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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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SUNY Upstate Medical University, Pharmacology Resource Report Resource Website |
SUNY Upstate Medical University, Pharmacology (RRID:SCR_007481) | data or information resource, department portal, organization portal, portal | Research in the Department of Pharmacology focuses on three major areas: 1) cardiovascular science 2) cell signaling 3) cancer biology and therapeutics. Within those areas, research ranges from basic biological problems to those with clinical orientations. The cardiovascular science research strives to understand the normal and abnormal functioning of the heart at the molecular, cellular and organ levels, and is exceptionally strong in cardiac electrophysiology and the mechanisms of cardiac arrhythmia. The cell signaling research concerns regulation of cell function by extracellular factors, the molecular biology of signaling pathways, cell communication, and intracellular proteolysis. The cancer biology and therapeutics research is focused on molecular mechanisms regulating cell death and survival in human malignancies, development and testing of novel cancer therapeutics, novel tumor markers, oncogenic transformation and apoptosis, regulation of tumor suppressors and molecular mechanisms of leukemogensis. The Pharmacology Department has multiple research grants for the next five years. Most of the funding comes from the National Institutes of Health (NIH), with additional funding from the Association for International Cancer Research, the American Society of Hematology, the Department of Defense and the American Heart Association. | nif-0000-02084 | SCR_007481 | SciCrunch Registry | SUNY Upstate | 2026-09-26 02:14:18 | 0 | |||||||||||
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University of Salamanca; Salamanca; Spain Resource Report Resource Website 1+ mentions |
University of Salamanca; Salamanca; Spain (RRID:SCR_007833) | USAL | university | Spanish higher education institution, located in the city of Salamanca, west of Madrid, in the autonomous community of Castile and León. It was founded in 1134 and given the Royal charter of foundation by King Alfonso IX in 1218. |
is parent organization of: ProbeExplorer is parent organization of: Agile Protein Interactomes DataServer |
Wikidata:Q308963, grid.11762.33, nlx_149149, ISNI:0000 0001 2180 1817 | https://ror.org/02f40zc51 | SCR_007833 | SciCrunch Registry | Universidad de Salamanca, University of Salamanca | 2026-09-26 02:14:20 | 2 | ||||||||
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Solanaceae Phenotype Ontology Resource Report Resource Website |
Solanaceae Phenotype Ontology (RRID:SCR_007832) | SPTO | controlled vocabulary, data or information resource, ontology | Ontology for Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance. | obo | is listed by: BioPortal | nlx_157592 | SCR_007832 | SciCrunch Registry | 2026-09-26 02:14:20 | 0 | |||||||||
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INVERTER Resource Report Resource Website 1+ mentions |
INVERTER (RRID:SCR_007956) | INVERTER | software resource | Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface. | is listed by: OMICtools | OMICS_00108 | SCR_007956 | SciCrunch Registry | 2026-09-26 02:14:20 | 3 | ||||||||||
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MetaCore Resource Report Resource Website 1000+ mentions |
MetaCore (RRID:SCR_008125) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. An integrated software suite for functional analysis of experimental data. The scope of data types includes microarray and SAGE gene expression, SNPs and CGH arrays, proteomics, metabolomics, pathway analysis, Y2H and other custom interactions. MetaCore is based on a proprietary manually curated database of human protein-protein, protein-DNA and protein compound interactions, metabolic and signaling pathways and the effects of bioactive molecules in gene expression. | expression, gene, dna, interaction, metabolomics, microarray, pathway, protein, proteomic, software | is listed by: Metabolomics Workbench | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-20874 | http://www.genego.com/metacore.php | SCR_008125 | SciCrunch Registry | 2026-09-26 02:14:22 | 1182 | ||||||||
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MedGene Resource Report Resource Website 1+ mentions |
MedGene (RRID:SCR_008122) | software resource | An algorithm that generates lists of genes associated with a gene or one or more disorders. The algorithm can be used in high-throughput screening experiments, can create disease-specific micro-arrays, and can sort the results of gene profiling data. Based on the co-citations of all Medline records, MedGene can retrieve the following relationships: 1. A list of human genes associated with a particular human disease in ranking order 2. A list of human genes associated with multiple human diseases in ranking order 3. A list of human diseases associated with a particular human gene in ranking order 4. A list of human genes associated with a particular human gene in ranking order 5. The sorted gene list from other disease related high-throughput experiments, such as micro-array 6. The sorted gene list from other gene related high-throughput experiments, such as micro-array | gene, disease, human order, microarray | has parent organization: Harvard University; Cambridge; United States | nif-0000-20869 | SCR_008122 | SciCrunch Registry | MedGene | 2026-09-26 02:14:22 | 4 | |||||||||
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BAMS Thesaurus Resource Report Resource Website |
BAMS Thesaurus (RRID:SCR_008003) | thesaurus | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19,2022. The BAMS Thesaurus is a part of the larger BAMS The Foundational Model of Connectivity (FMC). The principle of constructing the resource are: 1. Systematic attempts to produce internally consistent classifications and taxonomies require theoretical frameworks for deciding between alternatives. 2. Alternate classification and taxonomy schemes are always possible and must be accommodated. 3. The FMC is based on evidence, not authority. All components are justified by reference to the best observational or experimental evidence from the literature, combined with reference to priority when possible, not by undocumented statements from textbooks, the Web, or elsewhere. 4. The FMC is based on evolving evidence and concepts, revisions are based on enforced rules, and versioning is systematic and historical. The first version of FMC and the foundation of this online version was published in Swanson & Bota (2010). Please cite this reference whenever any part of the FMC is used in any way. This online version of FMC has the following main parts: 1. Thesaurus, which includes an alphabetical list of all concepts and terms used in FMC to date. The preferred terms are in bold. Clicking on each term of the Thesaurus will retrieve its definition, reference, list of synonyms, and a comment form that can be used by registered users. 2. References, which includes an alphabetical list of the literature used to construct FMC. Listed references are associated with the definitions included in the Thesaurus, and PubMed links. 3. Search form that can be used to search for terms defined in FMC, included in their definitions, their abbreviations, and references (search by authors). We strongly recommend to read FMC rules and notations before starting to use the online version. | brain, anatomy, connectivity, thesaurus, | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-07739 | SCR_008003 | SciCrunch Registry | 2026-09-26 02:14:21 | 0 | ||||||||||
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BigWig and BigBed Resource Report Resource Website 10+ mentions |
BigWig and BigBed (RRID:SCR_007708) | BigWig and BigBed | software resource | Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. |
is listed by: OMICtools is related to: UCSC Genome Browser is related to: bedGraphToBigWig has parent organization: University of California at Santa Cruz; California; USA |
OMICS_00626 | SCR_007708 | SciCrunch Registry | 2026-09-26 02:14:20 | 43 | ||||||||||
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HighSSR Resource Report Resource Website 1+ mentions |
HighSSR (RRID:SCR_007949) | HighSSR | software resource | Software that predicts microsatellites with Tandem Repeats Finder (TRF). |
is listed by: OMICtools has parent organization: Google Code |
PMID:22954626 | OMICS_00107 | SCR_007949 | SciCrunch Registry | highssr - Microsatellites prediction and analysis with next generation sequencing data | 2026-09-26 02:14:20 | 1 | ||||||||
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NMPDR Resource Report Resource Website 1+ mentions |
NMPDR (RRID:SCR_007821) | NMPDR | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The National Microbial Pathogen Data Resource provides curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma. This edition of the NMPDR includes 47 archaeal, 725 bacterial, and 29 eukaryal genomes with 3,257,100 genetic features, of which 1,338,895 are in FIGfams curated using 616 active subsystems. ''''''Notice to NMPDR Users'''''' - The NMPDR BRC contract ended in December 2009. At that time we ceased maintenance of the NMPDR web resource and data. Bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. | has parent organization: University of Chicago; Illinois; USA | NIAID contract HHSN266200400042C | PMID:17145713 | nif-0000-03193 | http://www.nmpdr.org | SCR_007821 | SciCrunch Registry | NMPDR - National Microbial Pathogen Data Resource, National Microbial Pathogen Data Resource, NMPDR BRC, NMPDR Bioinformatics Resource Center | 2026-09-26 02:14:20 | 3 | ||||||
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GenoTan Resource Report Resource Website 1+ mentions |
GenoTan (RRID:SCR_007935) | GenoTan | software resource | A free software tool to identify length variation of microsatellites from short sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24135263 | GNU General Public License, v3 | biotools:genotan | https://bio.tools/genotan | SCR_007935 | SciCrunch Registry | GenoTan - Genotyping of microsatellite loci | 2026-09-26 02:14:20 | 1 | |||||
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University of Pennsylvania Medical Center Neuroscience Resource Report Resource Website |
University of Pennsylvania Medical Center Neuroscience (RRID:SCR_007978) | data or information resource, department portal, organization portal, portal | The Department of Neuroscience is located in the School of Medicine at the University of Pennsylvania. Founded in 1992 to recognize the growing importance of neuroscience as a scientific discipline, the Department laboratories pursue a wide variety of research interests reflecting the entire range of modern neuroscience. The Department lies at the heart of the campus-wide Mahoney Institute of Neurological Sciences, the first research organization to receive NIH funding for training in the neurosciences. | nif-0000-03991 | SCR_007978 | SciCrunch Registry | U Penn | 2026-09-26 02:14:21 | 0 | |||||||||||
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VISTA Enhancer Browser Resource Report Resource Website 100+ mentions |
VISTA Enhancer Browser (RRID:SCR_007973) | VISTA Enhancer Browser | data or information resource, data repository, database, service resource, storage service resource | Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth. | human, noncoding fragment, mutant mouse strain, molecular neuroanatomy resource, image, telencephalon, development, genome, enhancer, dna fragment, embryo, embryonic mouse, brain, neural tube, eye, ear, heart, tail, limb, nose, cranial nerve, trigeminal, dorsal root ganglia, face, branchial arch, gene expression, annotation, vector, transgenic embryo, lacz reporter vector, lacz, biomaterial supply resource, in vivo, image collection, transcriptional enhancer, chip-seq, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NIF Data Federation is related to: One Mind Biospecimen Bank Listing is related to: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
American Heart Association ; DOE contract DE-AC02-05CH11231; DOE DE020060; NHGRI HG003988; NHLBI HL066681; NIDCR ; NINDS NS062859 |
PMID:17130149 | Free, Freely available | nif-0000-03637, OMICS_01568, biotools:vista_enhancer_browser | https://bio.tools/vista_enhancer_browser | SCR_007973 | SciCrunch Registry | 2026-09-26 02:14:20 | 249 | |||||
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GoatMap Database Resource Report Resource Website |
GoatMap Database (RRID:SCR_008144) | data or information resource, data repository, database, portal, service resource, storage service resource, topical portal | 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. | farm, gene, animal, caprine, cartography, genome, genomic, goat, homologue, locus, map, mapping, phene, sequence | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20978 | SCR_008144 | SciCrunch Registry | GoatMap | 2026-09-26 02:14:23 | 0 | |||||||||
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Cellular Open Resource Resource Report Resource Website 10+ mentions |
Cellular Open Resource (RRID:SCR_008022) | data or information resource, database, software resource | Cellular Open Resource is a Microsoft Windows environment for cellular modeling that is built around CellML (except for reactions and metadata which are not supported). It offers, through CellML, an ''out of the box'' access to a large database of single cell models. COR was among the early adopters of this standard, eventually forming the first publicly available CellML-based modeling and collaboration environment. From the onset, COR was designed to provide an environment that could not only be used by experienced modelers, but also by experimentalists, teachers and students. It therefore tries to combine a user-friendly interface with a computationally efficient numerical engine. In this paper, we introduce the philosophy behind COR, explain its user interface and current functionality, including the editing and running of CellML files, highlight lessons learned from user feedback and problems experienced during the development of COR and conclude by exploring future development potential. Sponsors: This study has been supported by a grant from the UK Biotechnology and Biological Sciences Research Council (BB/E024955/1). Keyword: Cell, Model, Cellular, Modeling, Open resource, Microsoft, Environment, Database, Experimentalist, Teacher, Student, Modeler, Computationally, Development, | has parent organization: University of Oxford; Oxford; United Kingdom | nif-0000-10187 | SCR_008022 | SciCrunch Registry | COR | 2026-09-26 02:14:21 | 15 | ||||||||||
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Annotation-Modules Resource Report Resource Website |
Annotation-Modules (RRID:SCR_008025) | Annotation-Modules | software resource | A tool for finding significant combinations of multisource annotations in gene lists. | is listed by: OMICtools | OMICS_00630 | SCR_008025 | SciCrunch Registry | 2026-09-26 02:14:21 | 0 | ||||||||||
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Buzsaki Lab Resource Report Resource Website 10+ mentions |
Buzsaki Lab (RRID:SCR_008020) | Buzsaki Lab | data analysis software, data or information resource, data processing software, laboratory portal, organization portal, portal, software application, software resource | Lab interested in understanding how neuronal circuitries of the brain support its cognitive capacities. Its goal is to provide rational, mechanistic explanations of cognitive functions at a descriptive level. In the lab''s view, the most promising area of cognitive faculties for scientific inquiry is memory, since it is a well-circumscribed term, can be studied in animals and substantial knowledge has accumulated on the molecular mechanisms of synaptic plasticity. Available software: * NeuroScope: NeuroScope can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities. * Klusters: Klusters is a powerful and easy-to-use cluster cutting application designed to help neurophysiologists sort action potentials from multiple neurons on groups of electrodes (e.g., tetrodes or multisite silicon probes). * KlustaKwik: KlustaKwik is a program for automatic cluster analysis, specifically designed to run fast on large data sets. * MATLAB m-files: A selection of MATLAB files developed in the lab., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, electrode, environment, funtion, animal, application, behavioral, brain, capacity, circuit, cluster, cognitive, hippocampal, hippocampus, laboratory, local field potential, mechanism, memory, molecular, neuron, neuronal, plasticity, research, scientific, spike, synaptic, tetrode |
has parent organization: Rutgers University; New Jersey; USA is parent organization of: NeuroScope |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10182 | http://osiris.rutgers.edu/frontmid/indexmid.html | SCR_008020 | SciCrunch Registry | Buzsaki''s Lab | 2026-09-26 02:14:21 | 15 | ||||||
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Bacterial Genomes Resource Report Resource Website 10+ mentions |
Bacterial Genomes (RRID:SCR_008141) | data analysis software, data or information resource, data processing software, database, software application, software resource | This website includes a list of projects that the Sanger Institute is currently working on or completed. All projects consist of the genomic sequencing of different bacteria. Each description of the bacteria includes its classification, a description, and the types of diseases that the bacteria is likely to cause. The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing users to search the sequences with their own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. The primary sequence viewer and annotation tool, Artemis is available for download. This is a portable Java program which is used extensively within the Microbial Genomes group for the analysis and annotation of sequence data from cosmids to whole genomes. The Artemis Comparison Tool (ACT) is also useful for interactive viewing of the comparisons between large and small sequences. | bacteria, bacterial, classification, description, disease, genomic, model, organism, pathogen, sequence, sequencing, model |
is listed by: 3DVC has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
nif-0000-20963 | SCR_008141 | SciCrunch Registry | Bacterial Genomes | 2026-09-26 02:14:22 | 12 | |||||||||
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Soy Ontology Resource Report Resource Website |
Soy Ontology (RRID:SCR_007847) | SOY | controlled vocabulary, data or information resource, ontology | Growth, trait and development ontology for soybean | obo |
is listed by: BioPortal has parent organization: SoyBase |
nlx_157593 | SCR_007847 | SciCrunch Registry | 2026-09-26 02:14:20 | 0 | |||||||||
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HPID - Human Protein Interaction database Resource Report Resource Website 1+ mentions |
HPID - Human Protein Interaction database (RRID:SCR_007724) | HPID | data or information resource, data repository, database, service resource, storage service resource | Database that provides human protein interaction information and integrated interaction and also finds proteins from databases that can potentially react with proteins submitted by users. The human protein interaction information was pre-computed by a statistical method from existing structural and experimental data, while the integrated human protein interactions are derived from BIND, DIP and HPRD. A score composed of three parts is assigned to the predicted interaction data, and those interactions with high scores were found reliable. HPID allows the user to use the protein IDs in EMBL, Ensembl, MIM, RefSeq, HPRD and NCBI to search protein interactions of interest. A set of web-based software tools has also been developed so that users can visualize and analyze protein interaction networks. | human protein, protein, interaction, protein superfamily, yeast, visualize, analyze, protein interaction network | has parent organization: Inha University; Incheon; South Korea | Ministry of Information and Communication of Korea IMT2000-C3-4 | PMID:15117749 | nif-0000-02984 | http://www.hpid.org | SCR_007724 | SciCrunch Registry | 2026-09-26 02:14:20 | 2 |
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