This appendix provides brief descriptions of the major databases and repositories relevant to life sciences research. Researchers should consult with their institutional librarians for guidance on database access, search strategy development, and interlibrary loan services.
PubMed/MEDLINE
PubMed is the primary free interface to MEDLINE, the National Library of Medicine’s flagship bibliographic database covering biomedical and life sciences literature. MEDLINE indexes more than 30 million citations from over 5,000 journals in biomedicine, nursing, dentistry, veterinary medicine, and allied health sciences, with coverage dating back to the 1950s. A distinctive and powerful feature of PubMed is its use of Medical Subject Headings (MeSH), a controlled vocabulary of biomedical terms that indexes articles by concept rather than keyword. Searching with MeSH terms allows researchers to retrieve relevant articles regardless of the specific language used by individual authors. PubMed is freely accessible to anyone worldwide through the National Library of Medicine’s website and requires no institutional subscription. For many life sciences researchers, PubMed is the first and most important database to master.
Web of Science
Web of Science, produced by Clarivate, is a multidisciplinary citation indexing database covering science, social sciences, arts, and humanities. Its Science Citation Index Expanded component is the most important for life sciences researchers, indexing approximately 9,200 of the world’s most impactful journals. Web of Science is particularly valuable for citation analysis: it allows researchers to see how many times a paper has been cited, who has cited it, and how those citations are distributed over time. Journal Impact Factors are calculated from Web of Science data. The database also provides author profiles, h-index calculations, and tools for visualizing citation networks. Access to Web of Science typically requires an institutional subscription.
Scopus
Scopus, produced by Elsevier, is a comprehensive abstract and citation database that indexes over 27,000 peer-reviewed journals across science, technology, medicine, and social sciences. It has broader coverage than Web of Science in some fields, including engineering, social sciences, and non-English-language journals. Scopus provides citation analysis tools, including author h-index calculations through Scopus Author ID profiles, journal rankings through CiteScore and SJR (SCImago Journal Rank), and institutional research analytics. Researchers comparing citation statistics between databases should note that Scopus’s broader journal coverage often results in higher citation counts than Web of Science for the same author or paper.
Embase
Embase, produced by Elsevier, is a biomedical and pharmacological database with particular strength in drug-related research, clinical pharmacology, and adverse drug reactions. It covers approximately 8,500 journals and indexes conference abstracts more comprehensively than PubMed, making it especially valuable for systematic reviews in clinical and pharmaceutical contexts. Embase uses Emtree, its own controlled vocabulary, which is distinct from PubMed’s MeSH. For comprehensive systematic reviews in clinical topics, searching both PubMed and Embase is standard practice because their journal coverage overlaps substantially but is not identical.
bioRxiv and medRxiv
bioRxiv (pronounced “bio-archive”) and medRxiv (“med-archive”) are preprint servers operated by Cold Spring Harbor Laboratory. bioRxiv covers biological sciences broadly, including cell biology, genetics, neuroscience, ecology, and biochemistry; medRxiv covers health sciences, including clinical medicine, epidemiology, and public health. Preprints are manuscripts posted publicly before peer review, allowing rapid dissemination of findings and community feedback prior to formal publication. Both servers screen submissions for basic scientific standards but do not peer-review them. Preprints can be searched through the respective server websites and are indexed by Google Scholar.
ClinicalTrials.gov
ClinicalTrials.gov is a registry and results database for clinical studies conducted in the United States and internationally, operated by the National Library of Medicine. It is a resource both for identifying registered trials and for finding results summaries of completed trials. Trial registration is required by major journals, the ICMJE, and many funders as a condition of publication for interventional studies. Researchers can search ClinicalTrials.gov to identify ongoing or completed trials relevant to their question and to find unpublished results that may reduce publication bias in a systematic review.
GenBank, UniProt, and PDB
Biological databases containing molecular sequence and structure data are essential infrastructure for modern life sciences research. GenBank, operated by the National Center for Biotechnology Information (NCBI), is the primary repository for nucleotide sequences, including genomic DNA, mRNA transcripts, and raw next-generation sequencing data. UniProt is the primary repository for protein sequences and functional annotation; its Swiss-Prot component is manually curated and highly authoritative. The Protein Data Bank (PDB) archives three-dimensional structural data for biological macromolecules determined by X-ray crystallography, NMR spectroscopy, cryo-electron microscopy, and other methods. Depositing sequence and structure data in these repositories at the time of publication is required by most major journals and by NIH funding policy.
Dryad, Zenodo, and Figshare
General-purpose research data repositories allow researchers to deposit data, code, and supplementary materials associated with publications. Dryad is a nonprofit repository specifically designed for research data associated with published papers, with particular strength in ecology, evolution, and the life sciences. Zenodo, operated by CERN and the European OpenAIRE program, is a free, general-purpose repository for research outputs of all types, including data, software, preprints, and presentations. Figshare is a commercial repository that supports a variety of data types with DOI minting. All three repositories mint Digital Object Identifiers for deposits, enabling persistent citation and discovery.
Google Scholar
Google Scholar is a freely accessible academic search engine that indexes scholarly literature across disciplines from a wide variety of sources, including journal articles, theses, books, preprints, conference papers, and grey literature. Its coverage is extremely broad but its quality control is limited: it indexes some non-peer-reviewed and low-quality sources alongside high-quality literature. Google Scholar is particularly useful for finding grey literature, locating specific papers when you know the title or author, and tracking citations through its Cited by function. Researchers should be aware that Google Scholar citation counts are typically higher than those from Web of Science or Scopus, reflecting its broader source coverage. Google Scholar should not be used as a sole source for formal systematic reviews but is an excellent complement to database searching.