Date: Thursday, February 1, 2018
Time: 10:00am – 11:45pm
Presenter: Marcus Spann
Location: Street Level Classroom
This class is designed to help individuals with database searching and planning.
Provider: Springer Science & Business Media LLC
Contents: E-books, full text, handbook, images, journals, links, links to full text, mobile access, protocols, video
Access Level: Licensed, On-Site Visitor, Partially Open, TMC Academic User
Descriptions: SpringerProtocols is said to be the most comprehensive and trustworthy online database of reproducible laboratory protocols in the biomedical and life sciences. From the book series Methods in Molecular Biology and numerous other sources, this collection offers researchers access to decades of step-by-step protocols for use in the lab. With an emphasis on clarity, each protocol is organized in an easily-reproduced, recipe style. All protocols have been written by experts in the field, and are reviewed first by editors distinguished in the relevant specific subject areas, and then by Springer's own editorial staff. Contains some open-access protocols. Mobile version of website available.
Keywords: assay, bioassay, bioinformatics, biotechnology, cell biology, genetics, genomics, immunology, infectious diseases, laboratory methods, microbiology, molecular medicine, neuroscience, pharmacology, plants, proteins, protocols, radiology
Provider: Kyoto University Bioinformatics Center
Descriptions: GenomeNet is a network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. The service was first developed at Kyoto University as part of a group of research projects begun in 1991 under the Japanese human genome program. It includes bioinformatics tools in sequence, chemical and genome analysis; community databases dealing with cyanobacteria, bacillus subtilis, and gene expression profiles; ontologies; and more. The KEGG database, which has its own entry in this list, is a part of GenomeNet.
Keywords: biomedical research, database, genome, genomics
Provider: Johns Hopkins University School of Medicine
Contents: brief records, index, links, links to full text
Access Level: Free, Open Access, Partially Open
Descriptions: OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and the entries contain copious links to other genetics resources. Registration required for ftp downloading on the part of nonprofit entities; commercial use/use by a commercial entity requires a license.
Keywords: diseases, genetics, genome, genomics
Provider: Nature Education
Descriptions: Scitable is a free website with international participation; its current focus is on all aspects of genetics. Created for educators and students working at the graduate and undergraduate levels, it may well be accessible enough for some high school students. Includes many free articles within "topic rooms," and offers blogging, the ability to post questions, opportunities to contribute as writer or mentor, and formation of groups for discussion or curriculum. Free registration required for full participation.
Keywords: blog, courseware, education, faculty, genetics, genomics, science, student
Provider: U.S. Department of Health and Human Services/Stanford University
Descriptions: PharmGKB's mission is "to collect, encode, and disseminate knowledge about the impact of human genetic variations on drug response. We curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways."
Keywords: clinical studies, collaborative, database, dosage, drug pathways, drugs, figures, free, genetics, genomics, genotype, images, pharmacogenomics, pharmacokinetics, phenotype, research, scientist
Provider: National Institutes of Health
Descriptions: The Neuroscience Information Framework (NIF) is a semantically-enhanced portal to a dynamic inventory of Web-based neuroscience resources. An initiative of the NIH Blueprint for Neuroscience Research, NIF enhances discovery and access to often unindexed but publicly available research data, datasets, software and tools in the deep web, as well as linking to PubMed records and open-access literature. The NIF Project provides the NIF Registry, Antibody Registry, Drug Related Gene Database, neuroscience ontology and a way to contribute to it (via the NeuroLex wiki) and semantic tagging services. NIF Navigator, a customizable, stand-alone search tool for incorporation into websites or wikis, draws query results from all the NIF's own components and from other sites and accessible databases. The valuable resources at NIF are too numerous to be described adequately here.
Keywords: biomedical research, clinical trials, data, data-sharing, datasets, disease, drugs, federal agencies, full text, genes, genomics, grants, images, informatics, links, networking, neuroscience, NIH, portal, research, scientist, social networking, software
Provider: Netherlands BioInformatics Centre
Descriptions: NBIC is engaged in bioinformatics research and education. Its website includes free software downloads, information on databases and projects, a journal and newsletter, and secondary-level education materials.
Keywords: biomedical research, blog, conference, data analysis, DNA, genes, genome, genomics, informatics, journal, news, open source, partial open access, pharmacogenomics, research, scientist, sequencing, software
Provider: NIGMS - National Institute of General Medical Sciences
Descriptions: "The mission of [NIGMS] is to support research that increases understanding of life processes and lays the foundation for advances in disease diagnosis, treatment, and prevention." NIGMS provides training and career grants, including a grants and opportunities program for minorities. This website is a gold mine for educators, providing scientist interviews, short films on special topics, an image database, posters, fact sheets, even interactive games. One can access or sign up for Biomedical Beat, the free NIGMS online newsletter, as well as order many other free publications. For researchers there is a blog, NIGMS Feedback Loop, that keeps one up to date on funding opportunities and future plans.
Keywords: biomedical research, blog, disease, federal agencies, free, gateway, genomics, grants, health sciences, images, informatics, life sciences, medicine, NIH, open access, pharmacogenomics, podcasts, research, science, scientist, video
Provider: Gene Ontology Project
Contents: datasets, open-source, standards, websites
Access Level: Free, Open Access
Descriptions: "The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data." The Ontologies describe three aspects of molecular biology- biological processes, cellular components, and molecular functions. Gene Ontology's collected tools list includes hundreds from all over the world: specialized browsers, search engines, statistical analysis and visualization tools, and many other kinds. This project began as a collaboration between three model organism databases, FlyBase (Drosophila), the Saccharomyces Genome Database and the Mouse Genome Database in 1998. Since then, the GO Consortium has grown to include many other databases, including several of the world's major repositories for plant, animal and microbial genomes. See the GO Consortium page for a full list of member organizations.
Keywords: animal, bioinformatics, collaborative, genetics, genome, genomics, ontologies, plants, taxonomy
Contents: E-books, full text
Access Level: Licensed, On-Site Visitor, TMC Academic User
Descriptions: An expanding collection with more than 100,000 titles in trade, reference, science, technology, medicine and literature. Some content is out of copyright, free with subscription; some is licensed by the Texas State Library for TexShare; and some is provided by the University of Texas at Austin.
Keywords: cell biology, chemistry, cognitive science, genomics, healthcare policy, healthcare system, medicine, microbiology, multidisciplinary, nanoscience, nursing, nutrition