Top Level Ontologies Daniel Schober (EBI, Metabolomics Society O-WG) FuGO Workshop, Philadelphia, February 13 th -15 th 2006.

Presentation on theme: "Top Level Ontologies Daniel Schober (EBI, Metabolomics Society O-WG) FuGO Workshop, Philadelphia, February 13 th -15 th 2006."— Presentation transcript:

1 Top Level Ontologies Daniel Schober (EBI, Metabolomics Society O-WG) FuGO Workshop, Philadelphia, February 13 th -15 th 2006

2 schober@ebi.ac.ukFuGO-Workshop-Philadelphia  Top level Ontologies Whats that ? Why that ? Which one ? TLO_KB.pprj Naming Conventions ? Talk Structure

3 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Top Level Ontologies (TLO) TLO  Reference O., Generic O. Core O., Foundational O., High-level O, Upper O. task & problem- solving ontology application ontology domain ontology [Guarino, 98] describe very general concepts like space, time, event, which are independent of a particular problem or domain describe the vocabulary related to a generic domain by specializing the concepts introduced in the top-level ontology. describe the vocabulary related to a generic task or activity by specializing the top-level ontologies. the most specific ontologies. Concepts in application ontologies often correspond to roles played by domain entities while performing a certain activity.

4 schober@ebi.ac.ukFuGO-Workshop-Philadelphia TLO Attributes: KR-Format, granularity, axiomatisation, extension of conceptual coverage, reused, soundness,..., others.... TLO-Library  TLO-KB.pprj (28 TLO´s) Requirements: Domain independent (general) Language independent (not dictated by the lexicalisation patterns of a particular language) Consistent Understandable accd. to common sense (vs) Well-formed (axiomatic) Set of mutually disjoint notions (e.g.cont vs occur) Hard to define border to domain top level. (Some TLOs contain quite specific things...)

5 schober@ebi.ac.ukFuGO-Workshop-Philadelphia TLO goals/usage Quality assurance: (Hopefully) Clear classification principles and definitions derived from TLO Taxonomic guidance (10 Questions): –Help domain experts rate their starting points and patterns. –Classes that are related to disjoint top-level concepts cannot be matched & confused –Attribute inheritance makes misclassifications obvious Ontology Alignment, Mapping –(Re-use, integration, interoperability) Ontol Library schemata Homonym disambiguation (NLP, see picture) Synonym detection –(Avoid Redundancies) [Hefflin and Hendler 2000]

6 schober@ebi.ac.ukFuGO-Workshop-Philadelphia How to get a useful TLO ? 3 ways: Look at existing TLO´s Look at Ontology Library Schemata (OBO Core) & Ontology Alignment Mappings Build own TLO bottom up: which TLO classes are implied by collected Bioontology upper level classes? –Done so by FuGo (e.g. „Characteristic“, Fugo- devel- email Barry 18Jan06)

7 schober@ebi.ac.ukFuGO-Workshop-Philadelphia TLO (Size/Precision vs. Formality) WordNet Cyc SUMO DOLCE Lexicons Formal Ontology Taxonomy Size UMLS Yahoo! Formality

8 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Self-standing vs Refining (A. Rector, GALEN-ULO) Self-standing Hand, Person, Computer, Idea… Refining Left, Size, severity, … Self_standing_entity is_refined_by Refining_entity –Establishes the domain & range of a top property distinction Does it make sense on its own? Yes  Self_standing

9 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Continuant vs Occurrent Thing vs Process –Organ vs Metabolism Physical (material) vs Non_physical –Non_physical is_manifested_by Physical Continuants participate_in Occurrents –“Things participate in Processes” “Processes happen to Things” Continuants (“perdurants”) –Things that retain their form over time People, books, desks, water, ideas, universities, … Occurrents –Things that occur during time Living, writing a book, sitting at a desk, the flow of water, thinking, building the university,... Question: Do things happen to it?  Continuant Does it happen or occur?  Occurrent

10 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Material vs Non-material Within Physical: Chest vs Chest_cavity –The problem of holes: Material defines non_material (things define “holes”) The intersection of the walls defines the corner

11 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Discrete vs Mass Discrete_entities are constituted of Mass_entities –Organ made_of Tissue Discrete things can be counted Mass things can only be measured –Guarino calls them “Amount of matter” Questions: Can I count it? Yes  Discrete If I make a plural, is it odd or something different? e.g. “waters”, “papers”, “thinkings” Do I say pieces/drops/lumps of it? Yes  Mass

12 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Taxonomic Guidance 10 Questions  What is an “Organelle”? Is it Continuant or Occurrent? Continuant –Does it happen or do things happen to it? Is it physical? Yes Is it Discrete or mass? Discrete –(Can you count it?) Is it material or non-material ? Material Is it part of something? Yes Has it a definite number or not? Yes Collectives of Organels are part of Cytoplasm`  ”Organelle” is_a “Cell_part” is_a “Biological_object”

13 schober@ebi.ac.ukFuGO-Workshop-Philadelphia What is “Digestion”? Is it Continuant or occurrent? occurrent Is it physical? Yes Is it discrete or mass? ??? Is it biological?Yes If so is it pathologicalNo  “Digestion” is_a “Biological_physical_occurrent”

14 schober@ebi.ac.ukFuGO-Workshop-Philadelphia UMLS Semantic Net

15 schober@ebi.ac.ukFuGO-Workshop-Philadelphia UMLS Inconsistencies Idea or Concept Functional Concept Qualitative Concept Quantitative Concept Spatial Concept Body Location or Region Body Space or Junction Geographic Area Molecular Sequence Amino Acid Sequence Carbohydrate Sequence Nucleotide Sequence “Philadelphia”  Idea or Concept ???

16 schober@ebi.ac.ukFuGO-Workshop-Philadelphia TAMBIS Upper Level

17 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Sowa´s TLO

18 schober@ebi.ac.ukFuGO-Workshop-Philadelphia DOLCE (WonderWeb, EU)

19 schober@ebi.ac.ukFuGO-Workshop-Philadelphia OBR (Barry Smith)

20 schober@ebi.ac.ukFuGO-Workshop-Philadelphia SUMO (IEEE-SUO-WG) entity physical ( things which have a position in space/time) object  FuGo top level (indept cont) selfconnected object process  FuGo top level (dept occur) abstract (don´t have a position in space/time) quantity number attribute  FuGo top level „Characteristic“ (dept cont) set or class relation proposition + FOL Axioms

21 schober@ebi.ac.ukFuGO-Workshop-Philadelphia “Blood” in the UMLS Blood Tissue Entity Physical Object Anatomical Structure Fully Formed Anatomical Structure An aggregation of similarly specialized cells and the associated intercellular substance. Tissues are relatively non-localized in comparison to body parts, organs or organ components Body SubstanceBody FluidSoft Tissue

22 schober@ebi.ac.ukFuGO-Workshop-Philadelphia “Blood” in WordNet Blood Humor the four fluids in the body whose balance was believed to determine our emotional and physical state As well as phlegm, yellow and black bile Entity Physical Object Substance Body Substance Body Fluid

23 schober@ebi.ac.ukFuGO-Workshop-Philadelphia “Blood” in GALEN Blood SoftTissue As well as Lymphoid Tissue, Integument, and Erectile Tissue DomainCategory Phenomenon Blood has two states, LiquidBlood and CoagulatedBlood Substance Tissue GeneralisedSubstanceSubstanceorPhysicalStructure

24 schober@ebi.ac.ukFuGO-Workshop-Philadelphia “Blood” in SNOMED Blood Liquid Substance Substance categorized by physical state Body fluid Body Substance Substance As well as lymph, sweat, plasma, platelet rich plasma, amniotic fluid, etc

25 schober@ebi.ac.ukFuGO-Workshop-Philadelphia “Blood” in Digital Anatomist Blood Body Substance Anatomical Entity Physical Anatomical Entity a physical anatomical entity and a substance in gaseous, liquid, semisolid or solid state, with or without the admixture of cells, which is produced by anatomical structures or derived from inhaled and ingested substances that become modified by anatomical structures as they pass into or through the body As well as saliva, semen, growth hormone, inhaled air, feces, lymph Tissue is an Organ Part.

26 schober@ebi.ac.ukFuGO-Workshop-Philadelphia „Conclusions“ Diverse TLO´s. All have Pros & Cons, many have inconsistencies Different „Time“ representation (... if any) „There is no one way! No matter how much some people want to make it a matter of dogma“ (Alan Rector) Current Fugo TLO is quite in accordance to most TLOs, but misses „middle level“ Has to be expanded Maybe build our own (bottom up) as needed?

27 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Next Steps TLO_KB Naming Conventions Textmining: –Co-op with Inhouse NLP-Groups Ontology refinement Harvest PubMed and WWW Morpheme & Lexical Analysis

28 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Of Advantage for “Binning“... Higher semantics (more info)  Easier Binning TLP & Naming Conventions help –also for Domain CVs (MIAXXXX) Similarity metric of OWL-L Ontologies exploitable for O. Merging/alignment: e.g. [Euzenat, Volchev 04] KR-Idioms harvestable: Hierarchy (Sub & Superclasses), classes/ Defs (DL Expr), properties incl. Ranges, Facets & restrictions on these properties Others: Instance similarities, Defs (NL)

29 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Acknowledgements Gilberto Fragoso Barry Smith & Alan Rector...from which many slides shown „Inherited“ Susanna Sansone, Phillipe Rocca-Serra Project Website http://www.ebi.ac.uk/microarray/Projects/tox-nutri/

30 schober@ebi.ac.ukFuGO-Workshop-Philadelphia KR-Naming Conventions Conventions: Completeness vs pragmatics No Problems arosed from „KR-semantics name heterogenity“ so far Few, if any, Problems arosed from KR- Metaidiom Name heterogenity  concentrate on KR-Naming

31 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Naming Conventions Different communities  Different notions AI: Frame DL: Concept name OOM: Class

32 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Semantic Triangle “Jaguar“ Concept [Ogden, Richards, 1923 ]

33 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Nonphysical entities (complicated) What is “Faust” ? The script for Faust in the library? The historic person Dr. Faustus ? A performance? –Faust has_manifestation Book_of_Faust Performance_of_Faust ?

34 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Domain Ontology Middle Ontology Top-Level Ontology

35 schober@ebi.ac.ukFuGO-Workshop-Philadelphia General Problems (From Barry`s tutorial) Don’t confuse entities with concepts Don’t confuse domain entities with logical structures Don’t confuse ontology with epistemology Don’t confuse is_a with has_role  Unintuitive rules for classification lead to coding errors, difficulties in training of curators, in ontology and in harvesting content in automatic reasoning systems

36 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Collective vs Individual Collectives of discrete entities at one level of granularity form mass entities at the next –Cells form Tissue Collectives –Object is_grain_of Collective Red_blood_cell is_grain_of Blood_cell_fraction –The concern is with the collective as a whole not its ‘grains’ –Loss or gain of grains does not affect identity of multiple –Grains are always smaller than the multiples they make up

37 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Hard to define (perspective dependent) "On those remote pages it is written that animals are divided into: a. those that belong to the Emperor b. embalmed ones c. those that are trained d. suckling pigs e. mermaids f. fabulous ones g. stray dogs h. those that are included in this classification i. those that tremble as if they were mad j. innumerable ones k. those drawn with a very fine camel's hair brush l. others m. those that have just broken a flower vase n. those that resemble flies from a distance" From: The Celestial Emporium of Benevolent Knowledge, Borges

38 schober@ebi.ac.ukFuGO-Workshop-Philadelphia OWL-S –A TLO for Services ResourceService Service profile Service model Service grounding provides presents describedBy supports What it does How it works How to access it description functionalities functional attributes

39 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Ontology Libraries WebOnto (http://eldora.open.ac.uk:3000/webonto): Knowledge Media Institute, Open University, UK, Ontolingual (http://www-ksl-svc.stanford.edu:5915/): Knowledge Systems Laboratory, Stanford University, USA) DAML Ontology library system (http://www.daml.org/ontologies/): DAML, DAPAR, USA SHOE (http://www.cs.umd.edu/projects/plus/SHOE/): University of Maryland, USA Ontology Server (http://www.starlab.vub.ac.be/research/dogma/OntologyServer.htm): Vrije Universiteit, Brussels, Belgium IEEE Standard Upper Ontology (http://suo.ieee.org/refs.html): IEEE OntoServer (http://ontoserver.aifb.uni-karlsruhe.de/): AIFB, University of Karlshruhe, Germany ONIONS ( http://saussure.irmkant.rm.cnr.it/onto/ ): Biomedical Technologies Institute (ITBM) of the Italian National Research Council (CNR), Italy

40 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Information systems & resources Information systems & resources Databases, RDF Instance stores, … (“individuals”) The Ontology Pyramid Domain Content Ontologies Top Domain Ontologies Top Domain Ontologies Top Level Ontologies Top Level Ontologies OWL classes Meta Ontologies FoL / HoL

41 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Aristotle’s Categories From Porphyry’s Commentary on Aristotles’s Categories

42 schober@ebi.ac.ukFuGO-Workshop-Philadelphia GUM

43 schober@ebi.ac.ukFuGO-Workshop-Philadelphia TLO-Representation examples: “Blood” in Cyc Blood Mixture A tangible stuff composed of two or more different constituents which have been mixed. These constituents do not form chemical bonds, and later the mixture may be resolved by some separation event. A mixture has a composition but not a structure As well as mud, air and carbonate beverage TangibleThing #$genls ExistingStuffType #$isa #$genls The function Separation-Event can apply to it.

44 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Domain Top Level Ontologies Synonymes: Task O., Application O., Middle level Ontologies Experiment Ontology, Tambis Upper Level O., MBO

45 schober@ebi.ac.ukFuGO-Workshop-Philadelphia Interpretation Continuum