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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Human Proteinpedia Resource Report Resource Website 10+ mentions |
Human Proteinpedia (RRID:SCR_002948) | Human Proteinpedia | data or information resource, data repository, database, service resource, storage service resource | A community portal for sharing and integration of human protein data that allows research laboratories to contribute and maintain protein annotations. The Human Protein Reference Database (HPRD) integrates data that is deposited along with the existing literature curated information in the context of an individual protein. Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted. | enzyme, protein expression, post-translational modification, protein-protein interaction, subcellular localization, enzyme substrate, tissue expression, protein, protein binding, peptide, mass spectrometry, mass spectrometry spectra, immunohistochemistry, western blotting, microarray, co-immunoprecipitation, fluorescence, annotation, cell line expression, disease tissue expression, FASEB list |
is listed by: re3data.org is related to: HPRD - Human Protein Reference Database has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
PMID:18259167 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02999, r3d100010985 | https://doi.org/10.17616/R3V62C | SCR_002948 | SciCrunch Registry | 2026-11-07 11:55:04 | 32 | ||||||
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PLEXdb - Plant Expression Database Resource Report Resource Website 10+ mentions |
PLEXdb - Plant Expression Database (RRID:SCR_006963) | PLEXdb | analysis service resource, data analysis service, data or information resource, data repository, database, portal, production service resource, service resource, storage service resource, topical portal | PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets. | gene expression, plant, plant pathogen, genotype, phenotype, genetic, physical, pathway, plant biology, compare, functional genomics, expression profiling, expression atlas, pathogen, genome, anova, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: FuncExpression has parent organization: Iowa State University; Iowa; USA |
UniNSF DBI-0543441; NSF IOS-0922746; USDA 3625-21000-049-00D |
PMID:22084198 | biotools:plexdb, r3d100011516, nlx_149236 | https://bio.tools/plexdb, https://doi.org/10.17616/R39D13 | SCR_006963 | SciCrunch Registry | PLEXdb - Gene expression resources for plants and plant pathogens, Plant Expression Database | 2026-11-07 12:00:34 | 21 | |||||
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Science Careers Resource Report Resource Website |
Science Careers (RRID:SCR_005156) | Science Careers | data or information resource, job resource, narrative resource | The journal Science is one of the most prestigious and widely cited scientific journals in the world. Founded by Thomas Edison in 1880, Science has been publishing breaking news and seminal research for more than 125 years. Science Careers is the careers component of Science that scientists rely on for career information and job postings. Science Careers offers a wide variety of content designed to assist scientists of all disciplines, backgrounds and experience levels navigate their career path. This includes over 3,000 job listings that are updated daily, thousands of career advice articles written by the Science Careers editorial staff, graduate program information, meetings and event information, funding opportunities on GrantsNet, and a Career Forum where scientists can join a community of experts and peers engaging in real time discussions around career issues. For employers, Science Careers provides multiple platforms for recruiting scientists and extending their employment brand including job postings, banner advertisements, email and newsletters and sponsorships. | job seeker, employer, career, employment, job posting, resume, database, community building portal, data storage repository, postdoctoral program resource |
is used by: NIF Data Federation is related to: Integrated Jobs |
The materials on this Website are protected by United States copyright law except that no copyright is claimed in any work of the US government. For personal, Noncommercial use only. Except where otherwise permitted, Any further reproduction, Distribution, Transmission, Display, Publication, Or broadcast requires the prior written permission of The American Association for the Advancement of Science. | nlx_144181 | SCR_005156 | SciCrunch Registry | 2026-11-07 12:00:46 | 0 | ||||||||
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Minimal information about Adaptive Immune Receptor Repertoires Resource Report Resource Website |
Minimal information about Adaptive Immune Receptor Repertoires (RRID:SCR_022596) | MiAIRR | data or information resource, narrative resource, portal, standard specification, topical portal | Checklist of minimally required information that we recommend journals adopt, and that could form requirements for submission to public data repository. AIRR sequencing studies apply high throughput sequencing technologies to profile B cell receptors (BCRs) and T cell receptors (TCRs). Standards were developed by AIRR Community Minimal Standards Working Group. | Checklist of minimally required information journals adopt, public data repository requirements, AIRR Community Minimal Standards Working Group standards | is related to: AIRR Data Commons | Free, Freely available | https://fairsharing.org/FAIRsharing.31hec1 | SCR_022596 | SciCrunch Registry | 2026-11-07 12:00:49 | 0 | ||||||||
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BRAIN Commons Resource Report Resource Website |
BRAIN Commons (RRID:SCR_023140) | data repository, service resource, storage service resource | Scalable cloud-based platform for computational discovery designed for the brain health community.The BRAINCommons empowers the global research community by providing access to multi-model data, state-of-the-art tools and a secure interoperable system for data sharing. | is listed by: DataCite | Free, Freely available | DOI:10.48478 | https://doi.org/10.48478, https://dx.doi.org/10.48478 | SCR_023140 | SciCrunch Registry | BRAIN Commons | 2026-11-07 12:01:03 | 0 | ||||||||
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WebArrayDB Resource Report Resource Website 1+ mentions |
WebArrayDB (RRID:SCR_005577) | WebArrayDB | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource | An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters. | is listed by: OMICtools | Prostate Cancer Foundation ; Mary Kay Ash Foundation ; NIH ; NIAI R01AI034829; NIAI R01AI052237; NCI R01CA68822; NCI U01CA114810 |
PMID:19602526 | Open source, Account required, The software package is available for the use on a public web server or can be downloaded | OMICS_00782 | SCR_005577 | SciCrunch Registry | 2026-11-07 11:55:35 | 8 | |||||||
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NIH Neuroscience Microarray Consortium Resource Report Resource Website 1+ mentions |
NIH Neuroscience Microarray Consortium (RRID:SCR_004930) | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2012. (no longer being funded) The NIH Microarray Consortium provides for-fee services to a community of NIH grantees, together with a more limited set of services to the public. The primary goal of this consortium is to move basic and translational research forward through acquisition and dissemination of high quality genomic data. This site includes a repository of microarray data sets and offers one-click links to public projects. These datasets were generated by various researchers on these platforms: Affymetrix, Agilent, Ambion, cDNA, Illumina, and Operon. The species currently covered are: Arabidopsis, Bovine, chicken, C. Elegans, Drosophila, Human, Macaca mulatta (Rhesus macaque), Mouse, Rat, Songbird, Xenopus, Yeast, and zebra finch. Basic search functions allows users to choose multiple options for finding the projects that interest them, and raw data files can also be downloaded after user registration. Web-based data analysis tools are also available. Scientists can analyze microarray data from the consortium repository or investigators can upload outside data for analysis. | arabidopsis, bos taurus, chicken, caenorhabditis elegans, drosophila, human, rhesus monkey, mouse, rat, songbird, xenopus, yeast, zebra finch |
is used by: NIF Data Federation is related to: Songbird Brain Transcriptome Database has parent organization: National Institutes of Health |
NIH Blueprint for Neuroscience Research | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00074 | http://arrayconsortium.tgen.org, http://np2.ctrl.ucla.edu/np2/home.do | SCR_004930 | SciCrunch Registry | NIH Neuroscience Microarray Consortium | 2026-11-07 11:55:40 | 4 | ||||||
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UNC Microarray Database Resource Report Resource Website 10+ mentions |
UNC Microarray Database (RRID:SCR_010979) | UNC MD, UNCMD | data or information resource, data repository, database, service resource, storage service resource | Database for microarray data storage, retrieval, analysis, and visualization. | microarray, FASEB list |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Account required, The community can contribute to this resource | OMICS_00872 | SCR_010979 | SciCrunch Registry | UNC-Chapel Hill Microarray Database | 2026-11-07 11:57:20 | 33 | |||||||
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YPED Resource Report Resource Website 1+ mentions |
YPED (RRID:SCR_001436) | YPED | data or information resource, data repository, database, service resource, storage service resource | Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards. | proteomics, protein, database, mass spectrometry, neuroscience, data analysis service, small molecule, source code, peptide, protein expression, phosphoprotein, mudpit, dige, icat, itraq |
uses: PANTHER is used by: Integrated Datasets is related to: Integrated Manually Extracted Annotation has parent organization: Yale School of Medicine; Connecticut; USA |
NIDA P30 DA018343; NHLBI N01-HV-28186 |
PMID:17867667 | Free, Freely Available | nlx_152660 | http://medicine.yale.edu/keck/nida/yped.aspx | SCR_001436 | SciCrunch Registry | Yale Protein Expression Database | 2026-11-07 11:54:31 | 4 | ||||
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MassBank Resource Report Resource Website 1000+ mentions |
MassBank (RRID:SCR_015535) | data or information resource, database | Public repository of mass spectral data which allows users to search similar spectra on a peak-to-peak basis, on a neutral loss-to-neutral loss basis, or by the m/z value and molecular formula, search chemical compounds by substructures, and keyword search chemical compounds | mass spectrometry, ms database, mass spectrometry database, chemical structure, chemical identification, FASEB list | Institute for Bioinformatics Research and Development Japan Science and Technology Agency ; National Bioscience Database Center Japan Science and Technology Agency ; Mass Spectorometry Society of Japan |
SCR_015535 | SciCrunch Registry | 2026-11-07 12:03:15 | 1429 | |||||||||||
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Gabi Primary Database Resource Report Resource Website 10+ mentions |
Gabi Primary Database (RRID:SCR_002755) | GABI | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource |
Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research. GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated. * GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload. |
molecular plant physiology, plant genome, genome, blast, sequence, snp, mapping, proteomics, image collection | has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany | German Resource Center for Genome Research RZPD GmbH ; Max Planck Society ; BMBF 0312272; BMBF 0313112; BMBF 0315046 |
PMID:18812395 | Free, Freely available | nif-0000-02866, r3d100012432 | http://gabi.rzpd.de/, https://doi.org/10.17616/R3QB61 | SCR_002755 | SciCrunch Registry | GabiPD | 2026-11-07 11:54:46 | 13 | ||||
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The Eye Lab Image Database Resource Report Resource Website 10+ mentions |
The Eye Lab Image Database (RRID:SCR_002038) | data or information resource, database | The Image Repository contains a collection of images produced by the research of John Clark's Eye Lab. Experiments include: Irradiated CP49 KO and wildtype, Hypothesis: CP49 KO mice will be more sensitive to X-irradiation than controls Huntington Mice Cataract ID, Hypothesis: Individuals can be identified by the pattern of their cataract. Alpha-Synuclein Mice, Hypothesis: Mice transgenic for the EGFP-tagged, mutant and WT strains of human alpha-synuclein gene, will provide a model for the testing of drugs on aggregation of the protein. alpha B Crystallin/SPARC DKO, Hypothesis: The absence of the chaperone protein, alpha B-Crystallin, causes a greater intensity and earlier onset in the opacifying effects of an absence of the matricellular protein, SPARC. Survey of SPARC KO and WT Survey of SPARC KO and WT Mice The repository is being built through a collaboration between the University of Washington's Department of Biological Structure, led by John Clark, and the Structural Informatics Group, led by Jim Brinkley. As an aim of the Biomedical Information Sciences Technology Initiative (BISTI), members of the Structural Informatics Group have been talking with biomedical researchers to find out their informatics needs. Tools such as this repository are being created in response to those needs. This web tool allows the researchers to add their images to a repository facilitating the organization and management of their data. | eye, alpha b-crystallin, alpha-synuclein, cataracts, cp49 ko, huntington, images, lens, mice, sparc, FASEB list | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-11980 | SCR_002038 | SciCrunch Registry | The Eye Lab | 2026-11-07 12:01:56 | 37 | |||||||||
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Neurodatabase.org Resource Report Resource Website 1+ mentions |
Neurodatabase.org (RRID:SCR_007091) | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 09, 2015. A repository of neurophysiology data conforming to BrainML data models and protocols: BrainML-formatted experimental data submissions are published in searchable, browsable form. Registered users may submit new experiments. The site contains spike trains, voltage time series, and some derived histograms from single cell and multi-unit activity. The database focuses on in vivo somatosensory and visual activity during task performance. This resource contains only a few datasets, but they are of high quality and have been used for reanalysis by several parties. There are three primary interfaces for querying data from this repository: a web-based browse interface, a web-based HTML query form, and a Java web start desktop application. In addition, there is an XML interface useful for direct access by software clients. To download the source code, please read and acknowledge the license agreement. | neurophysiology, source code, spike train, voltage time series, histogram, single cell, multi-unit, in vivo, somatosensory, visual, task, data set |
uses: BrainML is used by: NIF Data Federation has parent organization: Weill Cornell Medical College; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00001 | http://neurodatabase.org/dataserver/goto.do?page=.home | SCR_007091 | SciCrunch Registry | Neurodatabase.org: Laboratory of Neuroinformatics Weill Medical College, Neurodatabase, neurodatabase.org Laboratory of Neuroinformatics Weill Medical College of Cornell University, LNI: neurodatabase.org | 2026-11-07 11:56:08 | 7 | |||||||
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ALFRED Resource Report Resource Website 50+ mentions |
ALFRED (RRID:SCR_001730) | ALFRED | data or information resource, data repository, database, service resource, storage service resource | A public curated compilation of allele frequency data on anthropologically defined human population samples linked to the molecular genetics-human genome databases. Only data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. Researchers wishing to have their data entered into ALFRED should contact them. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching. ALFRED provides easy searching options including versatile "Keyword search" and also has numerous summary tables providing quick overviews of contents by chromosome, population, average heterozygosity, Fst and others, all available under various tabs from the ALFRED homepage. | allele frequency, dna polymorphism, haplotype, high throughput, genome, population, sample, education, polymorphism, allele, chromosome, heterozygosity, fst, loci, pathway, genetics, FASEB list | has parent organization: Yale School of Medicine; Connecticut; USA | NIGMS P01GM 57672 | PMID:19325849 PMID:11125124 PMID:12209575 |
Free, Freely Available | nif-0000-02541, r3d100012700 | https://doi.org/10.17616/R3GZ2J | SCR_001730 | SciCrunch Registry | The ALlele FREquency Database, ALlele FREquency Database | 2026-11-07 11:54:31 | 74 | ||||
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University Health Network Princess Margaret Living PDX Core Facility Resource Report Resource Website 1+ mentions |
University Health Network Princess Margaret Living PDX Core Facility (RRID:SCR_027523) | PMLB PDX Core | access service resource, biobank, core facility, material storage repository, service resource, storage service resource | Core provides services for the use of Xenograft (PDX) models listed in open global catalogue of PDX models for comprehensive search and attribute filtering support for clinico-pathological and molecular data. Molecular data and visualization of profiled models could be accessed through the institute's portal. | ABRF, services for use of Xenograft (PDX) models, open global catalogue of PDX models, |
is listed by: ABRF CoreMarketplace has parent organization: University Health Network |
ABRF_5428 | https://coremarketplace.org/RRID:SCR_027523/?citation=1 | SCR_027523 | SciCrunch Registry | Princess Margaret Living Biobank (PDX) | 2026-11-07 12:06:50 | 1 | |||||||
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eyeMoviePedia Resource Report Resource Website |
eyeMoviePedia (RRID:SCR_003541) | eyeMoviePedia | data or information resource, data repository, database, service resource, storage service resource | Archive and access films from the field of Ophthalmology for free on highly secure servers for permanent access and citeability. A citeable identification number (specific addressing using DOI), allows for citation of individual films in journal publications. Films may be commented by the author either in speech, or in text. Key wording provided by the authors at the time of submission, make each film recognizable to internet search machines. | ophthalmology, database, data sharing, eye, clinical, doi, publish, video resource, medicine | is listed by: re3data.org | Creative Commons Attribution-NoDerivs License, v3 Germany, The community can contribute to this resource | nlx_157655, r3d100012558 | https://doi.org/10.17616/R3DF7N | SCR_003541 | SciCrunch Registry | 2026-11-07 11:55:06 | 0 | |||||||
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Nucleotide database Resource Report Resource Website 100+ mentions |
Nucleotide database (RRID:SCR_004630) | nucest | data or information resource, data repository, database, service resource, storage service resource | Nucleotide database as collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. | Genome, gene, transcript sequence data, GenBank, RefSeq, TPA, PDB, gold standard |
is listed by: re3data.org is related to: BMAP cDNA Resources is related to: GenBank has parent organization: NCBI |
PMID:8401577 | Free, Freely available | SCR_016578, nlx_62971 | SCR_004630 | SciCrunch Registry | 2026-11-07 11:55:33 | 167 | |||||||
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Animal Toxin Database Resource Report Resource Website 1+ mentions |
Animal Toxin Database (RRID:SCR_007035) | ATDB | controlled vocabulary, data or information resource, data repository, database, ontology, service resource, storage service resource | Database of animal toxins, this most recent release (2009) focused on constructing a global-scale animal toxin-channel interaction network based on literature and database annotations through the integration of an ion channel database into ATDB 2.0. Most ion channel sequences were categorized and annotated with a hierarchic controlled term system (Ion Channel Ontology). More than 55,022 possible T-C interactions were extracted by text mining which link the toxin and ion channel database. These interaction data were classified carefully based on evidence type, in which 9,193 high confidence interactions were annotated in active site level. A web-based T-C interaction network view was build to visualize and make data access easy. The features and updates of ATDB 2.0 are summarized as follows: # AN interaction dataset including 55,022 toxin-channel interactions # Ion channel database (5,097 entries) # Ontology for ion channel classification (Ion Channel Ontology) # 3000 maps for toxins and ion channels interaction # More than 600 additional toxin entries # PDB view to visualize 3-D structure of molecule # More flexible option for data downloads. You may submit new toxins to the database. | toxin, ion channel, interaction, blast, ligand, 3d structure, data analysis service | has parent organization: Hunan Normal University; Changsha; China | National Laboratory of Protein Engineering and Plant Genetic Engineering at Peking University ; National Science Foundation of China 30430170; National Science Foundation of China 30670640 |
PMID:17933766 PMID:20685369 |
Free, For Public, Non-Profits, Academic Institutions, And Private Individuals using the GNU General Public License, The community can contribute to this resource | nlx_62001 | SCR_007035 | SciCrunch Registry | 2026-11-07 11:56:08 | 2 | ||||||
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DDBJ Sequence Read Archive Resource Report Resource Website 50+ mentions |
DDBJ Sequence Read Archive (RRID:SCR_001370) | DRA | data or information resource, data repository, database, service resource, storage service resource | Archive database for output data generated by next-generation sequencing machines including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA). Please submit the trace data from conventional capillary sequencers to DDBJ Trace Archive., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, next-generation sequencing, sequence read, FASEB list |
is listed by: OMICtools is affiliated with: INSDC is related to: NCBI Sequence Read Archive (SRA) is related to: European Nucleotide Archive (ENA) is related to: NCBI Sequence Read Archive (SRA) has parent organization: DNA DataBank of Japan (DDBJ) |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:22009675 PMID:21062823 |
THIS RESOURCE IS NO LONGER IN SERVICE | r3d100013696, OMICS_01027, nlx_152515 | http://trace.ddbj.nig.ac.jp/dra/ | SCR_001370 | SciCrunch Registry | 2026-11-07 11:54:17 | 95 | |||||
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BioData Management Portal Resource Report Resource Website |
BioData Management Portal (RRID:SCR_023138) | data repository, service resource, storage service resource | Portuguese distributed infrastructure for biological data and Portuguese node of ELIXIR. | is listed by: DataCite | Free, Freely available | DOI:10.34636 | https://doi.org/10.34636, https://dx.doi.org/10.34636 | SCR_023138 | SciCrunch Registry | BioData Management Portal | 2026-11-07 12:00:41 | 0 |
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