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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NCBI Resource Report Resource Website 10000+ mentions |
NCBI (RRID:SCR_006472) | NCBI | nonprofit organization | A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease. | biomedical, genomic, molecular biology, health, disease, database, computational biology, bio.tools |
is used by: NIF Data Federation is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: NCBI Viral Genomes is related to: Clone DB is related to: PubReader is related to: OMIA - Online Mendelian Inheritance in Animals is related to: European Nucleotide Archive (ENA) is related to: Plant Co-expression Annotation Resource is related to: METAGENOTE is related to: Phyutility is related to: CaspBase is related to: Prokaryotic Genomes Automatic Annotation Pipeline has parent organization: National Library of Medicine is parent organization of: MedGen is parent organization of: dbSTS is parent organization of: PubMed Health is parent organization of: BLASTP is parent organization of: GQuery is parent organization of: BLASTN is parent organization of: GTEx eQTL Browser is parent organization of: BLASTX is parent organization of: Homology Maps Page is parent organization of: PEDHUNTER is parent organization of: Conserved Domain Database is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: High Throughput Genomic Sequences Division is parent organization of: AceView is parent organization of: dbMHC is parent organization of: dbSNP is parent organization of: Entrez Gene is parent organization of: NCBI Genome is parent organization of: NCBI database of Genotypes and Phenotypes (dbGap) is parent organization of: GenBank is parent organization of: International HapMap Project is parent organization of: IgBLAST is parent organization of: Lowes Syndrome Mutation Database is parent organization of: HomoloGene is parent organization of: Influenza Virus Resource is parent organization of: Distant Regulatory Elements is parent organization of: e-PCR is parent organization of: MapViewer is parent organization of: Primer-BLAST is parent organization of: dbVar is parent organization of: NCBI Taxonomy is parent organization of: NCBI Protein Database is parent organization of: Gene Reference into Function is parent organization of: Protein Clusters is parent organization of: RefSeq is parent organization of: TPA is parent organization of: GENSAT at NCBI - Gene Expression Nervous System Atlas is parent organization of: COBALT: Constraint-based Multiple Alignment Tool is parent organization of: PubMed Central is parent organization of: UniLib is parent organization of: NCBI Structure is parent organization of: PubChem is parent organization of: Anopheles gambiae (African malaria mosquito) genome view is parent organization of: UniGene is parent organization of: NLM Catalog is parent organization of: Entrez GEO Profiles is parent organization of: Nucleotide database is parent organization of: NCBI BioSystems Database is parent organization of: CBLAST is parent organization of: NCBI BioProject is parent organization of: NCBI Probe is parent organization of: PubMed is parent organization of: NCBI BioSample is parent organization of: NCBI Nucleotide is parent organization of: NCBI Structure: Cn3D is parent organization of: NCBI BLAST is parent organization of: IBIS: Inferred Biomolecular Interactions Server is parent organization of: NCBI Sequence Read Archive (SRA) is parent organization of: Gene Expression Omnibus (GEO) is parent organization of: NCBI Popset is parent organization of: PIE the search is parent organization of: Genetic Testing Registry is parent organization of: NCBI Resource List is parent organization of: NCBI dbRBC is parent organization of: NCBI YouTube Channel is parent organization of: NCBI Epigenomics is parent organization of: ClinVar is parent organization of: Genome Reference Consortium is parent organization of: GeneReviews is parent organization of: Molecular Imaging and Contrast Agent Database is parent organization of: Consensus CDS is parent organization of: UniSTS is parent organization of: HIV-1 Human Protein Interaction Database is parent organization of: Assay Guidance Manual is parent organization of: Bookshelf is parent organization of: COG is parent organization of: Gene Expression Omnibus is parent organization of: Molecular Modelling DataBase is parent organization of: Organelle Genome Resources is parent organization of: SKY/M-FISH/CGH is parent organization of: dbEST is parent organization of: JournalReview.org is parent organization of: NCBI GenBank via FTP is parent organization of: PubChem Compound is parent organization of: Molecular Modeling DataBase is parent organization of: Vector Alignment Search Tool is parent organization of: PubChem BioAssay is parent organization of: NCBI Genome Workbench is parent organization of: TBLASTN is parent organization of: TBLASTX is parent organization of: Mega BLAST is parent organization of: Genetic Codes is parent organization of: HIV-1, Human Protein Interaction Database is parent organization of: PubReader is parent organization of: PubChem Substance is parent organization of: OMIA - Online Mendelian Inheritance in Animals is parent organization of: OMIM is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: GeneTests is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: MagicBlast is parent organization of: RefSeq is parent organization of: Sequin is parent organization of: Batch Entrez is parent organization of: Entrez is parent organization of: tbl2asn is parent organization of: Whole Genome Shotgun (WGS) Project is parent organization of: Digital Differential Display (DDD) is parent organization of: BLASTClust is parent organization of: PASC is parent organization of: Open Reading Frame Finder is parent organization of: Genotyping works with: Human Mouse Disease Connection works with: A plasmid Editor works with: Database of genes related to Repeat Expansion Diseases |
Public, The community can contribute to this resource | nif-0000-00139, biotools:ncbi_resources | https://bio.tools/ncbi_resources | http://www.ncbi.nih.gov/ | SCR_006472 | National Center for Biotechnology Information, NCBI - National Center for Biotechnology Information | 2025-05-19 01:34:39 | 23705 | |||||
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Xiamen University; Xiamen; China Resource Report Resource Website |
Xiamen University; Xiamen; China (RRID:SCR_006509) | university | Xiamen University, colloquially known as Xia Da in Mandarin Chinese or Ha Tai in Xiamen dialect, is public research university in Xiamen, Fujian, China with strengths in economics and management, fine arts, law, chemistry, journalism, communication, and mathematics. | is parent organization of: CytoSVM statistics | nlx_64389 | http://www.xmu.edu.cn/english/ | SCR_006509 | XMU | 2025-05-19 01:34:40 | 0 | |||||||||
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University of Picardie Jules Verne; Amiens; France Resource Report Resource Website |
University of Picardie Jules Verne; Amiens; France (RRID:SCR_006540) | UPJV | university | Public university organized into five main faculties. One of the top 60 universities of France. |
is parent organization of: Biobanque de Picardie is parent organization of: RESP ESP charged Database |
nlx_144284 | http://www.u-picardie.fr/jsp/fiche_pagelibre_accueil.jsp?CODE=95546447&LANGUE=1 | SCR_006540 | Université de Picardie Jules Verne, University of Picardie Jules Verne | 2025-05-19 01:34:40 | 0 | ||||||||
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F1000: Faculty of 1000 Post-Publication Peer Review Resource Report Resource Website 10+ mentions |
F1000: Faculty of 1000 Post-Publication Peer Review (RRID:SCR_006537) | F1000 | commercial organization | Service that identifies and evaluates the most important articles in biology and medical research publications. The selection process comprises a peer-nominated global ''Faculty'' of the world''s leading scientists and clinicians who rate the best of the articles they read and explain their importance. Faculty Members and their evaluations are organized into over 40 Faculties (subjects), which are further subdivided into over 300 Sections. On average, 1500 new evaluations are published each month; this corresponds to approximately the top 2% of all published articles in the biological and medical sciences. F1000 is a subscription service paid for by academic and corporate institutions. Users at subscribing institutions automatically receive full access to the F1000 service when using internet facilities provided by their institution. | biology, medicine, biomedical science, clinical, database, peer review, medical research |
is used by: PrePubMed is listed by: FORCE11 is related to: Overleaf has parent organization: Science Navigation Group is parent organization of: F1000 Reports is parent organization of: Faculty of 1000 - YouTube is parent organization of: F1000 Posters is parent organization of: Naturally Selected |
Subscription | nlx_71290, Wikidata: Q5428884, grid.466681.b, ISNI: 0000 0000 8758 3069 | https://ror.org/019tc7185 | http://www.facultyof1000.com/ | SCR_006537 | F1000 Evaluations, Faculty of 1000, F1000 Evaluated Articles | 2025-05-19 01:34:40 | 13 | |||||
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Tucker-Davis Technologies Resource Report Resource Website 50+ mentions |
Tucker-Davis Technologies (RRID:SCR_006495) | TDT | commercial organization | Commercial organization that provides products for basic and applied research in the neurophysiology, hearing, and speech sciences as well as for general data acquisition applications. It offers a complete line of modular DSP-based data acquisition and stimulus generation systems, ranging in complexity from a simple audio stimulator to a complete multichannel sensory and behavioral neurophysiology system for awake, behaving subjects. | neurophysiology, evoked potential, psychoacoustics, data acquisition, virtual acoustics, bioacoustics, hearing, speech, stimulus, audio, sensory, behavior |
is parent organization of: BioSigRP is parent organization of: BioSigRZ is parent organization of: OpenEx |
rid_000061, grid.421888.f | https://ror.org/0014wkh93 | SCR_006495 | Tucker-Davis Technologies (TDT) | 2025-05-19 01:34:39 | 64 | |||||||
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Concept Web Alliance Resource Report Resource Website |
Concept Web Alliance (RRID:SCR_006490) | CWA | knowledge environment | CWA is an open collaborative community that is actively addressing the challenges associated with the production of unprecedented volumes of academic and professional data. This international effort seeks to organize the massive amounts of information flooding the biological sciences and other scientific disciplines. Challenges include storage, interoperability and analysis of such massive and disparate data sets. CWA''s agreed approach is a ''Semantic Web'' strategy, meaning that disparate data on the internet are now structurally connected to each other. As the amount of scholarly communication increases, it is increasingly difficult for specific core scientific statements to be found, connected and curated. Additionally, the redundancy of these statements in multiple fora makes it difficult to determine attribution, quality, and provenance. To tackle these challenges, the Concept Web Alliance has promoted the notion of nanopublications (core scientific statements with associated context) in a manner allowing for meaningful Web-wide interconnectivity. The notion of a ''nanopublication'' is basically a general scientific assertion, written using semantic-web standard formats with additional meta-data concerning provenance. |
has parent organization: Netherlands Bioinformatics Centre is parent organization of: Conceptweblog is parent organization of: Nanopub.org |
Netherlands Bioinformatics Centre | nif-0000-03147 | SCR_006490 | 2025-05-19 01:34:39 | 0 | |||||||||
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American Society for Microbiology Resource Report Resource Website 10+ mentions |
American Society for Microbiology (RRID:SCR_006551) | ASM | professional organization | The American Society for Microbiology is the oldest and largest single life science membership organization in the world. Membership has grown from 59 scientists in 1899 to more than 39,000 members today, with more than one third located outside the United States. The members represent 26 disciplines of microbiological specialization plus a division for microbiology educators. Eligibility for Full Membership is open to any person who is interested in microbiology and holds at least a bachelor''s degree or equivalent experience in microbiology or related field. Many members hold advanced degrees, including a large number at the master''s, PhD, ScD, DrPH and MD level. A regularly matriculated student of microbiology or a related field is eligible to become a student member. There are also separate membership categories for postdoctoral fellows and for transitional scientists in the early years of a career. Microbiologists study microbes--bacteria, viruses, rickettsiae, mycoplasma, fungi, algae and protozoa--some of which cause diseases, but many of which contribute to the balance of nature or are otherwise beneficial. Microbiological research includes infectious diseases, recombinant DNA technology, alternative methods of energy production and waste recycling, new sources of food, new drug development, and the etiology of sexually transmitted diseases, among other areas. Microbiology is also concerned with environmental problems and industrial processes. Microbiology boasts some of the most illustrious names in the annals of science--Pasteur, Koch, Fleming, Leeuwenhoek, Lister, Jenner and Salk--and some of the greatest achievements for mankind. Within the 20th century, a third of all Nobel Prizes in Physiology or Medicine have been bestowed upon microbiologists. The mission of the American Society for Microbiology is to advance the microbiological sciences as a vehicle for understanding life processes and to apply and communicate this knowledge for the improvement of health and environmental and economic well being worldwide. To achieve these goals, ASM will: * Support programs of education, training and public information; * Publish journals and books; convene meetings, workshops and colloquia; * Promote the contributions and promise of the microbiological sciences; * Recognize achievement and distinction among its practitioners; * Set standards of ethical and professional behavior. | microbiology, society, virus, bacteria, rickettsiae, mycoplasma, fungus, algae, protozoa, infectious disease, recombinant dna technology, energy production, waste recycling, drug development |
uses: Publons is parent organization of: MicrobeWorld |
Wikidata: Q466809, Crossref funder ID: 100005430, nlx_151570, grid.280767.c, ISNI: 0000 0000 9729 747X | https://ror.org/04xsjmh40 | SCR_006551 | American Society For Microbiology | 2025-05-19 01:34:41 | 15 | |||||||
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ProSpec Resource Report Resource Website 1000+ mentions |
ProSpec (RRID:SCR_006584) | commercial organization | An Antibody supplier | nlx_152436 | SCR_006584 | 2025-05-19 01:34:41 | 1223 | ||||||||||||
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Webtracks Resource Report Resource Website |
Webtracks (RRID:SCR_006615) | Webtracks | knowledge environment | This project will develop an approach and mechanism to address the construction and propagation of linked data in the context of research and academic endeavour. The proposed work will build experiments in previous projects (Claddier, StoreLink) to develop a peer-to-peer protocol to underpin the construction of a web of linked data. This set of semantically annotated links between data resources forms a graph of citation and provenance and the project will build value added services to exploit these features. The project will address the following specific objectives: * To specify and implement the Intercom Protocol so that it can communicate a range of types of semantic links between resources via a secure communication mechanism. * To develop a practical working scenario involving data repositories, publication repositories, open science notebooks and publishers. * To develop aggregation techniques supporting added value services in search and impact analysis. * To evaluate of the approach with the identified stakeholders groups. | has parent organization: JISC | nlx_46790 | SCR_006615 | 2025-05-19 01:34:42 | 0 | ||||||||||
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casper Resource Report Resource Website 100+ mentions |
casper (RRID:SCR_006613) | casper | software resource | Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | biotools:casper, OMICS_01270 | https://bio.tools/casper | SCR_006613 | casper - Characterization of Alternative Splicing based on Paired-End Reads, Characterization of Alternative Splicing based on Paired-End Reads | 2025-05-19 01:34:42 | 133 | ||||||
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NIMH Repository and Genomics Resources Resource Report Resource Website 50+ mentions |
NIMH Repository and Genomics Resources (RRID:SCR_006698) | NRGR, RGR | institution | Collaborative venture between the National Institute of Mental Health (NIMH) and several academic institutions. Repository facilitates psychiatric genetic research by providing patient and control samples and phenotypic data for wide-range of mental disorders and Stem Cells.Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness. | biosamples, genetic, pedigree, clinical, data |
is listed by: One Mind Biospecimen Bank Listing is related to: NIMH Stem Cell Center is related to: Rutgers Cell and DNA Repository is related to: Sequenced Treatment Alternatives to Relieve Depression Study is related to: CATIE - Clinical Antipsychotic Trials in Intervention Effectiveness is related to: Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD) is related to: NKI-RS Enhanced Sample has parent organization: Rutgers University; New Jersey; USA has parent organization: Washington University in St. Louis; Missouri; USA has parent organization: University of Southern California; Los Angeles; USA |
Bipolar Disorder, Schizophrenia, Alzheimer's disease, Autism, Attention deficit-hyperactivity disorder, Depression, Control, Obsessive-Compulsive Disorder, Anorexia Nervosa, Relative, Mental disorder, Brain disorder, Relative | NIH Blueprint for Neuroscience Research ; National Institute for Mental Health |
Restricted | grid.482687.7, nif-0000-00186, SCR_016318 | https://ror.org/026dax180 | SCR_006698 | NIMH: Center for Collaborative Genetic Studies, NIMH Human Genetics Initiative, NIMH Center for Genetic Studies, NIMH Genetics, Center for Collaborative Genomic Studies on Mental Disorders, NIMH Repository and Genomics Resources (NRGR) | 2025-05-19 01:34:45 | 60 | ||||
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ProSci Resource Report Resource Website 500+ mentions |
ProSci (RRID:SCR_006609) | commercial organization | An Antibody supplier | nlx_152435 | SCR_006609 | ProSci Incorporated, ProSci Inc | 2025-05-19 01:34:42 | 786 | |||||||||||
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Progen Resource Report Resource Website 1000+ mentions |
Progen (RRID:SCR_006726) | commercial organization | Antibody and density gradient media supplier. | nlx_152433 | https://www.progen.de/ | SCR_006726 | 2025-05-19 01:34:46 | 1981 | |||||||||||
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SpliceTrap Resource Report Resource Website 10+ mentions |
SpliceTrap (RRID:SCR_006728) | SpliceTrap | software resource | A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3?/5? splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Cold Spring Harbor Laboratory |
PMID:21896509 | biotools:splicetrap, OMICS_01292 | https://bio.tools/splicetrap | SCR_006728 | 2025-05-19 01:34:46 | 16 | |||||||
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BEDTools Resource Report Resource Website 5000+ mentions |
BEDTools (RRID:SCR_006646) | BEDTools | software resource | A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line. | genomics, bed, sam, bam, overlap, sequencing, intersect, coverage, gff, vcf, bedgraph, interval, genome arithmetic, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Hydra is related to: pybedtools is required by: SL-quant |
PMID:20110278 DOI:10.1093/bioinformatics/btq033 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01159, biotools:bedtools | https://code.google.com/p/bedtools/ https://bio.tools/bedtools https://sources.debian.org/src/bedtools/ |
SCR_006646 | bedtools - a swiss army knife for genome arithmetic, bedtools: a flexible suite of utilities for comparing genomic features | 2025-05-19 01:34:43 | 8910 | |||||
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Down Syndrome Research and Treatment Foundation Resource Report Resource Website |
Down Syndrome Research and Treatment Foundation (RRID:SCR_006637) | DSRTF | institution | The Down Syndrome Research and Treatment Foundation is dedicated to finding a treatment to improve cognition including learning, memory and speech for individuals with Down syndrome. Since our founding in 2004 we have become the leading private source of funding in the United States for Down syndrome cognition research. The mission of DSRTF is to stimulate biomedical research that will accelerate the development of treatments to significantly improve cognition, including memory, learning and speech, for individuals with Down syndrome in order that they: * participate more successfully in school; * lead more active and independent lives; * and avoid the early onset of Alzheimer''s Disease. DSRTF is funding research that applies the information, tools and techniques resulting from the genome project along with recent advances in brain research to the study of cognition in Down syndrome. Our goal is the development of treatments that will improve learning, memory, and speech, and therefore enhance the lives of those with Down syndrome and their families. The majority of individuals with Down syndrome fall into the mild to moderate range of cognitive impairment. For many of these individuals, a 10%-20% improvement in cognitive ability would provide them with the ability to live independently, hold a job and be fully integrated within their communities. | grid.478821.0, ISNI: 0000 0004 5902 2167, nlx_143653, Crossref funder ID: 100006836 | https://ror.org/02m0a5h24 | SCR_006637 | 2025-05-19 01:34:43 | 0 | ||||||||||
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NiftySim Resource Report Resource Website 1+ mentions |
NiftySim (RRID:SCR_006591) | NiftySim | software resource | A high-performance nonlinear finite element solver. A key feature is the option of GPU-based execution, which allows the solver to significantly out-perform equivalent commercial packages. | pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
BSD License | nlx_155900 | http://www.nitrc.org/projects/niftysim | SCR_006591 | Nifty Sim | 2025-05-19 01:34:42 | 2 | ||||||
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LexGrid Resource Report Resource Website 1+ mentions |
LexGrid (RRID:SCR_006627) | LexGrid | software resource | LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, parse, ontology |
is listed by: BioPortal is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: European Bioinformatics Institute has parent organization: National Cancer Institute |
NIH ; Cancer Biomedical Informatics Grid ; NLM LM07319 |
PMID:19261933 | Free for academic use | nlx_149194 | http://www.lexgrid.org/ | SCR_006627 | Lexical Grid | 2025-05-19 01:34:42 | 1 | ||||
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ALEXA-Seq Resource Report Resource Website 1+ mentions |
ALEXA-Seq (RRID:SCR_006700) | ALEXA-Seq | software resource | A method for using massively parallel paired-end transcriptome sequencing for ''alternative expression analysis''. | is listed by: OMICtools | OMICS_01328 | SCR_006700 | 2025-05-19 01:34:45 | 6 | ||||||||||
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Hiclib Resource Report Resource Website 10+ mentions |
Hiclib (RRID:SCR_005535) | Hiclib | software resource | An Software resource | is listed by: OMICtools | OMICS_00521 | SCR_005535 | 2025-05-19 01:34:05 | 21 |
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