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Key Things You Need to Know About RDF and Why They Are Important David Booth, Ph.D. HRG & Rancho BioSciences david@dbooth.org Smart Data Conference 18-Aug-2015 Latest version of these slides: http://dbooth.org/2015/key/ RDF is

  1. Key Things You Need to Know About RDF and Why They Are Important David Booth, Ph.D. HRG & Rancho BioSciences david@dbooth.org Smart Data Conference 18-Aug-2015 Latest version of these slides: http://dbooth.org/2015/key/

  2. RDF is fundamentally different from other data formats – XML, JSON, etc. This presentation explains why. But first, some background . . . 2

  3. Comparing RDF with XML or JSON WARNING: Improper comparison! • XML, JSON or any other format could be used in special ways to achieve all of RDF's features – But that isn't how they are normally used • This talk compares RDF with XML and JSON as they are normally used 3

  4. What is RDF? • "Resource Description Framework" – But think "Reusable Data Framework" • Language for representing information • International standard by W3C • Mature: 10+ years • Used in many domains, including biomedical and pharma 4

  5. RDF Assertions (a/k/a "Triples") PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . ex:obs_001 v:units v:mmHg . 5

  6. RDF Assertions (a/k/a "Triples") Predicate Subject Object or Property or Value PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . ex:obs_001 v:units v:mmHg . 6

  7. RDF Assertions (a/k/a "Triples") Equivalent English sentence: PREFIX ex: <http://.../data/> Patient319 has full name "John Doe". PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . ex:obs_001 v:units v:mmHg . 7

  8. RDF Assertions (a/k/a "Triples") Equivalent English sentence: PREFIX ex: <http://.../data/> Patient319 has a systolic blood pressure observation obs_001. PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . ex:obs_001 v:units v:mmHg . 8

  9. RDF Assertions (a/k/a "Triples") PREFIX ex: <http://.../data/> Equivalent English sentence: PREFIX v: <http://.../vocab/> Obs_001 has a value of 120. ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . ex:obs_001 v:units v:mmHg . 9

  10. RDF Assertions (a/k/a "Triples") PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . Equivalent English sentence: Obs_001 has units of mmHg. ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . ex:obs_001 v:units v:mmHg . 10

  11. RDF Assertions (a/k/a "Triples") PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . ex:obs_001 v:units v:mmHg . Sets of assertions form an RDF graph . . . 11

  12. RDF Graph PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . RDF graph ex:obs_001 v:units v:mmHg . 12

  13. RDF Graph PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . RDF graph ex:obs_001 v:units v:mmHg . 13

  14. RDF Graph PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . RDF graph ex:obs_001 v:units v:mmHg . 14

  15. RDF Graph PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . RDF graph ex:obs_001 v:units v:mmHg . 15

  16. RDF Graph PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . RDF graph ex:obs_001 v:units v:mmHg . 16

  17. What is RDF good for? • Large-scale information integration • Semantically connecting diverse data models and vocabularies • Translating between data models and vocabularies • Smarter data use Let's see why . . .

  18. Key things you need to know about RDF #5: RDF is self describing – RDF uses URIs as identifiers #4: RDF is easy to map from other data representations – RDF data is made of assertions #3: RDF captures information – not syntax – RDF is format independent #2: Multiple data models and vocabularies can be easily combined and interrelated – RDF is multi-schema friendly #1: RDF enables smarter data use and automated data translation – RDF enables inference

  19. #5: RDF is self describing • Uses URIs as identifiers http://www.drugbank.ca/drugs/DB00945 19

  20. #5: RDF is self describing • Uses URIs as identifiers http://www.drugbank.ca/drugs/DB00945 drugbank: DB00945 Often abbreviated in RDF: PREFIX drugbank: <http://www.drugbank.ca/drugs/> drugbank:DB00945 . . . . 20

  21. #5: RDF is self describing • Uses URIs as identifiers http://www.drugbank.ca/drugs/DB00945 21

  22. Why is this important? • Terms, data models, vocabularies, etc., can be linked to definitions • Definition can be found by any party – Reduces ambiguity • Aids in bootstrapping new terms toward standardization Supports standards and innovation 22

  23. Terms are self describing ? ✔ • XML: – Can be just as good as RDF if namespaces are properly used – In practice, namespaces are not always used or clickable to definitions ½ • JSON: – In theory, could be used like RDF – In practice, almost never done 23

  24. #4: RDF is easy to map from other data representations • RDF represents information as triples • Triples form a graph 24

  25. RDF Graph PREFIX ex: <http://.../data/> PREFIX v: <http://.../vocab/> ex:patient319 v:fullName "John Doe" . ex:patient319 v:systolicBP ex:obs_001 . ex:obs_001 v:value 120 . RDF graph ex:obs_001 v:units v:mmHg . 25

  26. Why does this matter? • Easy to represent any data model – Hierarchical, relational, graph, etc. • Easy to map any data format to RDF – E.g., XML, JSON, CSV, SQL tables, etc. Great for data integration! 26

  27. Hierarchical data model in RDF 27

  28. Relational data model in RDF People Addresses ID fname addr ID City State 7 Bob 18 18 Concord NH 8 Sue 19 19 Boston MA See W3C Direct Mapping of Relational Data to RDF: 28 http://www.w3.org/TR/rdb-direct-mapping/

  29. Combined: Hierarchical + Relational 29

  30. Combined: Hierarchical + Relational Hierarchical Portion 30

  31. Combined: Hierarchical + Relational Relational Portion 31

  32. Easy to map from other formats? ½ • XML: – Graphs are possible but messy ✔ • JSON: – Except cyclic graphs 32

  33. #3: RDF captures information – not syntax • RDF is format independent • There are multiple RDF syntaxes: Turtle, N-Triples, JSON-LD, RDF/XML, etc. • The same information can be written in different formats • Any data format can be mapped to RDF 33

  34. RDF examples RDF (Turtle) RDF graph @prefix ex: <http://example/ex/> . @prefix loinc: <http://loinc.org/> . @prefix v: <http://example/v/> . ex:obs_001 a v:Observation ; v:code loinc:3727-0 ; v:display "BPsystolic, sitting" ; v:value 120 ; v:units v:mmHg . RDF (N-Triples) <http://example/ex/obs_001> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://example/v/Observation> . <http://example/ex/obs_001> <http://example/v/code> <http://loinc.org/3727-0> . <http://example/ex/obs_001> <http://example/v/display> "BPsystolic, sitting" . <http://example/ex/obs_001> <http://example/v/value> "120"^^<http://www.w3.org/2001/XMLSchema#integer> . <http://example/ex/obs_001> <http://example/v/units> <http://example/v/mmHg> . Same information! 34

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