HCLSIG/LODD/Data/DataSetEvaluation

This page provides an overview about the characteristics of datasets that could be relevant for the HCLSIG LODD effort.

LODD-related datasets that are already available as Linked Data

Project Home Page	Topic	Short Description	Size	License	Data dumps	Status/ Activity	Possible Linking to Other Datasets	Example Instances
chEBI	Chemical Compounds	dictionary of molecular entities focused on small chemical compounds	15,548 annotated entities	free	structured text files	updated monthly	CAS, KEGG
DailyMed	Drugs	information about approved prescription drugs, includes FDA approved labels (package inserts)	96,000 triples; 4,039 drugs		XML, SPL	updated regularly (RSS)	RX Norm, NDC	"Sterile Water (Irrigant)" via Marbles, via OpenLink Data Explorer
DBpedia	Drugs/ Diseases/ Proteins	RDF data about 2.49 million things that has been extracted from Wikipedia	218 million RDF triples; 2,300 drugs, 2,200 proteins	free	RDF	updated every 3 months	ATC, CAS, DrugBank, EntrezGene, HGNCid, OMIM, PubChem, ChemSpider	Aspirin, HIV
Diseasome	Diseases / Genes	characteristics of disorders and disease genes linked by known disorder–gene associations	87,000 triples; 2,600 genes	free	structured text files	updated 2006	OMIM, Entrez Gene	Alzheimer's via Marbles, via OpenLink Data Explorer
Drug Bank	Drugs	drug (i.e., chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e., sequence, structure, and pathway) information	1.1 million triples; 4,800 drugs, 2,500 protein sequences	permission of authors needed	structured text files (FASTA, SDF, DrugCard)	updated August 2008, irregular	PubChem, FDA/NDA, ChEBI, IUPAC, INCHI, CAS, KEGG	Varenicline via Marbles, via OpenLink Data Explorer
LinkedCT	Clinical Trials	Linked data source of trials from ClinicalTrials.gov	7 million triples, 62000 trials	free - with Terms and Conditions	Available upon request	preview release	DBpedia, GeoNames, Bio2RDF	Influenza (Intervention), A Trial, AIDS (condition), A reference, A location
OMIM	Genes	compendium of human genes and genetic phenotypes	12,000 genes	license from the Johns Hopkins University needed	structured text files	updated daily		CHONDROSARCOMA via Marbles, via OpenLink Data Explorer; TUMOR PROTEIN p53 via Marbles, via OpenLink Data Explorer

LODD-related datasets that are already RDFized but not served as Linked Data on the Web

Datasets RDFized by the Linked Life Data project (UniProt, Entrez Gene, Gene Ontology, Reactome, BioCyc, ...)
Datasets RDFized by the BioRDF project (GO, Mesh, Reactome, UniProt, ...)

LODD-related datasets that are not available as Linked Data yet

Project Home Page	Topic	Short Description	Size	License	Data dumps	Status/Activity	Possible Linking to Other Datasets	Example Instances
Adis R&D Insight	Drugs	comprehensively reports on the latest developments of drugs in active research and development internationally	19,000 drugs	written permission of Adis Data Information BV needed		updated weekly	CAS
ChemBlast	Atoms	information on all the ligands (HIV-related) and their scaffolds			Molecule pictures, (MDL, Excel)?	updated April 2008	IUPAC, PubChem
ChemSpider	Chemical Compounds	database of organic molecules containing more than 20 million compounds from many different providers	>20,000,000 chemical compounds		HTML, no downloads	updated regularly	ChEBI, DailyMed, KEGG, PubChem, Wikipedia, DrugBank, InChI, MESH
ClinicalTrials.gov	Trials	federally and privately supported clinical trials conducted worldwide; information about a trial's purpose, who may participate, locations, and phone numbers for more details	62,693 trials	accompanied by origin and date of data, and modifications made	HTML		ChemIDplus
Citeline TrialTrove	Trials	information about ongoing clinical trials		proprietary
DrugDB	Drugs	(offline)
Drug Ontology	Drugs	ontology including concepts such as indications, interactions, formulary, etc.			OWL schema only	updated 2005
DrugDigest	Drugs	usage advise for drugs, vitamins, and herbs	1,500 drugs	permission needed	HTML	updated daily
DrugInfo	Drugs	covers drugs in clinical trials, approval processes and on the market; information collected from other NLM services mostly	15,000 drugs	permission needed	HTML	updated daily	CAS, CT.gov, DailyMed, Medline, PubChem
Investigational Drug Database	Drugs	investigational drug development, from first patent to eventual launch or discontinuation	107,000 therapeutic patents; 23,000 drugs; 80.000 chemical structures	proprietary
IMS	Drugs	information about development, efficacy, and status of pharmaceuticals from early clinical testing through to launch	16,800 drug summaries	proprietary		updated weekly
KEGG Drug	Drugs	chemical structure based information resource for all approved drugs in Japan and the U.S.A; each is identified by the D number, and is associated with generic names, trade names, efficacy, target information, etc.		academic usage	structured text files	updated July 2008	DailyMed, PubChem
LillyTrials	Trials	clinical trials sponsored by Eli Lilly and Company			HTML, PDF	updated regulary	NDA
MedMaster	Drugs	information on drugs and their interactions, herbs and supplements	>1000 drugs	permission needed	HTML	updated daily	NDA
National Drug Code	Drugs	prescription drugs and insulin products that have been manufactured, prepared, propagated, compounded, or processed by registered establishments for commercial distribution		free	structured text files	updated regularly	NDA
Orange Book	Drugs	Generic product ANDA (Abbreviated New Drug Approval) approvals		free	structured text files	updated daily	NDA, FDA
Pharmaprojects	Drugs	drugs and their bindings to proteins		proprietary			Entrez Gene
PubChem	Chemical Compounds	chemical structures of small organic molecules and information on their biological activities		free	ASN.1, XML, SDF	updated daily	IUPAC, InChI
RxNorm	Drugs	standard names for clinical drugs		login required			National Drug Code