Reasoning Requirements for Bioscience

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Reasoning Requirements for Bioscience

  1. 1. <ul><li>Emanuele Della Valle </li></ul><ul><li>[email_address] </li></ul><ul><li>http://emanueledellavalle.org </li></ul>Reasoning requirements for Bioscience
  2. 2. Share, Remix, Reuse — Legally <ul><li>This work is licensed under the Creative Commons Attribution 3.0 Unported License. </li></ul><ul><li>Your are free: </li></ul><ul><ul><li>to Share — to copy, distribute and transmit the work </li></ul></ul><ul><ul><li>to Remix — to adapt the work </li></ul></ul><ul><li>Under the following conditions </li></ul><ul><ul><li>Attribution — You must attribute the work by inserting </li></ul></ul><ul><ul><ul><li>“ © applied-semantic-web.org” at the end of each reused slide </li></ul></ul></ul><ul><ul><ul><li>a credits slide stating “These slides are partially based on “Querying the Semantic Web with SPARQL” by Emanuele Della Valle http://applied-semantic-web.org/2010/03/05_SPARQL.ppt </li></ul></ul></ul><ul><li>To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ </li></ul>
  3. 3. Reasoning Requirements (for Bioscience) [KeetRM07] <ul><li>Supporting the ontology development process </li></ul><ul><ul><li>Finding source of errors </li></ul></ul><ul><ul><li>Classification </li></ul></ul><ul><ul><li>Supporting changes </li></ul></ul><ul><li>Model checking (violation) </li></ul><ul><li>Finding gaps in an ontology </li></ul><ul><li>Discovering new relations and concepts </li></ul><ul><li>Comparison of two ontologies </li></ul><ul><li>Mereologic reasoning </li></ul><ul><li>Finding inconsistencies in a hierarchy of relations </li></ul><ul><li>Reasoning across linked ontologies </li></ul><ul><li>Complex queries </li></ul>
  4. 4. Supporting the ontology development process Finding source of errors <ul><li>IDEA : Help in finding the source of errors </li></ul><ul><ul><li>Instead of all the logical consequences of a modeling error </li></ul></ul><ul><li>Example [ ParsiaSK05 ]: Swoop UI guides the user in locating and understanding bugs in the ontology by narrowing them down to their exact source . </li></ul><ul><ul><li>gene-part makes is inconsistent because the class dna-part and the class expression part-of.gene are inconsistent </li></ul></ul><ul><ul><li>Users can follow these dependencies and reach the root cause of the inconsistency, e.g., the class which is independently inconsistent in its definition </li></ul></ul>
  5. 5. Supporting the ontology development process Classification 1/3 <ul><li>IDEA : People do the basic modeling, machine complete the work </li></ul><ul><li>Example [Rector06] : </li></ul><ul><ul><li>Using a classifier to make life easier </li></ul></ul>
  6. 6. Supporting the ontology development process Classification 2/3 <ul><li>Substance </li></ul><ul><li>Protein </li></ul><ul><ul><li>Insulin </li></ul></ul><ul><ul><li>ATPase </li></ul></ul><ul><li>Steroid </li></ul><ul><ul><li>Cortisol </li></ul></ul><ul><li>PhsioloicRole </li></ul><ul><li>HormoneRole </li></ul><ul><li>CatalystRole </li></ul><ul><li>Hormone ≡ Substance   playsRole.HormoneRole </li></ul><ul><li>ProteinHormone ≡ Protein   playsRole.HormoneRole </li></ul><ul><li>SteroidHormone ≡ Steroid   playsRole.HormoneRole </li></ul><ul><li>Catalyst ≡ Substance   playsRole.CatalystRole </li></ul><ul><li>Enzyme ≡ Protein   playsRole.CatalystRole </li></ul><ul><li>Insulin   playsRole.HormoneRole </li></ul><ul><li>Cortisol   playsRole.HormoneRole </li></ul><ul><li>ATPase   playsRole.CatalystRole </li></ul>
  7. 7. Supporting the ontology development process Classification 3/3 <ul><li>Substance </li></ul><ul><ul><li>Protein </li></ul></ul><ul><ul><ul><li>ProteinHormone </li></ul></ul></ul><ul><ul><ul><ul><li>Insulin+ </li></ul></ul></ul></ul><ul><ul><ul><li>Enzyme </li></ul></ul></ul><ul><ul><ul><ul><li>ATPase+ </li></ul></ul></ul></ul><ul><ul><li>Steroid </li></ul></ul><ul><ul><ul><li>SteroidHormone+ </li></ul></ul></ul><ul><ul><ul><ul><li>Cortisol+ </li></ul></ul></ul></ul><ul><ul><li>Hormone </li></ul></ul><ul><ul><ul><li>ProteinHormone+ </li></ul></ul></ul><ul><ul><ul><ul><li>Insulin+ </li></ul></ul></ul></ul><ul><ul><ul><li>SteroidHormone+ </li></ul></ul></ul><ul><ul><ul><ul><li>Cortisol+ </li></ul></ul></ul></ul><ul><ul><li>Catalyst </li></ul></ul><ul><ul><ul><li>Enzyme+ </li></ul></ul></ul><ul><ul><ul><ul><li>ATPase+ </li></ul></ul></ul></ul>
  8. 8. Supporting the ontology development process Supporting changes <ul><li>IDEA : asking the modeler to do minimal changes and let the reasoner do the hard job </li></ul><ul><li>Example [Rector06] : </li></ul><ul><ul><li>What do we have to do to organise hormones as metabolic hormones and sex hormones and stress hormones and add in testosterone? </li></ul></ul><ul><ul><li>The hard way </li></ul></ul><ul><ul><ul><li>Know exactly where to introduce the new concepts in the polyherarchy </li></ul></ul></ul><ul><ul><li>The easy way </li></ul></ul><ul><ul><ul><li>Declare the semantics of metabolic hormones, sex hormones, stress hormones and testosterone </li></ul></ul></ul><ul><ul><ul><li>Let the reasoner classify </li></ul></ul></ul><ul><ul><ul><li>Check for other required changes </li></ul></ul></ul>
  9. 9. Supporting the ontology development process Supporting changes - Declare the semantics <ul><li>Substance </li></ul><ul><ul><li>Protein </li></ul></ul><ul><ul><ul><li>Insulin </li></ul></ul></ul><ul><ul><ul><li>ATPase </li></ul></ul></ul><ul><li>Steroid </li></ul><ul><ul><li>Cortisol </li></ul></ul><ul><ul><li>Testosterone </li></ul></ul><ul><li>PhsioloicRole </li></ul><ul><ul><li>HormoneRole </li></ul></ul><ul><ul><ul><li>SexHR </li></ul></ul></ul><ul><ul><ul><li>MetabHR </li></ul></ul></ul><ul><ul><ul><li>StressHR </li></ul></ul></ul><ul><ul><li>CatalystRole </li></ul></ul><ul><li>SexHrmn ≡ Substance   playsRole.SexHR </li></ul><ul><li>MetabolicHrmn ≡ Substance   playsRole.MetabHR </li></ul><ul><li>StressHrmn ≡ Substance   playsRole.StressHR </li></ul><ul><li>Testosterone   playsRole. SexHR </li></ul><ul><li>Cortisol   playsRole.StressHR </li></ul>
  10. 10. Supporting the ontology development process Supporting changes – classify and check <ul><li>Substance </li></ul><ul><ul><li>Protein </li></ul></ul><ul><ul><ul><li>ProteinHormone </li></ul></ul></ul><ul><ul><ul><ul><li>Insulin+ </li></ul></ul></ul></ul><ul><ul><li>Steroid </li></ul></ul><ul><ul><ul><li>SteroidHormone+ </li></ul></ul></ul><ul><ul><ul><ul><li>Cortisol+ </li></ul></ul></ul></ul><ul><ul><li>Hormone </li></ul></ul><ul><ul><ul><li>ProteinHormone+ </li></ul></ul></ul><ul><ul><ul><ul><li>Insulin+ </li></ul></ul></ul></ul><ul><ul><ul><li>SteroidHormone+ </li></ul></ul></ul><ul><ul><ul><ul><li>Cortisol+ </li></ul></ul></ul></ul><ul><ul><ul><li>SexHrmn </li></ul></ul></ul><ul><ul><ul><ul><li>Testosterone </li></ul></ul></ul></ul><ul><ul><ul><li>StressHrmn </li></ul></ul></ul><ul><ul><ul><ul><li>Cortisol+ </li></ul></ul></ul></ul><ul><ul><ul><li>MetabHrmn </li></ul></ul></ul><ul><ul><ul><ul><li>Insulin+ </li></ul></ul></ul></ul><ul><ul><li>Catalyst </li></ul></ul><ul><ul><ul><li>Enzyme+ </li></ul></ul></ul><ul><ul><ul><ul><li>ATPase+ </li></ul></ul></ul></ul>Declare Insulin   playsRole.MetabRole and classy once more
  11. 11. Model checking <ul><li>IDEA : test the ontology (at the type-level) against instance data that ought to conform to the logical theory </li></ul><ul><li>Example [ParsiaSK05]: </li></ul><ul><ul><li>Cow are herbivores, </li></ul></ul><ul><ul><ul><li>herbivore   eats.(plant  (  part_of.plant) </li></ul></ul></ul><ul><ul><li>Mad cows are cows that eats brains and other part of sheeps </li></ul></ul><ul><ul><ul><li>mad-cow  cow, eats.(brain  (  part_of.sheep) </li></ul></ul></ul>
  12. 12. Finding gaps in an ontology 1/2 <ul><li>IDEA : find out relations and concepts that are known, but that have not yet been added to the ontology </li></ul><ul><li>Example [KeetRM07]: </li></ul><ul><ul><li>Problem </li></ul></ul><ul><ul><ul><li>Foundational Model of Anatomy (FMA) has about 72000 concepts and 1.9 million relations among them and is known to be incomplete in particular at the cellular and sub-cellular levels of granularity </li></ul></ul></ul><ul><ul><ul><li>How can we know what is missing? </li></ul></ul></ul><ul><ul><li>Possible solutions </li></ul></ul><ul><ul><ul><li>Manual browsing: unrealistic </li></ul></ul></ul><ul><ul><ul><li>Targeted queries by domain experts: can help </li></ul></ul></ul><ul><ul><ul><li>Automated Reasoning: nice to have </li></ul></ul></ul>
  13. 13. Finding gaps in an ontology 2/2 <ul><li>Targeted queries by domain experts </li></ul><ul><li>Context </li></ul><ul><ul><li>there are 17 types of Macrophage (types of cells of the immune system) in the FMA, which must be part of or contained in something </li></ul></ul><ul><li>Query (a recoursive one) [Keet06] </li></ul><ul><ul><li>Find organ with macrophages </li></ul></ul><ul><ul><ul><li>all x of class Macrophage (and of its sub-class) </li></ul></ul></ul><ul><ul><ul><li>all y of class Organ (and of its sub-class) </li></ul></ul></ul><ul><ul><ul><li>where x is a part of y or x is contained in y </li></ul></ul></ul><ul><li>Each one of the 17 types of macrophages is expected to be related to at least one organ, but in FMA only Hepatic macrophage are known to be part of the Liver. The relations of the other 16 are missing. </li></ul>
  14. 14. Discovering new relations and concepts 1/4 <ul><li>IDEA : Finding new types of relations and DL-concepts by using instances </li></ul><ul><li>Example [KeetRM07]: </li></ul><ul><ul><li>correlation between two roles </li></ul></ul><ul><ul><li>examining if the data supports some subconcept X’ or a quaternary role </li></ul></ul><ul><ul><li>Path query that may be of arbitrary length, with any roles and concepts that relate to X </li></ul></ul>
  15. 15. Discovering new relations and concepts 2/4 <ul><li>Correlation between two roles </li></ul><ul><li>Formally </li></ul><ul><ul><li>for each x:X, y:Y, r:R, XRY, does there exist a z:Z, s:S, such that there exist  1 x and xsz? </li></ul></ul><ul><li>Example </li></ul><ul><ul><li>querying if more than 50% of the patients that suffer from lactose intolerance also have the symptom of being nauseous </li></ul></ul><ul><ul><ul><li>X = Patient, </li></ul></ul></ul><ul><ul><ul><li>R = has disease, </li></ul></ul></ul><ul><ul><ul><li>Y = Lactose intolerance, </li></ul></ul></ul><ul><ul><ul><li>S = has symptom, and </li></ul></ul></ul><ul><ul><ul><li>Z = Nausea </li></ul></ul></ul><ul><ul><ul><li>Challenging on large set of instances, but feasible </li></ul></ul></ul>
  16. 16. Discovering new relations and concepts 3/4 <ul><li>examining if the data supports some subconcept X’ or a quaternary role </li></ul><ul><li>Formally </li></ul><ul><ul><li>for each x:X, y:Y, r:R, XRY, </li></ul></ul><ul><ul><li>does there exist an xsz and an xta </li></ul></ul><ul><ul><li>where z:Z, s:S, a:A, t:T hold? </li></ul></ul><ul><ul><ul><li>brute force leads to a combinatorial explosion </li></ul></ul></ul>
  17. 17. Discovering new relations and concepts 4/4 <ul><ul><li>Path query that may be of arbitrary length, with any roles and concepts that relate to X </li></ul></ul><ul><ul><li>Formally </li></ul></ul><ul><ul><ul><li>for each x:X, return any r1, ...rn, their type of role and the concepts Y1, ...Yn they are related to </li></ul></ul></ul><ul><ul><li>Example </li></ul></ul><ul><ul><ul><li>establish if a protein is in some way related to anything else </li></ul></ul></ul><ul><ul><li>Exploring the search space of sequences of conjunctive queries of not-predefined arbitrary length may not be realistic </li></ul></ul><ul><ul><li>Feasible example </li></ul></ul><ul><ul><ul><li>discover the relationships between Histone code, DNA sequence, and Gene expression regulation </li></ul></ul></ul>
  18. 18. Comparison of two ontologies <ul><li>IDEA : similar to the problem of ontology matching but finding differences matters more than finding similarities </li></ul><ul><li>Example [KeetRM07]: </li></ul><ul><ul><li>Treating ontologies as formal rendering of a scientific theory </li></ul></ul><ul><ul><ul><li>any discrepancies between two competing theories can provide an impetus for experimentation to resolve the issues. </li></ul></ul></ul><ul><ul><li>biological pathway comparison </li></ul></ul><ul><ul><ul><li>Across species </li></ul></ul></ul><ul><ul><ul><li>Canonical vs. changed by toxins or genetic defects </li></ul></ul></ul><ul><li>Not feasible in the general case </li></ul>
  19. 19. Mereologic Reasoning <ul><li>IDEA : Reasoning with mereological parthood and other (part-whole) relations </li></ul><ul><li>Example [Rector06]: </li></ul><ul><ul><li>Complex and largely investigated field [ Winston87 ] </li></ul></ul><ul><li>OWL has not native primitives, but can be use to model the classical part-whole relations </li></ul>
  20. 20. Mereologic Reasoning- Five families of relations <ul><li>Partonomic </li></ul><ul><ul><li>Parts and wholes </li></ul></ul><ul><ul><ul><li>The lid is part of the box </li></ul></ul></ul><ul><ul><li>Constitution </li></ul></ul><ul><ul><ul><li>The box is made of cardboard </li></ul></ul></ul><ul><ul><li>Membership </li></ul></ul><ul><ul><ul><li>The box is part of the shipment </li></ul></ul></ul><ul><li>Nonpartonomic </li></ul><ul><ul><li>Containment </li></ul></ul><ul><ul><ul><li>The gift is contained in the box </li></ul></ul></ul><ul><ul><li>Connection/branching/Adjacency </li></ul></ul><ul><ul><ul><li>The box is connected to the container by a strap </li></ul></ul></ul>[Rector06]
  21. 21. Mereologic Reasoning – Transitivity 1/2 <ul><li>True kinds of part-of are transitive and a fault to the part is a fault in the whole </li></ul><ul><ul><li>The finger nail is part of the finger is part of the hand is part of the upper extremity is part of the body </li></ul></ul><ul><ul><ul><li>Injury to the fingernail is injury to the body </li></ul></ul></ul><ul><ul><li>The tail-light is part of the electrical system is part of the car </li></ul></ul><ul><ul><ul><li>A fault in the tail light is a fault in the car </li></ul></ul></ul><ul><li>Membership is not transitive </li></ul><ul><ul><li>The foot of the goose is part of the goose but not part of the flock of geese </li></ul></ul><ul><ul><ul><li>Damage to the foot of the goose is not damage ot the flock of geese </li></ul></ul></ul>[Rector06]
  22. 22. Mereologic Reasoning – Transitivity 2/2 <ul><li>Containment is transitive but things contained are not necessarily parts </li></ul><ul><ul><li>A fault (e.g. souring) to the milk contained in the bottle is not damage to the bottle </li></ul></ul><ul><li>Some kinds of part-whole relation are questionably transitive </li></ul><ul><ul><li>Is the cell that is part of the finger a part of the body? </li></ul></ul><ul><ul><ul><li>Is damage to the cell that is part of the finger damage to the body? </li></ul></ul></ul><ul><ul><ul><ul><li>Not necessarily, since the cells in my body die and regrow constantly </li></ul></ul></ul></ul>[Rector06]
  23. 23. Mereologic reasoning – 1 st Implementation Patterns <ul><li>IDEA : Transitive properties with non-transitive “direct” subproperties </li></ul><ul><li>Transitive properties should have non-transitive children </li></ul><ul><ul><li>isPartOf : transitive </li></ul></ul><ul><ul><ul><li>isPartOfDirectly : non-transitive </li></ul></ul></ul><ul><li>Split which is used in partial descriptions and complete definitions </li></ul><ul><ul><li>Necessary conditions use non-transitive version </li></ul></ul><ul><ul><li>Definitions use transitive version </li></ul></ul><ul><li>Benefits </li></ul><ul><ul><li>Allows more restrictions in domain/range constraints and cardinality </li></ul></ul><ul><ul><ul><li>Allows the hierarchy along that axis to be traced one step at a time </li></ul></ul></ul><ul><ul><ul><li>Allow a good approximation of pure trees </li></ul></ul></ul><ul><ul><ul><ul><li>Make the nontransitive subproperty functional </li></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>Transitive properties can (almost) never be functional (by definition, a transitive property has more than one value in any non-trivial system) </li></ul></ul></ul></ul></ul><ul><ul><ul><li>Constraints on transitive properties easily lead to unsatisfiability </li></ul></ul></ul>[Rector06]
  24. 24. Mereologic reasoning – 1 st Implementation Patterns <ul><li>Example : </li></ul><ul><ul><li>Finger isPartOfDirectly Hand </li></ul></ul><ul><ul><li>Hand isPartOfDirectly Arm </li></ul></ul><ul><ul><li>Arm isPartOfDirectly Body </li></ul></ul>body arm hand finger isPartOfDirectly isPartOfDirectly isPartOfDirectly isPartOf isPartOf isPartOf isPartOf isPartOf isPartOf isPartOf
  25. 25. Mereologic reasoning – 2 nd Implementation Patterns <ul><li>IDEA : “Adapted SEP Triples” [ SeidenbergR06] </li></ul><ul><li>Example [Rector06] : </li></ul><ul><ul><li>Body (‘as a whole’) </li></ul></ul><ul><ul><ul><li>Body </li></ul></ul></ul><ul><ul><li>The Body’s parts </li></ul></ul><ul><ul><ul><li> isPartOf.Body </li></ul></ul></ul><ul><ul><li>The Body and it’s parts </li></ul></ul><ul><ul><ul><li>Body   isPartOf.Body </li></ul></ul></ul><ul><ul><li>Note: the “and” in natural language is capture by “or” (unionOf) </li></ul></ul><ul><ul><li>Repeat for all parts </li></ul></ul>
  26. 26. Mereologic reasoning – Using part-of 1/2 <ul><li>Example [Rector06] </li></ul><ul><ul><li>Injury_to_Hand ≡ Injury   has_locus.( Hand   isPartOf.Hand ) </li></ul></ul><ul><ul><li>Injury_to_Arm = Injury   has_locus.( Arm   isPartOf.Arm ) </li></ul></ul><ul><ul><li>Injury_to_Body = Injury   has_locus.( Body   isPartOf.Body ) </li></ul></ul><ul><ul><li>After classification </li></ul></ul><ul><ul><li>we get the expected hierarchy from point of view of anatomy </li></ul></ul>
  27. 27. Mereologic reasoning – Using part-of 2/2 <ul><li>Example [ SeidenbergR06] </li></ul><ul><ul><li>Burn is found to be a subclass of LegInjury </li></ul></ul>
  28. 28. <ul><li>Example [Rector06] </li></ul><ul><ul><li>The Brain is contained in the Cavity defined by the Cranium which is a structural part of the skull. </li></ul></ul>Mereologic reasoning – Multiple “views” Both views: The Brain is located in the skull but not part of the skull Clinician’s view : Pericardium is part of heart & Pericardiitis is a kind of Heart Disease Anatomist’s view: Pericardium is a distinct organ that develops separately from Heart
  29. 29. Finding inconsistencies in a hierarchy of relations <ul><li>IDEA : checking if hierarchy of relations are correctly modeled as normally done for concepts </li></ul><ul><li>EXAMPLE [KeetRM07]: </li></ul><ul><ul><li>asymmetry implies irreflexivity, </li></ul></ul><ul><ul><li>therefore any subrole of an asymmetric role should not be irreflexive </li></ul></ul><ul><li>At present, automated reasoners assumes relations to have been modeled correctly </li></ul><ul><ul><li>never return an inconsistency on a property </li></ul></ul><ul><ul><li>inconsistent or erroneous re-classified concepts are the results of incorrect relation modeling </li></ul></ul>
  30. 30. Reasoning across linked ontologies <ul><li>IDEA : reason across multiple interlinked ontology without creating a huge (and unmanageable) ontology by merging multiple ontologies, but beneficing from (expressive) reasoning occurring locally to each ontology </li></ul><ul><li>Example [KeetRM07]: </li></ul><ul><ul><li>reasoning across </li></ul></ul><ul><ul><ul><li>MGED Ontology for microarray experiments, </li></ul></ul></ul><ul><ul><ul><li>BioPax for biological pathways, </li></ul></ul></ul><ul><ul><ul><li>Cell type, and </li></ul></ul></ul><ul><ul><ul><li>Mammalian Phenotype </li></ul></ul></ul><ul><li>Coordinated modularization and linking of ontologies on demand would be required </li></ul>
  31. 31. Complex queries <ul><li>IDEA : queries that require use of part-whole relations or cycles among the concepts in the ontology </li></ul><ul><li>Examples [KeetRM07, Keet06]: </li></ul><ul><ul><li>using of part-whole relations </li></ul></ul><ul><ul><ul><li>retrieve all biological pathways that contain a give protein e.g., Ubiquitin </li></ul></ul></ul><ul><ul><ul><li>what are the cellular components of blood? </li></ul></ul></ul><ul><ul><li>involving adjacent levels of granularity (e.g., Cell-level and SubcellularOrganelle-level) </li></ul></ul><ul><ul><ul><li>which cell type(s) do(es) not have a nucleus as part? </li></ul></ul></ul><ul><ul><li>using of cycles among the concepts </li></ul></ul><ul><ul><ul><li>retrieve the place of a give animal, e.g., Hedgehog, in food webs </li></ul></ul></ul><ul><ul><li>requiring to exploit two different part of relations (i.e., a structural one for the kidney and a functional one for the hormones) </li></ul></ul><ul><ul><ul><li>Which hormones are located in the kidney, and where in the kidney? </li></ul></ul></ul><ul><ul><li>Requiring to exploit one a part of and two sub class of relations </li></ul></ul><ul><ul><ul><li>In which organs are macrophages located? </li></ul></ul></ul>
  32. 32. Reasoning Requirements (for Bioscience) [KeetRM07] <ul><li>Supporting the ontology development process :-| </li></ul><ul><ul><li>Finding source of errors :-| </li></ul></ul><ul><ul><li>Classification :-D </li></ul></ul><ul><ul><li>Supporting changes :-) </li></ul></ul><ul><li>Model checking (violation) :-) </li></ul><ul><li>Finding gaps in an ontology :-( </li></ul><ul><li>Discovering new relations and concept :-/ </li></ul><ul><li>Comparison of two ontologies :-(( </li></ul><ul><li>Mereologic reasoning :-) </li></ul><ul><li>Finding inconsistencies in a hierarchy of relations :-( </li></ul><ul><li>Reasoning across linked ontologies :-(( </li></ul><ul><li>Complex queries :-) </li></ul>
  33. 33. Credits and References <ul><li>[KeetRM07] C. Maria Keet, Marco Roos, M. Scott Marshall: A Survey of Requirements for Automated Reasoning Services for Bio-Ontologies in OWL. OWLED 2007 </li></ul><ul><ul><li>http://www.webont.org/owled/2007/PapersPDF/submission_20.pdf </li></ul></ul><ul><li>[Rector06] Alan Rector. GALEN Revisited. </li></ul><ul><ul><li>http://www.cs.man.ac.uk/~rector/presentations/Reasoning-web-rector-GALEN-2006.ppt </li></ul></ul><ul><li>[ ParsiaSK05 ] Bijan Parsia, Evren Sirin, Aditya Kalyanpur: Debugging OWL ontologies. WWW 2005: 633-640 </li></ul><ul><ul><li>http://www2005.org/cdrom/docs/p633.pdf </li></ul></ul><ul><li>[Keet06] Keet, C.M. Granular information retrieval from the Gene Ontology and from the Foundational Model of Anatomy with OQAFMA. KRDB Research Centre Technical Report KRDB06-1, Free University of Bozen-Bolzano, 6 April 2006. 19p. </li></ul><ul><ul><li>http://www.inf.unibz.it/krdb/pub/TR/KRDB06-1.pdf </li></ul></ul><ul><li>[ Winston87 ] Winston, M., R. Chaffin, et al. (1987). &quot;A taxonomy of part-whole relations.&quot; Cognitive Science 11: 417-444. </li></ul><ul><ul><li>http://csjarchive.cogsci.rpi.edu/1987v11/i04/p0417p0444/MAIN.PDF </li></ul></ul><ul><li>[ SeidenbergR06] Julian Seidenberg, Alan L. Rector: Representing Transitive Propagation in OWL. ER 2006: 255-266 </li></ul><ul><ul><li>http://www.springerlink.com/content/02kk647893q43700/ </li></ul></ul>
  34. 34. <ul><li>Emanuele Della Valle </li></ul><ul><li>[email_address] </li></ul><ul><li>http://emanueledellavalle.org </li></ul>Reasoning requirements for Bioscience

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