The document summarizes statistics about quantifying RDF data sets. It provides counts of triples, literals, URIs, subjects, predicates, objects, and other metrics for several RDF datasets, including LinkedCT, BioGrid, RxNorm, SUNY Reach, and DrugBank. For each dataset, it lists the top 5 subjects, objects, and predicates as well as overall statistics like literalness, uniqueness, coverage, and type frequencies.

1. Quantifying RDF data sets
(a start)
Janos G. Hajagos
Stony Brook University
School of Medicine
1

2. Resource Description Framework
Graph based data model:
– Vertices or nodes are identified by URIs
<http://dbpedia.org/resource/Aspirin>
– Vertices can be typed: rdf:type
– Directed edges or links are specified with URIs
– Parallel edges are allowed (multi-graph)
– Literals are properties of vertices
2

3. http://challenge.semanticweb.org/submissions/swc2010_submission_15.pdf
3

4. • Pure Python library • No SPARQL support
• In-memory only • Ignores types
• PyPy JIT for speed • No named graphs
• API for pattern matching • No http access
4

5. Counting: 1, 2, 3, . . .
• Number of triples (Nt)
• Number of literals (Nl)
• Number of object URIs (No)
• Number of distinct literals (type removed) (Ndl)
• Number of distinct objects (Ndo)
• Number of distinct subjects (Nds)
• Number of distinct URIs (Nu)
• Number of typed instances (Ni)
• Number of instances of type t (Nit)
• Number of distinct classes (Nc)
• Number of distinct predicates (Ndp)
5

6. Simple fractions
“Literalness” = Nl / Nt
“Literal uniqueness” = Ndl / Nl
“Object uniqueness” = Ndo / No
“Structure” = 1 - (Ni + Nl) / Nt
“Subject coverage” = Nds / Nu
“Object coverage” = Ndo / Nu
“Type frequency of class t” = {Nit / Ni , . . .}
6

7. LODD + Comparisons
Source: http://dx.doi.org/10.1186/1758-2946-3-19
7

8. Linked CT
Top 5 subjects:
Statistics:
<http://data.linkedct.org/resource/country/united-states>, 60,980
Number of triples (Nt): 27,965,909
<http://data.linkedct.org/resource/state/california>, 15,775
Number of literals (Nl): 11,153,086
<http://data.linkedct.org/resource/state/texas>, 13,264
Number of objects (No): 16,812,823
<http://data.linkedct.org/resource/state/new-york>, 13,172
Number of typed instances (Ni): 3,033,501
<http://data.linkedct.org/resource/oversight_info/7eb3d38adc47e7e583ab6031
Number of URIs excluding predicates (Nu): 3,269,681
fe2948ba>, 11,963
Number of distinct classes (Nc): 30
Number of distinct subjects (Nds): 3,033,495
Number of distinct predicates (Ndp): 123 Top 5 objects including literals:
Number of distinct objects (Ndo): 3,148,210 "No", 525,210
Number of distinct literals (Ndl): 5,496,593 <http://data.linkedct.org/vocab/resource/location>, 477,926
Number of distinct lexical symbols (Ndls): 8,621,986 <http://data.linkedct.org/vocab/resource/facility>, 387,542
<http://data.linkedct.org/vocab/resource/outcome>, 376,231
Literalness (Nl/Nt): 0.399 <http://data.linkedct.org/vocab/resource/external_linkage>, 271,431
Literal uniqueness (Ndl/Nl): 0.493 <http://data.linkedct.org/resource/linkage_method/standardized-string-
Object uniqueness (Ndo/No): 0.187 matching>, 185,902
Structure (1 - (Nl+Ni)/Nt): 0.492
Subject coverage (Nds/Nu): 0.927
Object coverage (Ndo/Nu): 0.962 Top 5 predicates:
Class coverage: [0.15, 0.13, 0.12, 0.08, 0.05, 0.04, 0.04, <http://data.linkedct.org/vocab/resource/has_provenance>, 7,482,352
0.04, 0.04, 0.04, 0.04, 0.03, 0.03, 0.03, 0.03, 0.02, 0.01,
0.01, 0.009, 0.008, 0.007, 0.007, 0.006, 0.002, 0.002, <http://www.w3.org/2000/01/rdf-schema#label>, 3,142,207
0.001, 6.0e-05, 4.0e-05, 9.2e-06, 6.6e-07] <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>, 3,033,501
<http://data.linkedct.org/vocab/resource/trial_location>, 982,202
<http://data.linkedct.org/vocab/resource/location_facility>, 477,923
8

9. BioGrid in BioPax
Top 5 subjects:
Statistics:
<http://cbio.mskcc.org/cpath#CPATH-716194>, 470
Number of triples (Nt): 14,326,621
Number of literals (Nl): 5,680,921
<http://cbio.mskcc.org/cpath#CPATH-156001>, 362
Number of objects (No): 8,645,700 <http://cbio.mskcc.org/cpath#CPATH-738240>, 292
Number of typed instances (Ni): 4,229,345 <http://cbio.mskcc.org/cpath#CPATH-818091>, 266,
Number of URIs excluding predicates (Nu): 4,229,358 <http://cbio.mskcc.org/cpath#CPATH-726044>, 229
Number of distinct classes (Nc): 12
Number of distinct subjects (Nds): 4,229,345 Top 5 objects including literals:
Number of distinct predicates (Ndp): 23 <http://www.biopax.org/release/biopax-level2.owl#unificationXref>,
Number of distinct objects (Ndo): 4,009,607 1,249,232
Number of distinct literals (Ndl): 1,145,973 <http://www.biopax.org/release/biopax-
Number of distinct lexical symbols (Ndls): 5,375,354 level2.owl#openControlledVocabulary>, 659,251
"PSI-MI", 659,250
Literalness (Nl/Nt): 0.400 "PUBMED", 439,528
Literal uniqueness (Ndl/Nl): 0.202 <http://www.biopax.org/release/biopax-
Object uniqueness (Ndo/No): 0.464 level2.owl#publicationXref>, 439,528
Structure (1 - (Nl+Ni)/Nt): 0.309
Subject coverage (Nds/Nu): 0.999 Top 5 predicates:
Object coverage (Ndo/Nu): 0.948 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>, 4,229,345
Class coverage: [0.295, 0.156, 0.104, 0.104, 0.104, 0.066, <http://www.biopax.org/release/biopax-level2.owl#DB>, 1,966,356
0.052, 0.052, 0.052, 0.007, 0.007, 2.3e-07]
<http://www.biopax.org/release/biopax-level2.owl#ID>, 1,966,356
<http://www.biopax.org/release/biopax-level2.owl#XREF>, 1,933,616
<http://www.biopax.org/release/biopax-level2.owl#TERM>, 659,251
9

10. RxNorm
Top 5 subjects:
Statistics:
<http://link.informatics.stonybrook.edu/rxnorm/RXCUI/317541>, 11,804
Number of triples (Nt): 9,169,907
<http://link.informatics.stonybrook.edu/rxnorm/RXAUI/3149147>, 9,943
Number of literals (Nl): 4,557,110
<http://link.informatics.stonybrook.edu/rxnorm/RXCUI/316949>, 8,668
Number of objects (No): 4,612,797
<http://link.informatics.stonybrook.edu/rxnorm/RXCUI/316968>, 6,464
Number of typed instances (Ni): 628,852
<http://link.informatics.stonybrook.edu/rxnorm/RXCUI/316965>, 4,605
Number of URIs excluding predicates (Nu): 808,979
Number of distinct classes (Nc): 6
Number of distinct subjects (Nds): 807,722
Number of distinct predicates (Ndp): 193 Top 5 objects including literals:
Number of distinct objects (Ndo): 471,847 <http://link.informatics.stonybrook.edu/rxnorm/RXAUI>, 470,170
Number of distinct literals (Ndl): 2,577,006 <http://link.informatics.stonybrook.edu/rxnorm/RXCUI>, 158,457
Number of distinct lexical symbols (Ndls): 3,385,997 <http://link.informatics.stonybrook.edu/rxnorm/SAB/RXNORM> 143,622
<http://link.informatics.stonybrook.edu/rxnorm/SAB/NDFRT>, 134,049
Literalness (Nl/Nt): 0.497 <http://link.informatics.stonybrook.edu/rxnorm/TTY/CD>, 101,246
Literal uniqueness (Ndl/Nl): 0.565
Object uniqueness (Ndo/No): 0.102
Structure (1 - (Nl+Ni)/Nt): 0.434
Subject coverage (Nds/Nu): 0.998 Top 5 predicates:
Object coverage (Ndo/Nu): 0.583 <http://www.w3.org/2000/01/rdf-schema#label>, 807,705
Class coverage: [0.748, 0.252, 0.0003, 5. 6e-05, 9.5e-06, <http://link.informatics.stonybrook.edu/rxnorm/ATN#NDC>, 634,124
6.360e-06] <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>, 628,852
<http://link.informatics.stonybrook.edu/rxnorm/REL#has_related_form>,
571,320
<http://link.informatics.stonybrook.edu/umls/hasCUI>, 507,950
10

11. SUNY Reach in VIVO
Top 5 subjects:
Statistics:
<http://reach.suny.edu/individual/team_1>, 599
Number of triples (Nt): 1,278,216
<http://reach.suny.edu/individual/Faraone_Stephen>, 404
Number of literals (Nl): 562,262
<http://reach.suny.edu/individual/Hopkins_L>, 298
Number of objects (No): 715,954
<http://reach.suny.edu/individual/Genco_Robert>, 272
Number of typed instances (Ni): 243,263
<http://reach.suny.edu/individual/Jusko_William>, 257
Number of URIs excluding predicates (Nu): 174,488
Number of distinct classes (Nc): 71
Number of distinct subjects (Nds): 161,459 Top 5 objects including literals:
Number of distinct predicates (Ndp): 109 <http://vivoweb.org/ontology/core#Authorship>, 95,303
Number of distinct objects (Ndo): 172,991 <http://xmlns.com/foaf/0.1/Person>, 32,040
Number of distinct literals (Ndl): 224,290 <http://reach.suny.edu/ontology/core#Other_Investigator>, 31,170
Number of distinct lexical symbols (Ndls): 398,887 <http://vivoweb.org/ontology/core#Relationship>, 20,176
<http://vivoweb.org/ontology/core#InformationResource>, 18,301
Literalness (Nl/Nt): 0.440
Literal uniqueness (Ndl/Nl): 0.399
Object uniqueness (Ndo/No): 0.241 Top 5 predicates:
Structure (1 - (Nl+Ni)/Nt): 0.369 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>, 243,263
Subject coverage (Nds/Nu): 0.925 <http://vivoweb.org/ontology/core#freetextKeyword>, 199,327
Object coverage (Ndo/Nu): 0.991 <http://www.w3.org/2000/01/rdf-schema#label>, 144,653
Class coverage: <http://vivoweb.org/ontology/core#informationResourceInAuthorship>,
[0.391, 0.132, 0.128, 0.083, 0.075, 0.040, 0.037, 0.017,. . .] 95,105
<http://vivoweb.org/ontology/core#authorInAuthorship>, 95,101
11

12. DrugBank
Top 5 subjects:
Statistics:
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/targets/587>, 3767
Number of triples (Nt): 766,920
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/targets/3722>, 3032
Number of literals (Nl): 494,028
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/targets/357>, 2780
Number of objects (No): 272,892
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/targets/146>, 2570
Number of typed instances (Ni): 24,522
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/targets/136>, 2504
Number of URIs excluding predicates (Nu): 103,847
Number of distinct classes (Nc): 8 Top 5 objects including literals:
Number of distinct subjects (Nds): 19,693 <http://www4.wiwiss.fu-
Number of distinct predicates (Ndp): 119 berlin.de/drugbank/resource/drugbank/drug_interactions>,10,153
Number of distinct objects (Ndo): 89,685 "physiological process", 8,001
Number of distinct literals (Ndl): 186,457 <http://www4.wiwiss.fu-
Number of distinct lexical symbols (Ndls): 290,307 berlin.de/drugbank/resource/references/17016423>, 7,191
<http://www4.wiwiss.fu-
Literalness (Nl/Nt): 0.644 berlin.de/drugbank/resource/references/17139284>, 7,191),
Literal uniqueness (Ndl/Nl): 0.377 "catalytic activity", 6,841
Object uniqueness (Ndo/No): 0.329
Structure (1 - (Nl+Ni)/Nt): 0.324 Top 5 predicates:
Subject coverage (Nds/Nu): 0.190 <http://www4.wiwiss.fu-
Object coverage (Ndo/Nu): 0.863 berlin.de/drugbank/resource/drugbank/generalReference>, 72,359
Class coverage: [0.41, 0.20, 0.20, 0.19, 0.004, 0.004, <http://www4.wiwiss.fu-
0.002, 0.0002] berlin.de/drugbank/resource/drugbank/goClassificationFunction>, 72,232
<http://www4.wiwiss.fu-
berlin.de/drugbank/resource/drugbank/goClassificationProcess>, 63,520
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/synonym>,
44,949
<http://www4.wiwiss.fu-
berlin.de/drugbank/resource/drugbank/cellularLocation>, 26,258
12

13. DailyMed
Top 5 subjects:
Statistics: <http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/2245>, 240
Number of triples (Nt): 164,276 <http://www4.wiwiss.fu-berlin.de/dailymed/resource/organization/Hospira,_Inc.>,
Number of literals (Nl): 59,885 216
Number of objects (No): 104,391 <http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/2019>, 200
<http://www4.wiwiss.fu-
Number of typed instances (Ni): 14,934
berlin.de/dailymed/resource/organization/Teva_Pharmaceuticals_USA, 193
Number of URIs excluding predicates (Nu): 22,365 <http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/3505>, 170
Number of distinct classes (Nc): 6
Top 5 objects including literals:
Number of distinct subjects (Nds): 10,015
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/ingredients>,
Number of distinct predicates (Ndp): 28 5,577
Number of distinct objects (Ndo): 21,968 http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/drugs>, 4,308
Number of distinct literals (Ndl): 45,814 <http://www4.wiwiss.fu-berlin.de/drugbank/vocab/resource/class/Offer>,
Number of distinct lexical symbols (Ndls): 68,181 4308
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/routeOfAdministration/Oral>,
2,465
Literalness (Nl/Nt): 0.364 <http://www4.wiwiss.fu-
Literal uniqueness (Ndl/Nl): 0.765 berlin.de/dailymed/resource/ingredient/magnesium_stearate>, 1,405
Object uniqueness (Ndo/No): 0.210
Structure (1 - (Nl+Ni)/Nt): 0.544 Top 5 predicates:
<http://www.w3.org/2002/07/owl#sameAs>, 31,929
Subject coverage (Nds/Nu): 0.448
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/inactiveIngredient>,
Object coverage (Ndo/Nu): 0.982 28,403
Class coverage: [0.37, 0.29, 0.29, 0.05, 0.002, 0.0003] <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>, 14,934
<http://www.w3.org/2000/01/rdf-schema#label>, 10,596
<http://www4.wiwiss.fu-
berlin.de/dailymed/resource/dailymed/possibleDiseaseTarget>, 6,124
<http://www4.wiwiss.fu-
berlin.de/dailymed/resource/dailymed/routeOfAdministration>, 4,308
13

14. Building a co-author network from VIVO
with a twist
14

15. VIVO ontology modeling of authorship
The twist is to include only members of the Reach site
15

16. Graph processing and extraction
• Follow
– Multiple linked steps are allowed
• Collapse parallel edges
– Add weight to edges based on
on counts
• Export
– Standard graph format like GraphML, an XML format for
graph exchange
16

17. Network analysis with NetworkX
17

18. Network analysis with Mathematica
18

19. Network visualization with Gephi
19

20. For Your Information
- Linked CT: http://queens.db.toronto.edu/~oktie/linkedct/
- BioGrid in PAX: http://www.pathwaycommons.org/pc-
snapshot/current-release/biopax/by_source/
- Drugbank: http://www4.wiwiss.fu-
berlin.de/drugbank/drugbank_dump.nt
- DailyMed: http://www4.wiwiss.fu-
berlin.de/dailymed/dailymed_dump.nt
- RxNorm is available at:
http://link.informatics.stonybrook.edu/rxnorm/
- Reach VIVO site is at: http://reach.sunysb.edu
SPARQL endpoint:
http://link.informatics.stonybrook.edu/sparql/
named graph http://reach.sunysb.edu
20

21. The End
http://ctsaconnect.org/
21