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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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IPBIR - Integrated Primate Biomaterials and Information Resource Resource Report Resource Website |
IPBIR - Integrated Primate Biomaterials and Information Resource (RRID:SCR_004614) | IPBIR | biomaterial supply resource, cell repository, material resource | The purpose of the IPBIR - Integrated Primate Biomaterials and Information Resource is to assemble, characterize, and distribute high-quality DNA samples of known provenance with accompanying demographic, geographic, and behavioral information in order to stimulate and facilitate research in primate genetic diversity and evolution, comparative genomics, and population genetics. Further research in these areas will advance our understanding of human origins, the biological basis of cognitive processes, evolutionary history and relationships, and social structure, and will provide critical scientific information needed to facilitate conservation of biological diversity. The derived DNA will be openly available to the broad scientific community who agree to restrict use to non-commercial purposes. DNA and cell culture samples are distributed only to qualified professional persons who are associated with recognized research, medical, or educational organizations engaged in research. | demographic data, geographic data, behavioral data, genetic diversity, evolution, comparative genomics, population genetics, dna, cell culture, frozen |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Coriell Cell Repositories |
All | NSF 0629321 | Public, Non-commercial, The derived DNA will be openly available to the broad scientific community | nlx_143841 | SCR_004614 | SciCrunch Registry | Integrated Primate Biomaterials and Information Resource, IPBIR Repository, IPBIR - Integrated Primate Biomaterials Information Resource, Integrated Primate Biomaterials Information Resource | 2026-10-17 01:31:55 | 0 | |||||
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DataLad Resource Report Resource Website 50+ mentions |
DataLad (RRID:SCR_003931) | DataLad | data or information resource, portal, software resource | Project to adapt model of open source software distributions to address technical limitations of data sharing and develop all components of data distribution. Builds on top of git-annex and extends it with intuitive command line interface. Enables users to operate on data using familiar concepts, such as files and directories, while transparently managing data access and authorization with underlying hosting providers. Can create DataLad datasets using any data files published on the web. | Data sharing, aggregator, federated platform, distributed version control system, data set |
uses: OpenNeuro uses: CRCNS uses: NeuroImaging Tools and Resources Collaboratory (NITRC) uses: NIH Human Connectome Project uses: Mind Research Network - COINS uses: 1000 Functional Connectomes Project uses: Git uses: git-annex is related to: datasets.datalad.org has parent organization: Dartmouth College; New Hampshire; USA has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany has parent organization: Research Center Jülich; Jülich; Germany works with: ReproIn: The ReproNim image input management system (featuring DataLad) |
BMBF 01GQ1411; BMBF 01GQ1905; Deutsche Forschungsgemeinschaft SFB1451-INF; European Union’s Horizon 2020 research and innovation programme 826421; European Union’s Horizon 2020 research and innovation programme 945539; German federal state of Saxony-Anhalt and the European Regional Development Fund ; NIH 1P41EB019936-01A1; NIH 1R24MH117295-01A1; NSF 1429999; NSF 1912266 |
DOI:10.21105/joss.03262 | Free, Freely available | nlx_158300 | https://github.com/datalad/datalad.org | SCR_003931 | SciCrunch Registry | DataGit, Data Lad | 2026-10-17 01:32:55 | 58 | ||||
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DELSA Resource Report Resource Website 1+ mentions |
DELSA (RRID:SCR_006231) | DELSA | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 1, 2022. Organization whose mission is to build and promote a sustainable ecosystem of professional societies, funding agencies, foundations, companies, and citizens together with life science researchers and innovators in computing, infrastructure and analysis with the expressed goal of translating new discoveries into tools, resources and products. | life science, collective innovation, framework, data sharing, science, education, environment, energy, ecology, food, healthcare, transdiscipline, collaboration | NSF | PMID:22523528 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_151790 | SCR_006231 | SciCrunch Registry | Data-Enabled Life Sciences Alliance, DELSAglobal, DELSA: Data-Enabled Life Sciences Alliance, DELSA Global, Data-enabled Life Science Initiative | 2026-10-17 01:32:17 | 2 | ||||||
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Human Brain Atlas Resource Report Resource Website 1+ mentions |
Human Brain Atlas (RRID:SCR_006131) | Human Brain Atlas | atlas, data or information resource, video resource | A labeled three-dimensional atlas of the human brain created from MRI images. In conjunction are presented anatomically labeled stained sections that correspond to the three-dimensional MRI images. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies. The MRI subject was a 22-year-old adult male. Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process. The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp | human, adult, mri, fiber stain, anatomy, normal, neuroanatomy, nissl stain, image, brainstem, cell body, nerve fiber, brain, coronal, sagittal, horizontal, 3d model, montage, weil, hypothalamus |
is used by: NIF Data Federation has parent organization: Michigan State University; Michigan; USA |
NSF IBN 0131267; NSF 0131826; NSF 0131028 |
Copyrighted, Public, Request that you secure their permission, Acknowledgement required | nif-0000-00088 | SCR_006131 | SciCrunch Registry | MSU Brain Biodiversity Bank - Human Brain Atlas, Michigan State University Brain Biodiversity Bank - Human Brain Atlas | 2026-10-17 01:31:57 | 3 | ||||||
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XSEDE - Extreme Science and Engineering Discovery Environment Resource Report Resource Website 10+ mentions |
XSEDE - Extreme Science and Engineering Discovery Environment (RRID:SCR_006091) | XSEDE | data or information resource, portal | XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools. | data sharing, computing, supercomputer, data, tool, visualization, data analysis, cyberinfrastructure, digital service, high performance computing, high throughput computing, visualization, storage, data service |
is related to: Neuroscience Gateway has parent organization: San Diego Supercomputer Center |
NSF OCI-1053575 | nlx_151554, grid.501421.3 | https://ror.org/05524hb64 | SCR_006091 | SciCrunch Registry | XSEDE - Extreme Science Engineering Discovery Environment, Extreme Science and Engineering Discovery Environment | 2026-10-17 01:32:17 | 29 | ||||||
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Cellpack Resource Report Resource Website 1+ mentions |
Cellpack (RRID:SCR_006831) | cellPack | data processing software, software application, software resource | A specialized version of autoPack designed to pack biological components together. The current version is optimized to pack molecules into cells with biologically relevant interactions to populate massive cell models with atomic or near-atomic details. Components of the algorithm pack transmembrane proteins and lipids into bilayers, globular molecules into compartments defined by the bilayers (or as exteriors), and fibrous components like microtubules, actin, and DNA. | 3d packing software, pack, molecule, cell |
is related to: Autopack has parent organization: Autopack |
QB3 at UCSF Fellowship ; NSF 07576; NCRR P41 RR08605 |
GNU Lesser General Public License | nlx_151792 | https://sites.google.com/site/autofill21/, http://code.google.com/p/autofill/ | SCR_006831 | SciCrunch Registry | 2026-10-17 01:32:59 | 9 | ||||||
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Neuroscience Gateway Resource Report Resource Website 10+ mentions |
Neuroscience Gateway (RRID:SCR_008915) | NSG | data or information resource, portal, project portal, software resource | Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. | Large, scale, modeling, data, computing, neuroscience, neuron, BRAIN Initiative |
is recommended by: BRAIN Initiative lists: ModelRun is related to: XSEDE - Extreme Science and Engineering Discovery Environment is related to: NEURON is related to: GENESIS Neural Database and Modelers Workspace has parent organization: San Diego Supercomputer Center has parent organization: Neuroscience Information Framework has parent organization: Yale School of Medicine; Connecticut; USA |
BBSRC N005236; NIBIB R01 EB023297; NSF 1146949; NSF 1339856; NSF 1458495; NSF 1458840 |
Free, Freely available | nlx_151553, SCR_015767 | http://www.nitrc.org/projects/nsg/ | SCR_008915 | SciCrunch Registry | Neuroscience Gateway - A Portal for Computational Neuroscience, Neuroscience Gateway, Neuroscience Gateway (NSG) Portal | 2026-10-17 01:32:21 | 25 | |||||
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Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core Resource Report Resource Website 1+ mentions |
Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core (RRID:SCR_007342) | Tulane Tissue Culture Core | biomaterial supply resource, cell repository, material resource | The Stem Cell Research and Regenerative Medicine''s Tissue Culture Core provides cells for research use within the department, as well as for distribution to other facilities. The core obtains hMSCs from bone marrow donor samples and expands these cells for research use. The hMSC''s are also characterized for bone, fat and cartilage differentiation, and are stored on site for use. The Tissue Culture Core also handles the expansion and characterization of mouse and rat MSC''s. The animal cells are cultured in a separate area, and never interact with human derived cells. We also have a supply of hMSC''s marked with GFP+, Mito Red and Mito Blue available. | stem cell, mesenchymal stem cell, marrow stromal cell, frozen, adult, bone marrow, adipose tissue, bone, fat, cartilage |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Tulane University School of Medicine; Louisiana; USA |
United States Department of DefenseBlueprint for Neuroscience Research ; NSF ; NIH |
Public: The Tissue Culture Core provides cells for research use within the department, As well as for distribution to other facilities. | nif-0000-00246 | http://www.som.tulane.edu/gene_therapy/distribute.shtml | SCR_007342 | SciCrunch Registry | Tulane Stem Cell Research Regenerative Medicine Tissue Culture Core | 2026-10-17 01:32:19 | 1 | |||||
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ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | data processing software, software application, software resource | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch, https://bio.tools/scaffmatch | SCR_017025 | SciCrunch Registry | 2026-10-17 01:32:04 | 1 | ||||||
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FlowCal Resource Report Resource Website 1+ mentions |
FlowCal (RRID:SCR_018140) | data processing software, software application, software resource | Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots. | Converting flow cytometry data, arbitrary unit, calibrated unit, data gating, statistic, plot, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NDSEG Fellowship ; NIAID R21 AI115014; NSF Graduate Research Fellowship DGE 0940902; NSF EFRI 1137266; NSF MCB 1244135; Office of Naval Research MURI N000141310074; Office of Naval Research YIP N000141410487; Welch Foundation |
PMID:27110723 | Free, Available for download, Freely available | biotools:flowcal | https://bio.tools/flowcal | SCR_018140 | SciCrunch Registry | Python Flow Cytometry Calibration Library | 2026-10-17 01:32:12 | 6 | |||||
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UniProt Resource Report Resource Website 10000+ mentions |
UniProt (RRID:SCR_002380) | UniProt | data or information resource, database | Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB. | collection, protein, sequence, annotation, data, functional, information |
is used by: LIPID MAPS Proteome Database is used by: ChannelPedia is used by: Open PHACTS is used by: DisGeNET is used by: Smart Dictionary Lookup is used by: MitoMiner is used by: Cytokine Registry is used by: MobiDB is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Phospho.ELM is used by: GEROprotectors is used by: SwissLipids is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: LabWorm is related to: Clustal W2 is related to: UniProt DAS is related to: UniParc at the EBI is related to: ProDom is related to: LegumeIP is related to: Pathway Commons is related to: NIH Data Sharing Repositories is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: 3D-Interologs is related to: Biomine is related to: EBIMed is related to: STOP is related to: Coremine Medical is related to: BioExtract is related to: STRAP is related to: GOTaxExplorer is related to: GoAnnotator is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: Whatizit is related to: MOPED - Model Organism Protein Expression Database is related to: Polbase is related to: PredictSNP is related to: PSICQUIC Registry is related to: IntAct is related to: p300db is related to: UniProt Proteomes is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: Protein Information Resource is parent organization of: UniProtKB is parent organization of: NEWT is parent organization of: UniParc is parent organization of: UniProt Chordata protein annotation program is parent organization of: UniRef works with: Genotate works with: CellPhoneDB works with: MOLEonline works with: MiMeDB |
ARUK ; British Heart Foundation ; EMBL ; NCI ; NCRR P20 RR016472; NEI ; NHGRI P41 HG02273; NHGRI U24 HG007722; NHGRI U41 HG006104; NHLBI ; NIAID ; NIA ; NIDDK ; NIGMS 5R01GM080646; NIGMS R01 GM080646; NIMH ; NLM G08 LM010720; NSF DBI-0850319; PDUK |
PMID:19843607 PMID:18836194 PMID:18045787 PMID:17142230 PMID:16381842 PMID:15608167 PMID:14681372 |
nif-0000-00377, SCR_018750, r3d100010357 | http://www.ebi.uniprot.org, http://www.uniprot.org/uniprot/, http://www.pir.uniprot.org, ftp://ftp.uniprot.org, https://doi.org/10.17616/R3BW2M | SCR_002380 | SciCrunch Registry | , The Universal Protein Resource, Universal Protein Resource, UNIPROT Universal Protein Resource | 2026-10-17 01:32:44 | 19823 | |||||
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Mutation Annotation and Genomic Interpretation Resource Report Resource Website |
Mutation Annotation and Genomic Interpretation (RRID:SCR_002800) | MAGI | analysis service resource, data analysis service, production service resource, service resource | A tool for annotating, exploring, and analyzing gene sets that may be associated with cancer. | mutation, interaction, transcript, copy number aberration, network |
uses: The Cancer Genome Atlas uses: HINT uses: HPRD - Human Protein Reference Database uses: Pfam uses: SMART uses: Conserved Domain Database is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
Cancer | NSF ; NIH ; Brown University; Rhode Island; USA |
Free, Freely available, Available for download | OMICS_06145 | SCR_002800 | SciCrunch Registry | MAGI - A tool for Mutation Annotation and Genomic Interpretation | 2026-10-17 01:32:47 | 0 | |||||
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Phenoscape Knowledgebase Resource Report Resource Website 10+ mentions |
Phenoscape Knowledgebase (RRID:SCR_002821) | Phenoscape Knowledgebase | data or information resource, database | Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26. | fish, gene, anatomy, model organism, ostariophysan, phenotype, taxis, ontology, anatomy, variation, taxon, genetic, evolution, development, web service, source code |
uses: Teleost Anatomy Ontology is related to: Zebrafish Information Network (ZFIN) is related to: Catalog of Fishes is related to: FishBase is related to: AmphibiaWeb is related to: NCBI Taxonomy is related to: Catalogue of Life has parent organization: NESCent - National Evolutionary Synthesis Center has parent organization: Phenoscape is parent organization of: Teleost Taxonomy Ontology |
NSF DBI-1062404; NSF DBI-1062542; NSF EF-0905606; NSF BDI-0641025; NSF EF-0423641 |
PMID:22736877 PMID:20505755 |
Free, Freely available | nif-0000-24925 | SCR_002821 | SciCrunch Registry | 2026-10-17 01:33:47 | 14 | ||||||
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Nucleic Acid Database Resource Report Resource Website 10+ mentions |
Nucleic Acid Database (RRID:SCR_003255) | NDB | data or information resource, database | A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF). | nucleic acid, dna, nucleopeptide, nucleoprotein, nucleotide, rna, transfection, sequence, structure, function, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: MINAS - Metal Ions in Nucleic AcidS is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Jenalib: Jena Library of Biological Macromolecules has parent organization: Rutgers University; New Jersey; USA |
NSF ; DOE ; NIH |
PMID:24185695 PMID:1384741 |
Free, Available for download, Freely available | nif-0000-03184, biotools:ndb, r3d100010415 | https://bio.tools/ndb, https://doi.org/10.17616/R3531R | SCR_003255 | SciCrunch Registry | 2026-10-17 01:32:50 | 37 | |||||
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ASAP: the Alternative Splicing Annotation Project Resource Report Resource Website 10+ mentions |
ASAP: the Alternative Splicing Annotation Project (RRID:SCR_003415) | ASAP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases. | gene, genome, human, isoform, mechanism, metazoa, molecular, mrna, nucleus, process, protein, sequence, splice, tissue specificity, transcription, transcript, alternate splicing, microarray, alternative splicing, biological process, alternatively spliced isoform, contig, cancer, image |
is listed by: Biositemaps is related to: Alternative Splicing Annotation Project II Database has parent organization: University of California at Los Angeles; California; USA |
NSF 0082964; NSF DGE-9987641; DOE DEFG0387ER60615 |
PMID:12519958 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33105 | SCR_003415 | SciCrunch Registry | Alternative Splicing, Alternative Splicing Annotation Project, Alternative Splicing Annotation Project database | 2026-10-17 01:32:51 | 33 | |||||
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MITOMAP - A human mitochondrial genome database Resource Report Resource Website 100+ mentions |
MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) | MITOMAP | data or information resource, database | Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf. | gene, genome, diabetes, disease, disease-association, high resolution screening, human, inversion, metabolism, mitochondrial dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletion, FASEB list |
is used by: HmtVar is listed by: OMICtools is related to: Hereditary Hearing Loss Homepage has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA has parent organization: Emory University School of Medicine; Atlanta; Georgia; USA |
NIH ; Muscular Dystrophy Foundation ; Ellison Foundation ; Diputacion General de Aragon Grupos consolidados B33 ; NIGMS GM46915; NINDS NS21328; NHLBI HL30164; NIA AG10130; NIA AG13154; NINDS NS213L8; NHLBI HL64017; NIH Biomedical Informatics Training Grant T15 LM007443; NSF EIA-0321390; Spanish Fondo de Investigacion Sanitaria PI050647; Ciber Enfermedades raras CB06/07/0043 |
PMID:17178747 PMID:15608272 PMID:9399813 PMID:9016535 PMID:8594574 |
Except where otherwise noted, Creative Commons Attribution License, The community can contribute to this resource | nif-0000-00511, OMICS_01641 | SCR_002996 | SciCrunch Registry | 2026-10-17 01:32:37 | 405 | ||||||
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bioPIXIE Resource Report Resource Website 1+ mentions |
bioPIXIE (RRID:SCR_004182) | bioPIXIE | analysis service resource, data analysis service, production service resource, service resource | bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it). | prediction, bayesian network, probabilistic, interaction, network | has parent organization: Princeton University; New Jersey; USA | NHGRI T32 HG003284; NIGMS R01 GM071966; NHGRI R01 HG003471; NIGMS P50 GM071508; NSF DGE-9972930; NSF IIS-0513552 |
PMID:16420673 | nlx_20893 | SCR_004182 | SciCrunch Registry | biological Process Inference from eXperimental Interaction Evidence | 2026-10-17 01:33:13 | 1 | ||||||
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SGN Resource Report Resource Website 1000+ mentions |
SGN (RRID:SCR_004933) | SGN, SGN ref | data or information resource, database | A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions. | database, clade, genomic, sequence, phenotype, pathway, genetic, taxonomy, annotation, blast, plant genome, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Sol Genomics Network - Bulk download is related to: AmiGO has parent organization: Boyce Thompson Institute for Plant Research |
USDA ; ATC Inc. Advanced Technologies Cambridge ; NSF 0116076; NSF 9872617; NSF 975866; NSF 0421634 |
PMID:20935049 PMID:16010005 |
Public, The community can contribute to this resource | r3d100012078, nlx_89764, biotools:sol_genomics_network | https://bio.tools/sol_genomics_network, https://doi.org/10.17616/R3FS95 | http://www.sgn.cornell.edu/ | SCR_004933 | SciCrunch Registry | SGN ref, Sol Genomics Network | 2026-10-17 01:32:49 | 1261 | |||
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Phenologs Resource Report Resource Website 1+ mentions |
Phenologs (RRID:SCR_005529) | Phenologs | data or information resource, database | Database for identifying orthologous phenotypes (phenologs). Mapping between genotype and phenotype is often non-obvious, complicating prediction of genes underlying specific phenotypes. This problem can be addressed through comparative analyses of phenotypes. We define phenologs based upon overlapping sets of orthologous genes associated with each phenotype. Comparisons of >189,000 human, mouse, yeast, and worm gene-phenotype associations reveal many significant phenologs, including novel non-obvious human disease models. For example, phenologs suggest a yeast model for mammalian angiogenesis defects and an invertebrate model for vertebrate neural tube birth defects. Phenologs thus create a rich framework for comparing mutational phenotypes, identify adaptive reuse of gene systems, and suggest new disease genes. To search for phenologs, go to the basic search page and enter a list of genes in the box provided, using Entrez gene identifiers for mouse/human genes, locus ids for yeast (e.g., YHR200W), or sequence names for worm (e.g., B0205.3). It is expected that this list of genes will all be associated with a particular system, trait, mutational phenotype, or disease. The search will return all identified model organism/human mutational phenotypes that show any overlap with the input set of the genes, ranked according to their hypergeometric probability scores. Clicking on a particular phenolog will result in a list of genes associated with the phenotype, from which potential new candidate genes can identified. Currently known phenotypes in the database are available from the link labeled ''Find phenotypes'', where the associated gene can be submitted as queries, or alternately, can be searched directly from the link provided. | gene, phenotype, ortholog, genotype, human, mouse, yeast, worm | has parent organization: University of Texas at Austin; Texas; USA | Texas Advanced Research Program ; Welch Foundation ; Packard Fellowship ; March of Dimes ; Texas Institute for Drug and Diagnostic Development ; NSF ; NIH ; NIGMS |
PMID:20308572 | nlx_144624 | SCR_005529 | SciCrunch Registry | phenologs.org, Phenologs - Systematic discovery of non-obvious disease models and candidate genes | 2026-10-17 01:34:06 | 4 | ||||||
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Tree of Life Web Project Resource Report Resource Website 10+ mentions |
Tree of Life Web Project (RRID:SCR_005673) | ToL | data or information resource, database | A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups. | genomics, invertebrate, taxonomy, image, phylogeny, FASEB list |
is listed by: re3data.org has parent organization: University of Arizona; Arizona; USA |
NSF DBI-0078294; NSF DUE-0333715; NSF EF-0531754 |
The community can contribute to this resource, Acknowledgement requested, Copyrighted, Creative Commons Attribution-NonCommercial License, (ToL Glossary), Creative Commons Attribution License | r3d100010351, nif-0000-03586 | https://doi.org/10.17616/R30K6X | http://phylogeny.arizona.edu/tree/phylogeny.html | SCR_005673 | SciCrunch Registry | Tree of Life | 2026-10-17 01:33:10 | 39 |
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