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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Beaumont Hospitals Biobank Resource Report Resource Website |
Beaumont Hospitals Biobank (RRID:SCR_004666) | Beaumont BioBank | biomaterial supply resource, material resource, tissue bank | BioBank is a new Beaumont research center that is focused on developing innovative methods for early detection of disease and personalized treatment plans through leading edge analysis techniques and state of the art technologies. Biomarkers from tissue, blood or fluids, are used to develop the next generation of care management, taking it from bench to bedside. Beaumont BioBank will work to: * collect high-quality biological specimens from any specialty at Beaumont * store, analyze and record specimens in an efficient, organized and accessible manner using leading-edge technologies * connect specialties and specialists with each other across traditional hospital or laboratory departments to provide a multidisciplinary research structure * facilitate translational research that links molecular laboratory techniques that enable us to apply biomarker discoveries to clinical outcome studies in a speedy and direct manner | tissue, blood, fluid |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Beaumont Health System; Michigan; USA |
All | nlx_66501 | SCR_004666 | 2026-08-04 09:41:11 | 0 | ||||||||
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New York Organ Donor Network - NYODN Resource Report Resource Website |
New York Organ Donor Network - NYODN (RRID:SCR_004659) | NYODN | biomaterial supply resource, material resource, tissue bank | The New York Organ Donor Network is the nonprofit, federally designated organ procurement organization (OPO) for the greater New York Metropolitan area. Established in 1978, the Donor Network is the second largest OPO in the United States, serving a culturally and ethnically diverse population of 13 million people. Working closely with transplant centers and hospitals, we: * Coordinate organ, tissue and eye donation for transplant in the New York region * Educate the public and health care professionals about donation and transplantation * Promote the importance of signing up on the New York State Donate Life Registry. We work closely with 10 transplant centers, more than 90 hospitals, and various tissue and eye banks. The Donor Network is accredited by the Association of Organ Procurement Organizations (AOPO) and a member of the United Network for Organ Sharing (UNOS), which oversees the organ transplant waiting list in the U.S. |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Donate Life America |
nlx_66050 | SCR_004659 | New York Organ Donor Network | 2026-08-04 09:41:11 | 0 | |||||||||
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Integrated Disease Resource Report Resource Website |
Integrated Disease (RRID:SCR_004892) | database, data or information resource | A virtual database currently indexing authoritative information on disease and treatment options from NINDS Disorder List and PubMed Health. | disease, treatment, disorder, health, database |
is used by: NIF Data Federation is related to: NINDS Disorder Index is related to: PubMed Health has parent organization: Integrated |
Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource | nlx_86401 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-6 http://neuinfo.org/nif/nifgwt.html?query=nlx_86401, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_86401-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-6 | SCR_004892 | NIF Integrated Disease View, NIF Integrated Disease, Integrated Disease View | 2026-08-04 09:41:15 | 0 | |||||||
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Queen Square Brain Bank Resource Report Resource Website |
Queen Square Brain Bank (RRID:SCR_004652) | QSBB | biomaterial supply resource, material resource, tissue bank | A brain bank which holds an archive of brains donated by individuals with neurodegenerative disease and others who serve as neurologically normal controls. It specializes in parkinsonian movement disorders, including Parkinson's disease and multiple system atrophy, and holds the national collection of brains donated by individuals with progressive supranuclear palsy (PSP). Recently the collection has been developed to include donated brains from prospectively studied people with familial dementias. The QSBB also banks brains donated by people with dystonia and Gilles de la Tourette syndrome. The Brain Bank aims to provide brain tissue for neuropathological studies and for scientific research both in the UK and worldwide. The large collection of tissue is backed up by clinical documentation and all material is fully evaluated by the neuropathologists at QSBB. Brain tissue is stored as formalin-fixed, wax embedded blocks and is frozen, either at -20 degrees C or at -80 degrees C (flash-frozen). Tissue can be provided as slide-mounted sections, or as small blocks for neurochemistry, proteomics and DNA and RNA analysis. Flash-frozen material has excellent histological preservation and is suitable for in situ hybridization and immunohistochemistry. Case-control studies are matched for post-mortem delay and agonal status and are supplied blind. | neurological disorder, parkinsons disease, clinical data, human brain, brain tissue, neurodegenerative disease, neurologically normal control, progressive supranuclear palsy, parkinsonian movement disorder, multiple system atrophy, dementia, dystonia, tourettes disorder |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University College London; London; United Kingdom |
Neurodegenerative disease, Progressive Supranuclear Palsy, Parkinsonian movement disorder, Parkinson's disease, Multiple system atrophy, Dementia, Dystonia, Tourettes Disorder | UCL Institute of Neurology ; Reta Lila Weston Institute of Neurological Studies UCL ; PSP Association |
Available for neuropathological studies, Tissue requests from within the UK will be covered by the QSBB ethics approval, Requesters from outside the UK must provide evidence of approval from the Human Research Ethics Committee (or equivalent) of their parent institution | nlx_143854 | SCR_004652 | Queen Square Brain Bank for Neurological Disorders, UCL Brain Bank | 2026-08-04 09:41:11 | 0 | |||||
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Boston University Biospecimen Archive Research Core Resource Report Resource Website 1+ mentions |
Boston University Biospecimen Archive Research Core (RRID:SCR_005363) | BU BARC | biomaterial supply resource, material resource, tissue bank | Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org | disease, normal, cancer, tumor, colon, inflammatory bowel disease, rectal cancer, colon cancer, tonsil, obstructive sleep apnea, tonsillitis, parathyroid, parathyroid adenoma, stomach, stomach cancer, prostate, prostate cancer, uterus, uterine cancer, lung, squamous cell carcinoma, adenocarcinoma, ovary, ovarian cancer, thyroid, thyroid papillary carcinoma, kidney, papillary renal cell carcinoma, renal cell carcinoma, clear cell carcinoma, breast, ductal carcinoma in situ, invasive ductal carcinoma, invasive lobular carcinoma, tissue, cancer tissue, colon tissue, tonsil tissue, parathyroid tissue, stomach tissue, prostate tissue, uterine tissue, lung tissue, ovarian tissue, thyroid tissue, kidney tissue, breast tissue, frozen, paraffin block, blood, biopsy, heart disease, diabetes, brain, brain tissue, adrenal, adrenal tissue, parotid, parotid tissue, thymus, pancreas, cervix, esophagus, thymus tissue, pancreatic tissue, cervical tissue, esophageal tissue |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Boston University Medical Campus; Massachusetts; USA has parent organization: Boston University School of Medicine; Massachusetts; USA |
Disease, Cancer, Tumor, Normal, Heart disease, Diabetes, Inflammatory bowel disease, Rectal cancer, Colon cancer, Obstructive sleep apnea, Tonsillitis, Parathyroid adenoma, Stomach cancer, Prostate cancer, Uterine cancer, Squamous cell carcinoma, Adenocarcinoma, Ovarian cancer, Thyroid papillary carcinoma, Papillary renal cell carcinoma, Renal cell carcinoma, Clear cell carcinoma, Ductal carcinoma in situ, Invasive ductal carcinoma, Invasive lobular carcinoma | Public: The mission of the Biospecimen Archive Research Core (BARC) is to collect high quality samples of normal and diseased human material with appropriate clinical annotation and make these materials, Known as biospecimens, Available to qualified researchers while ensuring the informed consent, Safety and anonymity of all providers. | nlx_144430 | SCR_005363 | BU Biospecimen Archive Research Core, Boston University Biospecimen Archive Research Core (BARC), Biospecimen Archive Research Core Boston University Medical Center, Boston University Medical Center Biospecimen Archive Research Core, BUMC BARC, BUMC Biospecimen Archive Research Core | 2026-08-04 09:41:21 | 1 | ||||||
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Emory Neurology Database Resource Report Resource Website |
Emory Neurology Database (RRID:SCR_005277) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9, 2025. A database which retains extensive clinical information about study subjects recruited by the Alzheimer's Disease Research Center Clinical Core, as well as other individuals with neurological diseases. In addition to clinical information, the database has basic demographics, medical history (including risk factors such as smoking), and a detailed family history from all subjects. Some entries have neuropsychological measures. Users can access a Summary Database which contains the most commonly requested variables. A data dictionary describing the variables in the Summary Database is available. | alzheimer's disease, mild cognitive impairment, dementia, lewy body disease, parkinson's disease, movement disorder, amyotrophic lateral sclerosis, stroke, sleep disorder, clinical data, family history |
is affiliated with: Emory Alzheimer's Disease Research Center is related to: Emory ADRC Tissue and Biospecimen Banking Facility |
Alzheimer's disease, Mild Cognitive Impairment, Frontotemporal dementia, Dementia, Lewy body disease, Parkinson's disease, Amyotrophic lateral sclerosis, Stroke, Sleep disorder | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144309 | SCR_005277 | 2026-08-04 09:41:20 | 0 | ||||||||
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DTI White Matter Atlas Resource Report Resource Website |
DTI White Matter Atlas (RRID:SCR_005279) | DTI White Matter Atlas | atlas, data or information resource | DTI white matter atlases with different data sources and different image processing. These include single-subject, group-averaged, B0 correction, processed atlases (White Matter Parcellation Map, Tract-probability maps, Conceptual difference between the WMPM and tract-probability maps), and linear or non-linear transformation for automated white matter segmentation. # Adam single-subject white matter atlas (old version): These are electronic versions of atlases published in Wakana et al, Radiology, 230, 77-87 (2004) and MRI Atlas of Human White Matter, Elsevier. ## Original Adam Atlas: 256 x 256 x 55 (FOV = 246 x 246 mm / 2.2 mm slices) (The original matrix is 96x96x55 (2.2 mm isotropic) which is zerofilled to 256 x 256 ## Re-sliced Adam Atlas: 246 x 246 x 121 (1 mm isotropic) ## Talairach Adam: 246 x 246 x 121 (1 mm isotropic) # New Eve single-subject white matter atlas: The new version of the single-subject white matter atlas with comprehensive white matter parcellation. ## MNI coordinate: 181 x 217 x 181 (1 mm isotropic) ## Talairach coordinate: 181 x 217 x 181 (1 mm isotropic) # Group-averaged atlases: This atlas was created from their normal DTI database (n = 28). The template was MNI-ICBM-152 and the data from the normal subjects were normalized by affine transformation. Image dimensions are 181x217x181, 1 mm isotropic. There are two types of maps. The first one is the averaged tensor map and the second one is probabilistic maps of 11 white matter tracts reconstructed by FACT. # ICBM Group-averaged atlases: This atlas was created from ICBM database. All templates follow Radiology convention. You may need to flip right and left when you use image registration software that follows the Neurology convention. | white matter, brain, template, human, magnetic resonance imaging, diffusion tensor imaging, adult human, male, female, cerebellum, mni, talairach | has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA | Normal | NCRR P41RR015241 | Account required | nlx_144313 | SCR_005279 | 2026-08-04 09:41:19 | 0 | ||||||
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Brown Brain Tissue Resource Center Resource Report Resource Website 1+ mentions |
Brown Brain Tissue Resource Center (RRID:SCR_005392) | BTRC | biomaterial supply resource, material resource, tissue bank | A tissue resource center which facilitates research into the relationship between Alzheimer's disease and other brain disorders such as strokes and mental illnesses. Most donations have been obtained from Alzheimer's patients. Normal controls are available, many of which are from subjects with close relatives with Alzheimer's. The Brown BTRC also supports a collection of brain tumor cases that were harvested from patients who underwent surgery and who were enrolled in a clinical trial for the development of new treatments for brain cancer. | alzheimer's disease, brain disorder, stroke, mental disease, memory disorder, lewy body disease, parkinson's disease, brain tumor, brain cancer, dementia, downs syndrome, brain tissue, tumor tissue, brain, clinical trial |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Brown Alpert Medical School; Rhode Island; USA |
Alzheimer's disease, Brain disorder, Stroke, Mental disease, Memory disorder, Lewy Body Disease, Parkinson's disease, Brain tumor, Brain cancer, Dementia, Downs syndrome | Available for affiliates of Brown Medical School, Available to the research community | nlx_144502 | SCR_005392 | Brown Alpert Medical School BTRC, Brown University Medical School BTRC, Brown Alpert Medical School Brain Tissue Resource Center | 2026-08-04 09:41:21 | 1 | ||||||
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dbNSFP Resource Report Resource Website 500+ mentions |
dbNSFP (RRID:SCR_005178) | dbNSFP | database, data or information resource | A database for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Version 2.0 is based on the Gencode release 9 / Ensembl version 64 and includes a total of 87,347,043 nsSNVs and 2,270,742 essential splice site SNVs. It compiles prediction scores from six prediction algorithms (SIFT, Polyphen2, LRT, MutationTaster, MutationAssessor and FATHMM), three conservation scores (PhyloP, GERP++ and SiPhy) and other related information including allele frequencies observed in the 1000 Genomes Project phase 1 data and the NHLBI Exome Sequencing Project, various gene IDs from different databases, functional descriptions of genes, gene expression and gene interaction information, etc. Some dbNSFP contents (may not be up-to-date though) can also be accessed through variant tools, ANNOVAR, KGGSeq, UCSC Genome Browser''s Variant Annotation Integrator, Ensembl Variant Effect Predictor and HGMD. | non-synonymous single-nucleotide variant, function, annotation, functional prediction, non-synonymous mutation, splice site mutation, FASEB list |
is used by: Exomiser is listed by: OMICtools has parent organization: University of Texas Health Science Center at Houston; Texas; USA has parent organization: Google Sites |
PMID:23843252 PMID:21520341 |
Acknowledgement requested, Free, Public | OMICS_00172 | SCR_005178 | 2026-08-04 09:41:18 | 648 | |||||||
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SwissRegulon Resource Report Resource Website 10+ mentions |
SwissRegulon (RRID:SCR_005333) | SwissRegulon | database, data or information resource | A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format. | genome, binding site, transcription factor, genome-wide annotation, annotation, chip-chip, chip-seq, non-coding region, promoter, motif, transcript, regulatory motif, genome browser, FASEB list |
is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:23180783 PMID:17130146 |
Acknowledgement requested | nif-0000-03524, OMICS_00543 | SCR_005333 | SwissRegulon Database | 2026-08-04 09:41:20 | 44 | ||||||
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Einstein-Montefiore Institute for Clinical and Translational Research Biorepository Resource Report Resource Website 1+ mentions |
Einstein-Montefiore Institute for Clinical and Translational Research Biorepository (RRID:SCR_005297) | Einstein-Montefiore ICTR Biorepository | biomaterial supply resource, material resource, tissue bank | Patient-derived specimens are essential to research in genomics, proteomics, and biomarkers. We provide banking for biological fluid and tissue specimens as well as human DNA and RNA. We provide secure archival sample storage as well as clinically-annotated specimen biobanks for defined research projects. The core serves the human research blood and tissue banking needs of clinical and translational researchers. Samples can be banked by an individual PI or by a consortium of investigators. All samples are tracked and archived using a secure tracking database, the Einstein-Montefiore Bio-Repository Databank (EM-BRED), http://informatics30.aecom.yu.edu/em-bred/default.aspx. EM-BRED provides qualified investigators with a solution to securely link patient specimens to clinical and pathological data. It consists of a user-friendly query engine that allows for comprehensive specimen search, and ultimately to build clinical annotations of relevance. The facility works under the best practices set out by NCI and ISBER (2006) for collection, storage, and retrieval of human biological materials for research. | blood, tissue, dna, rna, clinical data, pathological data, frozen, flash frozen, oct embedded, paraffin embedded, tumor, cancer, non-tumor, adenoma, biliary atresia, carcinoma, clm, liver disease, colorectal metastasis, cryptogenic, etoh, familial hypercholestrolemia, hepatic artery injury, hepatitis b, hepatitis c, primary sclerosing cholangitis, recurrent pyogenic cholangitis with hepatolithiasis, subacute fulminant hepatic failure drug toxicity, database |
is listed by: One Mind Biospecimen Bank Listing is related to: Einstein-Montefiore ICTR Research Informatics Core has parent organization: Albert Einstein College of Medicine; New York; USA has parent organization: Montefiore Medical Center; New York; USA |
Tumor, Cancer, Non-tumor, Adenoma, Biliary atresia, Carcinoma, CLM, Liver disease, Colorectal metastasis, Cryptogenic, ETOH, Familial hypercholestrolemia, Hepatic artery injury, Hepatitis B, Hepatitis C, Primary sclerosing cholangitis, Recurrent pyogenic cholangitis with hepatolithiasis, Subacute fulminant hepatic failure drug toxicity | Varying: The core serves the human research blood and tissue banking needs of clinical and translational researchers. Samples can be banked by an individual PI or by a consortium of investigators. Owners of the samples grant permission. | nlx_144342 | SCR_005297 | Einstein-Montefiore Bio-Repository Databank, Einstein-Montefiore Bio-Repository Databank (EM-BRED), Einstein-Montefiore Institute for Clinical Translational Research Biorepository, Einstein-Montefiore Institute for Clinical & Translational Research Biorepository, EM-BRED | 2026-08-04 09:41:20 | 1 | ||||||
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Now at NEJM Resource Report Resource Website |
Now at NEJM (RRID:SCR_005239) | Now(at)NEJM | blog, narrative resource, data or information resource | A blog produced by the NEJM publishing communications team about new and innovative content in the New England Journal of Medicine (NEJM.org). Our goal is to inform you about what''s new and provide some additional context to complement the content published in NEJM. Each week we post a piece under Insights about one of the latest research papers in NEJM, discussing its clinical significance, where it may lead us in practice and research, and often giving an editor''s thoughts about why it was important to publish. We pose questions to stimulate your thinking and discussion. The idea is to make it easy for you to give us your views on a particular topic and make the conversation accessible to other doctors and physicians-in-training. Posts contain links to the full article, which will be free to all visitors for a limited time. We also feature two posts from the Resident e-Bulletin each week, with an article summary, Clinical Pearls, and Morning Report Questions teaching points that many of you find so useful in your roles as teachers or trainees. The blog gives us a new way to distribute and store this educational information on the social web, again, inviting comment and discussion. You''ll also hear about new products and applications as we bring them out, such as new Interactive Medical Cases, or iPhone applications, like NEJM This Week and the Image Challenge. We link to videos on the NEJMvideo channel on YouTube, share our Twitter feed, and links to NEJM in the News, too. We''d like this to be an open forum, complementary to the core content of NEJM, engaging you in a new experience beyond the journal page in a more interactive community. | medicine, doctor, physician, resident |
is used by: NIF Data Federation is used by: Integrated Blogs |
Protected by copyright; for your personal noncommercial use. http://www.nejm.org/page/about-nejm/terms-of-use | nlx_144240 | SCR_005239 | NowatNEJM, Now at NEJM - A blog for physicians about NEJM, Now_at_NEJM | 2026-08-04 09:41:19 | 0 | |||||||
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Spliceman Resource Report Resource Website 1+ mentions |
Spliceman (RRID:SCR_005354) | Spliceman | data analysis service, analysis service resource, production service resource, service resource | An online tool that takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation includes 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish. | dna sequence, pre-mrna, splicing, pre-mrna splicing, point mutation, mutation, sequence variation, fasta |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
PMID:22328782 | Free, Non-commercial, Commercial use requires license | OMICS_02259 | SCR_005354 | 2026-08-04 09:41:20 | 5 | |||||||
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BiGG Database Resource Report Resource Website 100+ mentions |
BiGG Database (RRID:SCR_005809) | BiGG | database, data or information resource | A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest. | biochemical, genetics, genomics, genome, metabolic network, reconstruction, model, metabolic pathway, gene, protein, reaction, metabolite, metabolic reconstruction, compound, pathway, FASEB list |
uses: SBML is used by: BiGGR is listed by: 3DVC has parent organization: University of California at San Diego; California; USA |
NIH ; Ruth L. Kirschstein National Research Service Award - NIH Bioinformatics Training ; University of California at San Diego; California; USA ; Calit2 summer research scholarship ; NIGMS GM00806-06 |
PMID:20426874 | nlx_149299, r3d100011567 | https://doi.org/10.17616/R3MG9M | SCR_005809 | BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions, BiGG - a Biochemical Genetic and Genomic knowledgebase | 2026-08-04 09:41:26 | 124 | |||||
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UniPROBE Resource Report Resource Website 100+ mentions |
UniPROBE (RRID:SCR_005803) | UniPROBE | database, data or information resource | Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. | protein, in vitro, dna binding, protein binding, genetics, dna, nucleotide sequence, sequence variant, k-mer, position weight matrix, graphical sequence logo, motif, motif similarity, binding site, microarray, protein-dna interaction, protein binding microarray probe sequence, probe, FASEB list |
is listed by: re3data.org is listed by: OMICtools |
PMID:21037262 PMID:18842628 |
Acknowledgement requested, Academic research use license | nif-0000-03611, OMICS_00546, r3d100010557 | http://thebrain.bwh.harvard.edu/pbms/webworks_pub/, https://doi.org/10.17616/R35C9J | SCR_005803 | UniPROBE Database, Universal Protein Binding Microarray Resource for Oligonucleotide Binding Evaluation, Universal PBM Resource for Oligonucleotide Binding Evaluation | 2026-08-04 09:41:26 | 149 | |||||
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Peptide Sequence Database Resource Report Resource Website |
Peptide Sequence Database (RRID:SCR_005764) | PepSeqDB | database, data or information resource | The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases. | peptide, sequence | has parent organization: Edwards Lab | nlx_149230 | SCR_005764 | 2026-08-04 09:41:26 | 0 | |||||||||
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Recon x Resource Report Resource Website 10+ mentions |
Recon x (RRID:SCR_006345) | Recon x | database, data or information resource | A comprehensive biochemical knowledge-base on human metabolism, this community-driven, consensus metabolic reconstruction integrates metabolic information from five different resources: * Recon 1, a global human metabolic reconstruction (Duarte et al, PNAS, 104(6), 1777-1782, 2007) * EHMN, Edinburgh Human Metabolic Network (Hao et al., BMC Bioinformatics 11, 393, 2010) * HepatoNet1, a liver metabolic reconstruction (Gille et al., Molecular Systems Biology 6, 411, 2010), * Ac/FAO module, an acylcarnitine/fatty acid oxidation module (Sahoo et al., Molecular bioSystems 8, 2545-2558, 2012), * a human small intestinal enterocytes reconstruction (Sahoo and Thiele, submitted). Additionally, more than 370 transport and exchange reactions were added, based on a literature review. Recon 2 is fully semantically annotated (Le Nov��re, N. et al. Nat Biotechnol 23, 1509-1515, 2005) with references to persistent and publicly available chemical and gene databases, unambiguously identifying its components and increasing its applicability for third-party users. Here you can explore the content of the reconstruction by searching/browsing metabolites and reactions. Recon 2 predictive model is available in the Systems Biology Markup Language format. | metabolism, annotation, metabolite, reaction, genome, reconstruction | has parent organization: University of Iceland; Reykjavik; Iceland | Knut and Alice Wallenberg Foundation ; Marie Curie International Reintegration Grant 249261; European Research Council 232816; Rannis research 100406022; Manchester Centre for Integrative Systems Biology BB/C008219/1; Bioprocessing Research Industry Club ; European Union FP7 201142; BBSRC BB/F005938; BBSRC BB/F00561X; DFG 0315756; DFG 0315741; NIGMS GM088244; NSF 0643548; Cystic Fibrosis Research Foundation 1060 |
PMID:23455439 | Free, Acknowledgement requested | nlx_152079 | SCR_006345 | Recon x Reconstruction of The Human Genome, Recon x - Reconstruction of The Human Genome, Recon x: Reconstruction of The Human Genome, Recon 2 | 2026-08-04 09:41:34 | 11 | |||||
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DisGeNET Resource Report Resource Website 1000+ mentions |
DisGeNET (RRID:SCR_006178) | DisGeNET | database, data or information resource | Database and discovery platform containing publicly available collections of genes and variants associated to human diseases. Integrates data from curated repositories, GWAS catalogues, animal models and scientific literature. | gene, disease, gene-disease association, gene-disease ontology, gene-disease text mining, text mining, genotype-phenotype, rdf, genotype, phenotype, gene-disease, variant-disease, FASEB list |
uses: Comparative Toxicogenomics Database (CTD) uses: Genetic Association Database uses: UniProt uses: Mouse Genome Database uses: Reactome uses: Unified Medical Language System uses: Entrez Gene uses: MEDLINE uses: National Center for Biomedical Ontology uses: National Cancer Institute Thesaurus uses: Human Phenotype Ontology uses: Semanticscience Integrated Ontology uses: Cytoscape uses: Literature-derived human gene-disease network uses: Rat Genome Database (RGD) uses: National Library of Medicine uses: PsyGeNET is used by: HmtPhenome is listed by: 3DVC is affiliated with: Gene-Disease Association Type Ontology has parent organization: Pompeu Fabra University; Barcelona; Spain |
EFPIA ; Instituto de Salud Carlos III-Fondo Europeo de Desarrollo Regional ; Elixir-Excelerate ; Innovative Medicines Initiative Joint Undertaking ; European Union Seventh Framework Programme ; European Union Horizon 2020 |
PMID:27924018 PMID:25877637 PMID:21695124 PMID:20861032 |
Restricted | nlx_151710, r3d100013301 | https://doi.org/10.17616/R31NJMR9 | SCR_006178 | database of gene disease associations | 2026-08-04 09:41:32 | 2210 | ||||
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SNPedia Resource Report Resource Website 50+ mentions |
SNPedia (RRID:SCR_006125) | SNPedia | database, data or information resource | Wiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we''''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.php | dna, genetics, gene, genome, genoset, genotype, medicine, medical condition, genetic variation, dna, genetic variation, genomics, single nucleotide polymorphism, medical association, phenotypic association, genealogical association, variation, genome annotation, phenotype, web service, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:22140107 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | biotools:snpedia, grid.465250.0, nlx_151604 | https://ror.org/0253rdk33, https://bio.tools/snpedia | SCR_006125 | 2026-08-04 09:41:30 | 62 | ||||||
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FaceBase Biorepository Resource Report Resource Website 1+ mentions |
FaceBase Biorepository (RRID:SCR_006001) | FaceBase Biorepository | biomaterial supply resource, material resource, tissue bank | THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. FaceBase Biorepository is now collecting biological samples from people with cleft lip/palate and their family members. Information for Prospective Cases: Clefts of the lip and/or palate can be caused by a wide range of genetic, environmental and other factors. The FaceBase Biorepository will serve as a common source of both biological samples and information that can be made available to investigators trying to determine the underlying cause of these common birth defects. Genetic studies, in particular, will benefit from both family history information and having samples from affected individuals as well as their family members. DNA is the information containing molecules found in all the cells of our body and can be easily obtained from material such as blood or saliva samples. As part of the FaceBase Biorepository, we are requesting families to submit biological samples from specific family members as well as information from other family members that might be affected with either the same condition or a similar condition. The medical and family history information that is collected includes other relevant information such as exposure to possible environmental causes during pregnancy. The biorepository is managed by Nichole Nidey, a research study coordinator, and Jeff Murray, a pediatric clinical geneticist and researcher. They are available to speak with family members regarding questions they may have, including providing information about the biorepository and making arrangements for the collection of samples for those who wish to participate. All participation is voluntary. Your name or other personally identifiable information (name, address, etc) will be removed before information is placed in the biorepository. Summary data to show how the database itself has been used overall as well as updates on whether specific findings might have been made using this database will be available on the FaceBase website at www.facebase.org. A newsletter containing this information will also be given to families and referring clinicians so that they may discuss the specifics with the families if there appears to be information that might be relevant in a particular case. Families will also need to sign a consent form that has been approved by the Institutional Review Board at the University of Iowa. Also, any submitted samples or data can also be removed from the database at any time should the family no longer wish to participate. Investigators interested in requesting DNA samples or for more information, please contact cleftresearch (at) uiowa.edu, Nichole Nidey, nichole-nidey (at) uiowa.edu or (319) 353-4365, or Jeff Murray, jeff-murray (at) uiowa.edu. | birth defect, genetic, environment, gene |
is listed by: One Mind Biospecimen Bank Listing has parent organization: FaceBase |
Cleft lip, Cleft palate, Family member, Campomelic Dysplasia, Chromosome Abnormality, Congenital Heart Disease, Facial clefting-Tessier Type 4, Gordon Syndrome, Hemifacial Microsomia, Idiopathic Short Stature, Marshall/Stickler, Microtia, Multiple Congenital Anomaly, Neurofibromatosis, Pierre Robin, Popliteal Pterygium Syndrome, Robinow, Downs syndrome, Townes-Brock Syndrome, Van der Woude Syndrome, Popliteal Pterygium Syndrome, Wildervanck Syndrome | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151379 | SCR_006001 | 2026-08-04 09:41:29 | 1 |
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