Linked Life Data 0.2.x
Data integration process
FIXME: Improve the section
- Requirements to database (stable vs unstable id)
- Plan the data source cross links
- Develop a test SPARQL endpoint
- Test the data source cross links
- Consolidate the data in a single repository
- Calculate the inference closure
Data sources overview
Concept type |
Primary data source |
Secondary data source |
SNP |
||
Target |
HMDB (Human Metabolome Database) |
|
UMLS (Unified Medical Language System) (SNOMEDCT, ICD10) |
||
Clinical trials (patient) |
- |
|
Adverse event (patient) |
FDA AERS (Adverse Events Reporting System) |
- |
Additional datasources
Databse |
Description |
Possible cross-links between datasources
Protein concept database links
Database |
Category |
Link to database |
Link to concept |
Comment |
Uniprot |
GeneID |
Entrezt Gene |
Gene |
|
Uniprot |
Features |
dbSNP |
SNP |
|
Uniprot |
Binary Interactions |
Intact |
Interaction |
|
Uniprot |
Ontologies |
Uniprot |
Disease |
Keywords assigned to proteins involved in a specific disease |
Uniprot |
Comments |
? |
Disease |
Concepts occurred in textual field |
Uniprot |
Other Resources |
Drugbank |
Drug |
|
Gene concept database links
Database |
Category |
Link to database |
Link to concept |
Comment |
Entrez Gene |
mRNA and Protein(s) |
Uniprot |
Protein |
|
Entrez Gene |
Genotypes |
dbSNP |
SNP |
|
Entrez Gene |
Interactions |
BIND |
interaction |
|
Entrez Gene |
See related |
OMIM |
Disease |
|
Entrez Gene |
Phenotypes |
OMIM |
Disease |
|
Entrez Gene |
Additional Links |
OMIM |
Disease |
|
SNP (Single Nucleotide Polymorphisms) concept database links
Database |
Category |
Link to database |
Link to concept |
Comment |
dbSNP |
geneID |
Entrez Gene |
Gene |
|
Hapmap |
dbSNP report |
dbSNP |
SNP |
|
Hapmap |
Ensembl SNPview |
Ensembl |
SNP |
|
Drug concept database links
Database |
Category |
Link to database |
Link to concept |
Comment |
Drugbank |
Target Gene Name |
Drugbank |
Target |
Links to internal database identifiers |
Drugbank |
Target UniprotKB/Swiss-Prot ID |
Drugbank |
Target |
Links to internal database identifiers |
Drugbank |
Target Gene Name |
dbSNP |
Drugbank |
Links to internal database identifiers |
Drugbank |
Indication |
UMLS |
Disease |
Concepts occurred in textual field |
Drugbank |
Indication |
OMIM |
Disease |
Concepts occurred in textual field |
Drugbank |
FDA label |
FDA |
Adverse event |
Concepts occurred in PDF documents |
Drugbank |
CAS Registry Number |
DBpedia |
Drug |
|
DBpedia |
drugbank |
Drugbank |
Drug |
|
Drug targets concept database links
Database |
Category |
Link to database |
Link to concept |
Comment |
Drugbank |
Target Gene Name |
Entrez Gene |
Gene |
|
Drugbank |
Target UniprotKB/Swiss-Prot ID |
Uniprot |
protein |
|
Drugbank |
Target Gene Name |
dbSNP |
SNP |
Via Entrez-Gene cross-reference links |
Drugbank |
Target UniprotKB/Swiss-Prot ID |
Intact, DIP |
Interaction |
Via Uniprot cross-reference links |
Drugbank |
Indication |
UMLS |
Disease |
Concepts occurred in textual field |
Drugbank |
Indication |
OMIM |
Disease |
Concepts occurred in textual field |
Protein-Protein Interactions concept database links
Database |
Category |
Link to database |
Link to concept |
Comment |
Intact |
Interacting molecules(Identifier) |
Uniprot |
Protein |
|
BioGRID |
Links |
Uniprot |
Protein |
|
BioGRID |
Links |
Entrez-Gene |
Gene |
|
BioGRID |
Links |
HGNC |
Gene |
|
BioGRID |
Links |
OMIM |
Disease |
|
DIP |
Cross Reference(Swiss-Prot) |
Uniprot |
Protein |
|
Adverse events concept database links
Database |
Category |
Link to database |
Link to concept |
Comment |
FDA AERS |
Drug |
Drugbank |
Drug |
Concepts occurred in textual field |
FDA AERS |
Indications |
UMLS |
Disease |
Concepts occurred in textual field |
TODO: Generate datasources integration schema image
Database specific information
Database name |
Concepts topic |
Last processed release |
Download link |
Schema |
Converter |
Size as NTriples (Mb) |
Entrez-Gene |
gene |
Sep 23, 2008 |
EntrezGene.owl (custom) |
|
500 |
|
Uniprot |
protein |
14.4 |
core.owl (original by the provider) |
|
56400 |
|
BioGRID |
Interaction/Pathway |
2.0.39 |
biopax-level2.owl (original by the provider) |
|
322 |
|
dbSNP |
SNP |
|
|
|
|
|
Drugbank |
Drug, Target |
2.5 |
|
|
|
|
LinkedCT |
Clinical Trials |
|
|
|
|
|
FDA AERS |
adverse events |
|
|
|
|
|
DBpedia |
Drug, Protein, Gene |
- |
dbpedia-ontology.owl (original by the provider) |
|
|