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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | data analysis software, data processing software, data visualization software, software application, software resource | Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. | biological, network, visualization, analysis, data, gene, pathway, molecular, interaction, FASEB list |
is used by: CytoSPADE is used by: HDBase is used by: DisGeNET is used by: categoryCompare lists: PEPPER is listed by: Debian is listed by: SoftCite is related to: PhosphoSitePlus: Protein Modification Site is related to: TRIP Database is related to: CoryneRegNet is related to: AltAnalyze - Alternative Splicing Analysis Tool is related to: MiMI Plugin for Cytoscape is related to: Network Data Exchange (NDEx) is related to: GeneMANIA is related to: DroID - Drosophila Interactions Database is related to: Network-based Prediction of Human Tissue-specific Metabolism is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: DaTo is related to: PiNGO is related to: iBIOFind is related to: cPath is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: ClueGO is related to: RamiGO is related to: EGAN: Exploratory Gene Association Networks has parent organization: Institute for Systems Biology; Washington; USA has parent organization: University of California at San Diego; California; USA is parent organization of: JEPETTO has plug in: CluePedia Cytoscape plugin has plug in: CytoSPADE has plug in: EnrichmentMap has plug in: cytoHubba has plug in: iRegulon works with: NetCirChro works with: IMEx - The International Molecular Exchange Consortium works with: yFiles Layout Algorithms works with: RCy3 |
National Resource for Network Biology ; NCRR RR031228; NIGMS GM070743 |
PMID:21149340 PMID:14597658 |
Free, Available for download, Freely available | nif-0000-30404 | https://sources.debian.org/src/cytoscape/ | SCR_003032 | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-09-19 12:50:10 | 25317 | |||||
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i2b2 Cross-Institutional Clinical Translational Research project Resource Report Resource Website |
i2b2 Cross-Institutional Clinical Translational Research project (RRID:SCR_003367) | i2b2CICTR, i2b2-CICTR | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies. | exchange, biomedical, clinical, medical, pilot, retrospective, translational, integration, interoperability, information exchange environment, software network, data sharing, network, federation |
is listed by: Biositemaps is related to: SHRINE has parent organization: Informatics for Integrating Biology and the Bedside has parent organization: University of Washington; Seattle; USA |
NCRR Contract HHSN268200700031C | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33108 | SCR_003367 | 2026-09-19 12:50:18 | 0 | |||||||
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IMOD Resource Report Resource Website 1000+ mentions |
IMOD (RRID:SCR_003297) | IMOD | data processing software, image analysis software, image processing software, software application, software resource, source code | A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X | electron microscopy, magnetic resonance, tomographic reconstruction, reconstruction, segmentation, 3d volume |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
NCRR ; NIGMS ; NIBIB |
PMID:27444392 | Free, Available for download, Freely available | nif-0000-31686 | http://www.nitrc.org/projects/imod | SCR_003297 | IMOD - 3D Reconstruction and Analysis | 2026-09-19 12:50:16 | 1685 | ||||
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Pharmabase - an open content cheminformatics resource linking physiology with pharmacology Resource Report Resource Website |
Pharmabase - an open content cheminformatics resource linking physiology with pharmacology (RRID:SCR_002462) | Pharmabase | data or information resource, database, image collection | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2015. Open content cheminformatics database linking physiology with pharmacology, it targets the action and use of pharmacological compounds in modifying protein function, while revealing molecular relationships and linking out to related databases and sites. Pharmabase has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research. It has several navigational routes, including a graphics browser (shows graphics of cell types and pathways) and membrane transport, which also illustrates the diversity of mechanisms that are covered. Users have access to detailed compound records with interactive features, and a form to send comments to the editor. Investigators are encouraged to alert the editors to mistakes, omissions or new compound information available from their reading and research. | function, cell, compound, graphic, illustration, membrane, molecular, pharmacological, pharmacology, protein, transport, metabolism, intracellular messenger, cell signaling, disease, tissue, cell type, pathway, pharmacology, channel, pump, carriers, protein transporter, membrane transport | has parent organization: BioCurrents Research Center | NCRR P41 RR001395 | PMID:18428760 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21324 | SCR_002462 | 2026-09-19 12:49:59 | 0 | ||||||
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Mouse BIRN Atlasing Toolkit Resource Report Resource Website 1+ mentions |
Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) | MBAT | data processing software, data visualization software, image analysis software, software application, software resource | Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels. | gene expression, microarray, light microscopy, electron microscopy, mri imaging, analyze, gnome, java, kde, magnetic resonance, nifti, os independent, win32 (ms windows), mri, registration, alignment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse Biomedical Informatics Research Network is related to: 3D MRI Atlas of Mouse Development has parent organization: Laboratory of Neuro Imaging |
NCRR U24 RR021760 | PMID:21176225 | Free, Freely available, Available for download | nif-0000-00039 | http://mbat.loni.ucla.edu/ | SCR_002814 | MouseBIRN Atlasing Toolkit | 2026-09-19 12:50:09 | 2 | ||||
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UMMC Center for Psychiatric Neuroscience Labs and Facilities Resource Report Resource Website |
UMMC Center for Psychiatric Neuroscience Labs and Facilities (RRID:SCR_002688) | UMMC CPN Labs & Facilities, UMMC CPN Labs and Facilities | biomaterial supply resource, brain bank, material resource, tissue bank | Core facility that provides access to psychiatrically characterized post-mortem brain specimens, state-of-the-art equipment, cutting-edge technologies and the technical advice of highly trained faculty members who serve as Core Directors. The sophisticated imaging systems and biotechnologically advanced molecular core resources are provided on a shared-use basis to CPN and UMMC researchers. The CPN Research Resources Cores include the Human Brain Collection Core, Animal Core, Imaging Core, Molecular Biology Core, and Information Technologies Core. | postmortem, brain, tissue, imaging, molecular biology, genomics |
is listed by: One Mind Biospecimen Bank Listing is listed by: ScienceExchange is related to: University of Mississippi Medical Center Labs and Facilities is related to: University of Mississippi Medical Center Animal Behavior Core Facility has parent organization: University of Mississippi Medical Center; Mississippi; USA |
Depression, Normal, Mental disease | NCRR | Free | SciEx_8930 | SCR_002688 | CPN Research Resource Cores, University of Mississippi Medical Center Center for Psychiatric Neuroscience, UMMC Center for Psychiatric Neuroscience Research Resource Cores, UMMC Center for Psychiatric Neuroscience Labs & Facilities, UMMC CPN Research Resource Cores | 2026-09-19 12:50:03 | 0 | |||||
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Washington National Primate Research Center Resource Report Resource Website 1+ mentions |
Washington National Primate Research Center (RRID:SCR_002761) | WaNPRC | biomaterial supply resource, material resource, organism supplier | Center that aims to provide an environment to support biomedical research directed towards human health issues and nonhuman primate health and biology. To meet this mission, the WaNPRC supports biomedical research activities, professional research staff, specifically bred and maintained nonhuman primate colonies, and dedicated facilities and equipment required for nonhuman primate research protocols. | aids, clinical, disease, monkey, developmental biology, functional genomics, immunology, reproduction, biology, neurophysiology, infectious disease, transplantation, stem cell, biology, virology, disease model, animal model, neurobiology, neuroscience, systems biology, baboon, long-tailed macaque, rhesus monkey, live animal, macaca nemestrina, macaca fascicularis, macaca mulatta, papio cynocephalus, papio anubis |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Washington; Seattle; USA has parent organization: National Center for Research Resources - Primate Resources is parent organization of: WaNPRC Pathology and Tissue Program |
NCRR ; NIH Office of the Director P51 OD010425; NIH Office of the Director U42 OD011123 |
Free | nif-0000-24361 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | http://www.wanprc.org/WaNPRC/index.php | SCR_002761 | 2026-09-19 12:50:05 | 4 | |||||
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LONI Visualization Tool Resource Report Resource Website |
LONI Visualization Tool (RRID:SCR_000765) | LONI Viz, LONI_Viz, LOVE | data processing software, data visualization software, software application, software resource | A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html | brain, atlas, visualization, gene mapping, atlas application, magnetic resonance, surface analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
Aging | NIA P50 AG16570; NLM 2R01 LM05639-06; NIA K08 AG100784; NCRR 2 P41 RR13642; NIMH 5 P01 MN52176; NSF DUE 0442992; NCRR U52 RR021813 |
PMID:16598642 | Free, Available for download, Freely available | nif-0000-23313 | http://www.nitrc.org/projects/incf_loni-viz | http://www.loni.ucla.edu/Software/LOVE | SCR_000765 | LONI Visualization Environment, LONI Viz environment, LOVE | 2026-09-19 12:49:29 | 0 | ||
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LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | data processing software, software application, software resource, workflow software | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-09-19 12:49:35 | 11 | |||
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Insight Segmentation and Registration Toolkit Resource Report Resource Website 50+ mentions |
Insight Segmentation and Registration Toolkit (RRID:SCR_001149) | ITK | data or information resource, portal, software resource, topical portal | Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. | registration, segmentation, multidimension, image processing, reusable library, analyze, bshort/bfloat, c++, console (text based), dicom, java, minc2, nifti, nrrd, os independent, philips par/rec, python, tcl/tk |
uses: Laplace Beltrami Filter on QuadEdge Meshes uses: VTK is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is used by: Displacement Field Viewer is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Vaa3D is related to: elastix is related to: VMTK in 3D Slicer is related to: NA-MIC Kit is related to: SimpleITK |
NIBIB EB006733; NIBIB EB008374; NIBIB EB009634; NCRR P41RR013218 |
Free, Available for download, Freely available | nif-0000-00319 | http://www.nitrc.org/projects/insighttoolkit | SCR_001149 | Insight Toolkit, National Library of Medicine Insight Segmentation and Registration Toolkit (ITK), Insight Segmentation and Registration Toolkit | 2026-09-19 12:49:35 | 84 | |||||
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Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | data analysis software, data processing software, software application, software resource | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NCRR P41 RR011823; NHLBI R01 HL082747; NIA P30 AG013280; NIDDK R01 DK069386 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-09-19 12:52:51 | 3040 | ||||||||
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Laplace Beltrami Filter on QuadEdge Meshes Resource Report Resource Website |
Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) | data acquisition software, data processing software, software application, software resource | A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface. | data acquisition software, filter, laplace beltrami, surface harmonic |
is used by: Insight Segmentation and Registration Toolkit is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
NIBIB R01-EB008171-01A1; NCRR P41-RR015241 |
Available to the research community | SCR_014133 | Laplace-Beltrami Filter on QuadEdge Meshes | 2026-09-19 12:52:52 | 0 | ||||||||
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Wisconsin National Primate Research Center Resource Report Resource Website 1+ mentions |
Wisconsin National Primate Research Center (RRID:SCR_012987) | WNPRC | data or information resource, portal, service resource, topical portal | Research center aimed towards increasing understanding of basic primate biology and improving human health and quality of life. Its goals include helping discover treatments, preventative measures and cures for human disease; gathering knowledge of primate biology and ecosystems; providing resources to scientists world wide; and collecting and disseminating research to the larger scientific community and public. | NPRC, NPRC Consortium, ORIP, ecosystem, embryonic, fertility, fetal, gene, animal, ctl, development, differentiation, disease, hiv, immunodeficiency, immunogenetic, medicine, metabolic, molecular, neuroendocrinology, obesity, ocular, ovarian, parkinson's disease, polycystic, presbyopia, primate, reproduction, restriction, stem cell, t-cell, vaccine, virology, virus, caloric restriction, obesity, diabetes mellitus, osteoporosis, ocular aging, glaucoma, neurodegeneration, gene expression profiling, simian immunodeficiency virus, cytotoxic t cell, embryonic stem cell, fertility regulation, embryonic differentiation, maternal-fetal health, reproductive neuroendocrinology, polycystic ovarian syndrome, endometriosis, reproductive tract, gene therapy |
is listed by: Biositemaps is listed by: National Primate Research Center Consortium is related to: NIA Nonhuman Primate Tissue Bank has parent organization: University of Wisconsin-Madison; Wisconsin; USA is parent organization of: Primate Info Net is parent organization of: Wisconsin National Primate Research Center Pathology Services Core Facility |
Aging | NCRR RR000167; NIH Office of the Director P51 OD011106 |
Available to the research community | nif-0000-24362 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | SCR_012987 | 2026-09-19 12:52:36 | 3 | |||||
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Resource Discovery System Resource Report Resource Website |
Resource Discovery System (RRID:SCR_005554) | RDS | data or information resource, database | Resource Discovery System is a web-accessible and searchable inventory of biomedical research resources. Powered by the Resource Discovery System (RDS) that includes a standards-based informatics infrastructure * Biositemaps Information Model * Biomedical Resource Ontology Extensions * Web Services distributed web-accessible inventory framework * Biositemap Resource Editor * Resource Discovery System Source code and project documentation to be made available on an open-source basis. Contributing institutions: University of Pittsburgh, University of Michigan, Stanford University, Oregon Health & Science University, University of Texas Houston. Duke University, Emory University, University of California Davis, University of California San Diego, National Institutes of Health, Inventory Resources Working Group Members | registry, web service, source code, biomedical, software resource, material resource, funding resource, service resource, training resource, people resource | has parent organization: Biositemaps | Clinical and Translational Science Awards Consortium ; National Centers for Biomedical Computing ; NCRR 3UL1RR024153-03S1; NCRR 5UL1RR024128-03S1; NCRR 1UL1RR025008-01; NCRR 1UL1RR024146-01; NCRR 1UL1RR024986-01; NCRR 1UL1RR024153-01; NIDA 3U54DA021519-04S1; NHGRI 3U54HG004028-04S |
nlx_144645 | SCR_005554 | 2026-09-19 12:56:52 | 0 | ||||||||
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Recombinase (cre) Activity Resource Report Resource Website 10+ mentions |
Recombinase (cre) Activity (RRID:SCR_006585) | Recombinase Activity | data or information resource, database | Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies. | cre, recombinase, transgene, knock-in, allele, expression, activity pattern, mutagenesis, promoter, driver, image, tissue, specificity assay |
is related to: International Mouse Strain Resource is related to: CREATE is related to: JAX Cre Repository is related to: Allen Institute for Brain Science is related to: CRE Driver Network is related to: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders is related to: EUCOMMTOOLS has parent organization: Mouse Genome Informatics (MGI) |
European Union HEALTH-F4-2009-223487; NCRR RR03 2656; NICHD HD062499 |
SCR_017520, nlx_152803 | http://www.creportal.org/ | SCR_006585 | Cre Portal | 2026-09-19 12:56:59 | 22 | ||||||
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SHRINE Resource Report Resource Website 1+ mentions |
SHRINE (RRID:SCR_006293) | SHRINE | software application, software resource, source code | Software providing a scalable query and aggregation mechanism that enables federated queries across many independently operated patient databases. This platform enables clinical researchers to solve the problem of identifying sufficient numbers of patients to include in their studies by querying across distributed hospital electronic medical record systems. Through the use of a federated network protocol, SHRINE allows investigators to see limited data about patients meeting their study criteria without compromising patient privacy. This software should greatly enable population-based research, assessment of potential clinical trials cohorts, and hypothesis formation for followup study by combining the EHR assets across the hospital system. In order to obtain the maximum number of cases representing the study population, it is useful to aggregate patient facts across as many sites as possible. Cutting across institutional boundaries necessitates that each hospital IRB remain in control, and that their local authority is recognized for each and every request for patient data. The independence, ownership, and legal responsibilities of hospitals predetermines a decentralized technical approach, such as a federated query over locally controlled databases. The application comes with the SHRINE Core Ontology but it can be used with any ontology, even one that is disease specific. The Core Ontology is designed to enable the widest range of studies possible using facts gathered in the EMR during routine patient care. SHRINE allows multiple ontologies to be used for different research purposes on the same installed systems. | software network, clinical database, data sharing, clinical, medical record, federated, platform, network |
is related to: i2b2 Cross-Institutional Clinical Translational Research project is related to: i2b2 Research Data Warehouse has parent organization: Harvard Medical School; Massachusetts; USA |
Informatics for Integrating Biology and the Bedside ; NLM 5 U54 LM008748; NCRR 1 UL1 RR025758-01 |
PMID:19567788 | Available under a BSD3 Open unspecified license Software license. | nlx_151949 | SCR_006293 | Shared Health Research Informatics NEtwork | 2026-09-19 12:56:57 | 8 | |||||
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Wake Forest Cynomolgus Breeding Colony Resource Report Resource Website |
Wake Forest Cynomolgus Breeding Colony (RRID:SCR_006605) | CBC, WFU CBC | biomaterial supply resource, material resource, tissue bank | The Wake Forest Cynomolgus Breeding Colony (CBC) is a colony of cynomolgus macaques (crab-eating macaques, Macaca fascicularis). The cynomolgus colony is designed to produce specific pathogen free (SPF) cynomolgus monkeys for use in biomedical research. The colony, supported by a grant from the NCRR, addresses the growing need for investigators to use in their protocols animals defined for the absence of specific diseases including CHV-1 (Herpes B), simian immunodeficiency virus, and simian retroviruses. An additional important characteristic of this colony is that, unlike many breeding colonies, the NHPs will be fed two defined diets. The first diet is a soy-free diet, not commercial monkey chow. The second diet has the same macronutrients but the protein source is from soy; similar in isoflavone content. A drawback of chow diets is that the exact nutritional product composition is unknown from lot to lot. However, they are always rich in soy bean meal, isoflavones and other constituents of soy bean meal that are known confounders of several types of research projects. All research using the cynomolgus colony must be reviewed and approved by the colony''s scientific board and the Wake Forest Animal Care and Use Committee (ACUC) before any work can be initiated. The scientific board meets regularly to assess the scientific value of each request and to determine whether or not animals/samples/data can be made available. This includes all requests for: # The purchase of animals for use outside the colony # The use of animals within the colony for the collection of blood/tissue samples, behavioral observations or other kinds of testing # The use of the CBC sample/tissue repository # The use of the CBC data repository | long-tailed macaque, non-human primate, blood, tissue, macaca fascicularis, animal model |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Wake Forest Primate Center |
Macaca fascicularis | NCRR | Public | nlx_146209 | SCR_006605 | WFU Cynomolgus Breeding Colony, Cynomolgus Breeding Colony | 2026-09-19 12:56:59 | 0 | |||||
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lapdftext Resource Report Resource Website |
lapdftext (RRID:SCR_006167) | lapdftext, LA-PDFText, | software application, software resource, text extraction software | Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise. | text mining, pdf, text extraction, natural language processing |
is listed by: FORCE11 has parent organization: University of Southern California; Los Angeles; USA |
NSF 0849977; NIGMS RO1-GM083871; NIMH 1R01MH079068-01A2; NCRR U24 RR025736-01 |
PMID:22640904 | Acknowledgement requested, GNU General Public License, v3 | nlx_151668 | SCR_006167 | Layout-Aware PDF Text Extraction, Layout-Aware Text Extraction from Full-text PDF of Scientific Articles, lapdftext: Layout-Aware Text Extraction from Full-text PDF of Scientific Articles | 2026-09-19 12:56:56 | 0 | |||||
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Homophila Resource Report Resource Website |
Homophila (RRID:SCR_007717) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 23, 2013. Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions. | homolog, human disease, human disease gene, human, gene, cognate |
is related to: OMIM has parent organization: University of California at San Diego; California; USA |
NCRR P 41 RR08605-06 | PMID:11752278 PMID:11381037 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02976 | SCR_007717 | Human disease to drosophila database | 2026-09-19 12:57:08 | 0 | ||||||
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Alternative Splicing Annotation Project II Database Resource Report Resource Website 1+ mentions |
Alternative Splicing Annotation Project II Database (RRID:SCR_000322) | ASAP II | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. An expanded version of the Alternative Splicing Annotation Project (ASAP) database with a new interface and integration of comparative features using UCSC BLASTZ multiple alignments. It supports 9 vertebrate species, 4 insects, and nematodes, and provides with extensive alternative splicing analysis and their splicing variants. As for human alternative splicing data, newly added EST libraries were classified and included into previous tissue and cancer classification, and lists of tissue and cancer (normal) specific alternatively spliced genes are re-calculated and updated. They have created a novel orthologous exon and intron databases and their splice variants based on multiple alignment among several species. These orthologous exon and intron database can give more comprehensive homologous gene information than protein similarity based method. Furthermore, splice junction and exon identity among species can be valuable resources to elucidate species-specific genes. ASAP II database can be easily integrated with pygr (unpublished, the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc. ASAP II can be searched by several different criteria such as gene symbol, gene name and ID (UniGene, GenBank etc.). The web interface provides 7 different kinds of views: (I) user query, UniGene annotation, orthologous genes and genome browsers; (II) genome alignment; (III) exons and orthologous exons; (IV) introns and orthologous introns; (V) alternative splicing; (IV) isoform and protein sequences; (VII) tissue and cancer vs. normal specificity. ASAP II shows genome alignments of isoforms, exons, and introns in UCSC-like genome browser. All alternative splicing relationships with supporting evidence information, types of alternative splicing patterns, and inclusion rate for skipped exons are listed in separate tables. Users can also search human data for tissue- and cancer-specific splice forms at the bottom of the gene summary page. The p-values for tissue-specificity as log-odds (LOD) scores, and highlight the results for LOD >= 3 and at least 3 EST sequences are all also reported. | exon, gene structure, genome, alternative splicing, cancer genome alignment, intron, isoform, orthologous exon, orthologous gene, orthologous intron, protein sequence, splice site, tissue, genome alignment, cancer |
is related to: ASAP: the Alternative Splicing Annotation Project has parent organization: University of California at Los Angeles; California; USA |
NCRR U54 RR021813; NIDCR DE-FC02-02ER63421 |
PMID:17108355 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02572 | SCR_000322 | ASAP II Database, Alternative Splicing Annotation Project II | 2026-09-19 12:56:25 | 2 |
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