 , Elena Beisswanger 2 , Udo Hahn 2 , Joachim Wermter 2 ,. 1 Freiburg University Hospital, Department of Medical Informatics, Germany 2 Jena University Language and Information Engineering (JULIE) Lab.

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Towards a Top-Level Ontology for Molecular Biology

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  1. Towards a Top-Level Ontology for Molecular Biology Stefan Schulz 1, Elena Beisswanger 2, Udo Hahn 2, Joachim Wermter 2, 1 Freiburg University Hospital, Department of Medical Informatics, Germany 2 Jena University Language and Information Engineering (JULIE) Lab

  2. What’s an ontology…?

  3. Our notion of ontology Universally accepted truths Consolidated but context-dependent facts Hypotheses, beliefs, statistical associations Domain Knowledge

  4. Ontology ! Universally accepted truths Consolidated but context-dependent facts Hypotheses, beliefs, statistical associations Domain Knowledge

  5. PubMed Raw Data ClinicalData Yeast FlyBase Mouse UniProt Data Sources in Biomedicine ONTOLOGIES Experimental Data Databases Literature Collection

  6. PubMed Raw Data ClinicalData Yeast Data Integration Data Annotation FlyBase Mouse UniProt Bioontologies are devised to support ONTOLOGIES Experimental Data Databases Literature Collection

  7. How can ontologies be structured?

  8. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers

  9. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers OBO (Gene Ontology, Sequence Ontology, Cell Ontology, Mouse Anatomy, ChEBI, …)

  10. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers • Transcription • DNA-dependent transcription • antisense RNA transcription • mRNA transcription • rRNA transcription • tRNA transcription • … • (from Gene Ontology) OBO (Gene Ontology, Sequence Ontology, Cell Ontology, Mouse Anatomy, ChEBI, …)

  11. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers DOLCE BFO OBO (Gene Ontology, Sequence Ontology, Cell Ontology, Mouse Anatomy, ChEBI, …)

  12. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers • Entity • Continuant • Dependent Continuant • Realizable Entity • Function • Role • Independent Continuant • Object • Object Aggregate • Occurrent • (from BFO) DOLCE BFO OBO (Gene Ontology, Sequence Ontology, Cell Ontology, Mouse Anatomy, ChEBI, …)

  13. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers DOLCE BFO OBO (Gene Ontology, Sequence Ontology, Cell Ontology, Mouse Anatomy, ChEBI, …)

  14. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers DOLCE BFO OBO (Gene Ontology, Sequence Ontology, Cell Ontology, Mouse Anatomy, ChEBI, …)

  15. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers DOLCE BFO • Biology Domain: • Organism • Body Part • Cell • Cell Component • Tissue • Protein • Nucleic Acid • DNA • RNA • Biological Function • Biological Process OBO (Gene Ontology, Sequence Ontology, Cell Ontology, Mouse Anatomy, ChEBI, …)

  16. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers DOLCE BFO Simple Bio Upper Ontology GFO-Bio GENIA OBO (Gene Ontology, Sequence Ontology, Cell Ontology, Mouse Anatomy, ChEBI, …)

  17. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontological Layers DOLCE BFO Simple Bio Upper Ontology GFO-Bio BioTop GENIA OBO (Gene Ontology, Sequence Ontology, Cell Ontology, Mouse Anatomy, ChEBI, …)

  18. GENIA as example for top level domain ontology.

  19. The GENIA Ontology “The GENIA ontology is intended to be a formal model of cell signaling reactions in human. It is to be used as a basis of thesauri and semantic dictionaries for natural language processing applications […] Another use of the GENIA ontology is to provide a basis for integrated view of multiple databases” http://www-tsujii.is.s.u-tokyo.ac.jp/~genia/topics/Corpus/genia-ontology.html • Developed at Tsujii Laboratory, University Tokyo • Taxonomy, 48 classes • Verbal definitions (“scope notes”) • No relations other than subclass relations • Purpose: Semantic annotation of biological papers

  20. GENIA Ontology http://www-tsujii.is.s.u-tokyo.ac.jp/~genia/ corpus/GENIAontology.owl

  21. GENIA Critique

  22. Insufficient Definitions • Amino Acid Monomer: • “An amino acid monomer, e.g.tyrosine, serine, tyr, ser” • DNA: • “DNAs include DNA groups, families, molecules, domains, and regions”

  23. False Taxonomic Parent GENIA: Source “Sources are biological locations where substances are found …” • ‘Organism’, ‘Tissue’, … are objects and not primarily sources! • ‘Source’ is a role …

  24. Misconception of “Type” GENIA: Cell Type • Are the instances of ‘Cell Type’ classes ? • Otherwise rename the class as ‘Cell’! “A cell type, e.g. T-Lymphocyte, T-cell, astrocyte, fibroblast”

  25. Non-Conformant Naming Policy GENIA: Amino Acid, GENIA: Protein “Proteins include protein groups, families, molecules, complexes, and substructures.” • Names suggest single molecules • Don’t work against biologists’ intuition! “An amino acid molecule or the compounds that consist of amino acids.”

  26. GENIA Redesign:BioTop

  27. BioTop • Ontologically founded Top level ontology for biology • Extensive use of formal relations (OBO) • Formal semantics (OWL-DL) • Use as a semantic glue between existing ontologies • Scope: as GENIA (in a 1st phase)

  28. BioTop Relations • partOf • properPartOf • locatedIn • derivesFrom • hasParticipant

  29. BioTop Relations • partOf • properPartOf • locatedIn • derivesFrom • hasParticipant • hasFunction (functionOf)

  30. BioTop Relations grainOf (hasGrain) componentOf (hasComponent) • partOf • properPartOf • locatedIn • derivesFrom • hasParticipant • hasFunction (functionOf)

  31. Collectives and hasGrain • hasGrain non-transitive subrelation of hasPart • Example: “Collective of Cell hasGrain only Cell” • Collectives can gain or lose grains without changing their identity

  32. Arginine Compounds and hasComponent • hasComponent non-transitive subrelation of hasPart • Example: Definition of Protein • Compounds are determined by their components Oxygen Carbon NH2 Protein

  33. Nucleotide Base Phosphate Ribose Full Definitions • Classes defined by necessary and sufficient conditions whenever possible • Rationales • Precise understanding of meaning • Empowering the classifier for automated validation processes • Required introduction of new • classes, e.g. Phosphate, Ribose Sufficient conditions for class ‘Nucleotide’

  34. GENIA BioTop properPartOf componentOf hasComponent Rearranged Classes

  35. BioTop Figures • BioTop.owl: • 143 non-taxonomic relation instances • (seven relation types) • 128 classes • BioTopGenia.owl: • Imports GENIA • Maps BioTop classes to GENIA classes

  36. BioTop OBO Ontologies Biological Process↔Biological ProcessGene Ontology Protein Function ↔ Molecular FunctionGene Ontology Cell Component ↔ Cellular ComponentGene Ontology Cell ↔ CellCell Ontology and CellFMA Atom ↔ AtomsChEBI Organic Compound↔ Organic Molecular EntitiesChEBI Tissue ↔ TissueFMA DNA, RNA ↔ DNASequence Ontology, RNASequence Ontology Protein ↔ ProteinSequence Ontology BioTop: Interfacing with OBO Ontologies

  37. Proposal: BioTop to enrich OBO Foundry

  38. OBO Foundry and BioTop BioTop BioTop BioTop BioTop BioTop BioTop

  39. BFO BioTop The OBO Foundryhttp://obofoundry.org/

  40. Outlook • Integration with BFO (work in process) • Completion of textual and formal definitions • Extension of process and function branch • Integration of BioTop in OBO foundry • Mapping BioTop to the UMLS Semantic Network • Use of BioTop in text mining: Experimental validation of added value compared to GENIA / thesaurus approach • Empirical Studies to create evidence of whether • Formal Ontologies better serve the needs of knowledge annotation / processing in biomedicine • Informal Thesauri are sufficient

  41. BioTop Redesign is going on Analyze/ complete textual class definitions Identify interfaces to existing biomedical ontologies Check ontological nature of classes Check inferred hierarchy for adequacy Check consistency Analyze/correct non-taxonomic relations, add descriptions Add /change necessary and (wherever possible) sufficient conditions if inadequate Connect classes to upper ontology if inconsistent Analyze/ clean taxonomic relations Select formal relations Make classes disjoint (wherever possible)

  42. BioTop Redesign is going on Contributions / Critiquewelcome: stschulz@uni-freiburg.de holger.stenzhorn@ifomis.uni-saarland.de Analyze/ complete textual class definitions Identify interfaces to existing biomedical ontologies Check ontological nature of classes Check inferred hierarchy for adequacy Check consistency Analyze/correct non-taxonomic relations, add descriptions Add /change necessary and (wherever possible) sufficient conditions if inadequate Connect classes to upper ontology if inconsistent Analyze/ clean taxonomic relations Select formal relations Make classes disjoint (wherever possible)

  43. Towards a Top-Level Ontology for Molecular Biology Stefan Schulz 1, Elena Beisswanger 2, Udo Hahn 2, Joachim Wermter 2, 1 Freiburg University Hospital, Department of Medical Informatics, Germany 2 Jena University Language and Information Engineering (JULIE) Lab

  44. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontology Layers

  45. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontology Layers OBO (GO, SO, ChEBI, …)

  46. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontology Layers DOLCE BFO OBO (GO, SO, ChEBI, …)

  47. Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology Ontology Layers DOLCE BFO OBO (GO, SO, ChEBI, …)

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