Table 2 Main data sources (Part I).

From: An ontology-based knowledge graph for representing interactions involving RNA molecules

Type

Data source

Species

RNAs

Format

API

Threshold

SI

Relation with

TI

Relation

miRNA

miRBase106

271

87,474

rel/CSV

no

validated

WR

miRNA

epi. mod.

WR

M

58,168

7

miRDB107

5

7,086

CSV

no

σ > 80

WR

mRNA

WR

3,519,884

miRNet108

10

7,928

rel/CSV

yes

 

WR

variant

gene

snoRNA

chemical

TF

epi. mod.

lncRNA

pseudogene

circRNA

disease

WR

WR

WR

M

M

M

WR

WR

WR

M

67,532

3,025,487

9,738

4,935

3,311

1,955

31,345

59,417

804,086

32,004

miRecords109

9

384

CSV

no

validated

WR

mRNA

M

1,529

HMDD110

HS

1,206

CSV

no

 

WR

disease

M

35,547

EpimiR111

7

617

CSV

no

 

WR

epi. mod.

M

1,974

miR2Disease112

HS

349

CSV

no

 

WR

disease

O

3,273

TargetScan113

5

5,168

CSV

no

validated

WR

gene

WR

2,850,014

SomamiR114

HS

1,078

CSV

no

validated

WR

mRNA

circRNA

lncRNA

disease

WR

WR

WR

M

2,313,416

428,237

127,025

2,424

TarBase115

18

2,156

rel/CSV

no

 

WR

gene

WR

665,843

miRTarBase116

28

4,630

CSV

no

 

WR

gene

WR

2,200,449

SM2miR117

21

1,658

CSV

no

 

WR

chemical

M

4,989

TransmiR118

19

785

CSV

no

validated

WR

TF

M

3,730

PolymiRTS119

HS

11,182

rel/CSV

no

validated

WR

disease

variant

mRNA

M

WR

WR

83,516

16,412

16,412

dbDEMC120

HS

3,268

CSV

no

pval < 0.01

WR

disease

M

160,800

TAM121

HS

1,209

CSV

no

 

WR

mol. function

miRNA

TF

disease

anatomy

M

WR

M

M

M

2,538

1,218

165

12,516

58

PuTmiR122

HS

1,296

CSV

no

 

WR

TF

M

12,097

miRPathDB123

HS, MM

29,430

CSV

no

FDR < 0.05

validated

WR

mol. function

bio. process

cell. component

pathway

O

O

O

WR

1,066,511

4,782,046

1,136,036

986,400

miRCancer124

HS

57,984

CSV

no

 

WR

disease

M

9,080

miRdSNP125

HS

249

CSV

no

validated

WR

disease

variant

mRNA

M

WR

WR

786

758

180

miRandola126

14

1,002

CSV

no

 

WR

extracell. form

chemical

M

M

3,262

25

mRNA vaccine

DrugBank127

 

4

rel/RDF

yesS

 

P

disease

M

8

  1. For each type of RNA molecule, the table reports the corresponding data sources. Moreover, for each data source, Species and RNAs columns specify the number of species and distinct sequences (HS and MM tags refer to specific species Homo sapiens and Mus musculus); Relation with and Relation columns specify the distinct relationships with bio-entities and their number; Format column refers to the data format (CSV for flatfiles, rel for relational tables, RDF, or HTML for web pages); API column reports the availability of API or SPARQL endpoints (the last one denoted with the superscript s) for data access; Threshold column provides identified quality threshold within the source. SI and TI columns contain the class of the identification schemes (WR – Well-Reputed, O – Ontology-based, M – Mapping- based, and P – Proprietary) adopted respectively by source and target(s) within a specific resource (the source is the RNA molecule specified in the Type column, whereas target(s) are specified in the Relation with column).
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