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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EMBRYS Resource Report Resource Website 1+ mentions |
EMBRYS (RRID:SCR_006689) | EMBRYS | data or information resource, database | Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System. | Gene, expression, pattern, mapped, whole mount, mouse, embryo, ICR strain, mid gestational stage, transcription, factor, cofactor, data |
uses: RIKEN uses: MGC uses: PANTHER |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japanese Ministry of Health Labor and Welfare |
Free, Freely available | nlx_153839 | http://embrys.jp/embrys/html/MainMenu.html | SCR_006689 | Embryonic Gene Expression Database for Biomedical Research Source, Embryonic gene expression Database as a Biomedical Research Source | 2026-07-28 09:41:36 | 8 | |||||
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Human Tumor Atlas Network Resource Report Resource Website 10+ mentions |
Human Tumor Atlas Network (RRID:SCR_023364) | HTAN | disease-related portal, data or information resource, atlas, topical portal, portal | HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP. | Three dimensional atlases, cancer transitions, diverse set of tumor types, map healthy organs, cancer genomics approaches, bulk sequencing at single point in time, data, precancerous lesions to advanced disease, | cancer | National Cancer Institut Cancer Moonshot Initiative | PMID:32302568 | Free, Freely available | SCR_023364 | 2026-07-28 09:45:54 | 27 | |||||||
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Charite University and Berlin Institute for Health Research Central Biobank Core Facility Resource Report Resource Website |
Charite University and Berlin Institute for Health Research Central Biobank Core Facility (RRID:SCR_023495) | ZeBanC | service resource, biobank, access service resource, material storage repository, storage service resource, core facility | Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management. | USEDit, ABRF, integrated healthcare biobank, biobank, biospecimens, data, data management, data storage, blood collection, DNA/RNA extraction, virtual microscopy |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
Open | ABRF_563 | https://coremarketplace.org/?FacilityID=563&citation=1 | SCR_023495 | , Charite/BIH (ZeBanC), Charite - Central Biobank Charite/BIH (ZeBanC), Central Biobank of the Charite | 2026-07-28 09:45:56 | 0 | ||||||
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loom-viewer Resource Report Resource Website |
loom-viewer (RRID:SCR_016683) | data visualization software, software resource, software application, data processing software | Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format. | sharing, browsing, visualizing, single, cell, data, stored, Loom, file, format | works with: LoomPy | Free, Available for download, Freely available | SCR_016683 | 2026-07-28 09:44:23 | 0 | ||||||||||
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MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | data visualization software, software resource, software application, data processing software | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/, http://www.mccauslandcenter.sc.edu/mricro/, http://www.nitrc.org/projects/mricron, http://neuro.debian.net/pkgs/mricron.html, https://bio.tools/MRIcron | SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-07-28 09:40:25 | 2194 | |||||
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Ensembl Covid-19 Resource Report Resource Website 1+ mentions |
Ensembl Covid-19 (RRID:SCR_024704) | disease-related portal, data or information resource, topical portal, portal | Ensembl SARS-Cov2 data portal. | Ensembl, SARS-Cov2, Covid -19, data | is listed by: Ensembl | Covid -19 | Free, Freely available | SCR_024704 | 2026-07-28 09:46:09 | 1 | |||||||||
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SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software toolkit, software resource | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-07-28 09:39:56 | 101 | |||
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Allen Institute for Brain Science Sleep Study Resource Report Resource Website 1+ mentions |
Allen Institute for Brain Science Sleep Study (RRID:SCR_002983) | Allen Sleep Study | data or information resource, data set, atlas | Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data. | gene, expression, brain, data, image, mice, microarray, nissl, sleep, deprivation, wake, cycle, wakefulness, neuroanatomy |
is listed by: 3DVC has parent organization: Allen Institute for Brain Science |
Free, Public | nif-0000-00507 | SCR_002983 | Sleep Study | 2026-07-28 09:40:34 | 2 | |||||||
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FluView: A Weekly Influenza Surveillance Report Resource Report Resource Website 1+ mentions |
FluView: A Weekly Influenza Surveillance Report (RRID:SCR_001118) | data or information resource, portal | This page contains the Influenza Surveillance Report during 2008-2009 Influenza Season Week 15, ending April 18, 2009. | influenza, disease, prevention, seasonal, data, portal | has parent organization: Centers for Disease Control and Prevention | CDC | nif-0000-30241 | SCR_001118 | FluView | 2026-07-28 09:40:12 | 2 | ||||||||
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Open Access Series of Imaging Studies Resource Report Resource Website 100+ mentions |
Open Access Series of Imaging Studies (RRID:SCR_007385) | OASIS | data or information resource, database | Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated. | early, stage, alzheimer, disease, mri, fmri, image, brain, dicom, magnetic, resonance, collection, data, FASEB list |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Automatic Registration Toolbox is related to: 2012 MICCAI Multi-Atlas Labeling Challenge Data has parent organization: Howard Hughes Medical Institute has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Biomedical Informatics Research Network is parent organization of: Cover Pages |
Alzheimer's disease, Dementia, Normal, Nondemented, Aging | NIA P50 AG05681; NIA P01 AG03991; NIA R01 AG021910; NIMH P50 MH071616; NCRR U24 RR021382; NIMH R01 MH56584 |
Free, Acknowledgement required | r3d100012182, nif-0000-00387 | http://www.nitrc.org/projects/oasis, https://doi.org/10.17616/R3RS8K | SCR_007385 | The Open Access Series of Imaging Studies, Open Access Series of Imaging Studies, OASIS | 2026-07-28 09:41:59 | 299 | ||||
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Allen Mouse Spinal Cord Atlas Resource Report Resource Website 10+ mentions |
Allen Mouse Spinal Cord Atlas (RRID:SCR_007418) | Mouse Spinal Cord Atlas | data or information resource, database, atlas | Platform for exploring spinal cord at cellular and molecular levels. Map of gene expression for adult and juvenile mouse spinal cord. Provides map of normal mouse when used to compare gene expression in diseased or injury models. Interactive database of gene expression mapped across all anatomic segments of mouse spinal cord at postnatal days 4 and 56. Indexed set of images based on RNA in situ hybridization data, searchable and sortable by gene, age, expression, cervical, thoracic, lumbar, sacral, and coccygeal segments. | gene, expression, adult, diseased, injury, juvenile, models, mouse, postnatal, RNA, hybridization, spinal, cord, molecular, neuroanatomy, data |
has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Free, Freely available | nif-0000-00510 | http://mousespinal.brain-map.org/ | SCR_007418 | 2026-07-28 09:41:48 | 29 | |||||||
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Topology Data Bank of Transmembrane Proteins Resource Report Resource Website 1+ mentions |
Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) | TOPDB | data or information resource, database | Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data. | collection, transmembrane, protein, dataset, topology, public, data, sequence, database |
has parent organization: Hungarian Academy of Sciences; Budapest; Hungary works with: CCTOP |
Hungarian research and development funds ; OTKA ; Öveges fellowship ; Bolyai János Scholarship |
PMID:17921502 | Free, Available for download, Freely available for non commercial users | nif-0000-03568 | SCR_007964 | Topology Data Bank of Transmembrane Proteins, TOPDB | 2026-07-28 09:42:15 | 6 | |||||
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Electroencephalogram Database: Prediction of Epileptic Seizures Resource Report Resource Website |
Electroencephalogram Database: Prediction of Epileptic Seizures (RRID:SCR_008032) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 29,2025. Electroencephalogram (EEG) data recorded from invasive and scalp electrodes. The EEG database contains invasive EEG recordings of 21 patients suffering from medically intractable focal epilepsy. The data were recorded during an invasive pre-surgical epilepsy monitoring at the Epilepsy Center of the University Hospital of Freiburg, Germany. In eleven patients, the epileptic focus was located in neocortical brain structures, in eight patients in the hippocampus, and in two patients in both. In order to obtain a high signal-to-noise ratio, fewer artifacts, and to record directly from focal areas, intracranial grid-, strip-, and depth-electrodes were utilized. The EEG data were acquired using a Neurofile NT digital video EEG system with 128 channels, 256 Hz sampling rate, and a 16 bit analogue-to-digital converter. Notch or band pass filters have not been applied. For each of the patients, there are datasets called ictal and interictal, the former containing files with epileptic seizures and at least 50 min pre-ictal data. the latter containing approximately 24 hours of EEG-recordings without seizure activity. At least 24 h of continuous interictal recordings are available for 13 patients. For the remaining patients interictal invasive EEG data consisting of less than 24 h were joined together, to end up with at least 24 h per patient. An interdisciplinary project between: * Epilepsy Center, University Hospital Freiburg * Bernstein Center for Computational Neuroscience (BCCN), Freiburg * Freiburg Center for Data Analysis and Modeling (FDM). | electrode, electroencephalogram (eeg), epilepsy, epileptic seizure, focal, algorithm, analysis, behavioral, brain, cardiac, computational, data, defibrillator, hippocampus, medically, modeling, neocortical, neuroscience, patient, predict, seizure, stimulation, structure, surgical, model |
is listed by: 3DVC has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
University of Freiburg; Baden-Wurttemberg; Germany | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10217 | SCR_008032 | EEG Database | 2026-07-28 09:42:01 | 0 | |||||||
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Migratory Locust EST Database Resource Report Resource Website 1+ mentions |
Migratory Locust EST Database (RRID:SCR_008201) | data or information resource, database | The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies. | ecologically, entomology, est, fruitfly, functional, gene, agronomically, analysis, annotation, codon, comparative, data, domain, genomic, hemimetabolous, homologous, honeybee, insect, invertebrate, invertebrate databases, locust, locusta migratoria, medically, migratory, molecular, mosquito, nematode, orthologous, orthopteran, pathway, pest, protein, sequence, silkworm, specie, transcriptome, transcriptomic, unigene, ontology | has parent organization: BGI; Shenzhen; China | nif-0000-21244 | SCR_008201 | LocustDB | 2026-07-28 09:42:05 | 7 | |||||||||
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PostgreSQL Resource Report Resource Website 100+ mentions |
PostgreSQL (RRID:SCR_021067) | data or information resource, database | Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems. | Object relational database system, SQL language, data storage, data, database system |
uses: pgAdmin is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | SCR_021067 | Postgres | 2026-07-28 09:45:10 | 108 | |||||||||
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Scopus Resource Report Resource Website 100+ mentions |
Scopus (RRID:SCR_022559) | data or information resource, database | Abstract and indexing database with full text links that is produced by Elsevier Co. Combines expertly curated abstract and citation database with enriched data and linked scholarly literature across wide variety of disciplines. | Elsevier Co, abstract and citation database, data, scholarly literature, abstract and indexing database, full text links | is listed by: SoftCite | PMID:16522216 | SCR_022559 | 2026-07-28 09:45:41 | 324 | ||||||||||
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ClinWiki Resource Report Resource Website |
ClinWiki (RRID:SCR_021297) | data or information resource, database | Clinical trials database. | Clinical trials, data, Wikidata | is related to: Wikidata | William Hoos | Free, Freely available | Wikidata_Q96777166 | https://www.wikidata.org/wiki/Q96777166 | SCR_021297 | 2026-07-28 09:45:16 | 0 | |||||||
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trinetx Resource Report Resource Website 100+ mentions |
trinetx (RRID:SCR_022760) | data or information resource, database | Network of healthcare organizations, together with data partners in Brazil, South Korea, and Japan, to bring clinical facts on more than 250 million patients around the world. Federated model so users of this data are ensured new patients, observations, and results every day, all harmonized to standard terminology like ICD-10 and LOINC without any data wrangling required at the point of care. The raw data is not available to authors of papers and papers in medicine are being retracted. | Data, medical data, clinical facts, patients around the world, raw data is not available to authors, papers in medicine are being retracted | Restricted | SCR_022760 | 2026-07-28 09:45:46 | 139 | |||||||||||
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CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software toolkit, software resource | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-07-28 09:39:59 | 31 | ||||||||
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Cross Validation Resource Report Resource Website |
Cross Validation (RRID:SCR_000702) | service resource, training service resource | A model evaluation method for training someone to read data. There are three methods: the holdout method, K-fold cross validation, and leave-one-out cross validation. | model, modeling, training, data, holdout, k fold, cross, validation | has parent organization: Carnegie Mellon University; Pennsylvania; USA | nlx_19901 | SCR_000702 | 2026-07-28 09:40:03 | 0 |
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