INTEROPERABILITY, ONTOLOGIES AND LINKED DATA THE LAY OF THE (IRE)LAND

Transcription

1 INTEROPERABILITY, ONTOLOGIES AND LINKED DATA THE LAY OF THE (IRE)LAND HRB Workshop, January 17, 2017

2 WHAT IS INTEROPERABILITY? The ability of independently-developed components to interact and cooperate with each other The ability of components to exchange data and services Interoperability is becoming the most relevant challenge in computer sciences

3 WHY IS INTEROPERABILITY DIFFICULT?

4 COMPUTER INTEROPERABILITY THROUGH TIME Components running on different hardware plagorms

5 COMPUTER INTEROPERABILITY THROUGH TIME Components running on different operahng systems

6 COMPUTER INTEROPERABILITY THROUGH TIME Components running on different network infrastructure

7 COMPUTER INTEROPERABILITY THROUGH TIME Components running on different communicahon protocols

8 COMPUTER INTEROPERABILITY THROUGH TIME Components using different data representahons

9 COMPUTER INTEROPERABILITY THROUGH TIME Components using different control models

10 COMPUTER INTEROPERABILITY THROUGH TIME Components implemenhng different semanhcs or semanhc interpretahons <student> <name>mary</name> <birthdate>01/13/1980</birthdate> <gender>female</gender> </student> <estudante> <nome>maria</nome> <datanascimento>01/13/1980</datanascimento> <sexo>feminino</sexo> </estudante>

11 SEMANTIC INTEROPERABILITY loo restroom

12 SEMANTIC INTEROPERABILITY plant

13 ULLMAN S TRIANGLE Concept (conceptualisahon) represents abstracts plant plandaí planta Symbol (language) refers to Thing (reality))

14 COMMUNICATION PROCESS semanhc distance interpretahon Tipperary won the 2016 Gaelic Athle?c Associa?on s All-Ireland Senior Hurling Championship

15 COMMUNICATION PROCESS Tipperary won the 2016 Gaelic Athle?c Associa?on s All-Ireland Senior Hurling Championship Hurler plays on Hurling Team competes Hurling Tournament has Champion is a is a County Team competes All-Ireland Senior Hurling Championship organises Gaelic Athletic Association is a edihon of Tipperary competes 2016 All-Ireland Senior Hurling Championship wins ConceptualisaHon (mental model) used to understand the sentence

16 COMMUNICATION PROCESS How can we communicate? We share mental models We are able to learn We are able to negohate meaning When do we have communica?on problems? Big semanhc distance False agreement (Guarino, 1998): The problem is not to disagree, it is to agree when, in fact, we disagree.

17 SOLUTION?

18 SOLUTION?

19 SOLUTION?

20 SOLUTION?

21 SOLUTION?

22 SOLUTION?

23 WHAT IS NOT AN ONTOLOGY

24 WHAT IS ONTOLOGY reality conceptualisahon ontology abstracted formalised explicit specificahon of a conceptualisahon (Gruber, 1993) formal specificahon of a shared conceptualisahon (Borst 1997)

25 REPRESENTATION SPECTRUM Terms Ad-hoc Hierarchies Thesauri XML DTDs DB Schema Data Models (UML, STEP) Logic Programming First-order, Higher-order, Modal Logic informal formal Ordinary Glossaries Data DicHonaries Structured Glossaries Informal Hierarchies XML Schema Formal Taxonomies DescripHon Logics

26 TYPES OF ONTOLOGIES There are many types of ontologies In literature they are commonly classified according to: Language: expressivity x tractability Modeling domain: generality x parhcularity ApplicaHon: IS x SemanHc Web x Community IMPORTANT ü Choose the appropriate language for your problem ü Use tools that are adequate to your context

27 TYPES OF ONTOLOGIES - LANGUAGE Reference Model Focus: expressivity User: human Technology: independent Ex.: OntoUML Implementa?on Model Focus: tractability User: computer Technology: dependent Ex.: OWL

28 TYPES OF ONTOLOGIES - DOMAIN FoundaHonal Ontologies (UFO, Dolce, BFO) Core Ontologies (UFO-S) Domain Ontologies (Gene Ontology, SNOMED CT) ApplicaHon Ontologies (Hospital X ontology)

29 PRINCIPLE OF IDENTITY =

30 PRINCIPLE OF IDENTITY

31 PRINCIPLE OF IDENTITY

32 PRINCIPLE OF IDENTITY A principle of idenhty support the judgment of whether two parhculars are the same. Every object in a conceptual model of the domain must be an instance of a class represenhng a sortal type. No enhty without idenhty (Quine, 1969) An individual cannot obey incompahble principles of idenhty.

33 ONTOLOGY EXAMPLE <<datatype>> DateTime Domain <<kind>> Recording Device <<kind>> Person start end <<complex event>> Recording Session producedby hasparticipant <<role>> RD as Recorder <<kind>> Record hasparticipant <<role>> Patient *Fragment of the ECG reference ontology: doi: /j.ini

34 BUT HOW ONTOLOGIES CAN HELP ON OUR SEMANTIC INTEROPERABILITY PROBLEMS? Tim Berners-Lee: The SemanHc Web is an extension of the current web in which informa?on is given well-defined meaning, beier enabling computers and people to work in cooperahon. Ontologies will be used by publishers to explicitly define their words and concepts.

35 WEB MINIMAL MACHINE-PROCESSABLE INFORMATION linksto Resource Resource linksto linksto Resource linksto linksto linksto Resource Resource Resource Resource linksto linksto linksto Resource Resource linksto linksto

36 SEMANTIC WEB MACHINE-PROCESSABLE INFORMATION m:pahentat JohnSmith St. James Hospital g:locatedin r:has g:livesin Dublin g:capitalof sn:diabetes Insipidus hpo:phenohpic abnormality r:isa Ireland x:mapsto hpo:diabetes insipidus r:isa hpo:abnormality of the endocrine s ystem

37 W3C S SEMANTIC WEB STANDARD STACK

38 W3C S SEMANTIC WEB STANDARD STACK interac?on trust query reasoning representa?on

39 WHAT IS LINKED DATA? Linked Data is a method of publishing structured data using standard Web technologies such as HTTP, RDF and URIs Tim Berners-Lee, 2006 Linked Data principles: Use URLs to name (idenhfy) things Provide useful informahon about a thing when it s looked up Refer to other things (using their URL) when publishing data on the Web

40 WHAT IS RDF? RDF stands for Resource: pages, concepts, ideas (everything that can have a URI Descrip?on: aiributes, features and relahons of the resources Framework: model, languages and syntaxes for these descriphons The Resource DescripHon Framework (RDF) is a standard model for data interchange on the Web

41 RDF GRAPH MulHple triples form a graph Object Subject Predicate Object / Subject Triple 1

42 RDF RDF is a triple model, i.e., every piece of knowledge is broken down into subject, predicate and object Subject Predicate Object Triple

43 HOW DO I PUBLISH MY DATA AS LINKED DATA? Use URLs to name (idenhfy) things Provide useful informahon about a thing when it s looked up Refer to other things (using their URL) when publishing data on the Web

44 USE URLs TO NAME (IDENTIFY) THINGS Mosquito transmits malaria

45 USE URLs TO NAME (IDENTIFY) THINGS mosquito transmits malaria

46 USE URLs TO NAME (IDENTIFY) THINGS Is there a URL for mosquito, transmits and malaria? Let s search for them! mosquito transmits malaria

47 USE URLs TO NAME (IDENTIFY) THINGS Is there a URL for mosquito, transmits and malaria? Let s search for them! mosquito transmits malaria

48 USE URLs TO NAME (IDENTIFY) THINGS mosquito transmits malaria

49 USE URLs TO NAME (IDENTIFY) THINGS mosquito transmits malaria

50 HOW DO I PUBLISH MY DATA AS LINKED DATA? Use URLs to name (idenhfy) things Provide useful informahon about a thing when it s looked up Refer to other things (using their URL) when publishing data on the Web

51 PROVIDE USEFUL INFORMATION ABOUT A THING WHEN IT S LOOKED UP What do these URLs resolve to? mosquito transmits malaria

52 PROVIDE USEFUL INFORMATION ABOUT A THING WHEN IT S LOOKED UP mosquito

53 PROVIDE USEFUL INFORMATION ABOUT A THING WHEN IT S LOOKED UP malaria

54 PROVIDE USEFUL INFORMATION ABOUT A THING WHEN IT S LOOKED UP transmits

55 HOW DO I PUBLISH MY DATA AS LINKED DATA? Use URLs to name (idenhfy) things Provide useful informahon about a thing when it s looked up Refer to other things

56 REFER TO OTHER THINGS For example: how to treat malaria? mosquito transmits malaria symptomahc relief analgesic treatment

57 Turtle TriG N-Triples N-Quads JSON-LD RDFa RDF HAS DIFFERENT SYNTAXES

58 HOW TO REPRESENT RDF? mosquito transmits malaria < < < n-triples

59 ! HOW TO REPRESENT RDF? mosquito transmits obo: < obo:miro_ obo:idomal_ obo:idomal_ ! Turtle

60 HOW TO REPRESENT RDF? mosquito transmits malaria <?xml version="1.0" encoding="utf-8"?>! <rdf:rdf xmlns:rdf=" xmlns:obo=" <rdf:description rdf:about=" <obo:idomal_ rdf:resource=" </rdf:description>! </rdf:rdf> RDF/XML

61 Q&A/CONTACT INFO Luiz Bonino CTO FAIR Data hip://