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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | data processing software, software application, software resource, data analysis software | Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq. | automate, cell, type, identification, pathway, analysis, gene, regulation, autocrine, paracrine, signaling, network, human, islet, scRNA-seq, dataset | NIDDK R24 DK096518; NHLBI R24 HL123482; NIDDK R01 DK115791; Fraternal Order of Eagles Diabetes Research Center ; University of Iowa Center for Gene Therapy ; Carver Chair in Molecular Medicine ; NIGMS T32 GM082729 |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-08-04 09:44:02 | 5 | |||||||||
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ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 1+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | portal, catalog, project portal, database, data or information resource | International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIH ; NIDDK |
SCR_016921 | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-08-04 09:44:01 | 9 | ||||||||
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Italian Institute for Genomic Medicine; Turin; Italy Resource Report Resource Website |
Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) | IIGM, HuGeF | topical portal, portal, data or information resource | Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience. | institute, private, research, human, genetic, genomic, epigenomic, immunogenetic, quantitative, biology, computational, neuroscience | is parent organization of: HaTSPiL | SCR_017062 | 2026-08-04 09:44:03 | 0 | ||||||||||
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Data Archive BRAIN Initiative Resource Report Resource Website 10+ mentions |
Data Archive BRAIN Initiative (RRID:SCR_017114) | DABI | storage service resource, data repository, data or information resource, service resource | Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves. | shared, archive, human, invasive, neurophysiology, data, brain, neurotechnology, dataset, BRAIN Initiative |
is recommended by: National Library of Medicine is recommended by: BRAIN Initiative has parent organization: University of Southern California; Los Angeles; USA has parent organization: BRAIN Initiative |
BRAIN Initiative | Restricted | SCR_017114 | Data Archive Brain Initiative, DABI | 2026-08-04 09:44:05 | 14 | |||||||
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SPARC Portal Resource Report Resource Website 100+ mentions |
SPARC Portal (RRID:SCR_017041) | SPARC.science | storage service resource, data repository, service resource | SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short. | Nervous system, periphery, organ, human, FASEB list, repository, curated |
uses: Protocols.io uses: Brain Imaging Data Structure (BIDs) uses: Physiome Model Repository uses: SciGraph uses: o²S²PARC uses: SODA uses: Blackfynn Discover uses: ApiNATOMY uses: Biolucida uses: TissueMaker uses: ScaffoldMaker uses: ScaffoldFitter uses: OpenCOR uses: Pennsieve Data Management Platform uses: InterLex uses: Neurolucida 360 uses: SciCrunch uses: Tissue Mapper uses: Vesselucida 360 uses: DataCite uses: TissueMaker is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is recommended by: National Library of Medicine is related to: SPARC Anatomy Working Group is related to: HORNET CENTER FOR AUTONOMIC NERVE RECORDING AND STIMULATION SYSTEMS is related to: NIH PRECISION Human Pain Network is related to: SCKAN Explorer is related to: SCKANNER works with: SPARC Data Standard has organization facet: o²S²PARC has organization facet: SODA has organization facet: SPARC Anatomy Working Group has organization facet: Blackfynn Discover has organization facet: ApiNATOMY has organization facet: Pennsieve Data Management Platform |
NIH Office of the Director OD025349; NIH Office of the Director OD030213; NIH Office of the Director OD032619; NIH Office of the Director OD030541; NIH Office of the Director OD026585; NIH Office of the Director OD024908; NIH Office of the Director OD025306; NIH Office of the Director OD023849 |
PMID:34248680 DOI:10.1101/2021.02.10.430563 |
Free, Freely available, | DOI:10.26275, r3d100013719 | https://commonfund.nih.gov/sparc, https://docs.sparc.science/, https://data.sparc.science/, https://doi.org/10.26275, https://doi.dx/10.26275, https://sparc.science/data?type=dataset, https://doi.org/10.17616/R31NJN2V | SCR_017041 | , SPARC Project, SPARC Repository, Stimulating Peripheral Activity to Relieve Conditions | 2026-08-04 09:44:03 | 115 | ||||
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-08-04 09:44:09 | 7 | ||||||||
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TissueAtlas Resource Report Resource Website 10+ mentions |
TissueAtlas (RRID:SCR_017352) | web service, software resource, data access protocol, atlas, database, data or information resource | Human miRNA tissue atlas. Database showing distribution of miRNA expression across human tissues. | Human, miRNA, tissue, atlas, data, distribution, expression | has parent organization: Saarland University; Saarbrucken; Germany | Saarland University ; Germany ; Siemens Healthcare ; FP7 project BestAgeing |
PMID:26921406 | Free, Freely available | SCR_017352 | 2026-08-04 09:44:07 | 29 | ||||||||
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Neuromorphometrics Resource Report Resource Website 100+ mentions |
Neuromorphometrics (RRID:SCR_005656) | Neuromorphometrics Inc. | portal, software resource, organization portal, service resource, web application, data or information resource | Neuromorphometrics provides brain labeling and measurement services. Given raw MRI brain scans, we make precise quantitative measurements of the volume, shape, and location of specific neuroanatomical structures. Web tool for brain measurement services. Used for modeling living human brain and make quantitative measurements of volume, shape, and location of specific neuroanatomical structures using given MRI brain scans. Automated analyses are manually guided, inspected and certified by a neuroanatomical expert. Resource of neuroanatomically labeled MRI brain scans database. Resource for neuroanatomical localization and identification: NeuAtlas. | brain, human, modeling, measurement, quantitative, volume, shape, location, neuroanatomical, structure, MRI, scan, analysis, database, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainColor: Collaborative Open Labeling Online Resource is related to: 2012 MICCAI Multi-Atlas Labeling Challenge Data is parent organization of: NVM is parent organization of: Manually Labeled MRI Brain Scan Database is parent organization of: MRI Neuroanatomy Labeling Services |
NIMH R43 MH084358 | Free Demo available for download, Commercially available, Discount for academic use available | SCR_014141, nlx_149079 | http://www.nitrc.org/projects/brain_labeling | SCR_005656 | MRI Brain Anatomy Labeling Services, Quantitative Measurements in MR Brain Images | 2026-08-04 09:41:24 | 363 | |||||
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ChemHealthWeb Resource Report Resource Website |
ChemHealthWeb (RRID:SCR_005851) | ChemHealthWeb | portal, video resource, topical portal, training material, narrative resource, data or information resource | Visit ChemHealthWeb for research highlights, chemist profiles, games and videos and other Web extras. The NIGMS Chemistry of Health booklet describes basic chemistry and biochemistry research that spurs a better understanding of human health. | chemistry, health, chemistry, biochemistry, research, human, game, puzzle, chemist, molecule, medicine, teacher | has parent organization: National Institute of General Medical Sciences | NIGMS | nlx_149382 | SCR_005851 | 2026-08-04 09:41:28 | 0 | ||||||||
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BrainSuite Resource Report Resource Website 50+ mentions |
BrainSuite (RRID:SCR_006623) | BrainSuite | data processing software, software resource, software application, image analysis software, data visualization software | Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction | brain, magnetic resonance, image, analysis, human, topology, segmentation, visualization, cortex, cortical, mri, tissue classification, topological correction, rendering, edit, cortical surface |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network |
NIBIB R01 EB002010; NCRR P41 RR013642; NIMH RO1-MH53213 |
PMID:12045000 | nif-0000-30214 | http://www.nitrc.org/projects/brainsuite | SCR_006623 | Brain Suite | 2026-08-04 09:41:39 | 93 | |||||
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MITRE Neuroinformatics Resource Report Resource Website |
MITRE Neuroinformatics (RRID:SCR_006508) | MITRE Neuroinfomatics | simulation software, data processing software, data analysis software, data distribution software, software resource, software application, data transfer software, data visualization software | This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality. | brain, data, diffusion tensor image, distorted, human, imagery, image, informatics, investigator, laboratory, magnetic resonance image, mapping, neuroscience, structural, visualization, neuroimaging | Human Brain Project ; MITRE Technology Program ; NSF ; NIMH R01-MH64417 |
nif-0000-10469 | http://neuroinformatics.mitre.org/ | SCR_006508 | Neuroinfomatics at MITRE, Neuroinformatics: Exploring the Human Brain | 2026-08-04 09:41:38 | 0 | |||||||
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Rat Genome Database (RGD) Resource Report Resource Website 100+ mentions |
Rat Genome Database (RGD) (RRID:SCR_006444) | RGD | storage service resource, data repository, service resource, database, data or information resource | Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources. | RIN, Resource Information Network, mouse, rat, human, gene, qtl, marker, map, strain, sequence, est, genome, ontology, pathway, comparative genomics, physiology, phenotype, disease, model organism, proteomics, function, genetic, genomic, variation, immunology, behavior, knockout, inbred rat strain, mutant, congenic rat, recombinant inbred rat, data analysis service, organism supplier, genotype, gold standard, FASEB list, RRID Community Authority |
uses: InterMOD is used by: ChannelPedia is used by: Resource Identification Portal is used by: DisGeNET is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is listed by: re3data.org is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: Rat Gene Symbol Tracker is related to: MPO is related to: NIF Data Federation is related to: MONARCH Initiative is related to: Vertebrate Trait Ontology is related to: Biositemaps is related to: One Mind Biospecimen Bank Listing is related to: AmiGO is related to: OMICtools is related to: re3data.org is related to: Integrated Manually Extracted Annotation is related to: OntoMate has parent organization: Medical College of Wisconsin; Wisconsin; USA is parent organization of: Diabetes Disease Portal is parent organization of: Rat Strain Ontology is parent organization of: Rat Strain Ontology is parent organization of: Renal Disease Portal is organization facet of: Alliance of Genome Resources |
NHLBI | PMID:23434633 PMID:18996890 PMID:17151068 |
Free, Freely available | nif-0000-00134, r3d100010417, OMICS_01660 | https://doi.org/10.17616/R3WK60 | SCR_006444 | , Rat Genome Database, RGD | 2026-08-04 09:41:35 | 272 | ||||
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Office of Behavioral and Social Sciences Research Resource Report Resource Website 1+ mentions |
Office of Behavioral and Social Sciences Research (RRID:SCR_006554) | OBSSR, NIH/OBSSR | portal, organization portal, data or information resource, funding resource | An NIH office devoted to the study of the role of behavioral and social factors in illness and health. Its mission is to stimulate behavioral and social sciences research throughout NIH and to integrate these areas of research more fully into others of the NIH health research enterprise, thereby improving our understanding, treatment, and prevention of disease. To provide the OBSSR with counsel in fulfilling its mission, the Behavioral and Social Sciences Research Coordinating Committee (BSSR CC) serves as an internal advisory board. The Office of Behavioral and Social Sciences Research (OBSSR) opened officially on July 1, 1995. The major responsibilities of the office and its director, set forth in its formal mission statement, are: * To provide leadership and direction in the development, refinement, and implementation of a trans-NIH plan to increase the scope of and support for behavioral and social sciences research. * To inform and advise the NIH director and other key officials of trends and developments having significant bearing on the missions of the NIH, DHHS, and other federal agencies. * To serve as the principal NIH spokesperson regarding research on the importance of behavioral, social, and lifestyle factors in the causation, treatment, and prevention of diseases; and to advise and consult on these topics with NIH scientists and others within and outside the federal government. * To develop a standard definition of behavioral and social sciences research, assess the current levels of NIH support for this research, and develop an overall strategy for the uniform expansion and integration * of these disciplines across NIH institutes and centers. * To develop initiatives designed to stimulate research in the behavioral and social sciences arena, integrate a bio-behavioral perspective across the research areas of the NIH, and encourage the study of behavioral and social sciences across NIH''s institutes and centers. * To initiate and promote studies to evaluate the contributions of behavioral, social, and lifestyle determinants in the development, course, treatment, and prevention of illness and related public health problems. * To provide leadership in ensuring that findings from behavioral and social sciences research are disseminated to the public. * To sponsor seminars, symposia, workshops, and conferences at the NIH and at national and international scientific meetings on state-of-the-art behavioral and social sciences research. Funding Opportunities Announcements (FOA) Since opening its doors in 1995, The Office of Behavioral and Social Sciences Research (OBSSR) has worked to achieve the goals of its authorizing legislation by effectively highlighting and supporting the scientific opportunities that exist in basic and applied behavioral and social sciences research. Guided by its Strategic Plan, OBSSR has been working actively with its IC partners to develop funding opportunities in the behavioral and social sciences. Although OBSSR does not have grant-making authority, it has been active in organizing and funding (through transfers to NIH Institutes and Centers) a variety of trans-NIH research programs. Scientific Areas The Office of Behavioral and Social Sciences Researchs (OBSSR) leadership is crucial at a time when exciting scientific opportunities, persistent public health needs, and emergent public health challenges face our nation. The vision of the office is to bring together the biomedical, behavioral, and social science communities to work more collaboratively to solve complex pressing health challenges. Notable areas of research where OBSSR has led efforts and encourages research include: * Biopsychosocial Interactions * Methodology (including Systems Science and CBPR) * Genes, Behavior and Environment * Social and Cultural Factors in Health * Health and Behavior * Translation OBSSR Training & Education Opportunities The Office of Behavioral and Social Sciences Research (OBSSR) develops and coordinates training and career development opportunities with the NIH Institutes and Centers. | educational material, educational opportunity, events, behavioral, career development, disease, health, human, illness, journal articles, news, prevention, publications, public health, research, social factors, social sciences, treatment, meeting |
has parent organization: NIH Blueprint for Neuroscience Research has parent organization: National Institutes of Health is parent organization of: e-Source: Behavioral and Social Sciences Research |
nif-0000-22618 | SCR_006554 | NIH OBSSR, NIH Office of Behavioral Social Sciences Research, Office of Behavioral Social Sciences Research | 2026-08-04 09:41:39 | 1 | ||||||||
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BrainVoyager Brain Tutor Resource Report Resource Website 1+ mentions |
BrainVoyager Brain Tutor (RRID:SCR_006737) | BV Brain Tutor | software resource, training material, software application, narrative resource, data or information resource | A free award-winning educational program that teaches you knowledge about the human brain through interactive exploration of rotatable 3D models. The models have been computed with BrainVoyager QX using original data from magnetic resonance imaging (MRI) scans. Besides having fun with the rotatable 3D models, the program contains information about the major lobes, gyri, sulci and Brodmann areas of the cerebral cortex. The program runs on Windows XP, Vista and Windows 7. | atlas, brain, cerebral cortex, lobe of cerebral cortex, brodmann partition scheme region, functional area, human, magnetic resonance imaging assay, mri, 3d model, c++, macos, microsoft, magnetic resonance, software, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVoyager has parent organization: Brain Innovation: Home of the BrainVoyager Product Family |
Free | nlx_144322 | http://www.nitrc.org/projects/bvbraintutor, http://www.brainvoyager.com/BrainTutor.html | SCR_006737 | 2026-08-04 09:41:39 | 2 | |||||||
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Hazardous Substances Data Bank Resource Report Resource Website 10+ mentions |
Hazardous Substances Data Bank (RRID:SCR_002374) | HSDB | database, data or information resource | A toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel. | emergency handling, environment, exposure, analytical, chemical, hazardous, human, hygiene, industrial, methodology, pharmacology, regulation, regulatory, substance, toxicology, toxicology database, transformation | has parent organization: National Library of Medicine | PMID:15138039 PMID:14728459 PMID:11164971 PMID:10164468 PMID:8545846 |
nif-0000-21201, r3d100011209 | https://doi.org/10.17616/R3BD01 | SCR_002374 | Hazardous Substances DataBank, HSDB - A TOXNET DATABASE | 2026-08-04 09:40:37 | 10 | ||||||
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NHGRI Dog Genome Project Resource Report Resource Website 1+ mentions |
NHGRI Dog Genome Project (RRID:SCR_002256) | NHGRI Dog Genome Project | database, data or information resource | The Dog Genome Project at the National Human Genome Research Institute is working to develop resources necessary to map and clone canine genes in an effort to utilize dogs as a model system for genetics and cancer research. The US National Human Genome Research Institute (NHGRI) agreed to fund a project to sequence the entire genome of a boxer dog named Tasha, because it recognized the value of the dog as an unrivaled model for the study of human disease. The National Human Genome Research Institute (NHGRI) led the National Institutes of Health's (NIH) contribution to the International Human Genome Project, which had as its primary goal the sequencing of the human genome. This project was successfully completed in April 2003. Now, the NHGRI's mission has expanded to encompass a broad range of studies aimed at understanding the structure and function of the human genome and its role in health and disease. To that end NHGRI supports the development of resources and technology that will accelerate genome research and its application to human health. A critical part of the NHGRI mission continues to be the study of the ethical, legal and social implications (ELSI) of genome research. NHGRI also supports the training of investigators and the dissemination of genome information to the public and to health professionals. | gene, genetic, cancer, canine, clone, disease, dog, genome, health, human, map, model, system | PMID:16102268 | nif-0000-20975 | SCR_002256 | National Human Genome Research Institute Dog Genome Project | 2026-08-04 09:40:36 | 1 | ||||||||
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Database of Transcribed Sequences Resource Report Resource Website 10+ mentions |
Database of Transcribed Sequences (RRID:SCR_002334) | database, data or information resource | DoTS (Database Of Transcribed Sequences) is a human and mouse transcript index created from all publicly available transcript sequences. The input sequences are clustered and assembled to form the DoTS Consensus Transcripts that comprise the index. These transcripts are assigned stable identifiers of the form DT.123456 (and are often referred to as dots). The transcripts are in turn clustered to form putative DoTS Genes. These are assigned stable identifiers of the form DG.1234356. As of September 1, 2004, the DoTS annotation team has manually annotated 43,164 human and 78,054 mouse DoTS Transcripts (DTs), corresponding to 3,939 human and 7,752 mouse DoTS Genes (DGs). Use the manually annotated gene query to see the DoTS Transcripts that have been manually annotated. The focus of the DoTS project is integrating the various types of data (e.g., EST sequences, genomic sequence, expression data, functional annotation) in a structured manner which facilitates sophisticated queries that are otherwise not easy to perform. DoTS is built on the GUS Platform which includes a relational database that uses controlled vocabularies and ontologies to ensure that biologically meaningful queries can be posed in a uniform fashion. An easy way to start using the site is to search for DoTS Transcripts using an existing cDNA or mRNA sequence. Click on the BLAST tab at the top of the page and enter your sequence in the form provided. All the transcripts with significant sequence similarity to your query sequence will be displayed. Or use one of the provided queries to retrieve transcripts using a number of criteria. These queries are listed on the query page, which can also be reached by clicking on the tab marked query at the top of the page. Finally, the boolean query page allows these queries to be combined in a variety of ways. Sponsors: Funding provided by -NIH grant RO1-HG-01539-03 -DOE grant DE-FG02-00ER62893 | expression, functional, gene, annotation, biological, cdna, genomic, human, index, model organisms and comparative genomics databases, mouse, mrna, sequence, structure, transcribed, transcript | has parent organization: University of Pennsylvania; Philadelphia; USA | nif-0000-21125 | SCR_002334 | DoTs | 2026-08-04 09:40:37 | 15 | |||||||||
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IPI Resource Report Resource Website 50+ mentions |
IPI (RRID:SCR_003012) | IPI | database, data or information resource | IPI provides a top level guide to the main databases (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, RefSeq, Ensembl, TAIR, H-InvDB, Vega) that describe the proteomes of higher eukaryotic organisms. IPI: :1. effectively maintains a database of cross references between the primary data sources :2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) :3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. As previously announced, the closure of IPI has been proposed for some time. Replacement data sets are now available through UniProt for human and mouse; sets for the other species contained within IPI are expected to be included as part of the UniProt release 2011_07. To allow users time to transition to using the new UniProt data sets, IPI releases will continue to be produced throughout the summer. The final release will be made in September 2011. Thereafter, the IPI website will cease to be maintained, although previous releases of the dataset will continue to be available from the FTP site. We would like to thank our users for their support and interest in this service. | human, mouse, rat, zebrafish, arabidopsis, chicken, cow, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProt DAS has parent organization: European Bioinformatics Institute works with: PremierBiosoft Proteo IQ Software |
PMID:15221759 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ipi, nif-0000-03043 | https://bio.tools/ipi | SCR_003012 | International Protein Index, IPI - International Protein Index | 2026-08-04 09:40:47 | 76 | |||||
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Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | database, data or information resource, service resource | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-08-04 09:40:55 | 0 | ||||||
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Biobanque de Picardie Resource Report Resource Website |
Biobanque de Picardie (RRID:SCR_004731) | biomaterial supply resource, material resource, tissue bank | A secure repository of biological samples and data dedicated for medical and research purposes. These biological samples are linked to consenting patient relative data. Biobanque de Picardie provides quality and traceability services for establishment, conservation and use of biological samples collections. It houses collections of human tissue in a variety of areas of disease. Samples are used in basic research and translational studies, physiopathology of diseases and identification of new diagnostic, and as prognostic or therapeutic biomarkers. Biobanque de Picardie also develops healthy or pathological human primary stem cell banks, such as: mesenchymal stem cells in umbilical cord (HUC-MSC), primary hepatocytes (HPH), peripheral blood mononuclear cells (PBMC), and fibroblasts. Biological samples are stored at - 80 degrees C in electric freezers, at - 196 degrees C in liquid nitrogen or -130 degrees C in nitrogen vapor. | tissue, stem cell, mesenchymal stem cell, fibroblast, frozen, liquid nitrogen, cryopreserved, fresh, normal control, internal medicine, pediatrics, biobank, human |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Picardie Jules Verne; Amiens; France |
Anti-phospholipid antibody syndrome, Ovarian cancer, Hepathocellular carcinoma, Chlamydia, Acute alcoholic hepatitis, Hepatitis B, Hepatitis C, HT 21, Celiac disease, Crohn's disease, Ulcerative colitis, Giant cell arteritis, Blood disorder, Leukemia, Mastocytosis, Lymphoma, Myeloma, Obesity, Acute Pancreatitis, Rheumatoid arthritis, Kidney transplant, Human immunodeficiency virus | French Ministry of Research ; FEDER |
For the scientific community | nlx_73857 | http://www.biobanque-picardie.com/indexang.htm | SCR_004731 | 2026-08-04 09:41:12 | 0 |
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