Databases

(NIH/NCI-F) - Access restricted to NIH & NCI-F sites | (NCI-F) - Access restricted to National Cancer Institute at Frederick

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Databases

 | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z |

A

  • ACD Labs NMR Predictors - online software for the prediction of NMR spectra, chemical shifts, and coupling constants for the following nuclei - 1H, 13C, 15N, 19F, and 31P. Chemical structures may be drawn, pasted, or imported into the program to obtain their predicted spectra. Alternatively, you may search the database for known structures using chemical shift, coupling constant, molecular weight, molecular formula, or reference information. ***Important Note: All structures searched will remain in the program's History. If you do not want others to view structures you have searched, you'll need to request a free personal account. This account will also allow you to access the predictors from outside of the NCIF IP range. To set up your personal account, send an e-mail to ilab@acdlabs.com. Include your full name, NCIF phone number and address in the body of the e-mail , and "NCIF" in the subject line. If you have any problems, contact dossal@mail.nih.gov(NCI-F only)
  • Allen Brain Atlases - Free Atlases in the data portal include the Mouse Brain, Developing Mouse Brain, Mouse Connectivity, Mouse Spinal Cord, Non-Human Primate, Human Brain, Developing Human Brain, Gioblastoma, and more. The portal is a growing collection of online public resources integrating extensive gene expression and neuroanatomical data, with a novel suite of search and viewing tools. For new and experienced users of the Allen Brain Atlas resources, view the Library of Tutorials for introductory overviews as well as guided tours focused on specific tools. Read more about the Allen Institute for Brain Science. (NIH/NCI-F)
  • AntiBase 2017 Update, the Natural Compound Identifier, is available to NCI at Frederick researchers as a networked CD-ROM via the Scientific Library. AntiBase is a comprehensive database of more than 44,000 natural compounds from micro-organisms and higher fungi. and includes descriptive data; physico-chemical data; spectroscopic data; biological data; information on origin and isolation and a summary of literature sources.
  •  For questions, please contact Alan Doss at x6249, or by e-mail at dossal@mail.nih.gov(NCI-F only)
    • NOTE: AntiBase will only open in ChemBioFinder. To have ChemBioFinder installed on your computer, as part of theChemBioOffice software package, contact DMS Computer Services Help Desk at x5115.
    • To access AntiBase, select the Windows Globe icon, at the lower left of your screen in MS Windows, copy the following file address (New Address for 2017 Update) - \\adsv11\Antibase2017\ANTIBASE_2017.cfx, and paste it into the search box and click the "Enter" button.

B

  • BindingDB - The Binding Database (BindingDB) is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be drug-targets with small, drug-like molecules. BindingDB also offers tools for virtual screening of candidate ligands. Learn more about BindingDB - Article 1Article 2.
  • Biobase Biological Databases - for access to the Human Gene Mutation Database (HGMD). Individual registration and login required. Enter the code 1881-6975-97565225 in the license field during the account registration process. For additional bioinformatics resources, see NIH's Analysis Tools & Databases list(NIH/NCI-F)
  • BioBrea - A vendor source for antibodies related to genes/proteins, targets or disease or an area of interest, BioBrea provides detailed product information and literature citations to aid scientists identify high quality antibodies frequently used by other scientists.
  • bioDBnet - biological D ata B ase n etwork, developed at the Advanced Biomedical Computing Center (ABCC), NCI atFrederick, integrates many public databases such as Ensembl, NCBI-Gene, GO, UniProt, Affy, etc. It has tools to get detailed annotation reports and also to convert between biological identifiers like proteins to genes or pathways to genes or RefSeq proteins to Ensembl proteins, etc. Any questions or requests to bioDBnet can be made through the bioDBnet Contact Form.
  • Bioinformatics Analysis Tools & Databases from NIH Library - See the list of bioinformatics resources licensed by the NIH Library. Access requirements vary so please read information accompanying each resource on list. (NIH/NCI-F)
  • BIOSIS Citation Index (1926-present) via Web of Science (WOS) - Use the pulldown menu next to Web of Science Core Collection to select the database.(NIH/NCI-F)
  • Book Citation Index (2005-present) via Web of Science (WOS) - Use the pulldown menu next to Web of Science Core Collection to select the database.(NIH/NCI-F)
  • BotDB - A Database Resource for Clostridial Neurotoxins, developed at the Advanced Biomedical Computing Center (ABCC), NCI at Frederick, BotDB serves as a comprehensive resource for botulinum research.
  • Britannica Online - Encyclopedia Britannica online - limited free access.

 

C

  • Cambridge Structural Database via WebCSD - Online portal to the Cambridge Structural Database. Read PMC article about WebCSD (NIH/NCI-F)
  • Carcinogenic Potency Database - From TOXNET, NLM's Toxicology Data Network.
  • CBL Nitric Oxide Database - Learn about Nitric Oxide Research in the Chemical Biology Laboratory, Frederick National Lab, using this searchable Nitric Oxide Diazeniumdiolate (or NONOates) Reagents Database.
  • ChemBank - a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG). This knowledge environment includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data so that biological and medical insights can be gained. Learn more about ChemBank Article 1, ChemBank Article 2.
  • Chemical Carcinogenesis Research Information Service (CCRIS) - From TOXNET, NLM's Toxicology Data Network, carcinogenicity and mutagenicity test results for over 8,000 chemicals.
  • ChemID Plus - From TOXNET, NLM's Toxicology Data Network, a searchable dictionary of over 370,000 chemicals (names, synonyms, and structures). Includes links to NLM and other databases and resources.
  • Chemistry Resources
  • ChemNavigator - Available to all NIH affiliated scientific researchers, NIH has made an agreement with ChemNavigator to provide a current and comprehensive database of commercially accessible drug discovery screening compounds. If you are an NIH researcher, once you register in the system, you'll have full access to the iResearch System. Then you will be able to perform chemical structure searches for compound samples of interest and purchase these samples through this on-line system. (NCI/NCI-F)
  • CINAHL Plus - via NIH's EbscoHost ; the Cumulative Index to Nursing and Allied Health Literature (CINAHL Plus) provides indexing for 4,500 journals from the fields of nursing and allied health, with indexing back to 1937. CINAHL Plus also contains searchable cited references for more than 1,340 journals. Full text material includes nearly 80 journals plus legal cases, clinical innovations, critical paths, drug records, research instruments and clinical trials.Click on EbscoHost Research Databases , then CINAHL Plus . (NIH/NCI-F)
  • ClinicalTrials.gov - (1982 - ). With over 70,000 trials in 167 countries, this database, a service of the NIH, is a registry of federally and privately supported clinical trials conducted in the United States and around the world. Find trials for a specific medical condition or other criteria in the registry.
  • Cochrane Library - The Cochrane Library is designed to provide information and evidence to support decisions taken in health care and to inform those receiving care. The Cochrane Library consists of a regularly updated collection of evidence-based medicine databases: The Cochrane Database of Systematic Reviews (Cochrane Reviews), Database of Abstracts of Reviews of Effects (DARE), The Cochrane Central Register of Controlled Trials (CENTRAL), The Cochrane Database of Methodology Reviews (Methodology Reviews), The Cochrane Methodology Register (Methodology Register), Health Technology Assessment Database (HTA), NHS Economic Evaluation Database (NHS EED) and About The Cochrane Collaboration and the Cochrane Collaborative Review Groups. Many of the reviews analyze the efficiency and adverse effect of pharmacological agents and provide a useful resource for completed or abandoned clinical trial . (NIH/NCI-F)
  • Cold Spring Harbor Protocols - over 700 methods in molecular and cell biology. Free individual registration is required prior to your first use. Login with your personal username and password for each future use. For more protocols, see also Springer Protocols,Methods in Enzymology and the Current Protocols series titles in the Online Books list. (NIH/NCI-F)
  • ConceptGen - from NCIBI, a gene set enrichment testing and gene set relation mapping tool that can help you identify, explore, and visualize relationships and significant overlaps among sets of genes (concepts). ConceptGen is built on a repository of conceptual data drawn from diverse areas.
  • Conference Proceedings Citation Index (1990-present) via Web of Science (WOS) - Use the pulldown menu next to Web of Science Core Collection to select the database.(NIH/NCI-F)
  • Contract-Awarded Labor Category (CALC) Tool - If you are looking for labor rates for specific positions and contractors, this site from the General Services Administration (GSA) allows contracting officers and specialists to conduct research and price analysis for professional labor categories across a database of contract awarded prices for 48,000 labor categories from more than 5,000 recent GSA contracts.  It lists examples from the rate lists it searches with links to those lists providing rates that are “fully burdened”. 
  • Current Chemical Reactions (1985-present) via Web of Science (WOS) - Use the pulldown menu next to Web of Science Core Collection to select the database.(NIH/NCI-F)
  • Current Contents Connect (1998-present) via Web of Science (WOS) - Use the pulldown menu next to Web of Science Core Collection to select the database.(NIH/NCI-F)
  • Current Index to Statistics Extended Database - from 1975, indexes publications in statistics and related fields. (NIH/NCI-F)
  • Cytoscape (software) - an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. This free software needs to be downloaded on individual computers. The MetScape Plugin for Cytoscape provides a bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data in the context of human metabolism.

 

D

  • DailyMed - A public service from NLM, provides information about marketed drugs including FDA approved labels (package inserts).
  • Data Citation Index (1900-present) via Web of Science (WOS) - Use the pulldown menu next to Web of Science Core Collection to select the database.(NIH/NCI-F)
  • DATA.gov - provides free public access to machine readable datasets generated by the Executive Branch of the Federal Government; includes access to searchable data catalogs - the "raw" data catalog, the tool catalog, and the geodata catalog.
  • DAVID - Database for Annotation, Visualization, & Integrated Discovery - the DAVID Bioinformatics Resources database, developed by the Laboratory of Human Retrovirology Immunoinformatics (LHRI), Leidos Biomedical Research, Inc., provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large lists of genes. Read an article published in Nature Protocols describing a step-by-step procedure for using DAVID. Contact DAVID Bioinformatic Team - Brad T Sherman, Bioinformatics Manager, (301) 846-7694.
    .
  • Derwent Innovations Index (1963-present) via Web of Science (WOS) - Use the pulldown menu next to Web of Science Core Collection to select the database.(NIH/NCI-F)
  • Dictionary of Natural Products (DNP) Online - a comprehensive database of 170,000 natural products which includes names and synonyms, formulae, chemical structures, CAS Registry Numbers, extensive source data, uses and applications, physical state, melting point, boiling point, pKa, and key literature citations, searchable by text or substructure. A comprehensive type of compound classification scheme brings together compounds that are biogenetically related. DNP is restricted to 1-2 concurrent NCI-F users; please logoff after each session. If needed, a free browser plug-in is available on the left side of the screen, "Get the Plug-in". Please call Alan Doss at x6249 for searching assistance. (NCI-F only)
  • DrugEXPERT - part of the ExPub Toxicology Collection database, delivers environmental health and safety-oriented data on thousands of pharmaceutical substances. (NIH/NCI-F)
  • DXplain - Diagnostic Decision Support (DXplain) is a decision support system using clinical findings (signs, symptoms, labs) to produce a ranked list of diagnoses. For each diagnosis, it provides justification for consideration, further clinical data to collect, and atypical findings. DXplain doesn't offer definitive medical consultation and should not be used as a substitute for physician diagnostic decision making. Access requires entering your NIH email address. (NIH/NCI-F)
  • DynaMedPlus - a clinical reference tool created by physicians for physicians, residents, nurse practitioners and other health care professionals for use at the point-of-care with clinically-organized summaries for more than 3,400 topics.  Editors monitor journals, journal review services, systematic review collections, guideline collections, drug information sources and other relevant sources. (NIH/NCI-F)

 

E

  • EbscoHost eBooks - Subscribed items in Library's collection available by title on Online Books list, in the Online Catalog, and via OneSearch on the Library's homepage. (NCI-F only)
  • Elsevier Pathway Studio Software - about | NCI researchers (includes NCI-F) have unlimited access to the latest version of Elsevier's Pathway Studio software with the Mammalian (protein-centric) knowledge base as well as the premium DiseaseFx (disease-centric), and ChemEffect (compound-centric) knowledgebases, as well as the MedScan text mining module. Researchers also have access to the NCI's high-quality HyNet Yeast 2-Hybrid Protein Interaction Database .The knowledge bases include molecular facts retrieved from Elsevier's journals as well as facts retrieved from articles from other leading scientific publishers and from PubMed abstracts. Pathway Studio lets molecular biologists work in an interactive graphical environment to connect findings from independent research projects, analyze experimental data, and to develop new findings and publish. Frederick Support: NCI investigators located in Frederick are asked to utilize the DMS Help Desk fredhelpdesk@mail.nih.gov for all Pathway Studio issues. Service requests submitted to DMS Help Desk for software registration should be directed to nciterpsysnetadmin@mail.nih.gov (NCI/NCI-F)
  • EcoSal Plus - Based on the classic print reference, Escherichia coli and Salmonella: Cellular and Molecular Biology, EcoSal Plus online publishes expert reviews covering E. coli, Salmonella, and other members of the family Enterobacteriaceae and their use as model microbes for biological explorations. (NIH/NCI-F)
  • Embase - With over 24 million indexed records and more than 7,600 currently indexed peer-reviewed journals, Embase is a  multipurpose and up-to-date database covering the most important international biomedical literature from 1947 to the present. Embase includes coverage and in-depth indexing of the drug-related and clinical literature, with a particular focus on comprehensive indexing of adverse drug reactions; emphasis on Evidence Based Medicine (EBM) indexing including systematic reviews, and coverage and indexing of journals and articles relevant to the development and use of medical devices. (NCI/NCI-F)
  • Ensembl - genome database and integrated browser, funded by the European Molecular Biology Laboratory and the Wellcome Trust Sanger Institute allows you to graphically navigate publicly available genomics data to quickly find Genes, SNPs, Regulatory features, and Sequences, and to compare sequences against multiple species. Filmed WorkshopOnline Tutorials.
  • Eureka! - Eureka! provides a simple one-button one-window access to MetaCore's manually curated databases. Users can query the database with gene, protein, compound, drug names, diseases, and processes, pathological or toxic categories in a free text format. The results, ranked based on relevance, will present all categories of information and data from the database and links to external databases including third party vendors. (NIH/NCI-F)

 

F

  • Faculty of 1000 Posters -  now merged with F1000Research, F1000Posters an open access repository, provides a permanent, structured environment for the deposition of posters and slide presentations as well as a trustworthy venue for ongoing discussion and development of the information being presented.(NIH/NCI-F)
  • Faculty of 1000 Prime - The core service of F1000Prime identifies and evaluates the most important articles in biology and medical research publications. Composed of 5,000 Faculty Members — senior scientists and leading experts in all areas of biology and medicine — plus their associates, the Faculty recommends the most important articles, rating them and providing short explanations for their selections.  F1000Prime is a combination of two earlier services: Faculty of 1000 Biology - launched in 2002, and Faculty of 1000 Medicine - launched in 2006. The two services were merged in 2009 to form F1000Prime. (NIH/NCI-F)
  • Faculty of 1000 Prime Reports - 2013-15 only.  See F1000 Faculty Reviews, 2015 to present. (NIH/NCI-F)
  • Faculty of 1000 Faculty Reviews - 2015 to present.  F1000 Faculty Reviews will continue to bring readers commissioned, open access reviews providing comprehensive coverage of the life sciences, expanding on the recommended literature coverage of F1000Prime. Articles published in F1000Prime Reports will continue to be fully accessible in their current location as well as on the new channel page. (NIH/NCI-F)
  • Faculty of 1000 Research - F1000Research is an Open Science publishing platform offering immediate publication of posters, slides and articles with no editorial bias. All articles benefit from transparent peer review and the inclusion of all source data. (NIH/NCI-F).
  • Faculty of 1000 Workspace - F1000Workspace is a workspace for scientists to collect, write & discuss scientific literature. Powered by a faculty of over 10,000 leading experts in biology and medicine. (NIH/NCI-F)

 

G

  • Gene2MeSH - an automated literature-based genome annotation using MeSH.
  • GeneSpring (Software) - from Agilent Technologies, includes GeneSpring GX for microarray data and Agilent's ArrayCGH Analytics ; combines a highly scalable architecture, a rich set of analysis tools, and a series of programmatic interfaces that enable multi-campus enterprises to maximize the value of their research; offers an expanding suite of applications designed to store multiple data types including gene expression, genotyping, comparative genomic hybridization, and proteomics data. Access Information: Contact the NIH Help Desk at 301-496-4357 (6:00 am - 6:00 pm); Email: helpdesk@nih.gov; Web: http://support.nih.gov (NIH/NCI-F)
  • Gene Ontology (GO) - 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.
  • GIDEON: Global Infectious Diseases & Epidemiology Network - GIDEON (Global Infectious Diseases and Epidemiology Online Network) is the world’s premier Global Infectious Disease knowledge management tool.  GIDEON is used for Diagnosis Support and Informatics in the fields of Tropical and Infectious diseases, Epidemiology, Microbiology and Antimicrobial Chemotherapy. (NIH/NCI-F)
  • Grant Forward - Infers and aggregates interests from several sources such as a researcher's CV, or publication history, matching the profile with relevant funding opportunities. Users must first create an account at: http://www.grantforward.com/signup, using an email address that ends in "nih.gov". (NIH/NCI-F)

 

H

  • Health and Psychosocial Instruments (HaPi) - On the EbscoHost databases platform, this comprehensive bibliographic database is abstracted from leading journals covering health sciences and psychosocial sciences with information about behavioral measurement instruments, including those from Industrial Organizational Behavior and Education. Records in HaPI provide information on questionnaires, interview schedules, vignettes/scenarios, coding schemes, rating and other scales, checklists, indexes, tests, projective techniques and more.  (NIH/NCI-F)
  • Henry Stewart Talks Collection (HSTalks) - Biomedical & Life Sciences: this series of over 1,500 specially prepared animated audiovisual presentations with synchronized narration by world leading scientists is keeping researchers informed throughout the world. The collection is constantly being expanded and updated and already over seven hundred leading world experts have recorded presentations especially for Henry Stewart Talks. (NCI-F only )
  • HIV Databases - These databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials. Also included is access to a large number of tools that can be used to analyze these data. This project is funded by the Division of AIDS of the National Institute of Allergy and Infectious Diseases (NIAID), NIH.
  • Human Gene Mutation Database (HGMD) Professional - From Biobase, the professional version of the Human Gene Mutation Database (HGMD) provides up-to-date information on human inherited gene mutations. It allows researchers to assess the novelty of identified gene mutations. The mutations in the database are manually curated from the scientific literature. They are mapped to the genome and can be searched by motif, type of nucleotide or amino acid substitution, and location within a splice site or regulatory region. View an introductory tutorial .

    Access is provided at https://portal.biobase-international.com/cgi-bin/portal/login.cgi/ . Individual registration and login required. Enter the code 1881-6975-97565225 in the license field during the account registration process. For additional bioinformatics resources, see NIH's Analysis Tools & Databases list. (NIH/NCI-F)

  • Human Metabolome Database (HMDB) - a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education.

 

I

  • IEEE Explore Digital Library - Resource for access to scientific and technical content published by the Institute of Electrical & Electronics Engineers (IEEE).  The database includes full-text, searchable content published since 1988, with select content dating back to 1872.  Includes conference proceedings, transactions, standards, and journal articles in biomedical engineering, data analysis, biomedical imaging, medical devices, health informatics, and more. (NIH/NCI-F)
  • Index Chemicus (1993-present) via Web of Science (WOS) - Use the pulldown menu next to Web of Science Core Collection to select the database.(NIH/NCI-F)
  • Ingenuity Pathways Analysis  (IPA) - a web-based bioinformatics tool from Ingenuity Systems allowing researchers to search, analyze, and graphically view molecular interactions, biological functions, and diseases. Access Information: IPA is available to all researchers affiliated with the NCI. Please use the registration link below to initiate your user account (NCI affiliated e-mail address required).REGISTRATION: Enrollment is open to all researchers within the NCI. You must first contact the NIH Computer Helpdesk to be placed on the list of authorized NCI users. Then you can proceed to the link shown below to activate your private user account: Help Desk Telephone: 301-496-4357 (open 6:00 am - 6:00 pm). Email: helpdesk@nih.gov / Web: http://support.nih.gov / NCI User Account Activation Request Form: https://apps.ingenuity.com/isa/account/signup/ipa?utm_source=ingenuity&utm_medium=website&utm_campaign=IPALoginPage(NIH/NCI-F)

 

J

  • Journal/Author Name Estimator (JANE) - A free resource tool for finding the perfect journal in which to publish your research, from The Biosemantics Group. Copy and paste your manuscript's abstract or type in the key concepts of your paper. You will get a list of journals, sorted by confidence score, once you click the Find Journals button. Learn more about JANE.
  • Journal Citation Reports (JCR) - consists of Journal Science Reports and Journal Social Science Reports and is a unique resource that allows you to evaluate and compare journals using citation data drawn from over 11,000 scholarly and technical journals from more than 3,300 publishers in over 80 countries. Data includes most frequently cited journals in a field; Highest impact journals in a field. (NIH/NCI-F)
  • JoVE Science Education Database - Learn or train others in laboratory fundamentals using easy-to-understand video demonstrations in 9 subject collections, each with 15 core videos, and 75 application videos. Topics include General Laboratory Methods; Basic Methods in Cellular & Molecular Biology; Essentials of Behavioral Science; Essentials of Biology 1: Yeast, Drosophila, C.elegans; Essentials of Biology II: Mouse, Zebrafish, Chick; Essentials of Cell Biology; Essentials of Developmental Biology; Essentials of Genetics; Essentials of Neuroscience. The database is part of the Journal of Visualized Experiments (JoVE), a PubMed-indexed video journal. (NIH/NCI-F)
  • JSTOR - this link takes you to the JSTOR Digital Archives website where you may find a list of journal holdings available to NIH & NCI-F employees by the NIH institutional license. Collections include - Life Sciences; Arts & Sciences I & II. The JSTOR Digital Archiveincludes more than 600 leading academic journals in the humanities, social sciences, and sciences available for NIH & NCI-F users.(NIH/NCI-F)

 

K

 

L

M

  • MedlinePlus - Free to all, a consumer health information service of the National Library of Medicine and the National Institutes of Health.
  • Metab2MeSH - From the National Center for Integrative Biomedical Informatics (NCIBI), a free web application that searches biological substances or MeSH terms and displays resulting pairs of substances and MeSH terms that match the search term.
  • MetaCore - MetaCore is a web-based bioinformatics suite that allows researchers to upload data analysis results from experiments such as microarray, next generation sequencing, metabolic, SAGE, siRNA, microRNA, and screening. It provides functional analysis to identify the most relevant pathways, networks, and cellular processes in the data. Additionally, gene, protein, compound, pathwaymap, and disease searches are available. The license for the Genomic Analysis Tool is included for studying genetic variance and is particularly useful for studying a set of variants resulting from next generation sequencing experiments.

Access requires a user account which is linked to your NIH email address. Sign up on the MetaCore registration page. If you do not get a response within two business days, please contact Dr. Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library. (NIH/NCI-F)

  • MetaDrug - (About MetaDrug) The NCI-F Scientific Library has added the MetaDrug tool (NCI-F only) to those already made available by NCI Bethesda to all NIH researchers, GeneGo, MetaCore, MetaRodent. MetaDrug is a platform that can help you predict possible Indications, Modes of Action, ADME, Phase I and Phase II metabolites, and Toxicities of novel compounds. It also allows you to view the predicted activities on pathway maps that can be validated by uploading experimental data for the compounds, once available. For an account to access MetaDrug contact Alan Doss, x6249. (NCI-F only)
  • MetScape Plugin for Cytoscape - provides a bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data in the context of human metabolism. It allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data. Gene expression and/or compound concentration data can be loaded from file(s) (in CSV, TSV, or Excel formats), or the user can directly enter individual compounds/genes (using KEGG compound IDs, or Entrez Gene IDs) to build metabolic networks without loading a file. MetScape uses an internal relational database stored at NCIBI that integrates data from KEGG and http://www.ehmn.bioinformatics.ed.ac.uk/.
  • Micromedex - The industry standard for more than 40 years, Micromedex Solutions provide hospitals and healthcare providers with a single source of clinical information — from need-to-know drug, pediatric, disease, lab, and toxicology information to comprehensive resources for patient and consumer education. (NIH/NCI-F)
  • MiMI (Michigan Molecular Interactions Database) - a database of protein interactions, pathways, and genes.
  • MiSearch - a literature search tool that works with NCBI Entrez and displays results in order of those most relevant to your research interests.
  • Molecular Imaging and Contrast Agent Database (MICAD) - MICAD is a free source of scientific information regarding molecular imaging and contrast agents (under development, in clinical trials or commercially available for medical applications) that have in vivo data (animal or human) published in peer-reviewed scientific journals. MICAD was established as a key component of the 'Molecular Libraries and Imaging" program of the NIH Common Fund (formerly NIH Roadmap), a set of inter-agency initiatives accelerating medical research. After June 30, 2013, new and revised chapters will no longer be uploaded to the MICAD website. However, the current chapters remain available online via PubMed.
  • Mouse Genome Informatics (MGI) Database - MGI, developed at the Jackson Laboratory in Bar Harbor, Maine, provides free, publicly available access to integrated data on the genetics, genomics and biology of the laboratory mouse.

 

N

  • NCBI BioSystems Database - biological pathways databases which can be searched directly or accessed via links from Entrez Gene, Protein, PubChem Compound, and more.
  • NCI at Frederick Scientific Publications Database (formerly NCI at Frederick-in-Print) - this database is a collection of citations for journal articles authored by employees and contractors of the NCI-F from 1997 through the present. Please bear in mind that this new product is a work in progress, and we welcome any comments you may have.
  • NCIBI Web Services - database integrates data through the application of research and open source software. Services include MiMI,Gene2MeSH, Metab2MeSH, Metabolomics, and Natural Language Processing. Access to this web service is provided free of charge. The NCIBI Web Services is an activity of the NIH's National Center for Integrative Biomedical Informatics (NCIBI).
  • NIH Intramural Database (NIDB) - NIDB collects and disseminates information about research being performed in the Intramural Programs of the Institutes and Centers of the National Institutes of Health
  • NIH OVID Databases - inlcudes Books@OVID and Journals@OVID Full Text. No login required; click on Start OvidSP if you are on a login page. Please Logoff after each session. (NIH/NCI-F)
  • NIH RePORTER - formerly known as CRISP, the information found in NIH RePORTER is drawn from eRA databases, Medline, PubMed Central, the NIH Intramural Database, and iEdison, using newly-formed linkages among the disparate data sources. The comprehensiveness of these databases varies, as does the quality of the linkages formed among them. The quality of RePORTER data should improve over time as a result of changes in both data collection (e.g., implementation of the NIH Public Access policy) and the increased ability to identify missing information that comes from making these data accessible to more people. (NIH/NCI-F)

 

O

  • OpenHelix - OpenHelix is a partly public, partly fee-based portal that assists researchers in conducting breakthrough research directing scientists to the most relevant publicly available bioinformatics and genomics resources on the web, and then gives them immediate access to tutorials, training materials, and useful tips and information developed by OpenHelix . Only the section of the portal that is publicly available can be accessed effective 2012.
  • Organohalogen Compounds Database - archives short papers presented at annual Dioxin Symposia from 1990 to date. Sponsored by the nonprofit group, Dioxin 20XX, of the International Advisory Board of the International Symposium of Halogenated Persistent Organic Pollutants (POPs), this free database includes scientific papers in pdf format and covers POPs as they relate to disciplines such as molecular biology, human health risk assessment, management risk assessment, and environmental and analytical chemistry.

 

P

  • Partek Genomics Suite (Software) - a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data. Designed for high-dimensional genomic studies containing thousands of samples, it is fast, memory efficient and will analyze large data sets on a personal computer. It supports a complete workflow including convenient data access tools, identification and annotation of important biomarkers, and construction and validation of predictive diagnostic classification systems. The software is Affymetrix GeneChip-compatibleT for gene expression analysis, exon expression analysis, and chromosomal copy number analysis. Access Information: Contact the NIH Help Desk at 301-496-4357 (6:00 am - 6:00 pm); or the NIH IT Service Desk.(NIH/NCI-F)
  • PATAI's Chemistry of Functional Groups - for the organic chemist, searchable database containing all 21 volumes of Patai's series published from 1996 to present. New content, initially 2 volumes per year, will be added. (NIH/NCI-F)
  • Pathway Studio Software (Elsevier) - about | NCI researchers (includes NCI-F) have unlimited access to the latest version of Elsevier's Pathway Studio software with the Mammalian (protein-centric) knowledge base as well as the premium DiseaseFx (disease-centric) and ChemEffect (compound-centric) knowledgebases, as well as the MedScan text mining module. Researchers also have access to the NCI's high-quality HyNet Yeast 2-Hybrid Protein Interaction Database .The knowledge bases include molecular facts retrieved from Elsevier's journals as well as facts retrieved from articles from other leading scientific publishers and from PubMed abstracts. Pathway Studio lets molecular biologists work in an interactive graphical environment to connect findings from independent research projects, analyze experimental data, and to develop new findings and publish. Frederick Support: NCI investigators located in Frederick are asked to utilize the DMS Help Desk fredhelpdesk@mail.nih.gov for all Pathway Studio issues. Service requests submitted to DMS Help Desk for software registration should be directed to nciterpsysnetadmin@mail.nih.gov (NCI/NCI-F)
  • Pharmaprojects - from Citeline, contains highly detailed profiles of over 50,000 drugs, covering all drugs for all diseases, from the preclinical to commercialization stage. Drug development information is updated in realtime by a team of experts. A brief, one time registration is required to use this database. (NIH/NCI-F)
  • Protein Lounge - systems biology resource - a collection of interactive web-based databases and tools to help life scientists assess and analyze gene-protein data. You may click on the Create Account button on the website to create an account under the NIH Library license.(NIH/NCI-F)
  • PsycINFO - (1806 - ) via the APA PsychNet gateway, provides citations with abstracts to the scholarly literature in the psychological, social, behavioral, and health sciences. (NIH/NCI-F)
  • PubChem - PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
  • PubMed @ NCIF | FAQ - Use the 'PubMed @ NCIF' link to view the Scientific Library's 'Full-Text' and 'Print' icons while searchingPubMed. PubMed is a free version of MEDLINE with access to an index of biomedical literature journals from 1950 forward, as well as a growing collection of free reference books [NCBI Bookshelf] that can be searched by keyword within the PubMed interface.
  • PubMed Central (PMC) - PMC is the NLM's digital archive of biomedical and life sciences journal literature, which is free and accessible on the web, in keeping with NLM's mandate to preserve the biomedical literature. PMC is also a repository for journal literature deposited by participating publishers and for author manuscripts submitted in compliance with NIH's Public Access Policy mandate . Read more aboutPMC and the mandate at http://www.ncbi.nlm.nih.gov/pmc/about/public-access-info. More information about the PMC Manuscript Submission System is available at http://www.nihms.nih.gov/.
  • PubMed Commons - is a system that enables researchers to share their opinions about scientific publications. Researchers can comment on any publication indexed by PubMed, and read the comments of others. PubMed Commons is a forum for open and constructive criticism and discussion of scientific issues. PubMed Commons is currently in a closed pilot testing phase, which means that only invited participants can add and view comments in PubMed. In order to complete the process you will also need to have a My NCBI account. If you don't already have one, register for a free account. (NCI/NCI-F)

 

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  • QUOSA Information Manager - QUOSA literature management software for biomedical researchers is a tool from Elsevier for downloading, organizing, and searching full-text PDFs retrieved from PubMed, Web of Science, Embase, Scopus, ScienceDirect, Google Scholar, and other databases. QUOSA Software is available to NCI-F employees via an NCI license and designed for individual desktops. Visit the Training and Support page for links to download either Windows or Mac Subscriber versions. See also tutorials onQUOSA's YouTube channel. Questions about the software or problems with access should be directed to support@quosa.com. (NCI/NCI-F)

 

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  • RAS Reference Library via EndNote Web - a list of RAS citations available to any NCI-F employee. EndNote Web, the software used for the RAS References Libary, requires a one-time registration. NOTE: If you are already using EndNote Web, please emailmeckleyr@mail.nih.gov, as this process could affect references already in EndNote WebRegistration instructions: 1) From a computer at NCI-F, go to the Web of Science (WOS) database. 2) Under "Customize Your Experience" on the right side, click "Register." 3) Enter your email address (The address does not have to be an NIH email address.). 4) Enter requested information. Be sure your password is at leasteight characters long and includes one symbol and one number. 5) Check your email for notification that your account was created. 6) After you receive confirmation, email Robin Meckley and provide the email address that you used to create your EndNote Web account. 7) You will receive a return email with information on how to view the RAS References Library. (NCI-F only)
  • RBdigital - (formerly OneClickdigital)  The RBdigital app provides access to audio recordings of several Great Courses lectures and a collection of free literary "classics."  Mobile apps are available for the iPhone®, Android™, and Kindle Fire. It is also possible to stream these files online.
  • Reaxys - See Changes for Registered Users. (References from 1771-; Patents from 1803-). Formerly known as Beilstein, contains enhanced access to Beilstein, Gmelin and Patent Chemistry databases. Reaxys connects validated experimental data from the three authoritative sources and provides workflow tools designed to support planning optimization in chemistry and related disciplines such as pharmacology, toxicology and ecology. It contains specific bioassay results, logPs, toxicity values, and other valuable data. To learn more about Reaxys, or view online training, click on links from within the Reaxys site. If you need any assistance using this database, please feel free to call Alan Doss at x6249 or via email(NIH/NCI-F)
  • RePORT (Research Portfolio Online Reporting Tools) - provides access to reports, data and analysis of NIH research activities including information on NIH expenditures and the results of NIH-funded research. For questions and comments, please contact the RePORT team.

 

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  • SciBX - Science-Business eXchange - a weekly publication that provides a timely, concise and understandable analysis of the scientific content and commercial potential of the most important translational research papers from across the life science literature. Editorial teams at SciBX mine articles across the literature each week, distilling information down to 25 most important developments. By reporting the industry viewpoint on key papers, SciBX provides a unique scientific and commercial perspective on today's breakthrough science.(NIH/NCI-F)
  • ScienceDirect Database - link to the main page of ScienceDirect's electronic collection of full-text science, technology, medical journals and books and bibliographic information; you can also find a wide variety of other features and content. (NIH/NCI-F)
  • SCOPUS - an abstract and indexing database from Elsevier Science, Scopus, offers access to over 14,000 peer-reviewed titles from more than 4,000 international publishers covering scientific, technical, medical, and social science literature and 15 million patents. In Scopus, you can set up an email alert to let you know each time a particular article of interest is cited in Scopus. (NIH/NCI-F)
  • SEER Cancer Statistics Review (CSR) - (1975-2014). The SEER Cancer Statistics Review (CSR), a report of the most recent cancer incidence, mortality, survival, prevalence, and lifetime risk statistics, is published annually by the Surveillance Research Program of the NCI.
  • Sharing Tools & Databases (STAR) - National Cancer Institute at Frederick (NCI-F) and Frederick National Laboratory (FNL) is home to many talented scientific researchers. This site is dedicated to them, and to their research, and is open to all NCI-F researchers who wish to share the fruits of their research with the rest of NCI-F, as well as with a larger, world-wide community of researchers, in the spirit of collaboration that moves research forward and makes breakthroughs more likely to happen. Please contact the Scientific Library for more information on how you can have your research represented on this site.
  • Springer Protocols - full-text access to over 16,000 online biomedical research protocols from Methods in Molecular Biology (1984-),Methods in Molecular Medicine (1996-), content found in Neuromethods, Methods in Pharmacology and Toxicology, and Methods in Biotechnology. Access individual titles in Springer Protocols from the Online Catalog using either the Series title or the unique volume title. (NIH/NCI-F)
  • STITCH - The Search Tool for Interactions of Chemicals ( STITCH ) is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. Read articles from Nucleic Acids Research about STICH: Article 1Article 2.
  • Structural Biology KnowledgeBase (SBKB) - The Structural Biology Knowledgebase (SGKB) is a free, comprehensive resource produced in a collaboration between the Protein Structure Initiative (PSI) and Nature Publishing Group (NPG). The site offers you an easy way of keeping abreast of developments both by the PSI and more generally in the fields of structural genomics and structural biology.

 

T

  • TOXNET - from NLM, the NLM Toxicology Data Network, databases on toxicology, hazardous chemicals, environmental health, and toxic release.
  • TRANSFAC + PROTEOME Professional – can be used for the identification of Experimentally Demonstrated Regulators for Eukaryotic cells, visualization of a gene’s promoter region and associated regulatory features, identification of experimentally demonstrated targets of transcription factors, predicted binding sites for a gene of interest, and analysis of microarray, ChiP-Seq, and RNA-seq data. Before accessing this resource, first setup an account at the Registration Site, using the following License Key: 1881-6975-97565225. Quick Start Guide, Video and Other Tutorials. (NIH/NCI-F)

 

U

  • Ulrichsweb Global Serials Directory - search source of detailed information on more than 300,000 periodicals / serials of all types: academic and scholarly journals, e-journals, peer-reviewed titles, popular magazines, newspapers, newsletters, and more. (NCI-F)
  • UpToDate - an evidence-based tool for answering clinical questions and identifying treatments with over 75,000 pages of peer-reviewed text, written and reviewed by clinicians. (NIH/NCI-F)

 

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W

  • Web of Science (WOS) - online version of ISI's Science Citation Index Expanded (1900 - present) & Social Sciences Citation Index, (1900 - present); with "Cited Reference Search," a unique tool for citation reference searching. WOS Interface also includes BIOSIS Citation Index; Current Contents Index; Data Citation Index; Derwent Innovations Index; Zoological Record; Book Citation Index; Conference Proceedings Index; Current Chemical Reactions; and Index Chemicus. Make your selection from the WOS Core Collection pulldown list. Also available from the WOS site are links to Journal Citation Reports and EndNote Web.(NIH/NCI-F)

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Y

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