# Linked Data for Life Sciences
## Preliminaries
### Data Sets  
Life sciences is rapidly becoming the most data intensive branch of sciences that is generating data from the molecular level to the population level. As a part of our case study we have chosen representative data sources, which are described in this section as part of our user scenario. It is important to mention, however, that the database selection in the case study is not exhaustive and inclusion of other databases is not only possible but also intended within the LD framework. MEDLINE: MEDLINE is the U.S. National Library of Medicine bibliographic database which contains more than 24 million references to journal articles in life sciences with a concentration on biomedicine. MEDLINE is continuously indexing articles from 5400 of the world's leading life sciences journals. A distinctive feature of MEDLINE is that the records are indexed with NLM MedicalSubject Headings (MeSH). PubMed ([[https://www.ncbi.nlm.nih.gov/pubmed](https://www.ncbi.nlm.nih.gov/pubmed)]([https://www.ncbi.nlm.nih.gov/pubmed](https://www.ncbi.nlm.nih.gov/pubmed))) provides free access to MEDLINE and links to full text articles when possible. Medical Subject Headings (MeSH): MeSH is curated and maintained by the National Library of Medicine and consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. At the most general level of the hierarchical structure are very broad headings. More specific headings are found at more narrow levels of the thirteen-level hierarchy. In the 2016 version of MeSH are defined 27,883 descriptors associated with over 87,000 entry terms to assist the users in finding the most appropriate MeSH Heading to their topic of interest. Gene Expression Omnibus (GEO): GEO ([[https://www.ncbi.nlm.nih.gov/geo/](https://www.ncbi.nlm.nih.gov/geo/)]([https://www.ncbi.nlm.nih.gov/geo/](https://www.ncbi.nlm.nih.gov/geo/))) is a publicly available, functional genomics data repository supporting MIME-compliant (Minimum Information about a Microarray Experiment) data submissions. Data that is array- and sequence-based is accepted. There are internal tools available to help users to query and download experiments from curated database profiles. There is also an online graphical user interface for data export and basic analysis [16]. ArrayExpress: ArrayExpress ([[https://www.ebi.ac.uk/arrayexpress/](https://www.ebi.ac.uk/arrayexpress/)]([https://www.ebi.ac.uk/arrayexpress/](https://www.ebi.ac.uk/arrayexpress/))) is the major repository for archiving functional genomics data from microarray and sequencing platforms to support reproducible research. ArrayExpress also facilitates submissions in compliance with Minimum Information about a Microarray Experiment (MIAME) and Minimum Information about a Sequencing Experiment (MINSEQE) guidelines [17]. STRING-db: STRING ([[https://string-db.org/](https://string-db.org/)]([https://string-db.org/](https://string-db.org/))) is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other databases [18]. As of 31 October 2017, STRING database covers 9,643,763 proteins from 2031 organisms. DrugBank: The DrugBank database ([[https://www.drugbank.ca/](https://www.drugbank.ca/)]([https://www.drugbank.ca/](https://www.drugbank.ca/))) is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e., chemical, pharmacological, and pharmaceutical) data with comprehensive drug target information. The database contains 9591 drug entries including 2037 FDA-approved small molecule drugs, 241 FDA-approved biotech (protein/peptide) drugs, 96 nutraceuticals, and over 6000 experimental drugs. Additionally, 4661 non-redundant protein sequences are linked to these drug entries.