This page provides an overview about the characteristics of datasets that could be relevant for the HCLSIG LODD effort.
Project Home Page
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Topic
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Short Description
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Size
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License
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Data dumps
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Status/ Activity
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Possible Linking to Other Datasets
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Example Instances
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chEBI
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Chemical Compounds
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dictionary of molecular entities focused on small chemical compounds
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15,548 annotated entities
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free
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structured text files
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updated monthly
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CAS, KEGG
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DailyMed
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Drugs
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information about approved prescription drugs, includes FDA approved labels (package inserts)
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96,000 triples; 4,039 drugs
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XML, SPL
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updated regularly (RSS)
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RX Norm, NDC
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"Sterile Water (Irrigant)" via Marbles, via OpenLink Data Explorer
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DBpedia
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Drugs/ Diseases/ Proteins
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RDF data about 2.49 million things that has been extracted from Wikipedia
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218 million RDF triples; 2,300 drugs, 2,200 proteins
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free
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RDF
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updated every 3 months
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ATC, CAS, DrugBank, EntrezGene, HGNCid, OMIM, PubChem, ChemSpider
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Aspirin, HIV
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Diseasome
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Diseases / Genes
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characteristics of disorders and disease genes linked by known disorder–gene associations
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87,000 triples; 2,600 genes
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free
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structured text files
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updated 2006
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OMIM, Entrez Gene
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Alzheimer's via Marbles, via OpenLink Data Explorer
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Drug Bank
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Drugs
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drug (i.e., chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e., sequence, structure, and pathway) information
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1.1 million triples; 4,800 drugs, 2,500 protein sequences
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permission of authors needed
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structured text files (FASTA, SDF, DrugCard)
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updated August 2008, irregular
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PubChem, FDA/NDA, ChEBI, IUPAC, INCHI, CAS, KEGG
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Varenicline via Marbles, via OpenLink Data Explorer
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LinkedCT
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Clinical Trials
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Linked data source of trials from ClinicalTrials.gov
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7 million triples, 62000 trials
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free - with Terms and Conditions
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Available upon request
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preview release
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DBpedia, GeoNames, Bio2RDF
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Influenza (Intervention), A Trial, AIDS (condition), A reference, A location
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OMIM
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Genes
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compendium of human genes and genetic phenotypes
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12,000 genes
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license from the Johns Hopkins University needed
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structured text files
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updated daily
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CHONDROSARCOMA via Marbles, via OpenLink Data Explorer; TUMOR PROTEIN p53 via Marbles, via OpenLink Data Explorer
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Project Home Page
|
Topic
|
Short Description
|
Size
|
License
|
Data dumps
|
Status/Activity
|
Possible Linking to Other Datasets
|
Example Instances
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Adis R&D Insight
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Drugs
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comprehensively reports on the latest developments of drugs in active research and development internationally
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19,000 drugs
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written permission of Adis Data Information BV needed
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updated weekly
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CAS
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ChemBlast
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Atoms
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information on all the ligands (HIV-related) and their scaffolds
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Molecule pictures, (MDL, Excel)?
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updated April 2008
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IUPAC, PubChem
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ChemSpider
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Chemical Compounds
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database of organic molecules containing more than 20 million compounds from many different providers
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>20,000,000 chemical compounds
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HTML, no downloads
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updated regularly
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ChEBI, DailyMed, KEGG, PubChem, Wikipedia, DrugBank, InChI, MESH
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ClinicalTrials.gov
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Trials
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federally and privately supported clinical trials conducted worldwide; information about a trial's purpose, who may participate, locations, and phone numbers for more details
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62,693 trials
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accompanied by origin and date of data, and modifications made
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HTML
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ChemIDplus
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Citeline TrialTrove
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Trials
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information about ongoing clinical trials
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proprietary
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DrugDB
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Drugs
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(offline)
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Drug Ontology
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Drugs
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ontology including concepts such as indications, interactions, formulary, etc.
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OWL schema only
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updated 2005
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DrugDigest
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Drugs
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usage advise for drugs, vitamins, and herbs
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1,500 drugs
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permission needed
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HTML
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updated daily
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DrugInfo
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Drugs
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covers drugs in clinical trials, approval processes and on the market; information collected from other NLM services mostly
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15,000 drugs
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permission needed
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HTML
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updated daily
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CAS, CT.gov, DailyMed, Medline, PubChem
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Investigational Drug Database
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Drugs
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investigational drug development, from first patent to eventual launch or discontinuation
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107,000 therapeutic patents; 23,000 drugs; 80.000 chemical structures
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proprietary
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IMS
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Drugs
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information about development, efficacy, and status of pharmaceuticals from early clinical testing through to launch
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16,800 drug summaries
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proprietary
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updated weekly
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KEGG Drug
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Drugs
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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.
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academic usage
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structured text files
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updated July 2008
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DailyMed, PubChem
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LillyTrials
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Trials
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clinical trials sponsored by Eli Lilly and Company
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HTML, PDF
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updated regulary
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NDA
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MedMaster
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Drugs
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information on drugs and their interactions, herbs and supplements
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>1000 drugs
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permission needed
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HTML
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updated daily
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NDA
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National Drug Code
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Drugs
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prescription drugs and insulin products that have been manufactured, prepared, propagated, compounded, or processed by registered establishments for commercial distribution
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free
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structured text files
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updated regularly
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NDA
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Orange Book
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Drugs
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Generic product ANDA (Abbreviated New Drug Approval) approvals
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free
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structured text files
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updated daily
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NDA, FDA
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Pharmaprojects
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Drugs
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drugs and their bindings to proteins
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proprietary
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Entrez Gene
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PubChem
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Chemical Compounds
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chemical structures of small organic molecules and information on their biological activities
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free
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ASN.1, XML, SDF
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updated daily
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IUPAC, InChI
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RxNorm
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Drugs
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standard names for clinical drugs
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login required
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National Drug Code
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