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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CellPhoneDB Resource Report Resource Website 100+ mentions |
CellPhoneDB (RRID:SCR_017054) | data or information resource, database | Collection of publicly available data of curated receptors, ligands and their interactions. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand or receptor or to interrogate single cell transcriptomics data. | collection, publicly, available, data, curated, receptor, ligand, interaction, heterometric, complex, dataset, cellular, transcriptomic, FASEB list |
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom works with: UniProt works with: Ensembl works with: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) works with: IMEx - The International Molecular Exchange Consortium works with: International Union of Basic and Clinical Pharmacology |
PMID:30429548 | Free, Available for download, Freely available | https://github.com/Teichlab/cellphonedb | SCR_017054 | 2026-08-29 11:30:23 | 469 | ||||||||
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ALZPEDIA Resource Report Resource Website 1+ mentions |
ALZPEDIA (RRID:SCR_017548) | AlzPedia | data or information resource, database | Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge. | Summary, gene, protein, pathophysiology, Alzheimer, neurodegenerative, disorder | is related to: Alzheimer's Research Forum | Free, Freely available | SCR_017548 | 2026-08-29 11:30:25 | 3 | |||||||||
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Medical Information Mart for Intensive Care-III Resource Report Resource Website 100+ mentions |
Medical Information Mart for Intensive Care-III (RRID:SCR_017384) | MIMIC-III, MIMIC 3 | data or information resource, database | Collection of comprising deidentified health related data associated with patients who stayed in critical care units of Beth Israel Deaconess Medical Center between 2001 and 2012. Database includes information such as demographics, vital sign measurements made at bedside (~1 data point per hour), laboratory test results, procedures, medications, caregiver notes, imaging reports, and mortality (both in and out of hospital). | deidentified, health-related data, Beth Israel Deaconess Medical Center, , FASEB list | NIBIB | Freely Available, Free, Available for Download | https://physionet.org/users/help/data-sharing/ | SCR_017384 | , MIMIC-III, MIMIC 3, 3, MIMIC, Medical Information Mart for Intensive Care, Medical Information Mart for Intensive Care-III | 2026-08-29 11:30:24 | 252 | |||||||
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Biospecimen Repository Access and Data Sharing Resource Report Resource Website 1+ mentions |
Biospecimen Repository Access and Data Sharing (RRID:SCR_017383) | BRADS | data or information resource, database | Access to data from the Division of Intramural Population Health Research (DIPHR) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) from completed studies, including biospecimens and ancillary data. | child, health, human, development, dataset | NICHD | Restricted | https://brads.nichd.nih.gov/AccessRequest/AccessRequest/ | SCR_017383 | , BRADS, Biospecimen Repository Access and Data Sharing | 2026-08-29 11:30:46 | 1 | |||||||
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Database of Open Chromatin Regions Resource Report Resource Website 1+ mentions |
Database of Open Chromatin Regions (RRID:SCR_016614) | data or information resource, database | Collection of open chromatin regions from sequencing data. Metadata as entire curated DNase-I hypersensitive sites (DHS) on the whole genome datasets and data specific to each chromosome. | collection, open, chromatin, region, sequencing, data, metadata, dataset | Free, Available for download, Freely available | SCR_016614 | 2026-08-29 11:30:22 | 3 | |||||||||||
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The 10000 Immunomes Resource Report Resource Website 1+ mentions |
The 10000 Immunomes (RRID:SCR_016624) | 10KIP | data or information resource, database | Collection of reference datasets for human immunology, derived from control subjects in the NIAID ImmPort database . Available data include flow cytometry, CyTOF, multiplex ELISA, gene expression, HAI titers, clinical lab tests, HLA type, and others. | collection, reference, dataset, human, immunology, control, subject, NIAID, ImmPort, database |
is related to: The Immunology Database and Analysis Portal (ImmPort) is related to: NIAID |
NIAID HHSN272201200028C | PMID:30304689 | Public, Free, Available for download, Freely available | SCR_016624 | 10K Immunomes Project, 000 Immunomes Project, 000 Immunomes, 10 | 2026-08-29 11:30:23 | 1 | ||||||
|
PlantGSEA Resource Report Resource Website 10+ mentions |
PlantGSEA (RRID:SCR_016866) | PlantGSEA | analysis service resource, data analysis service, production service resource, service resource | Websever for gene set enrichment analysis of plants. Used for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets. | gene, set, enrichement, analysis, plant | Ministry of Education of China ; Ministry of Science and Technology of China |
DOI:10.1093/nar/gkt281 | SCR_016866 | The Plant GeneSet Enrichment Analysis Toolkit, Plant GeneSet Enrichment Analysis, Gene Set Enrichment Analysis (GSEA) | 2026-08-29 11:30:23 | 18 | ||||||||
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Brain Maps Resource Report Resource Website 1+ mentions |
Brain Maps (RRID:SCR_017314) | atlas, data or information resource | Atlas with global nervous system nomenclature ontology and flatmaps for structure of rat brain. Open access resource for neuroscience community. | atlas, nervous, system, nomenclature, ontology, flatmap, structure, brain, rat | PMID:29277900 | Free, Freely available | SCR_017314 | Brain maps 4.0, Brain maps | 2026-08-29 11:30:34 | 5 | |||||||||
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Database of genes related to Repeat Expansion Diseases Resource Report Resource Website 1+ mentions |
Database of genes related to Repeat Expansion Diseases (RRID:SCR_018086) | DRED | data or information resource, database, service resource | Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest. | Gene, repeat expansion disease, unstable tandem repeat, abnormal repeat expansion, data |
works with: OMIM works with: NCBI works with: Ensembl |
Repeat Expansion Diseases | Free, Freely available | SCR_018086 | Database of genes related to Repeat Expansion Diseases | 2026-08-29 11:30:26 | 1 | |||||||
|
mqtldb Resource Report Resource Website 10+ mentions |
mqtldb (RRID:SCR_018002) | mqtldb | data or information resource, database | Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES). | Data, large scale, genome, DNA methylation, analysis, mother-child pair, serial time point, life course, aeries, methylation, quantitative trait loci, database | DOI:10.1186/s13059-016-0926-z | SCR_018002 | methylation quantitative trait loci database | 2026-08-29 11:30:46 | 47 | |||||||||
|
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 | 2026-08-29 11:30:35 | 166 | |||||||||
|
tfcheckpoint Resource Report Resource Website 1+ mentions |
tfcheckpoint (RRID:SCR_023880) | data or information resource, database | Collection of transcription factors annotated according to experimental and other evidence on their function as true DbTFs. Provides reference for both small scale experiments and genome scale studies. Curated compendium of specific DNA-binding RNA polymerase II transcription factors. | transcription factor, DNA-binding RNA polymerase II transcription factors, DNA-binding, RNA polymerase II transcription factors, | Liaison Committee between the Central Norway Regional Health Authority ; Norwegian Cancer Society ; Norwegian University of Science and Technology |
PMID:23933972 | Free, Freely available | SCR_023880 | 2026-08-29 11:30:34 | 4 | |||||||||
|
CaspBase Resource Report Resource Website 1+ mentions |
CaspBase (RRID:SCR_018975) | data or information resource, database | Database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference. Tool to rapidly disseminate organized caspase sequence data. Includes all animal species with currently available annotated genomes in NCBI genome database. Manually curated and not curated sequences are available to download. | Caspase sequences, curated data, caspase, caspase functional divergence, ancestral sequence inference, data analysis, dataset |
is related to: NCBI Genome is related to: NCBI |
PMID:30076665 | Free, Available for download, Freely available | SCR_018975 | Caspase Sequence Database | 2026-08-29 11:30:47 | 2 | ||||||||
|
Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform Resource Report Resource Website 500+ mentions |
Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (RRID:SCR_023757) | TCMSP | data or information resource, database | Pharmacology platform of Chinese herbal medicines that captures relationships between drugs, targets and diseases. Database includes chemicals, targets and drug-target networks, and associated drug-target-disease networks, as well as pharmacokinetic properties for natural compounds involving oral bioavailability, drug-likeness, intestinal epithelial permeability, blood-brain-barrier, aqueous solubility. | Pharmacology platform, Chinese herbal medicines, drugs, targets and diseases, drug-target networks, natural compounds, pharmacokinetic properties, | National Natural Science Foundation of China | PMID:24735618 | Free, Freely available | https://tcmsp-e.com/ | SCR_023757 | TCMSP database | 2026-08-29 11:30:36 | 577 | ||||||
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Adult Zebrafish Brain Atlas Resource Report Resource Website 1+ mentions |
Adult Zebrafish Brain Atlas (RRID:SCR_021732) | AZBA | atlas, data or information resource | Software tool as 3D adult zebrafish brain atlas for digital age. Built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains. | 3D adult zebrafish brain atlas, zebrafish brain, adult zebrafish brain, 3D brain | DOI:10.1101/2021.05.04.442625 | Free, Freely available | SCR_021732 | 2026-08-29 11:30:29 | 2 | |||||||||
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SIFT 4G Resource Report Resource Website 1+ mentions |
SIFT 4G (RRID:SCR_021850) | analysis service resource, data analysis service, production service resource, service resource | Software tool to predict whether amino acid substitution affects protein function. Faster version of SIFT that enables to scale up and provide SIFT predictions for more organisms. | sequence homology, amino acids physical properties, amino acid substitution, protein function | is related to: SIFT | Free, Available for download, Freely available | https://github.com/rvaser/sift4g | SCR_021850 | Sorting Intolerant From Tolerant For Genomes, SIFT4G | 2026-08-29 11:30:30 | 4 | ||||||||
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Blue Brain Cell Atlas Resource Report Resource Website 10+ mentions |
Blue Brain Cell Atlas (RRID:SCR_019266) | atlas, data or information resource | Describes number, types, and positions of cells in all areas of mouse brain. Provides densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and microglia in each of brain regions defined in Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, cell positions and types for modeling and visualizing brain areas. Underlying workflow uses imaging data from Allen Institute Common Coordinate Framework to generate cell positions and assign their type using API for data access. | Cell number, cell type, cell position, brain area, mouse brain, neuromodulatory neurons, astrocytes, oligodendrocytes, microglia, imaging data, Allen Institute Common Coordinate Framework |
is used by: BICCN is related to: Allen Mouse Brain Reference Atlas is related to: Allen Institute for Brain Science is provided by: Blue Brain Project |
Free, Freely available | SCR_019266 | The Blue Brain Cell Atlas | 2026-08-29 11:30:47 | 11 | |||||||||
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Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) | atlas, data or information resource | Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform. | Anatomical labels, Allen Common Coordinate Framework, Franklin and Paxinos labels, MRI atlas, segment labels, transgenic mice, dorsal striatum, cortico-striatal connectivity data, mouse brain anatomical structure |
is used by: BICCN is related to: Allen Institute for Brain Science |
NIH Office of the Director R24 OD018559; NIMH R01 MH116176; NINDS R01 NS10 8407; Pennsylvania Department of Health |
PMID:31699990 | Free, Freely available | SCR_019267 | 2026-08-29 11:30:29 | 2 | ||||||||
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Harvard Tissue Atlas Resource Report Resource Website 1+ mentions |
Harvard Tissue Atlas (RRID:SCR_022829) | HTA | atlas, data or information resource | Gathers together imaging and omic datasets into molecular maps of normal and diseased tissue from human and animal models, with emphasis on cancer. Used to access datasets, educational curriculum and talks, and recommended methods and software. | imaging and omic datasets, molecular maps, normal and diseased tissue, human and animal models, cancer datasets | has parent organization: Harvard University; Cambridge; United States | cancer | Free, Freely available | SCR_022829 | tissue-atlas.org | 2026-08-29 11:30:48 | 2 | |||||||
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EBSCO Dentistry and Oral Sciences Source Resource Report Resource Website 1+ mentions |
EBSCO Dentistry and Oral Sciences Source (RRID:SCR_022705) | data or information resource, database | Full text research database for dental practitioners and researchers. Offers top dental and oral sciences journals commonly purchased by dental schools and related institutions. | Dentistry journal, oral health | Free, Freely available | https://www.ebsco.com/products/research-databases/dentistry-oral-sciences-source | SCR_022705 | Dentistry and Oral Sciences Source | 2026-08-29 11:30:31 | 3 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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