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on page 1 showing 19 out of 19 results

Cite this (Animal Genome Size Database, RRID:SCR_007551)

URL: http://www.genomesize.com

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

Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff.

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    Arvados

Cite this (Arvados, RRID:SCR_002223)

URL: https://arvados.org/

Resource Type: Resource, service resource, data repository, storage service resource

A free and open source bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. The platform is designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. The platform is designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management.

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    ASPGD

Cite this (ASPGD, RRID:SCR_002047)

URL: http://www.aspgd.org/

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

Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.

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Cite this (BioBank Central., RRID:SCR_008645)

URL: http://www.biobankcentral.org/resource/wwibb.php

Resource Type: Resource, data or information resource, biospecimen repository, people resource, service resource, portal, storage service resource, data repository, community building portal, funding resource, material storage repository

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. Web-based portal to connect all the constituencies in the global biobank community. The project seeks to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum. Biobanks are the meeting point of two major information trends in biomedical research: the generation of huge amounts of genomic and other laboratory data, and the electronic capture and integration of patient clinical records. They are comprised of large numbers of human biospecimens supplemented with clinical data. Biobanks when implemented effectively can harness the power of both genomic and clinical data and serve as a critical bridge between basic and applied research, linking laboratory to patient and getting to cures faster. As science and technology leaders work to address the many challenges facing U.S. biobanks logistical, technical, ethical, financial, intellectual property, and IT BioBank Central will serve as an accurate and timely source of knowledge and news about biorepositories and their role in research and drug development. The Web site also provides a working group venue, patient and public education programs, and a forum for international collaboration and harmonization of best practices.

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    dbSTS

Cite this (dbSTS, RRID:SCR_000400)

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

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

THIS RESOURCE IS NO LONGER ACCEPTING SUBMISSIONS, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences.

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Cite this (Drug Related Gene Database, RRID:SCR_003330)

URL: https://confluence.crbs.ucsd.edu/display/NIF/DRG

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

Gene expression data from published journal articles that test hypotheses relevant to the neuroscience of addiction and addictive behavior. Data types include the effects of a particular drug, strain, or knock out on a particular gene, in a particular anatomical region. "Export" (Data Federation) for a fuller description of the methods, drug paradigm and the experimental values. Data submissions are welcome, https://confluence.crbs.ucsd.edu/display/NIF/DRG+Submission+Documentation Funded by an ARRA supplement from the National Institute of Drug Abuse (NIDA), the DRG database was created to facilitate discovery and use of resources relevant to drug abuse research. The database and associated tools were specifically created for providing data that is contained in tables, figures and supplementary materials from published papers in a way that facilitates search across the results of these studies. The current database mainly focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Once loaded, these data are available for query through the NIF interface. During this process, the content is standardized using a generic high level description of a relevant study and map terms to ontologies available through the NIF project (NIFSTD) to enhance semantic search of such data.

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Cite this (European Genome-phenome Archive, RRID:SCR_004944)

URL: http://www.ebi.ac.uk/ega/

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

A service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication.

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Cite this (GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database, RRID:SCR_007440)

URL: http://www.geisha.arizona.edu/geisha/

Resource Type: Resource, database, narrative resource, service resource, storage service resource, atlas, data repository, experimental protocol, data or information resource

Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA.

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Cite this (Genome survey sequence database, RRID:SCR_002146)

URL: https://www.ncbi.nlm.nih.gov/genbank/dbgss/

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

Database of unannotated short single-read primarily genomic sequences from GenBank including random survey sequences clone-end sequences and exon-trapped sequences. The GSS division of GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA). It should be noted that two classes (exon trapped products and gene trapped products) may be derived via a cDNA intermediate. Care should be taken when analyzing sequences from either of these classes, as a splicing event could have occurred and the sequence represented in the record may be interrupted when compared to genomic sequence. The GSS division contains (but is not limited to) the following types of data: * random single pass read genome survey sequences. * cosmid/BAC/YAC end sequences * exon trapped genomic sequences * Alu PCR sequences * transposon-tagged sequences Although dbGSS sequences are incorporated into the GSS Division of GenBank, annotation in dbGSS is more comprehensive and includes detailed information about the contributors, experimental conditions, and genetic map locations.

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Cite this (GoatMap Database, RRID:SCR_008144)

URL: http://locus.jouy.inra.fr/cgi-bin/lgbc/mapping/common/intro2.pl?BASE=goat

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This website contains information about the mapping of the caprine genome. It contains loci list, phenes list, cartography, gene list, and other sequence information about goats. This website contains 731 loci, 271 genes, and 1909 homologue loci on 112 species. It also allows users to summit their own data for Goatmap. ARK-Genomics is not-for-profit and has collaborators from all over the world with an interest in farm animal genomics and genetics. ARK-Genomics was initially set up in 2000 with a grant awarded from the BBSRC IGF (Investigating Gene Function) initiative and from core resources of the Roslin Institute to provide a laboratory for automated analysis of gene expression using state-of-the-art genomic facilities. Since then, ARK-Genomics has expanded considerably, building up considerable expertise and resources.

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Cite this (High Throughput Genomic Sequences Division, RRID:SCR_002150)

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

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

Database of high-throughput genome sequences from large-scale genome sequencing centers, including unfinished and finished sequences. It was created to accommodate a growing need to make unfinished genomic sequence data rapidly available to the scientific community in a coordinated effort among the International Nucleotide Sequence databases, DDBJ, EMBL, and GenBank. Sequences are prepared for submission by using NCBI's software tools Sequin or tbl2asn. Each center has an FTP directory into which new or updated sequence files are placed. Sequence data in this division are available for BLAST homology searches against either the htgs database or the month database, which includes all new submissions for the prior month. Unfinished HTG sequences containing contigs greater than 2 kb are assigned an accession number and deposited in the HTG division. A typical HTG record might consist of all the first-pass sequence data generated from a single cosmid, BAC, YAC, or P1 clone, which together make up more than 2 kb and contain one or more gaps. A single accession number is assigned to this collection of sequences, and each record includes a clear indication of the status (phase 1 or 2) plus a prominent warning that the sequence data are unfinished and may contain errors. The accession number does not change as sequence records are updated; only the most recent version of a HTG record remains in GenBank.

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Cite this (Influenza Research Database (IRD), RRID:SCR_006641)

URL: http://www.fludb.org/brc/home.do?decorator=influenza

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

The Influenza Research Database (IRD) serves as a public repository and analysis platform for flu sequence, experiment, surveillance and related data.

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Cite this (Kyoto Encyclopedia of Genes and Genomes Expression Database, RRID:SCR_001120)

URL: http://www.genome.jp/kegg/expression/

Resource Type: Resource, service resource, data repository, storage service resource

A repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.

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    NBRC

Cite this (NBRC, RRID:SCR_002660)

URL: http://www.nbrc.nite.go.jp/e/index.html

Resource Type: Resource, production service resource, biomaterial supply resource, biospecimen repository, database, material service resource, service resource, storage service resource, data or information resource, material resource, biomaterial manufacture, material storage repository

Collection of microbial resources and perform taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. NBRC is a member of WFCC, OECD Global BRC Network, ACM and JSCC. They are certified by quality management system ISO 9001. To provide attractive biological resources with useful information attached, they actively collect potentially useful biological resources (microorganisms and cloned genes) and distributes them to promote basic research as well as industrial applications. At the Biological Resource Center, they explore, isolate and identify microorganisms from various natural environments and at the same time accept scientifically and industrially useful microorganisms from researchers in academic and industrial sectors. The microbial DNA library constructed at the Biotechnology Development Center is also part of their collection. To improve and expand the collection, new methodologies for the isolation, identification and preservation of microorganisms and DNA will be investigated and developed so as to provide biological resources of higher quality. Their resources serve, for example, as the standard for determining antimicrobial activity, in aseptic tests as well as for the production of pharmaceutical substances and will be constantly reinforced for wider distribution to researchers in academia and industries. Please refer to the catalog shown at the NBRC website for details.

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Cite this (NeMOarchive, RRID:SCR_016152)

URL: https://nemoarchive.org/

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

Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification,
histone modification profiles and chromatin accessibility.

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Cite this (NIMH Data Archive, RRID:SCR_004434)

URL: https://nda.nih.gov/

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

Research data repository for data sharing and collaboration among autism spectrum disorder investigators. Used to accelerate scientific discovery through data sharing, data harmonization and reporting of research results.

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Cite this (NUgene Project, RRID:SCR_007426)

URL: https://www.nugene.org/

Resource Type: Resource, biomaterial supply resource, biospecimen repository, service resource, storage service resource, data or information resource, material resource, material storage repository

Collects and stores genetic (DNA) samples along with associated healthcare information from patients of Northwestern-affiliated hospitals and clinics. This resource is available to scientists to conduct groundbreaking genetic research. The information and blood samples provided will be used by researchers to examine the role genes play in the development and treatment of common diseases. The NUgene Project seeks to increase the understanding of genetic mechanisms underlying common diseases, assist in the development of DNA-based technology for diagnosis and treatment of disease, and aid physicians and other healthcare providers in the application of genetics to the practice of medicine. NUgene participants are recruited throughout the Northwestern-affiliated healthcare community in order to create an ethnically and medically diverse population for research. Participants must be 18 years of age or older and receive their medical care from a Northwestern-affiliated provider, regardless of health status. Consenting individuals complete all aspects of enrollment in a single meeting with a research coordinator. The enrollment process includes the donation of a single sample of blood and the completion of a self-administered questionnaire. Participants also sign a consent form during this encounter. The NUgene Project is an interdisciplinary project that relies on the expertise of individuals working in a variety of fields, including science, medicine, clinical research, statistics, epidemiology, and computational biology. NUgene''s multidisciplinary approach has spurred collaborations within Northwestern-affiliated institutions and with other outside institutions. This collaboration of ideas is the future of genetics and genomic research.

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Cite this (Rat Genome Database (RGD), RRID:SCR_006444)

URL: http://rgd.mcw.edu

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

Centralized database that collects, manages, and distributes data generated from ongoing rat genetic and genomic research efforts and makes these data widely available to the scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. It also facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include a comprehensive description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.

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Cite this (Zebra Model Organism Database (ZFIN), RRID:SCR_002560)

URL: http://zfin.org

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

ZFIN is a Model Organism Database that serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. ZFIN includes (i) access to images with associated curated data, (ii) gene expression and phenotype data, (iii) zebrafish models of human diseases, (iv) genomic features and molecular details, (v) a genome browser, (vi) transcripts, (vii) antibodies and (viii) a community wiki for protocols and antibodies. ZFIN welcomes direct data submissions. If you would like to make your unpublished expression or phenotype data available to the community, you can submit this data to ZFIN using Phenote program or contact zfinadmn@zfin.org for additional options and support. Additionally, data is downloadable as text files and available in the data mining platform zebrafishmine (zebrafishmine.org).

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