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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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UCL Motor Control Group Resource Report Resource Website 1+ mentions |
UCL Motor Control Group (RRID:SCR_005271) | Motor Control Group | data or information resource, topical portal, portal | Using robotic devices to investigate human motor behavior, this group develops computational models to understand the underlying control and learning processes. By simulating novel objects or dynamic environments they study how the brain recalibrates well-learned motor skills or acquires new ones. These insights are used to design fMRI studies to investigate how these processes map onto the brain. They have developed a number of novel techniques of how to study motor control in the MRI environment, and how to analyze MRI data of the human cerebellum. They also study patients with stroke or neurological disease to further determine how the brain manages to control the body. | motor cortex, motor control, brain, human, neurological disease, stroke, fmri, cerebellum, mri |
has parent organization: University College London; London; United Kingdom is parent organization of: Spatially unbiased atlas template of the cerebellum and brainstem is parent organization of: Probabilistic atlas of the human cerebellum |
Neurological disease, Stroke | Marie-Curie Program ; Wellcome Trust ; James S. McDonnell Foundation ; BBSRC |
nlx_144299 | SCR_005271 | 2026-07-28 09:41:12 | 1 | |||||||
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Genes to Cognition - Biological Resources Resource Report Resource Website 1+ mentions |
Genes to Cognition - Biological Resources (RRID:SCR_001675) | G2C Biological Resources | organism supplier, biomaterial supply resource, material resource | Biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6J | transgenic, mutant mouse strain, c57bl/6j, 129s5, transgenic mouse line, vector, es cell line, transgenic mouse |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
Free, Freely Available | nif-0000-10163 | http://www.genes2cognition.org/mice_resources/ | http://www.genes2cognition.org/resources.html | SCR_001675 | G2C Mice Resources, G2C Biological Resources, G2C-Biological Resources, G2C - Biological Resources | 2026-07-28 09:40:22 | 2 | ||||
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Flybrain at Stanford Resource Report Resource Website 1+ mentions |
Flybrain at Stanford (RRID:SCR_001877) | Flybrain(at)Stanford, FlybrainatStanford | software application, data or information resource, data processing software, software resource, image collection, image analysis software | Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer. | brain, cell, neuron, neuropil, olfactory, pheromone, confocal image, antennal lobe, axon trace, forum, neuronal tracing, image registration tool, analysis script, single-cell labeling, image registration, mushroom body, lateral horn, olfactory receptor neuron | has parent organization: Stanford University; Stanford; California | Wellcome Trust WT076726; Damon Runyon Cancer Research Foundation DRG-1766-03; NIAAA AA05965; NIAAA AA13521; NIDCD R01-DC005982 |
PMID:17382886 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10437 | SCR_001877 | Flybrain (at) Stanford - A warped brain is a good thing, Flybrain (at) Stanford | 2026-07-28 09:40:27 | 6 | |||||
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Ensembl Resource Report Resource Website 10000+ mentions |
Ensembl (RRID:SCR_002344) | data or information resource, database | Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. | collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Animal QTLdb is used by: ChannelPedia is used by: Blueprint Epigenome is used by: HmtPhenome lists: Ensembl Covid-19 is listed by: OMICtools is listed by: Biositemaps is listed by: re3data.org is listed by: LabWorm is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Ensembl Genomes is related to: GermOnline is related to: CandiSNPer is related to: Human Splicing Finder is related to: NGS-SNP is related to: Sanger Mouse Resources Portal is related to: DECIPHER is related to: Ensembl Genomes is related to: PeptideAtlas is related to: AnimalTFDB is related to: Bgee: dataBase for Gene Expression Evolution is related to: FlyMine is related to: Rat Gene Symbol Tracker is related to: UniParc at the EBI is related to: go-db-perl is related to: UniParc is related to: g:Profiler is related to: RIKEN integrated database of mammals is related to: VBASE2 is related to: p300db is related to: ShinyGO has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: Ensembl Metazoa is parent organization of: Ensembl Variation is parent organization of: Pre Ensembl is parent organization of: Variant Effect Predictor is parent organization of: Ensembl Bacteria is parent organization of: Ensembl Plants is parent organization of: Ensembl Fungi is parent organization of: Ensembl Protists is parent organization of: Ensembl Genome Browser works with: Genotate works with: CellPhoneDB works with: Open Regulatory Annotation Database works with: Database of genes related to Repeat Expansion Diseases works with: TarBase |
Wellcome Trust ; EMBL ; European Union ; FP7 ; FP6 ; MRC ; NHGRI ; BBSRC |
PMID:24316576 PMID:23203987 |
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 | https://bio.tools/ensembl, https://sources.debian.org/src/ensembl/, https://doi.org/10.17616/R39K5B | SCR_002344 | ENSEMBL | 2026-07-28 09:40:24 | 11652 | ||||||
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OME-TIFF Format Resource Report Resource Website |
OME-TIFF Format (RRID:SCR_002636) | OME-TIFF | data or information resource, narrative resource, standard specification | A standardized file format for multidimensional microscopy image data. OME-TIFF maximizes the respective strengths of OME-XML and TIFF. It takes advantage of the rich metadata defined in OME-XML while retaining the pixel structure in multi-page TIF format for compatibility with many image-processing applications. An OME-TIFF dataset has the following characteristics: * Image planes are stored within one multi-page TIFF file, or across multiple TIFF files. Any image organization is feasible. * A complete OME-XML metadata block describing the dataset is embedded in each TIFF file's header. Thus, even if some of the TIFF files in a dataset are misplaced, the metadata remains intact. * The OME-XML metadata block may contain anything allowed in a standard OME-XML file. * OME-TIFF uses the standard TIFF mechanism for storing one or more image planes in each of the constituent files, instead of encoding pixels as base64 chunks within the XML. Since TIFF is an image format, it makes sense to only use OME-TIFF as opposed to OME-XML, when there is at least one image plane. | microscopy, format, archiving, data management, annotation, mark up, metadata standard, standard, tiff, ome-xml |
is listed by: FORCE11 is related to: JCB DataViewer is related to: Cell Image Library (CIL) is related to: HMS LINCS Database is related to: Stowers Original Data Repository is related to: Bio-Formats has parent organization: OME - Open Microscopy Environment |
Wellcome Trust 68046 | PMID:15892875 | Free, Available for download, Freely available | nlx_156061 | SCR_002636 | OME-TIFF: Open Microscopy Environment Tagged Image File Format, Open Microscopy Environment Tagged Image File Format | 2026-07-28 09:40:38 | 0 | |||||
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Bio-Formats Resource Report Resource Website 50+ mentions |
Bio-Formats (RRID:SCR_000450) | Bio-Formats | software application, software resource, software library, standalone software, software toolkit | Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard. | Java library, reading microscopy image data files, writing image data, standardized format, open format, |
is listed by: FORCE11 is listed by: Debian is related to: OMERO is related to: OME-TIFF Format has parent organization: OME - Open Microscopy Environment |
Wellcome Trust | Free, Available for download, Freely available | nif-0000-30175 | http://www.force11.org/node/4810, http://www.loci.wisc.edu/software/bio-formats, https://sources.debian.org/src/libbio-formats-java/ | SCR_000450 | , BioFormats, Bio-Formats Library, The Bio-Formats Library | 2026-07-28 09:40:00 | 60 | |||||
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Zebrafish Brain Atlas Resource Report Resource Website 1+ mentions |
Zebrafish Brain Atlas (RRID:SCR_000606) | Zebrafish Brain Atlas | service resource, data or information resource, data repository, image repository, atlas, storage service resource | Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish. | brain, neuroanatomy, developing, transgene, antibody, confocal, section, reconstruction, high-resolution, developmental stage, embryo, brain structure, confocal imaging, comparative anatomy, transgenic, 3d spatial image, video, embryonic zebrafish, development, annotation, narrative resource, training material, cell repository |
recommends: Zebrafish Anatomical Ontology is listed by: One Mind Biospecimen Bank Listing has parent organization: University College London; London; United Kingdom |
European Union ; Wellcome Trust ; BBSRC |
Public, (Transgenic lines), Freely available for academic use, Creative Commons license, (pending verification), The community can contribute to this resource | nlx_149455 | http://zebrafishucl.org/ | http://www.ucl.ac.uk/zebrafish-group/zebrafishbrain/index.php | SCR_000606 | , zebrafishbrain.org, Zebrafish Brain Atlas | 2026-07-28 09:40:03 | 3 | ||||
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NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software application, data analysis software, software resource, data processing software, software toolkit | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-07-28 09:44:41 | 2 | |||||
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xiSEARCH Resource Report Resource Website 10+ mentions |
xiSEARCH (RRID:SCR_018395) | software application, data analysis software, algorithm resource, software resource, data processing software | Software and algorithm for analyzing protein protein cross linking mass spectrometry data. Library of routines for peptide based mass spectrometry. Contains search engine for identification of crosslinked peptides. | Protein analysis, mass spectrometry, protein cross linking, XL-MS, cross-linking mass spectrometry, data analysis, peptide mass spectrometry, crosslinked peptide identification | Wellcome Trust | PMID:26719564 | Free, Available for download, Freely available | https://github.com/Rappsilber-Laboratory/xisearch | SCR_018395 | 2026-07-28 09:44:45 | 22 | ||||||||
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Recombination Detection Program Resource Report Resource Website 100+ mentions |
Recombination Detection Program (RRID:SCR_018537) | RDP | software application, software resource, data analysis software, data processing software | Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes. | DNA sequence, alignment, phylogenetic tree, nucleotide analysis, sequence data analysis, genetic recombination identification, DNA sequence alignment, recombinant pattern analysis, virus genome | Wellcome Trust ; Fund for Scientific Research Flanders ; South African Centre of High Performance Computing ; European Research Council ; Spanish Ministry of Science and Education ; South African National Research Foundation ; University of Cape Town ; Polyomielitis Research Foundation ; Carnergie Corporation ; NIAID AI090970; NIGMS U01 GM110749; NIAID AI100665 |
PMID:27774277 PMID:20798170 |
Free, Available for download, Freely available | SCR_018537 | Recombination Detection Program, RDP4, RDP3 | 2026-07-28 09:44:46 | 483 | |||||||
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Tracer Resource Report Resource Website 1000+ mentions |
Tracer (RRID:SCR_019121) | software application, data analysis software, software resource, data processing software, data visualization software | Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. | Analysing trace files, files generated by Bayesian MCMC runs, MCMC trace files, conditional posterior distribution summary, demographic trajectory reconstruction, Bayesian phylogenetic inference, kernel density estimation, multivariate visualisation | Wellcome Trust ; European Union Seventh Framework Programme ; NSF DMS 1264153; NIAID R01 AI107034; NIAID U19 AI135995 |
PMID:29718447 | Free, Available for download, Freely available | https://github.com/beast-dev/tracer, http://gensoft.pasteur.fr/docs/Tracer/v1.6, http://beast.community/tracer, https://github.com/beast-dev/tracer/releases/tag/v1.7.1 | SCR_019121 | Tracer v1.7.1, Tracer v1.6 | 2026-07-28 09:44:56 | 1582 | |||||||
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NWB Explorer Resource Report Resource Website |
NWB Explorer (RRID:SCR_021151) | software application, data access protocol, software resource, web service, standalone software | Web application and standalone application to read, visualize and explore content of NWB:N 2 files.Used to share neurophysiological data in Neurodata Without Borders format. | Read NWB files, visualize NWB files, explore NWB files, NWB, neurophysiology data sharing, Neurodata Without Borders format, neurophysiology data |
uses: Jupyter Notebook uses: PyNWB is listed by: Neurodata Without Borders is related to: Metacell is related to: Open Source Brain |
Wellcome Trust | Free, Available for download, Freely available | https://www.nwb.org/tools/ | SCR_021151 | 2026-07-28 09:45:12 | 0 | ||||||||
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SpikeInterface Resource Report Resource Website 1+ mentions |
SpikeInterface (RRID:SCR_021150) | software application, data analysis software, software resource, data processing software, data visualization software | Software tool as unified framework for spike sorting. Python framework to unify preexisting spike sorting technologies into single codebase and to facilitate straightforward comparison and adoption of different approaches.Used to reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs. | Spike sorting, Python framework, unify preexisting spike sorting, single codebase, spike sorting algorithms | is listed by: Neurodata Without Borders | Wellcome Trust ; ETH Zurich Postdoctoral Fellowship ; University of Oslo ; Norwegian Ministry of Education ; Research and Church Affairs ; University of Edinburgh |
PMID:33170122 | Free, Available for download, Freely available | https://www.nwb.org/tools/, https://github.com/SpikeInterface/spikeinterface/blob/master/doc/index.rst | SCR_021150 | 2026-07-28 09:45:07 | 3 | |||||||
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CellML Model Repository Resource Report Resource Website 1+ mentions |
CellML Model Repository (RRID:SCR_008113) | CellML Repository | service resource, data repository, software resource, software repository, storage service resource | Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource. | cell function, cell model, model, cell, calcium dynamics, cardiovascularc circulation, cell cycle, cell migration, circadian rhythm, electrophysiology, endocrine, excitation-contraction coupling, gene regulation, hepatology, immunology, ion transport, mechanical constitutive law, metabolism, myofilament mechanics, neurobiology, ph regulation, pkpd, signal transduction, synthetic biology, image, exposure |
is used by: NIF Data Federation is listed by: 3DVC is listed by: Integrated Models is related to: Integrated Manually Extracted Annotation has parent organization: CellML |
Wellcome Trust ; Royal Society of New Zealand ; Maurice Wilkins Centre for Molecular Biodiscovery |
PMID:21216774 PMID:18658182 PMID:17947072 PMID:19162720 PMID:19380315 |
The community can contribute to this resource | nif-0000-20828 | SCR_008113 | 2026-07-28 09:42:16 | 6 | ||||||
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CellML Resource Report Resource Website 100+ mentions |
CellML (RRID:SCR_008061) | CellML | narrative resource, markup language, data or information resource, standard specification, interchange format | The CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org. | biological model, cell, mathematical model, mathematics, metadata, model structure, model, xml, annotation, mark up language, FASEB list |
is listed by: 3DVC is related to: PathGuide: the pathway resource list is related to: Physiome Model Repository has parent organization: University of Auckland; Auckland; New Zealand is parent organization of: CellML Model Repository |
VPH NoE ; Maurice Wilkins Centre for Molecular Biodiscovery ; International Union of Physiological Sciences: Physiome Project ; aneurIST ; NZIMA ; Foundation for Research Science and Technology ; Wellcome Trust |
PMID:15142756 PMID:18658182 PMID:19564239 PMID:19380315 PMID:18579471 PMID:17947072 PMID:17271569 |
The CellML project is built by an open, Democratic community on an Open unspecified license / free ethic. | nif-0000-10448 | SCR_008061 | CellML project, The CellML Project | 2026-07-28 09:42:01 | 146 | |||||
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ORCID - Open Researcher and Contributor ID Resource Report Resource Website 100+ mentions |
ORCID - Open Researcher and Contributor ID (RRID:SCR_008700) | ORCID | service resource, narrative resource, data or information resource, standard specification, international standard specification | Non-profit organization dedicated to solving the author/contributor name ambiguity problem in scholarly communications by creating a central registry of unique identifiers for individual researchers and an open and transparent linking mechanism between ORCID and other current author ID schemes. These identifiers, and the relationships among them, can be linked to the researcher''s output to enhance the scientific discovery process and to improve the efficiency of research funding and collaboration within the research community. The ideal solution is to establish a registry that is adopted and embraced as the de facto standard by the whole of the community. A resolution to the systemic name ambiguity problem, by means of assigning unique identifiers linkable to an individual''s research output, will enhance the scientific discovery process and improve the efficiency of funding and collaboration. The organization brings together the leaders of the most influential universities, funding organizations, societies, publishers and corporations from around the globe and is managed by a fourteen member Board of Directors. A disambiguated set of authors will allow new services and benefits to be built for the research community by all stakeholders in scholarly communication: from commercial actors to non-profit organizations, from governments to universities. | name ambiguity, scholarly communication, unique identifier, author identification, identifier service, people resource |
is used by: Academic Karma is listed by: FORCE11 is related to: Europe PubMed Central is related to: Academic Karma is parent organization of: ODIN |
American Physical Society ; Nature Publishing Group ; Wiley ; Hindawi ; Oxford University Press ; PLoS ; MIT Libraries ; Springer ; Wellcome Trust ; American Chemical Society ; Microsoft Research ; Elsevier ; American Institute of Physics ; Association for Computing Machinery ; Taylor and Francis Group ; Thompson Reuters |
nif-0000-37710 | SCR_008700 | ORCID: Open Researcher and Contributor ID, Open Reseacher & Contributor ID (ORCID), ORCID - Open Researcher Contributor ID, Open Researcher and Contributor ID, ORCID - Open Researcher and Contributor ID, ORCID - Open Reseacher & Contributor ID | 2026-07-28 09:42:22 | 476 | |||||||
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ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT082930MA; National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882 |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-07-28 09:44:08 | 8 | ||||||
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Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes. | Genome analysis, prokaryote pan genome, pan genome, gene identification, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools works with: Scoary |
Wellcome Trust | PMID:26198102 | Free, Available for download, Freely available | OMICS_09491, biotools:roary | https://github.com/sanger-pathogens/Roary, https://bio.tools/roary, https://sources.debian.org/src/roary/ | SCR_018172 | 2026-07-28 09:44:42 | 602 | ||||||
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GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | project portal, data or information resource, portal, dataset | Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. | human, mouse, genome, annotation, sequence, gene features, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: ENCODE |
NHGRI 5U54HG004555; Wellcome Trust WT098051 |
PMID:22955987 | Free | biotools:GENCODE | https://bio.tools/GENCODE | SCR_014966 | ENCODE | 2026-07-28 09:43:38 | 7700 | |||||
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eVOC Resource Report Resource Website 1+ mentions |
eVOC (RRID:SCR_010704) | eVOC | controlled vocabulary, data or information resource, ontology | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information. | mouse, mapping, cdna, development, microarray, expression, expressed sequence, anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation, treatment, gene expression, genome sequence, expression phenotype, genome, sequence, phenotype, anatomical system, cell type, pathology, anatomy |
is related to: OBO is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of the Western Cape; Bellville; South Africa |
South African National Research Foundation ; European Union ; Wellcome Trust ; South African Department of Arts Culture Science and Technology 32146 |
PMID:12799354 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_84448 | SCR_010704 | Expressed Sequence Annotation for Humans, eVOC (Expressed Sequence Annotation for Humans), eVOC Ontologies, eVOContology.org | 2026-07-28 09:42:55 | 4 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
