HCLSIG/LODD/Data

LODD-related datasets that the LODD group already made available as Linked Data

NOTE: WORK-IN-PROGRESS fu-berlin datasets are being hosted by Bio2RDF. Several are already there. Updates to this page and CKAN Datahub are pending..

A graph of some of the LODD datasets (dark grey), related biomedical datasets (light grey), related general-purpose datasets (white) and their interconnections. Line weights correspond to the number of links. The direction of an arrow indicates the dataset that contains the links, e.g., an arrow from A to B means that dataset A contains RDF triples that use identifiers from B. Bidirectional arrows usually indicate that the links are mirrored in both datasets. More on the interlinking methodology and statistics can be found on the Interlinking page.

The LODD datasets have been crawled by the SWSE Semantic Web search engine and can be accessed via a faceted browsing interface at [1] (Example query: Varenicline).

Most of the LODD datasets have also been integrated into the SPARQL endpoint of the HCLS Knowledge Base, see the wiki page of the HCLS KB for further information.

Bio2RDF Data Sets

The Bio2RDF project has published 40 biology-, gene- and medical-related datasets (altogether 2.3 billion triples). The datasets are available via SPARQL endpoints and as Linked Data. It is recommended that you use the Bio2RDF Java Servlet, and optionally download the databases for efficient personal use. Running your own instance of the OpenLink Virtuoso AMI for EC2 is also an option (and for basic URI resolution doesn't require the Java Servlet, although if you want advanced queries you should still download it and configure it to query your EC2 sparql endpoint).

• Bio2RDF sparql endpoint list Sparql endpoint list in RDF
• Identification of an autoimmune enteropathy-related 75-kilodalton antigen, via an OpenLink hosted edition of Bio2Rdf
• Structure of the gene encoding the human cyclin-dependent kinase inhibitor p18 and mutational analysis in breast cancer, via an OpenLink hosted edition of Bio2Rdf
• PubMed article viewed using the Marbles Linked Data browser.
• PubMed author viewed using the Marbles Linked Data browser.
• OMIM Killer Cell Lectin-Like Receptor viewed using the Marbles Linked Data browser.
• Falcons Search for KILLER CELL. The Bio2RDF data has been crawled by the Falcons Semantic Web Search engine. This is an example on how the data is accessed by humans using the search engine. Falcons also offers an API that can by used by applications to access the data.

Chem2bio2RDF

• Information about the chem2bio2rdf data sets

Data Sets for the LODD Task

To complement the drug-related Web of Data build by the LODD effort, the following data sets could/should also be published as Linked Data.

The LODD effort is currently gathering more information about relevant datasets. See also Evaluation of LODD Data Sets for current evaluation results.

• Adis R&D Insight
• chEBI
• ChemBlast
• ChemSpider
• ClinicalTrials.gov
• Citeline TrialTrove
• DailyMed
• DBpedia
• Diseasome
• Drug Bank
• DrugDB
• Drugome
• Drug Ontology
• Investigational Drug Database - Proprietary
• IMS
• KEGG Drug
• LillyTrials
• MedWatch
• National Drug Code
• OMIM
• Orange Book
• Pharmaprojects - Proprietary
• PubChem
• RxNorm
• VA NDF-RT
• Other data sources could include blogs, discussion boards, wikis, etc.
• and....
  • World Health Organization's Global Health Atlas
  • EpiSPIDER
  • Drugs@FDA - FDA Approved Drug Products
  • DrugDigest
  • HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism
  • Alzheimer Research Forum
  • RxTerms
  • HuDiNe
  • Medpedia
  • TCMGeneDIT and RDF dump
  • List of other possible data sources from page 66 onwards

Alternative Herbal Medicine use case

• TCMGeneDIT dataset

Identified Based Linkage Points

• INCHIs
• PubChem Compound ID (CID)
• PubChem NSC
• Chemical Abstract ID (CAS)
• New Drug Application (NDA)

Data Set Attributes

• Licensing
• Data Format
• Identifiers