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Basic Science Resources and Collections: Databases / Tools

A collection of basic science resources of interest to researchers and students.

End-user bioinformatics group

Join the End-User Bioinformatics Network (EBNET) and become a member of a grass root community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research at Yale.

Databases and Other Tools

REGISTER TO Ingenuity Pathway Analysis (IPA) an online software for the analysis of omics data. It is supported by a manually-curated knowledge base obtained from the peer-reviewed biomedical literature, public and private databases. With IPA you can identify relevant biomarkers, contextualize metabolomics, proteomics, toxicogenomics, and transcriptomics data, and perform network analysis among others. Login to IPA (once you are registered)

REGISTER TO ACCESS MetaCore (Thomson Reuters) MetaCore is an online software based on manually-curated knowledgebase of transcription factors, receptor/ligands, kinase, drugs from the biomedical literature. MetaCore can be used for the functional analysis of the NextGen sequence data, CNV, microarray, proteomics, metabolic, SAGE, proteomics, siRNA, microRNA, and screening data. Login to MetaCore (once you are registered)

BIOBASE Knowledge Library (INCLUDES Proteome Bioknowledge Library) The BIOBASE Knowledge Library™ (BKL), an expanded version of the Proteome Bioknowledge Database, is a collection of gene-regulation and protein oriented scientific databases created from the peer-reviewed scientific literature. The TRANSFAC®, TRANSPATH® and PROTEOME™ products are included in BIOBASE.

Neuroscience Information Framework is an inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet.

OvidSP Medline Ovid  Allows to search across a number of databases including    MEDLINE(R) 1946 to present; Embase 1974 to present; AMED (Allied and Complementary Medicine) 1985 to present; Books@Ovid May 15, 2014; Global Health 1910 to present; Health and; Psychosocial Instruments 1985 to April 2014; PsycBOOKS 1806 to present; PsycINFO 1967 to present

PubMed@Yale Enter PubMed through the Yale link to have access to all our licensed content.

SciFinder Scholar is the interface to the following databases: Chemical Abstracts, CASReact, Registry, CHEMCATS, and Medline. The SciFinder Scholar interface allows users to search these databases using a chemical structure, chemical reaction, research topic, and author information. Registration is required to use this database.

SCOPUS is the largest abstract and citation database of peer-reviewed literature, features smart tools to track, analyze and visualize research.

Find a Biomedical Resource by Title, Keyword, or Subject

Enzyme, Gene & Protein Databases

BioSystems Database (NCBI) The NCBI BioSystems Database provides integrated access to biological systems and their component genes, proteins, and small molecules, as well as literture describing those biosystems and other related data throughout Entrez.

BRENDA BRENDA is one of the main collection of enzyme functional data available to the scientific community. It isavailable free of charge.

Entrez Simultaneously search multiple life sciences databases at the National Center for Biotechnology Information (NCBI). Entrez provides integrated access to nucleotide and protein sequence data from >160,000 organisms, along with 3D protein structures, genomic mapping information, PubMed MEDLINE, and more. Sequence data are combined from various sources, including GenBank, EMBL, DDBJ, RefSeq, PIR-International, PRF, Swiss-Prot, and PDB.

European Bioinformatics Institute The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures. The Institute also provides an exhaustive web-based collection of tools for the field of bioinformatics. A number of applications and databases can be found at EBI that are not offered by other resources.

Use Yale Links!

Be sure to use Yale Links so that you are getting the most complete and efficient access to thousands of electronic journals.

Finding Patents

Scopus is a comprehensive scientific, medical, technical and social science database.  It allows users to limit search results to patents. Try it at SCOPUS. You can also find a link to Scopus under the Resources section of our website.

Also try SciFinder Scholar.  SciFinder Scholar requires that you download the application to your computer.

Other Yale sites with patent information include:

Biomedical Sciences Research Support

Rolando Garcia-Milian
Follow me on ResearchGate
Yale Medical Library, 333 Cedar St, Room L-111, New Haven CT 06520
Website / Blog Page

Yale Research Accelerator

 The YCCI Research Accelerator is designed to facilitate scientific collaboration and resource sharing throughout Yale and beyond. Researchers can share and discuss data, reagents, human samples, laboratory protocols, validated antibodies, cell lines, research projects and more.  The Accelerator can be modified to work with researchers in professional organizations as well.   Check it out!