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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HmtVar Resource Report Resource Website 10+ mentions |
HmtVar (RRID:SCR_017288) | data or information resource, database, service resource | Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. | manually, curated, data, variability, mitochondria, pathogenicity, mtDNA, variant, human, bio.tools |
uses: HmtDB - Human Mitochondrial DataBase uses: 1000 Genomes Project and AWS uses: MITOMAP - A human mitochondrial genome database uses: MutPred uses: SNPsandGO is listed by: Debian is listed by: bio.tools is affiliated with: University of Bologna; Bologna; Italy has parent organization: University of Bari; Bari; Italy |
DHOMOS Worldwide Cancer Research ; DISCO TRIP ; Italian Ministry of Health ; Rosa Maria Massari fellowship from the Italian Association for Cancer Research |
PMID:30371888 PMID:31821723 |
Free, Freely available | biotools:HmtVar | https://bio.tools/HmtVar | SCR_017288 | 2026-09-12 01:02:17 | 12 | ||||||
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EPSD Eukaryotic Phosphorylation Site Database Resource Report Resource Website 1+ mentions |
EPSD Eukaryotic Phosphorylation Site Database (RRID:SCR_016514) | EPSD | data or information resource, database | Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies. | protein, phosphorylation, site, eukaryotes, phosphoproteomic, data | has parent organization: Huazhong University of Science and Technology; Wuhan; China | Special Project on Precision Medicine under the National Key R&D Program 2017YFC0906600; the Fundamental Research Funds for the Central Universities 2017KFXKJC001; the Natural Science Foundation of China 31671360 |
Free, Freely available | SCR_016514 | Eukaryotic Phosphorylation Site Database, EPSD | 2026-09-12 01:02:17 | 1 | |||||||
|
fiddle Resource Report Resource Website 1+ mentions |
fiddle (RRID:SCR_017327) | FIDDLE | service resource, software application, software resource | Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community. | identify, publication, format, dataset, , result, file, drawer, data, liberation, effort | DOI:10.31219/osf.io/6mcu3 | Free, Freely available | https://github.com/quest-bih/FIDDLE | SCR_017327 | file drawer data liberation effort, fiddle | 2026-09-12 01:02:18 | 2 | |||||||
|
KEGG PATHWAY Database Resource Report Resource Website 1000+ mentions |
KEGG PATHWAY Database (RRID:SCR_018145) | data or information resource, database, service resource | Reference database for pathway mapping in KEGG Mapper. Collection of manually drawn pathway maps representing knowledge on molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organisms systems, human diseases, drug development. | Pathway mapping, reference database, KEGG Mapper, molecular interaction, reaction and relation network, metabolism, genetic information processing, cellular process, organism system, human disease, drug development, data | is related to: KEGG | Free, Freely available | SCR_018145 | KEGG PATHWAY | 2026-09-12 01:02:18 | 1224 | |||||||||
|
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 | 2026-09-12 01:02:17 | 469 | ||||||||
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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 | 2026-09-12 01:02:17 | 3 | |||||||||||
|
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 | 2026-09-12 01:02:18 | 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 | 2026-09-12 01:02:18 | 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 | 2026-09-12 01:02:19 | 166 | |||||||||
|
Scopus Resource Report Resource Website 500+ 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 | 2026-09-12 01:02:20 | 788 | ||||||||||
|
ClinWiki Resource Report Resource Website 1+ mentions |
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 | 2026-09-12 01:02:20 | 1 | |||||||
|
TFFACTOR Resource Report Resource Website |
TFFACTOR (RRID:SCR_000519) | data or information resource, data set |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 13, 2016. A dataset about transcriptional regulation in eukaryotic cells, including data such as transcription factors and their binding sites and profiles. Resource is in Chinese. |
data, transcription, regulation, eukaryotic, binding, site |
is related to: TFSEARCH: Searching Transcription Factor Binding Sites has parent organization: Computational Biology Research Center Core Facility |
PMID:9399875 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_39049 | SCR_000519 | 2026-09-12 01:03:09 | 0 | ||||||||
|
Genomedata Resource Report Resource Website 1+ mentions |
Genomedata (RRID:SCR_004544) | Genomedata | software resource, source code | A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems. | genome, data, format, linux, mac, functional genomics, function, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:20435580 | GNU General Public License | nlx_53677, biotools:genomedata, OMICS_02148 | https://bio.tools/genomedata | SCR_004544 | 2026-09-12 01:03:15 | 1 | ||||||
|
Matlab Health and Socio-Economic Survey Resource Report Resource Website |
Matlab Health and Socio-Economic Survey (RRID:SCR_008942) | MHSS | data or information resource, data set | A data set of the health and socioeconomic factors that affect the elderly in Matlab, a region of rural Bangladesh. The survey captures measurements and statistics such as adult survival, health status, health care utilization, resource flows between generations and the impact of community services and infrastructure on adult health care. Data was collected through surveys that touch on four topics: household and individual information; determinants of natural fertility; migration out of the community; and community and provider survey of healthcare and education infrastructure. | survey, bangladesh, adult, birth control, child development, culture, fertility, health behavior, health care, health care facility, health care service, health services utilization, health status, household budget, household expenditure, housing condition, infant feeding, reproductive history, school, social network, socioeconomic status, traditional medicine, women's health care, socioeconomic, behavior, family, community, household, woman, female, pregnancy status, outmigrant, family planning, international, questionnaire, clinical, interview, research, data |
is listed by: Inter-university Consortium for Political and Social Research (ICPSR) has parent organization: National Archive of Computerized Data on Aging (NACDA) |
Aging | NIA P01AG11952 | Public, Data and documentation may be used for academic and public policy research purposes only | nlx_151854 | SCR_008942 | Matlab Health and Socioeconomic Survey, Matlab Health and Socioeconomic Survey (MHSS), Matlab Health and Socio-Economic Survey (MHSS) | 2026-09-12 01:03:18 | 0 | |||||
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Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center Resource Report Resource Website |
Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) | BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics. | RT PCR, transcriptome, epigenome, metabolomics, profiling, assay, protein, expression, pathway, data, bioinformatics, analysis, next, generation, sequencing, human, mouse, array, tissue, imaging |
is listed by: Eagle I is related to: Beth Israel Deaconess Medical Center Labs and Facilities is related to: Harvard University Labs and Facilities has parent organization: Harvard University; Cambridge; Massachusetts |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156126 | http://www.bidmcgenomics.org/ | SCR_009668 | Beth Israel Deaconess Medical Center, BIDMC | 2026-09-12 01:03:19 | 0 | ||||||
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BIDMC Division of Digital Psychiatry LAMP platform Core Facility Resource Report Resource Website 1+ mentions |
BIDMC Division of Digital Psychiatry LAMP platform Core Facility (RRID:SCR_027767) | access service resource, core facility, data or information resource, service resource | Core collects data to capture and consider the real-time lived experiences of patients. Uses open-source digital platform and mobile app for neuropsychiatric research and clinical care, to monitor, support, and improve brain health by collecting real-time data (like location, activity, heart rate via sensors), conducting digital assessments (surveys, cognitive tests), and delivering interventions (meditation, journaling, psychoeducation) to patients and clinicians. It helps study behavioral patterns, track symptoms, and personalize mental health treatment through features organized around Learn, Assess, Manage, and Prevent. | ABRF, study behavioral patterns, track symptoms, personalize mental health treatment, data, neuropsychiatric research and clinical care management platform, run remote smartphone-based research studies, |
is listed by: ABRF CoreMarketplace has parent organization: Harvard Medical School; Massachusetts; USA |
ABRF_3107 | https://coremarketplace.org/?FacilityID=3107, https://docs.lamp.digital/, https://github.com/BIDMCDigitalPsychiatry/LAMP-platform/ | SCR_027767 | mindLAMP, BIDMC mindLAMP, Beth Israel Deaconess Medical Center mindLAMP | 2026-09-12 01:05:36 | 2 | ||||||||
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Collection of Alternative Methods for Regulatory Application (CAMERA) Resource Report Resource Website 1+ mentions |
Collection of Alternative Methods for Regulatory Application (CAMERA) (RRID:SCR_027893) | CAMERA | data or information resource, database | Interactive database and user interface providing online access to validated alternative methods for U.S. regulatory and other contexts of use. Central hub and unified resource of validated alternative methods that enhances accessibility to validation study reports, data, protocols / SOPs, and information on regulatory guidance.Users can filter searches by alternative method types, defined approaches, Test Method Endpoint, and regulatory guidance. | NAMSD, validated alternative methods, U.S. regulatory, validation study reports, data, protocols, SOPs, regulatory guidance, | Free, Freely available | SCR_027893 | Collection of Alternative Methods for Regulatory Application | 2026-09-12 01:05:38 | 1 | |||||||||
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OAI Knowledge base Resource Report Resource Website 50+ mentions |
OAI Knowledge base (RRID:SCR_028107) | data or information resource, knowledge base | Centralized, annotated repository for the Osteoarthritis Initiative (OAI) study, designed to accelerate research by organizing and linking extensive clinical, imaging (MRI/X-ray), and biomarker data. It aims to help researchers analyze knee osteoarthritis prevention, treatment, and progression. | DRKB, clinical, imaging, MRI, X-ray, biomarker, data, osteoarthritis | Free, Freely available, | SCR_028107 | Osteoarthritis Initiative Knowledge base | 2026-09-12 01:05:43 | 50 | ||||||||||
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Human Brain Variation Project Resource Report Resource Website 1+ mentions |
Human Brain Variation Project (RRID:SCR_028065) | data access protocol, data or information resource, portal, project portal, software resource, web service | Project provides data currently generated with support from the NIH Brain Initiative Cell Atlas Network (BICAN). Broad Institute collaboration supported by the NIH BRAIN Initiative, to create comprehensive atlas of cellular variation in the healthy human brain. It maps data from millions of cells across diverse individuals to understand how brain biology differs, helping researchers distinguish healthy variation from disease states. | Brain, data, healthy human brain, cells, |
is related to: BRAIN Initiative Cell Atlas Network is related to: BRAIN Initiative |
Free, Freely available | SCR_028065 | Human Brain Variation Project (McCarroll, Macosko) | 2026-09-12 01:05:42 | 1 | |||||||||
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MarmotGraph Resource Report Resource Website |
MarmotGraph (RRID:SCR_027452) | knowledge graph, software application, software resource | Knowledge graph system developed for managing and organizing rich metadata objects, initially for the Human Brain Project (HBP) and now extended to be a more generic, domain-agnostic solution. It is associated with CSCS (Swiss National Supercomputing Centre) and aims to provide a comprehensive toolset and API for working with knowledge graphs. | Metadata, managing, system, neuroscience, experimental, data, human, brain, graph, database, terminology, ontology | is related to: EBRAINS Knowledge Graph | Free, Freely available, | SCR_027452 | Management Applications for Rich Metadata ObjecTs Graph | 2026-09-12 01:05:27 | 0 |
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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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