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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VirusHunter Resource Report Resource Website |
VirusHunter (RRID:SCR_001198) | VirusHunter | software resource | A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses. | virus, next-generation sequencing, roche, 454, taxonomic classification, alignment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:24167629 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:virushunter, OMICS_02153 | https://bio.tools/virushunter | SCR_001198 | 2026-02-14 01:59:55 | 0 | ||||||
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Genome Trax Resource Report Resource Website 1+ mentions |
Genome Trax (RRID:SCR_001234) | Genome Trax | service resource | Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia. | next-generation sequencing, genome, exome, sequence, variation, mutation, pathogenic, database, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: BIOBASE Corporation |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02109, biotools:genome_trax | https://bio.tools/genome_trax | SCR_001234 | Genome Trax for Next Generation Sequencing | 2026-02-14 01:59:58 | 2 | ||||||
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ITALICS Resource Report Resource Website |
ITALICS (RRID:SCR_001274) | ITALICS | software resource | Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set. | affymetrix, copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18252739 | Free, Available for download, Freely available | OMICS_02064 | SCR_001274 | 2026-02-14 01:59:59 | 0 | |||||||
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DEXUS Resource Report Resource Website 1+ mentions |
DEXUS (RRID:SCR_001309) | DEXUS | software resource | Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power. | classification, differential expression, gene expression, hapmap, quality control, rna-seq, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24049071 | Free, Available for download, Freely available | biotools:dexus, OMICS_02024 | http://www.bioconductor.org/packages/release/bioc/html/dexus.html | SCR_001309 | DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates | 2026-02-14 02:00:00 | 1 | |||||
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Center for Biomedical OCT Research Resource Report Resource Website 1+ mentions |
Center for Biomedical OCT Research (RRID:SCR_001418) | CBORT | training resource | Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware. | imaging, optical coherence tomography, microscope, catheter, endoscopy, near infrared fluorescence | has parent organization: Harvard Medical School; Massachusetts; USA | NIBIB P41EB015903 | Free, Freely Available | nlx_152640 | SCR_001418 | Center for Biomedical OCT Research and Translation | 2026-02-14 02:00:03 | 2 | ||||||
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Flash Gviewer Resource Report Resource Website 1+ mentions |
Flash Gviewer (RRID:SCR_012870) | Flash GViewer | software resource | Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool | visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Medical College of Wisconsin; Wisconsin; USA |
Free for academic use | nlx_149333 | http://gmod.org/flashgviewer | SCR_012870 | 2026-02-14 02:02:24 | 2 | |||||||
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Children and Adults with Attention Deficit/Hyperactivity Disorder Resource Report Resource Website 1+ mentions |
Children and Adults with Attention Deficit/Hyperactivity Disorder (RRID:SCR_013384) | CHADD | nonprofit organization | Non-profit organization serving individuals with attention deficit-hyperactivity disorder (AD/HD) and their families. CHADD has over 16,000 members in 200 local chapters throughout the U.S. Chapters offer support for individuals, parents, teachers, professionals, and others. CHADD''s primary objectives are: to provide a support network for parents and caregivers; to provide a forum for continuing education; to be a community resource and disseminate accurate, evidence-based information about AD/HD to parents, educators, adults, professionals, and the media; to promote ongoing research; and to be an advocate on behalf of the AD/HD community. In general, CHADD works to improve the lives of people affected by AD/HD through: Collaborative Leadership, Advocacy, Research Education and, Support CHADD has three current priority objectives: (1) to serve as a clearinghouse for evidence-based information on AD/HD, (2) to serve as a local face-to-face family support group for families and individuals affected by AD/HD, and (3) to serve as an advocate for appropriate public policies and public recognition in response to needs faced by families and individuals with AD/HD. CHADD is a membership organization, produces the bi-monthly Attention! magazine (for members), and sponsors an annual conference. The National Resource Center on AD/HD (NRC) is the CDC-funded national clearinghouse for evidence-based information about AD/HD. | education, family, adult human, advocacy, attention, attention deficit disorder, caregiver, child, deficit, disorder, hyperactivity, hyperactivity disorder, individual, media, medication, news, parent, professional, research, support, teacher, treatment, young human | Attention deficit-hyperactivity disorder | ISNI: 0000 0004 0546 7056, nif-0000-10195, grid.433005.1 | https://ror.org/01ds3sh29 | SCR_013384 | 2026-02-14 02:02:51 | 2 | ||||||||
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National Drug Code Directory Resource Report Resource Website |
National Drug Code Directory (RRID:SCR_013721) | ndc | Drug database published by the Food and Drug Administration of unique universal product identifiers for all drugs manufactured, prepared, propagated, compounded, or processed by it for commercial distribution. | drug database, drug code, FDA | Free, public | SCR_013721 | 2026-02-14 02:02:30 | 0 | |||||||||||
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Approved Drug Products with Therapeutic Equivalence Evaluations Resource Report Resource Website 1+ mentions |
Approved Drug Products with Therapeutic Equivalence Evaluations (RRID:SCR_013727) | Orange Book | Database that contains drug products approved on the basis of safety and effectiveness by the Food and Drug Administration. | drugs, prescription drug, over-the-counter drug, OTC drug, Drug Products |
is listed by: U.S. Food and Drug Administration has parent organization: U.S. Food and Drug Administration |
Free, public | SCR_013727 | 2026-02-14 02:02:54 | 2 | ||||||||||
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Biospecimen Repository and Processing Core Resource Report Resource Website |
Biospecimen Repository and Processing Core (RRID:SCR_013792) | BRPC | information resource | A biomaterial supply and access service resource which provides a shared resource for coordinated tissue processing and biorepository services. Services include patient identification and informed consent, specimen collection, processing and banking, and annotation of banked specimens and specimen distribution. They provide biospecimen inventory management, services, and equipment. It is a shared resource of Duke University. | repository, biomaterial supply resource, shared resource, Duke University, biospecimen, tissue, tissue processing, informed consent, biobank |
is related to: Duke Cancer Institute is related to: Duke Biobank is related to: Duke University School of Medicine; North Carolina; USA has parent organization: Duke University; North Carolina; USA |
Available to the research and education community, Fee | http://www.dukecancerinstitute.org/research/shared-resources/Biospecimen%20Repository%20and%20Processing%20Core | SCR_013792 | 2026-02-14 02:02:34 | 0 | ||||||||
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National Database for Clinical Trials related to Mental Illness Resource Report Resource Website 1+ mentions |
National Database for Clinical Trials related to Mental Illness (RRID:SCR_013795) | NDCT | data resource | A database which houses human subjects clinical trial data. NDCT currently contains data on 13,409 subjects and has access to data on 100,500 subjects from the NIMH Data Archive. Users can also sign up for news updates and watch video tutorials. | database, human, clinical trial, mental health, mental illness |
uses: NIMH Data Archive uses: RDoCdb is listed by: NIH Data Sharing Repositories is related to: NIMH Data Archive is related to: RDoCdb is related to: RDoCdb |
NIH | Public, Only for research | SCR_013795 | 2026-02-14 02:02:51 | 2 | ||||||||
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Spatio-temporal transcriptome of the human brain Resource Report Resource Website |
Spatio-temporal transcriptome of the human brain (RRID:SCR_013743) | data or information resource, document, narrative resource | A research paper with supplementary materials reporting the generation and analysis of exon-level transcriptome and associated genotyping data. The experiment represented both males and females of multiple ethnicities and examines gene regulation and expression in different areas of the brain. A data set on the human brain transcriptome as well as insights into the transcriptional foundations of human neurodevelopment is provided. | spatio-temporal, transcriptome data, brain regions, human brain, gene expression, gene regulation |
is related to: Human Brain Transcriptome has parent organization: Yale University; Connecticut; USA |
Kavil Foundation ; NARSAD ; James S. McDonnell Foundation Scholar Award ; NIMH MH081896; NIMH MH089929; NINDS NS054273 |
PMID:22031440 | Public, Free | SCR_013743 | 2026-02-14 02:02:50 | 0 | ||||||||
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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) | 2026-02-14 02:01:14 | 66 | ||||
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GREC Corpus Resource Report Resource Website 1+ mentions |
GREC Corpus (RRID:SCR_006719) | GREC | training set | A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format | annotation, information extraction, text mining, semantic role, semantic search, gene, computational linguistics, gene regulation |
is listed by: FORCE11 is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:19852798 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, For Copyright of abstracts refer to PubMed. | nif-0000-06688 | SCR_006719 | Gene Event Regulation Corpus | 2026-02-14 02:01:12 | 3 | |||||
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InnateDB Resource Report Resource Website 100+ mentions |
InnateDB (RRID:SCR_006714) | InnateDB | data or information resource, database | Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice. | gene, immune response, pathway, protein, signaling pathway, interaction, immune, signaling response, gene, orthology prediction, orthology, ortholg, annotation, interactome, gene expression, molecule, protein-protein interaction, molecular interaction, visualization, nucleic acid-protein, nucleic acid, network, web service, transcription factor binding site, software resource, FASEB list |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: PSICQUIC Registry is related to: Gene Ontology is related to: IntAct has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada works with: IMEx - The International Molecular Exchange Consortium |
Microbial infection, Allergy, Asthma | Michael Smith Foundation for Health Research ; AllerGen 12ASI1; AllerGen 12B&B2; Teagasc RMIS6018; European Union PSIMEx project contract FP7-HEALTH-2007-223411 |
PMID:23180781 PMID:18766178 |
Free, Freely available | nif-0000-20808, r3d100010676 | https://doi.org/10.17616/R36S43 | SCR_006714 | A Knowledge Resource for Innate Immunity Interactions and Pathways, InnateDB: Systems Biology of the Innate Immune Response, InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways | 2026-02-14 02:01:14 | 496 | |||
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University of Quebec Hospital Centre; Quebec; Canada Resource Report Resource Website |
University of Quebec Hospital Centre; Quebec; Canada (RRID:SCR_006740) | CHUQ | university | Network of three teaching hospitals affiliated with the medical school of Université Laval and several specialized institutions in Quebec City. |
is related to: Cancer Research Network of the FRSQ has parent organization: Laval University; Quebec; Canada |
Wikidata:Q3145390, nlx_158566, grid.417661.3, ISNI:0000 0001 2190 0479 | https://ror.org/034sbqc84 | SCR_006740 | University of Quebec Hospital Center, University of Quebec Hospital Centre, CHU de Qu�bec, Centre hospitalier universitaire de Quebec, CHU de Quebec, Centre hospitalier universitaire de Qu�bec | 2026-02-14 02:01:12 | 0 | ||||||||
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National Institute of Child Health and Human Development Resource Report Resource Website 100+ mentions |
National Institute of Child Health and Human Development (RRID:SCR_011429) | NICHD | institution | A national institute that investigates human development throughout the entire life process, focusing on understanding developmental disabilities, including intellectual and developmental disabilities, and illuminating important events that occur during pregnancy. The NICHD conducts and supports laboratory research, clinical trials, and epidemiological studies that explore health processes; examines the impact of disabilities, diseases, and defects on the lives of individuals; and sponsors training programs for scientists, doctors, and researchers to ensure that NICHD research can continue. The Institute also supports research training across all its programs. In addition, an overarching responsibility of the NICHD is to disseminate information that emanates from Institute research programs to researchers, practitioners, other health care professionals, and the public. | human development, developmental disabilities, pregnancy, national institute |
has parent organization: NIH Blueprint for Neuroscience Research has parent organization: National Institutes of Health is parent organization of: NICHD Developmental Neuroethology - Laboratory of Comparative Ethology is parent organization of: TORTOISE is parent organization of: NCMRR - National Center for Medical Rehabilitation Research is parent organization of: GermSAGE is parent organization of: Traumatic Brain Injury Clinical Trials Network |
Available to the research community | nlx_inv_1005104, Crossref funder ID: 100000071, Wikidata: Q5409765, grid.420089.7, ISNI: 0000 0000 9635 8082 | https://ror.org/04byxyr05 | SCR_011429 | Eunice Kennedy Shriver National Institute of Child Health and Human Development | 2026-02-14 02:02:18 | 165 | ||||||
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Seattle Childrens Research Institute; Washington; USA Resource Report Resource Website 1+ mentions |
Seattle Childrens Research Institute; Washington; USA (RRID:SCR_011520) | institution | A top five pediatric research center in the nation that brings together the best minds in pediatric research to set new standards of pediatric care and find new cures for childhood diseases. Their goal is that every patient at Seattle Children''s has the opportunity to participate in, or benefit from, their groundbreaking research. The research institute is organized into nine centers, each one specializing in areas like cancer immunotherapy, neuroscience and child health and behavior. The centers are supported by faculty from the Treuman Katz Center for Pediatric Bioethics , the nation''s first pediatric bioethics center. |
is related to: Beta Cell Biology Consortium is parent organization of: Seattle Children's Research Institute Micro Computed Tomography Imaging and Visualization Lab Core Facility is parent organization of: Seattle Childrens Research Institute Behavioral Phenotyping Core Facility |
nlx_158444 | SCR_011520 | Seattle Childrens Research Institute, Seattle Children''s Research Institute | 2026-02-14 02:02:21 | 1 | ||||||||||
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University of Montreal Hospital Centre; Quebec; Canada Resource Report Resource Website |
University of Montreal Hospital Centre; Quebec; Canada (RRID:SCR_011686) | CHUM | university | Hôpital Saint-Luc was a hospital in Montreal, Quebec, Canada, at the intersection of Saint Denis Street and René Lévesque Boulevard in the borough of Ville-Marie. It was named in honor of Luke the Evangelist, who is the patron saint of doctors in the Roman Catholic religion. |
is related to: Cancer Research Network of the FRSQ has parent organization: University of Montreal; Quebec; Canada |
Wikidata:Q1054216, ISNI:0000 0001 0743 2111, nlx_158565, grid.410559.c | https://ror.org/0410a8y51 | SCR_011686 | Montreal University Health Centre, University of Montreal Hospital Centre, University of Montreal Hospital Center, Centre hospitalier de l''Universite de Montreal, Montreal University Hospital Centre, Centre hospitalier de l''Universit� de Montr�al, Montreal University Hospital Center | 2026-02-14 02:02:25 | 0 | ||||||||
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Vestische Children and Youth Clinic Dates; North Rhine-Westphalia; Germany Resource Report Resource Website |
Vestische Children and Youth Clinic Dates; North Rhine-Westphalia; Germany (RRID:SCR_011759) | hospital |
is related to: EMIF has parent organization: Witten/Herdecke University; North Rhine-Westphalia; Germany |
SCR_011759 | Vestische Kinder- und Jugendklinik Datteln, Vestische Children and Youth Clinic Dates | 2026-02-14 02:02:26 | 0 |
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