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Databases Picture by Jeremy Hiebert [http://www.flickr.com/photos/jeremyhiebert/] Graph Databases Motivation Andr Santanch e Patrcia Cavoto Institute of Computing UNICAMP August 2015 Graph Database Graph as the basic data model of

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Databases

Graph Databases

Motivation André Santanchè e Patrícia Cavoto Institute of Computing – UNICAMP

August 2015

Picture by Jeremy Hiebert [http://www.flickr.com/photos/jeremyhiebert/]

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Graph Database

Graph as the basic data model of a database

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Why Graphs?

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SLIDE 4

Why Graphs?

▪ The Web Effect

▫ Linked Data ▫ Social Networks and Social Content

▪ Sharing and interconnecting ▪ Complex Networks

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SLIDE 5

Why Graphs?

Linked Data

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SLIDE 6

Wikipedia

Infobox

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DBPedia

Île-de- France France Paris Departments Prefecture Country Region Yvelines Departments Region

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DBPedia (URIs)

http://en.wikipedia.org/wiki/Yvelines http://en.wikipedia.org/wiki/Île-de-France_(region) http://en.wikipedia.org/wiki/Paris http://en.wikipedia.org/wiki/France

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DBPedia – English

▪ 4 million things ▪ 3.22 million classified in a consistent ontology

▫ 832,000 persons ▫ 639,000 places (427,000 populated) ▫ 372,000 creative works

  • 116,000 music albums; 78,000 films; 18,500 video games

▫ 209,000 organizations ▫ 226,000 species ▫ 5,600 diseases.

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DBPedia – International

▪ 119 languages ▪ 24.9 million things ▪ 16.8 million interlinked with English ▪ 12.6 million unique things

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Datasets published following Linked Data ‘format’: 05/2007

Source: http://lod-cloud.net/

Linked Data

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Datasets published following Linked Data ‘format’: 11/2007

Source: http://lod-cloud.net/

Linked Data

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Datasets published following Linked Data ‘format’: 2008

Source: http://lod-cloud.net/

Linked Data

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Datasets published following Linked Data ‘format’: 2009

Source: http://lod-cloud.net/

Linked Data

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Datasets published following Linked Data ‘format’: 2010

Source: http://lod-cloud.net/

Linked Data

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Datasets published following Linked Data ‘format’: 2011

Linked Data

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Source: http://lod-cloud.net/

Linked Data

04/2014

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Why Graphs?

Social Networks and Social Content

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Searching Pet

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Pet Shop Boys

Anirudh Koul pet shop boys, pet, concert, tour

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cat, kittens, eyes, ears, pet, animal cat, kitten, garden, pet cat, kitty, eyes, pretty dog, pet, alaskan malamute dog, pet, animal, funny, glasses

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recycle, pet, plastic bottle, polyethylene terephthalate recycle, pet, plastic bottle, polyethylene terephthalate wine, pet, bottle

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cat, kittens, eyes, ears, pet, animal cat, kitten, garden, pet Jay Woodworth sfroehlich1121 cat, kitty, eyes, pretty sfroehlich1121 Edward Corpuz dog, pet, alaskan malamute dog, pet, animal, funny, glasses shorty_nz_2000

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SLIDE 24

recycle, pet, plastic bottle, polyethylene terephthalate Nemo's great uncle recycle, pet, plastic bottle, polyethylene terephthalate FaceMePLS Karl Baron wine, pet, bottle

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Graph users/tags/resources

dog cat bottle pet

tags users resources

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pet cat dog bottle Graph users/tags/resources

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pet cat pet cat pet dog pet bottle pet bottle cat kitty dog animal pet recycle bottle plastic

Co-ocurrences and Latent Semantics

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Co-ocurrences and Latent Semantics

cat pet dog kitty animal bottle recycle plastic pet

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Co-ocurrences and Latent Semantics

cat pet animal dog pet animal mouse pet animal snake animal tiger animal

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Co-ocurrences and Latent Semantics

cat pet animal dog mouse snake tiger

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Social Effect Suggested/Reinforced Tags

black, cat, kitty, katze, long, hair, blue, eyes, pretty, canon, t1i, 500d, ef 100mm f/2.8 usm macro sfroehlich1121

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Social Effect Suggested/Reinforced Tags

black, cat, kitty, katze, long,

hair, blue, eyes, pretty,

canon, t1i, 500d, ef 100mm f/2.8 usm macro sfroehlich1121

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SLIDE 33

M1 co-occurrences in a folksonomy

tags / co-occurrences w w w w

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Tagsets

tagsets tags tagsets

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M2 tagsets and their co-occurrences tagsets/co-occurrences w w w w w

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M4 Social Ontology

is-a tagsets / typed relations

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M3 simplified model of an ontology

part-of is-a is-a concepts/relations

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M5 Folksonomized Ontology (FO)

i i i i i i i i

is-a, w w w w w w w w concepts / typed relations (ontology) + information content / co-occurrences (folksonomy)

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Meaning of Pet needs meaning of other tags?

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Matrix What is the meaning of the word Love?

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Why Graphs?

Sharing and Interconnecting

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Models to Describe

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Describing Prehistoric Animals

Lyme Regis England Is a Plesiosaurus dolichodeirus Origin Recognized 1824 Size 5

MNHN A. C. 8592

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Describing Prehistoric Animals

Lyme Regis England Is a Plesiosaurus dolichodeirus Origin Recognized 1830 Size 5

SIPB R 90

  • St. Croix

Switzerland Is a Plesiosaurus gurgitis Origin Recognized 1964 Size 3.5

STC223

Is a Triceratops horridus Origin Lance Creek Recognized 1889 Size 9

MNHN 1912.20

EUA Hell Creek EUA

FMNH PR2081

Is a Tyrannosaurus rex Origin Recognized 1990

Sue

Size 12.3

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SLIDE 45

Table

STC223 Plesiosaurus gurgitis

  • St. Croix

1964 3.5 Id Is a MNHN 1912.20 Triceratops horridus Lance Creek 1889 9 FMNH PR2081 Tyrannosaurus rex Hell Creek 1990 12.3 Switzerland Origin Place Recognized Size Origin Country EUA EUA SIPB R 90 Plesiosaurus dolichodeirus Lyme Regis 1830 5 England MNHN A. C. 8592 Plesiosaurus dolichodeirus Lyme Regis 1824 5 England

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Table Excellent to Manage Data with Predictable Static Schema Sharing?

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Documents and XML

Plesiosaurus dolichodeirus Is a id=MNHN A. C. 8592 CodedDescription Origin Place Country Lyme Regis England 1824 Recognized 5 Size

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Documents and XML

Plesiosaurus dolichodeirus Is a id=MNHN A. C. 8592 CodedDescription Origin Place Country Lyme Regis England 1824 Recognized 5 Size Plesiosaurus dolichodeirus Is a id=SIPB R 90 CodedDescription Origin Place Country Lyme Regis England 1830 Recognized 5 Size Triceratops horridus Is a MNHN 1912.20 CodedDescription Origin Place Country Lance Creek EUA 1889 Recognized 9 Size Tyrannosaurus rex Is a FMNH PR2081 CodedDescription Origin Place Country Hell Creek EUA 1990 Recognized 12.3 Size

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Documents and XML

Plesiosaurus dolichodeirus Is a id=MNHN A. C. 8592 CodedDescription Origin Place Country Lyme Regis England 1824 Recognized 5 Size Plesiosaurus dolichodeirus Is a id=SIPB R 90 CodedDescription Origin Place Country Lyme Regis England 1830 Recognized 5 Size Triceratops horridus Is a MNHN 1912.20 CodedDescription Origin Place Country Lance Creek EUA 1889 Recognized 9 Size Tyrannosaurus rex Is a FMNH PR2081 CodedDescription Origin Place Country Hell Creek EUA 1990 Recognized 12.3 Size

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SLIDE 50

How much hierarchical is your data?

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Back to the Table

STC223 Plesiosaurus gurgitis

  • St. Croix

1964 3.5 Id Is a MNHN 1912.20 Triceratops calicornis Lance Creek 1888 9 FMNH PR2081 Tyrannosaurus rex Hell Creek 1990 12.3 Switzerland Origin Place Recognized Size Origin Country EUA EUA SIPB R 90 Plesiosaurus dolichodeirus Lyme Regis 1830 5 England MNHN A. C. 8592 Plesiosaurus dolichodeirus Lyme Regis 1824 5 England MNHN 1912.20b Triceratops horridus Lance Creek 1889 9 EUA

renamed near includes

Le Muséum national d'Histoire naturelle

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The tradeoff of Static Schemas

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XML Schema Not designed to mix

LSID Life Science Identifier GBIF Infrastructure Species 2000 Infrastructure ITIS Infrastructure EOL Schema Esquema SpeciesBase Darwin Core ABCD Species 2000 Standard dataset SDD Encyclopedia

  • f Life

speciesLink TDWG Standards Committee Xper2 Phenotypes and Identification Keys Lucid Phenotypes and Identification Keys Catalog of Life schema schema schema schema defines defines exports exports defines adopts adopts adopts adopts uses uses

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DataSpaces Pay-as-you-go Integration

Franklin, M., Halevy, A., & Maier, D. (2005). From databases to dataspaces: a new abstraction for information

  • management. SIGMOD Rec., 34(4), 27–33.
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DataSpaces and Linked Data

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Why Graphs?

Complex Networks

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SLIDE 57

Complex Networks

▪ Developed steadily since 1999 ▪ Discrete systems are represented in terms of

entities and relationships

(Luciano da F. Costa, 2013)

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Patient x Diagnosis

(Gomes-Jr, 2013)

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Complex Networks

▪ Physical relationships

▫ neurons – nodes; connections – edges

▪ Force relationships

▫ grains – nodes; force vectors – edges

▪ Social relationships ▪ Conceptual relationships

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Complex Networks Examples

http://www-personal.umich.edu/~mejn/networks/

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Les Miserables

(Neo4j example)

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Cadeia Alimentar FishBase

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Freshwater food web

Freshwater food web: Neo Martinez and Richard Williams.

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Contagion of TB

Contagion of TB, books on politics: Valdis Krebs, www.orgnet.com.

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Yeast proteins

Yeast proteins: Sergei Maslov and Kim Sneppen, Specificity and stability in topology of protein networks, Science 296, 910-913 (2002).

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What can I ask to a Graph?

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Triceratops in a Graph

Is a Triceratops horridus Origin Lance Creek Recognized 1889 Size 9

MNHN 1912.20

EUA

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Triceratops in a Graph

MNHN 1912.20 9 size Triceratops horridus is a Lance Creek

  • rigin

1889 recognized

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Triceratops in a Graph

MNHN 1912.20 9 size Triceratops horridus is a Lance Creek

  • rigin

1889 recognized Converse County Wyoming EUA part of part of part of

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Tyrannosaurus in a Graph

FMNH PR2081

12.3 size Tyrannosaurus rex is a Hell Creek

  • rigin

1990 recognized Cheyenne River Indian Reservation South Dakota EUA part of part of part of

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Analyzing in the Space

OpenStreetMap

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Analyzing in the Space

Hell Creek Cheyenne River Indian Reservation South Dakota EUA Lance Creek Converse County Wyoming

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Analyzing in the Space

Hell Creek Cheyenne River Indian Reservation South Dakota EUA Lance Creek Converse County Wyoming

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GeoNames

MNHN 1912.20 9 size Triceratops horridus is a Lance Creek http://www.geonames.org/5829995/

  • rigin

1889 recognized Niobrara County http://www.geonames.org/5833446 Wyoming http://www.geonames.org/5843591 United States http://www.geonames.org/6252001

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Processing the Query

▪ Process by pattern

▫ Find [species] whose [origin]

( → 0..*) part of → EUA

▪ Process by inference

▫ Find [species] whose [origin]

EUA →

▫ Rules:

  • If (A) origin (B) and (B) part of (C) => (A) origin (C)
  • If (A) part of (B) and (B) part of (C) => (A) part of (C)
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Looking the Topology

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Graph Topology

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Graph Topology

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Patient x Diagnosis

▪ Retrieve candidate diagnosis relevant to a

given patient based on her symptoms and correlations with other similar patients.

(Gomes-Jr, 2013)

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From Dataspaces to Ontologies

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From Dataspaces to Ontologies

Ontology Dataspace Linked Graph

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Building Patterns

Instances Schema ID

when where what what

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84

Data Exploration Prototype

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7 distinct morphological descriptions:

  • genus Varanus
  • V

a r a n u s g

  • u

l d i i

  • V

a r a n u s i n d i c u s

  • V

a r a n u s p r a s i n u s

  • V

a r a n u s s a l v a t

  • r
  • V

a r a n u s s p i n y

  • V

a r a n u s t i mo r e n s i s

Integrating phenotypes

85

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7 distinct morphological descriptions:

  • genus Varanus
  • V

a r a n u s g

  • u

l d i i

  • V

a r a n u s i n d i c u s

  • V

a r a n u s p r a s i n u s

  • V

a r a n u s s a l v a t

  • r
  • V

a r a n u s s p i n y

  • V

a r a n u s t i mo r e n s i s

Our approach

86

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7 distinct morphological descriptions:

  • genus Varanus
  • V

a r a n u s g

  • u

l d i i

  • V

a r a n u s i n d i c u s

  • V

a r a n u s p r a s i n u s

  • V

a r a n u s s a l v a t

  • r
  • V

a r a n u s s p i n y

  • V

a r a n u s t i mo r e n s i s

Our approach

87

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7 distinct morphological descriptions:

  • genus Varanus
  • V

a r a n u s g

  • u

l d i i

  • V

a r a n u s i n d i c u s

  • V

a r a n u s p r a s i n u s

  • V

a r a n u s s a l v a t

  • r
  • V

a r a n u s s p i n y

  • V

a r a n u s t i mo r e n s i s

Our approach

88

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7 distinct morphological descriptions:

  • genus Varanus
  • V

a r a n u s g

  • u

l d i i

  • V

a r a n u s i n d i c u s

  • V

a r a n u s p r a s i n u s

  • V

a r a n u s s a l v a t

  • r
  • V

a r a n u s s p i n y

  • V

a r a n u s t i mo r e n s i s

Our approach

89

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7 distinct morphological descriptions:

  • genus Varanus
  • V

a r a n u s g

  • u

l d i i

  • V

a r a n u s i n d i c u s

  • V

a r a n u s p r a s i n u s

  • V

a r a n u s s a l v a t

  • r
  • V

a r a n u s s p i n y

  • V

a r a n u s t i mo r e n s i s

Our approach

90

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SLIDE 91

7 distinct morphological descriptions:

  • genus Varanus
  • V

a r a n u s g

  • u

l d i i

  • V

a r a n u s i n d i c u s

  • V

a r a n u s p r a s i n u s

  • V

a r a n u s s a l v a t

  • r
  • V

a r a n u s s p i n y

  • V

a r a n u s t i mo r e n s i s

Our approach

91

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SLIDE 92

7 distinct morphological descriptions:

  • genus Varanus
  • V

a r a n u s g

  • u

l d i i

  • V

a r a n u s i n d i c u s

  • V

a r a n u s p r a s i n u s

  • V

a r a n u s s a l v a t

  • r
  • V

a r a n u s s p i n y

  • V

a r a n u s t i mo r e n s i s

Our approach

92

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SLIDE 93

7 distinct morphological descriptions:

  • genus Varanus
  • V

a r a n u s g

  • u

l d i i

  • V

a r a n u s i n d i c u s

  • V

a r a n u s p r a s i n u s

  • V

a r a n u s s a l v a t

  • r
  • V

a r a n u s s p i n y

  • V

a r a n u s t i mo r e n s i s

Our approach

93

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Evaluating Similarity

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Size of the Shared Universe

judge prosecutor

  • fficial

functionary person adjudicator child actor district attorney state attorney

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SLIDE 96

Size of the Shared Universe

judge prosecutor

  • fficial

functionary person adjudicator child actor district attorney state attorney

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SLIDE 97

Size of the Shared Universe

judge prosecutor

  • fficial

functionary person adjudicator child actor district attorney state attorney

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SLIDE 98

Size of the Shared Universe

People (judge + child) Official Functionary (judge + district attorney)

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SLIDE 99

Size of the Shared Universe

People (judge + child) Official Functionary (judge + district attorney)

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SLIDE 100

Similarity

▪ What is more

similar of a tobacco mosaic virus?

a)variola major virus b)plant

virus microorganism

  • rganism

bacteria plant variola virus poxvirus animal virus variola major virus tobacco mosaic virus plant virus

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SLIDE 101

Similarity

Minimum path length

▪ What is more

similar of a tobacco mosaic virus?

a)variola major virus b)plant (?)

virus microorganism

  • rganism

bacteria plant variola virus poxvirus animal virus variola major virus tobacco mosaic virus plant virus 5 edges 6 edges

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SLIDE 102

Similarity

More specialized common ancestor

▪ What is more

similar of a tobacco mosaic virus?

a)variola major virus b)plant

virus microorganism

  • rganism

bacteria plant variola virus poxvirus animal virus variola major virus tobacco mosaic virus plant virus more information content less information content

common ancestor (more specific) common ancestor (more generic)

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SLIDE 103

Similarity

Maximum information content

▪ What is more

similar of a tobacco mosaic virus?

a)variola major virus b)plant

virus microorganism

  • rganism

bacteria plant variola virus poxvirus animal virus variola major virus tobacco mosaic virus plant virus more information content less information content

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SLIDE 104

Similarity

Maximum information content

▪ What is more

similar of a tobacco mosaic virus?

a)variola major virus b)plant

virus microorganism

  • rganism

bacteria plant variola virus poxvirus animal virus variola major virus tobacco mosaic virus plant virus more information content less information content

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Graph Databases

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Graph Model

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Graph Model

RDF Graph

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RDF Graph

▪ Triple model: resource, property, value

resource value property

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RDF Graph

▪ Triple model: resource, property, value ▪ The value can be another resource

resource value property resource property value

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SLIDE 110

RDF Graph

▪ Triple model: resource, property, value ▪ The value can be another resource ▪ … described by a property,value

resource value property resource property value resource property value/resource value property

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Plesiosaurus dolichodeirus in RDF

▪ Triple: <MNHN A. C. 8592>, size, 5

MNHN A. C. 8592 5 size

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Plesiosaurus dolichodeirus in RDF

▪ Triple: <MNHN A. C. 8592>, size, 5 ▪ Triple: <MNHN A. C. 8592>, recognized, 1830

MNHN A. C. 8592 5 size 1830 recognized

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SLIDE 113

Plesiosaurus dolichodeirus in RDF

▪ <MNHN A. C. 8592>, is_a, <Plesiosaurus dolichodeirus>

MNHN A. C. 8592 5 size 1830 recognized Plesiosaurus dolichodeirus is a

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SLIDE 114

Plesiosaurus dolichodeirus in RDF

MNHN A. C. 8592 5 size Plesiosaurus dolichodeirus is a Lyme Regis

  • rigin

England country 1830 recognized

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SLIDE 115

MNHN A. C. 8592 5 size LSID:123456 is a Lyme Regis

  • rigin

England country 1830 recognized Plesiosaurus dolichodeirus label Plesiossauro popular@pt-BR

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SLIDE 116

Identifying by surrogates and LSID

MNHN A. C. 8592 5 size LSID:123456 is a Lyme Regis

  • rigin

England country 1830 recognized Plesiosaurus dolichodeirus label Plesiossauro popular@pt-BR

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SLIDE 117

Identifying by URIs

MNHN A. C. 8592 5 size LSID:123456 is a

http://en.wikipedia.org/wiki/Lyme_Regis http://en.wikipedia.org/wiki/England

country 1830 recognized Plesiosaurus dolichodeirus label Plesiossauro popular@pt-BR Lyme Regis label

  • rigin
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SLIDE 118

Short URIs (namespaces)

MNHN A. C. 8592 5 size LSID:123456 is a wiki:Lyme_Regis

  • rigin

wiki:England country 1830 recognized Plesiosaurus dolichodeirus label Plesiossauro popular@pt-BR Lyme Regis label

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SLIDE 119

RDF Graph

http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/publisher http://www.x.org/contratado http://www.x.org/razao_social http://purl.org/dc/elements/1.1/title http://www.x.org/edicao http://www.x.org/data_publicacao http://www.x.org/nome Horácio Montéquio Editora Edissauros Vida dos Dinossauros 17/05/2001 2

a

http://www.paleo.org/dinos.pdf mailto:horacio@paleo.org http://www.edissauros.com.br

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SLIDE 120

Graph Model

Property Graph

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SLIDE 121

Property Graph

▪ (node)

node

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SLIDE 122

Property Graph

▪ (node)

▫ Nodes can have properties

(node { property: value })

node node property: value

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SLIDE 123

Property Graph

▪ (node)

▫ Nodes can have properties

(node { property: value })

▪ (node)-[edge]->(node)

node node property: value node edge node

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SLIDE 124

Property Graph

▪ (node)

▫ Nodes can have properties

(node { property: value })

▪ (node)-[edge]->(node)

▫ Edges can have properties

(node)-[edge {property:value}]->(node)

node node property: value node edge node node edge property: value node

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SLIDE 125

Plesiosaurus in a Property Graph

MNHN A. C. 8592

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SLIDE 126

Plesiosaurus in a Property Graph

MNHN A. C. 8592 size: 5 recognized: 1830

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SLIDE 127

Plesiosaurus in a Property Graph

MNHN A. C. 8592 Plesiosaurus dolichodeirus is a Lyme Regis

  • rigin

England country size: 5 recognized: 1830

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SLIDE 128

LSID Surrogate

MNHN A. C. 8592 is a Lyme Regis

  • rigin

England country size: 5 recognized: 1830 LSID:123456 label: Plesiosaurus dolichodeirus popular@pt-BR: Plesiossauro

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SLIDE 129

URI Identifiers

MNHN A. C. 8592 is a wiki:Lyme_Regis

  • rigin

wiki:England country size: 5 recognized: 1830 LSID:123456 label: Plesiosaurus dolichodeirus popular@pt-BR: Plesiossauro label: Lyme Regis label: England

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SLIDE 130

Property in the origin edge

MNHN A. C. 8592 is a wiki:Lyme_Regis

  • rigin

wiki:England country size: 5 recognized: 1830 LSID:123456 label: Plesiosaurus dolichodeirus popular@pt-BR: Plesiossauro label: Lyme Regis label: England discovered: 1824

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SLIDE 131

Back to the Property Graph

MNHN A. C. 8592 5 size LSID:123456 is a wiki:Lyme_Regis

  • rigin

1830 recognized Plesiosaurus dolichodeirus label Plesiossauro popular: pt-BR

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SLIDE 132

Two properties for origin

MNHN A. C. 8592 5 size LSID:123456 is a wiki:Lyme_Regis 1830 recognized Plesiosaurus dolichodeirus label Plesiossauro popular: pt-BR

  • rigin

place 1824 discovered

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SLIDE 133

References

▪ GOMES-JR, L. C.; JENSEN, R.; SANTANCHÈ, A. (2013) Towards Query

Model Integration: Topology-aware, IR-inspired Metrics for Declarative Graph Querying, II Workshop on Querying Graph Structured Data 2013, Genoa.

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SLIDE 134

André Santanchè

http://www.ic.unicamp.br/~santanche

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SLIDE 135

Property

Label Detail var:origin Origin of the specimen This descriptor has to be used with great precaution...

var:origin

property

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SLIDE 136

Using the Property

CodedDescription taxa:V_bengalensis.html Label Detail state:asia Asia and austral isles The specimen is from Asia or the austral islands...

var:origin

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SLIDE 137

Connected Graph

... taxa:V_bengalensis.html state:asia

var:origin

...

var:origin var:origin

slide-138
SLIDE 138

Origin in GeoNames

taxa:V_bengalensis.html http://www.geonames.org/1269750/

var:origin

India

slide-139
SLIDE 139

Geo Tree

http://www.geonames.org/6255147/ http://www.geonames.org/1269750/

gn:parentFeature

India Asia

slide-140
SLIDE 140

Hypergraph

(Jaudete Daltio, 2013)

slide-141
SLIDE 141

Licença

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  • Commons. Sob as seguintes condições: Atribuição, Uso Não-

Comercial e Compartilhamento pela mesma Licença.

▪ Mais detalhes sobre a referida licença Creative Commons veja

no link: http://creativecommons.org/licenses/by-nc-sa/3.0/

▪ Fotografia de capa e fundos: web-drops por Jeremy Hiebert [

http://www.flickr.com/photos/jeremyhiebert/] dispinível em http://www.flickr.com/photos/jeremyhiebert/6081389428/