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on page 1 showing 20 out of 73 results from 1 sources

Cite this (Alignable Tight Genomic Cluster, RRID:SCR_001894)

URL: http://atgc.lbl.gov/atgc/

Resource Type: Resource, data or information resource, database

ATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis.

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Cite this (Array Information Library Universal Navigator, RRID:SCR_006967)

URL: http://ailun.stanford.edu/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Re-annotated gene expression / proteomics data from GEO by relating all probe IDs to Entrez Gene IDs once every three months, enabling you to find data from GEO, and compare them from different platforms and species. Platform Annotations adds the latest annotations to any uploaded probe / gene ID list file. Platform Comparison compares any two platforms to find corresponding probes mapping to the same gene. Cross-species mapping maps platform annotations to other species. Gene Search finds deposited platforms and samples in GEO that contain a list of genes. GPL ID Search finds the GPL ID (GEO platform ID) for your array. You can also download the latest annotations files for all arrays and their comprehensive universal gene identifier table, which relates all types of gene / protein / clone identifiers to Entrez Gene IDs for all species. Note: The database was last updated on 4/30/2011. They have successfully mapped 54932732 individual probes from 385099 GEO samples measuring 3519 GEO platforms across 217 species.

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Cite this (Automated Microarray Pipeline, RRID:SCR_001219)

URL: http://compbio.dfci.harvard.edu/amp/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis.

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    BECA

Cite this (BECA, RRID:SCR_015846)

URL: http://www.iu.edu/~beca/

Resource Type: Resource, software resource, image analysis software, data visualization software, data processing software, software application

Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.

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Cite this (Biological Magnetic Resonance Data Bank, RRID:SCR_002296)

URL: http://www.bmrb.wisc.edu/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance (NMR) spectroscopic investigations of biological macromolecules and metabolites. BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR. The BMRB archive consists of four main data depositories: quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors and derived data; databases for NMR restraints processed from original author depositions available from the Protein Data Bank; time-domain spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules; and a database of one- and two-dimensional (1)H and (13)C one- and two-dimensional NMR spectra for over 250 metabolites. BMRB has tools for querying the archive and retrieving information and an ftp site where data in the archive can be downloaded in bulk. BMRB accepts quantitative NMR data for a peptide, protein, nucleic acid, or polysaccharide and their ligands and cofactors assigned on an atom-specific basis, and data derived from the analysis of such data.

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Cite this (BrainInfo, RRID:SCR_003142)

URL: http://braininfo.rprc.washington.edu

Resource Type: Resource, topical portal, database, standard specification, narrative resource, portal, atlas, data or information resource

Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.

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Cite this (Clair library, RRID:SCR_007019)

URL: http://www.clairlib.org

Resource Type: Resource, data analysis software, data processing software, software application, text-mining software, software resource, software toolkit, text extraction software

A suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA). Its architecture also allows for external software to be plugged in with very little effort. The latest version of clairlib is 1.06 which was released on March 2009 and includes about 130 modules implementing a wide range of functionalities. Clairlib is distributed in two forms: * Clairlib-core, which has essential functionality and minimal dependence on external software, and * Clairlib-ext, which has extended functionality that may be of interest to a smaller audience. Much can be done using Clairlib on its own. Some of the things that Clairlib can do are: Tokenization, Summarization, Document Clustering, Document Indexing, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis, RandomWalks on Graphs, Tf-IDF, Perceptron Learning and Classification, and Phrase Based Retrieval and Fuzzy OR Queries.

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    ComiR

Cite this (ComiR, RRID:SCR_013023)

URL: http://www.benoslab.pitt.edu/comir/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.

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Cite this (Coremine Medical, RRID:SCR_005323)

URL: http://www.coremine.com/medical/#search

Resource Type: Resource, service resource

Service to access comprehensive information on diseases, drugs, treatments and medical biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to drill down to specific details. Search results are presented in a dashboard format comprized of panels containing various categories of information ranging from introductory sources to the latest scientific articles.

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Cite this (dbGaP at NCBI, RRID:SCR_002709)

URL: http://www.ncbi.nlm.nih.gov/gap

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype, including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. dbGaP provides two types of access for users, open and controlled. Summaries of studies and the contents of measured variables as well as original study document text are generally available to the public, while access to individual-level data including phenotypic data tables and genotypes require varying levels of authorization. The data in dbGaP will be pre-competitive, and will not be protected by intellectual property patents. Investigators who agree to the terms of dbGaP data use may not restrict other investigators' use of primary dbGaP data by filing intellectual property patents on it. However, the use of primary data from dbGaP to develop commercial products and tests to meet public health needs is encouraged. Submitters who are not Federally-funded and affiliated with an NIH IC will need to work with an NIH DAC so that proposed submission can be reviewed for consistency with appropriate policies to protect the privacy of research participants and confidentiality of their data. Submissions to dbGaP will not be accepted without assurance that the submitting institution approves the submission and has verified that the data submission is consistent with all applicable laws and regulations, as well as institutional policies. Submitters must also identify any limits on research uses of the data that are specifically set by individual research participants, e.g., through their informed consent. Open-access data can be browsed online or downloaded from dbGaP without prior permission or authorization.

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    dbSNP

Cite this (dbSNP, RRID:SCR_002338)

URL: http://www.ncbi.nlm.nih.gov/SNP/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database serving as a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Once discovered, these polymorphisms could be used by additional laboratories, using the sequence information around the polymorphism and the specific experimental conditions. (Note that dbSNP takes the looser "variation" definition for SNPs, so there is no requirement or assumption about minimum allele frequency.) The database accepts data submissions. dbSNP distinguishes a report of how to assay a SNP from the use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay a SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations.

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Cite this (Developmental and Reproductive Toxicology Database, RRID:SCR_002326)

URL: http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?DARTETIC

Resource Type: Resource, data or information resource, database

Bibliographic database providing references to developmental and reproductive toxicology literature on the National Library of Medicine's Toxicology Data Network. It covers teratology and other aspects of developmental and reproductive toxicology. It contains over 200,000 references to literature published since 1965. DART/ETIC is easily accessible and free of charge. Search by subject terms, title words, chemical name, Chemical Abstracts Service Registry Number (RN), and author. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order, but may be sorted by publication date, author or title.

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Cite this (Directory of Health Organizations Online, RRID:SCR_002331)

URL: http://dirline.nlm.nih.gov/

Resource Type: Resource, data or information resource, database

THIS RESOURCE HAS BEEN DISCONTINUED, documented July 15, 2016. Database containing location and descriptive information about a wide variety of information resources including organizations, research resources, projects, and databases concerned with health and biomedicine. This information may not be readily available in bibliographic databases. Each record may contain information on the publications, holdings, and services provided. These information resources fall into many categories including federal, state, and local government agencies; information and referral centers; professional societies; self-help groups and voluntary associations; academic and research institutions and their programs; information systems and research facilities. Topics include HIV/AIDS, maternal and child health, most diseases and conditions including genetic and other rare diseases, health services research and technology assessment. DIRLINE can be searched using subject words (such as disease or condition) including Medical Subject Headings (MeSH) or for the name or location of a resource. It now offers an A to Z list of over 8,500 organizations.

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Cite this (Distant Regulatory Elements, RRID:SCR_003058)

URL: http://dire.dcode.org

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

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Cite this (DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins, RRID:SCR_003039)

URL: http://lcg.rit.albany.edu/dp-bind

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

This web-server takes a user-supplied sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA. Prediction can be performed using a profile of evolutionary conservation of the input sequence automatically generated by the web-server or the input sequence alone. Three prediction methods are run for each input sequence and consensus prediction is generated.

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Cite this (Drug Information Portal, RRID:SCR_002818)

URL: http://druginfo.nlm.nih.gov/drugportal/drugportal.jsp

Resource Type: Resource, topical portal, database, portal, data or information resource

The NLM Drug Information Portal gives users a gateway to selected drug information from the U.S. National Library of Medicine and other key U.S. Government agencies. At the top of the page are links to individual resources with potential drug information, including summaries tailored to various audiences. Resources include the NLM search systems useful in searching for a drug, NLM research resources, resources organized by audience and class, and other NIH and government resources such as FDA and CDC. The search box in the middle of the page lets you search many of these resources simultaneously. More than 34,000 drugs can be searched using this facility. The portal covers drugs from the time they are entered into clinical trials (Clinicaltrials.gov) through their entry in the U.S. market place (Drugs@FDA). Many drugs in other countries are covered, but not as thoroughly as U.S. drugs. The PubMed link provides medical literature describing research, and TOXLINE provides toxicology literature. Resources such as MedlinePlus provide easy to read summaries of the uses and efficacy of a drug. You may search by a drug's trade name or generic name. For example, the trade name Advil and the generic name ibuprofen will retrieve the same drug record. As you type in a name, suggestions are given beneath the search box. A spell checker gives suggestions if the name is not found. You can find embedded portions of names by using an asterisk at the beginning and/or end of a search term. You can also search by the general Category of usage of a drug by checking that radio button. Suggestions are given as you type here too. Once a drug is found, a summary of the drug's type and usage is given, as well as links leading to further information at one of the portal's resources. Outside links open in a new window. Within a given drug record, you may click on the drug category and retrieve drugs with the same or similar uses. * View drug category descriptions. * View top By Name searches (previous seven days). * View top By Category searches (previous seven days). * View top dispensed prescriptions in the US Market, 2010. * View common drug name list. * View category name list. * View list of resources searched. JavaScript must be enabled in your browser for the NLM Drug Information Portal to work properly.

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Cite this (EDDA Study Design Terminology, RRID:SCR_010312)

URL: http://purl.bioontology.org/ontology/EDDA

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

Ontology terms useful for machine learning experiments. The terminology appearing in JMLA has been enriched with terms from MeSH and Emtree, the controlled vocabularies for MEDLINE and Embase, respectively. Synonyms include American and British variants and some inverted terms.

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    FLASH

Cite this (FLASH, RRID:SCR_005531)

URL: http://ccb.jhu.edu/software/FLASH/

Resource Type: Resource, software resource

A software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.

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    FMA

Cite this (FMA, RRID:SCR_003379)

URL: http://sig.biostr.washington.edu/projects/fm/

Resource Type: Resource, data analysis software, data processing software, database, software application, software resource, ontology, controlled vocabulary, data or information resource

A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model.

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    GenBank

Cite this (GenBank, RRID:SCR_002760)

URL: http://www.ncbi.nlm.nih.gov/Genbank/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

NIH genetic sequence database that provides an annotated collection of all publicly available DNA sequences for almost 280 000 formally described species. (Jan 2014) These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of the International Nucleotide Sequence Database Collaboration and daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.

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