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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

Physical Resource or Software Tool Software

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
UCSCinResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Beta software used to align and browse a genome.genomeSCR_000571(UCSCin, RRID:SCR_000571)University of Toronto; Ontario; Canada Last checked downnlx_144379
Pathology DiagnosticsResource, service resource, core facility, access service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented September 15, 2016. Pathology Diagnostics Ltd is an independent GCLP accredited histopathology research organisation delivering tissue, laboratory, and diagnostics services to industry Research and Development scientists engaged in drug and biomarker development.diagnostics, histopathology, commercial, research organization, drug development, biomarker developmentSCR_001033(Pathology Diagnostics, RRID:SCR_001033)listed by: Science ExchangeLast checked downSciEx_11698http://www.scienceexchange.com/facilities/pathology-diagnostics
iBIOFindResource, software resource, software application, service resource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 WPF / OWL / REST / JSON / SPARQL multi-threaded, parallel desktop application enables the construction of biomedical knowledge through PubMed, ScienceDirect, EndNote and NIH Grant repositories for tracking the work of medical researchers for ranking and recommendations. Users can crawl web sites, build latent semantic indices to generate literature searches for both Clinical Translation Science Award and non-CTSA institutions, examine publications, build Bayesian networks for neural correlates, gene to gene interactions, protein to protein interactions and as well drug treatment hypotheses. Furthermore, one can easily access potential researcher information, monitor and evolve their networks and search for possible collaborators and software tools for creating biomedical informatics products. The application is designed to work with the ModelMaker, R, Neural Maestro, Lucene, EndNote and MindGenius applications to improve the quality and quantity of medical research. iBIOFind interfaces with both eNeoTutor and ModelMaker 2013 Web Services Implementation in .NET for eNeoTutor to aid instructors to build neuroscience courses as well as rare diseases. Added: Rare Disease Explorer: The Visualization of Rare Disease, Gene and Protein Networks application module. Cinematics for the Image Finder from Yale. The ability to automatically generate and update websites for rare diseases. Cytoscape integration for the construction and visualization of pathways for Molecular targets of Model Organisms. Productivity metrics for medical researchers in rare diseases. iBIOFind 2013 database now includes over 150 medical schools in the US along with Clinical Translational Science Award Institutions for the generation of biomedical knowledge, biomedical informatics and Researcher Profiles.workflow, model, prediction, research trend, rare disease, resource discovery, biomedicine, genomic, neural network, visualization, reporting, search engine, genetic, neural, clinical translation science award, biomedical resource, funding, gene, protein, neuron, collaborator, publication, trend, grant, funding opportunity, reportSCR_001587(iBIOFind, RRID:SCR_001587)The Cromwell Workshop related to: ModelMaker, Neural Maestro, eNeoTutor, Cytoscape, Biomedical Resource Ontology, PubMedLast checked downnlx_153829
The Cromwell WorkshopResource, service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. Statistical and biomedical informatics software studio that develops neuroscience applications and brain computer interface games. They are dedicated to the integration of medical research, neuroscience, time series analysis, computer programming, statistics, sensor technologies, graphics design, artificial intelligence and entertainment to build gaming systems for neuroscientific research and intelligent tutoring in the classroom and lab. The current focus of The Cromwell Workshop/Neuronal Architects is on theoretical neuroscience and experimental modeling of psychological and neural processes that involve attention, emotion, motivation and executive functions that are impaired by neurological diseases. The outcome of this work is to use these results in the design of multiple genre brain computer interface gaming systems that can be used in both clinical and at home settings. If you would like to explore any collaborative opportunities to use their software or enhance your existing statistical products with their .NET, Java, R and Matlab code bases, let them know.statistical software, web design, medical research, neuroscience, time series analysis, computer programming, statistics, sensor technology, graphics design, artificial intelligence, entertainment, gaming system, modeling, psychological process, neural process, attention, emotion, motivation, executive function, neurological disease, brain computer interface, .net, java, r, matlab, computational neuroscience, time series, gamingSCR_001588(The Cromwell Workshop, RRID:SCR_001588)Last checked downnlx_153830
C. elegans Gene Knockout ConsortiumResource, organism supplier, production service resource, biomaterial supply resource, material service resource, service resource, material resource, biomaterial manufactureTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The mission of the C. elegans Gene Knockout Consortium is to facilitate genetic research of this important model system through the production of deletion alleles at specified gene targets. We choose targets based on investigator requests. Strains produced by the consortium are freely available with no restrictions to any investigator. At one time, our capacity dictated that we restrict requests to five per lab. This restriction no longer holds. Investigators are encouraged especially to register requests for functionally related groups of genes. Consortium strains are distributed by the C. elegans Genetic Center (CGC). In most cases, when you use the Consortium web site to request an existing allele, your request is forwarded automatically to the CGC. However, if you indicate that an existing allele is not satisfactory for your research, (for whatever reason), you may request that we generate another allele for the same target. Any information generated by the Consortium is entered into the official C. elegans data repository, WormBase.gene, locus, knockout, genetic, research, model, allele, target, strain, deletion allele, gene targetSCR_003000(C. elegans Gene Knockout Consortium, RRID:SCR_003000)Oklahoma Medical Research Foundation related to: Caenorhabditis Genetics Center, WormBaseLast checked downnif-0000-30230
SumsDBResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, atlas, image repository, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figuressegmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomySCR_002759(SumsDB, RRID:SCR_002759)Washington University School of Medicine in St. Louis; Missouri; USA Mental disease, Neurological disorder, NormalHuman Brain Project, NASA, National Partnership for Advanced Computational Infrastructure, NCI, NIMH, NLM, NSFrelated to: Computerized Anatomical Reconstruction and Editing Toolkit, Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by: Biositemaps, NeuroImaging Tools and Resources Collaboratory (NITRC), re3data.orgLast checked downnif-0000-00016http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb
Coddle-Codons Optimized to Discover Deleterious LEsionsResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene.codon, deleterious lesion, gene, coding, sequence, mutation, primer, protein sequence, cdna, sequence alignment, coding sequenceSCR_003003(Coddle-Codons Optimized to Discover Deleterious LEsions, RRID:SCR_003003)Fred Hutchinson Cancer Research Center DOE, Office of Energy Researchlisted by: 3DVCLast checked downnif-0000-30262
Amino Acid-Nucleotide Interaction DatabaseResource, service resource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. AANT, the Amino Acid-Nucleotide Interaction Database, contains information derived from all of the protein/nucleic acid complexes with experimentally determined structures in the Protein Data Bank. You can visualize the AANT models using the simple web interface, which relies on the Chime plug-in. You can also download these models for further analysis using publicly available tools for manipulating PDB structures. The software that generates AANT uses HBPLUS to predict hydrogen bond interactions between single bases and single amino acid residues within these complexes. The AANT software uses this information to break down a single PDB structure into scores of individual interactions between either the base, sugar, or phosphate of a nucleotide and the side chain or peptide backbone of a amino acid. The software then superimposes all the interactions between a particular moiety of a nucleotide and a particular moiety of a amino acid residue into a single 3D model, centering on a particular point in the base, sugar, or phosphate. The AANT software then groups geometrically similar interactions into clusters.SCR_004617(Amino Acid-Nucleotide Interaction Database, RRID:SCR_004617)University of Texas at Austin; Texas; USA PMID:14681388Last checked downnlx_61417
ETEX CorporationResource, commercial organization, production service resource, biomaterial supply resource, material service resource, service resource, material resource, biomaterial manufactureTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Develop, manufacture and market proprietary, nanocrystalline calcium-phosphate-based biomaterials that promote the repair and regeneration of bone damaged by trauma or disease. ETEX focuses on expanding applications through combinations with cells, biologics, or therapeutic agents delivered in minimally invasive and easy to use systems.calcium phosphate, bone substitute, bone substitute material, bone, bioresorbableSCR_004685(ETEX Corporation, RRID:SCR_004685)listed by: One Mind Biospecimen Bank ListingLast checked downnlx_68272
UMKC Neuroscience Brain Tissue Bank and Research LaboratoryResource, biomaterial supply resource, tissue bank, service resource, brain bank, storage service resource, material resource, material storage repositoryTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The UMKC Neuroscience Brain Tissue Bank and Research Laboratory has been established to obtain, process, and distribute human brain tissue to qualified scientists and clinicians dedicated to neuroscience research. No other living organ approaches the human brain in complexity or capacity. Healthy, it astounds and inspires miracles. Diseased, it confounds and diminishes hope. The use of human brain tissue for research will provide insight into the anatomical and neurochemical aspects of diseased and non-diseased brains. While animal models are helpful and necessary in understanding disease, certain disorders can be more efficiently studied using human brain tissue. Also, modern research techniques are often best applied to human tissue. We also need samples of brain tissue that have not been affected by disease. They help us to compare a 'normal' brain with a diseased one. Also, we have a critical need for brain donations from relatives who have genetically inherited disorders. Tissue preparation consists of fresh quick-frozen tissue blocks or coronal slices (nitrogen vapor frozen; custom dissection of specific anatomic regions) or formalin-fixed coronal slices (custom dissection of specific anatomic regions).brain tissue, brain, tissue, fresh quick-frozen, block, nitrogen vapor frozen, frozen, formalin-fixed, disease, normal, genetically inherited disorder, normal control, matched control, neuroscience, post-mortem, coronal sliceSCR_005148(UMKC Neuroscience Brain Tissue Bank and Research Laboratory, RRID:SCR_005148)University of Missouri-Kansas City School of Medicine; Missouri; USA Disease, Normal, Genetically inherited disorder, Normal control, Matched controllisted by: One Mind Biospecimen Bank ListingLast checked downnlx_144161
GeneMergeResource, data analysis service, production service resource, analysis service resource, software application, service resource, software resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblegene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarraySCR_005744(GeneMerge, RRID:SCR_005744)Harvard University; Cambridge; United States related to: Gene Ontology, listed by: Gene Ontology ToolsPMID:12724301Last checked downnlx_149203http://genemerge.cbcb.umd.edu/
MetaGeneProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Meta Gene Profiler (MetaGP) is a web application tool for discovering differentially expressed gene sets (meta genes) from the gene set library registered in our database. Once user submits gene expression profiles which are categorized into subtypes of conditioned experiments, or a list of genes with the valid pvalues, MetaGP assigns the integrated p-value to each gene set by combining the statistical evidences of genes that are obtained from gene-level analysis of significance. The current version supports the nine Affymetrix GeneChip arrays for the three organisms (human, mouse and rat). The significances of GO terms are graphically mapped onto the directed acyclic graph (DAG). The navigation systems of GO hierarchy enable us to summarize the significance of interesting sub-graphs on the web browser. Platform: Online toolgene, gene expression, differentially expressed, gene ontology, meta gene, gene set, statistical analysisSCR_005794(MetaGeneProfiler, RRID:SCR_005794)Institute of Statistical Mathematics; Tokyo; Japan related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked downnlx_149271
PubSearchResource, service resource, software resource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblegene, annotate, editor, literature curation tool, literature, ontology or annotation editorSCR_005830(PubSearch, RRID:SCR_005830)TAIR , Stanford University; Stanford; California NHGRIrelated to: Gene Ontology, listed by: Gene Ontology ToolsLast checked downnlx_149338
Expression ProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, geneSCR_005821(Expression Profiler, RRID:SCR_005821)European Bioinformatics Institute Estonian Science Foundation, European Union, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15215431Last checked downnlx_149323
Type 1 Diabetes Preclinical Testing Program Resource, service resource, resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Investigator access is provided to the established facilities and expertise needed to extend, enhance and validate preclinical studies of promising new therapeutics in cases where additional preclinical testing is needed to validate potential therapies under disease-specific conditions and in multiple animal models before therapeutics can enter the Type 1 Diabetes Rapid Access to Intervention Development (T1D-RAID) development pipeline. The T1D-RAID program provides resources for pre-clinical development of drugs, natural products, and biologics that will be tested as new therapeutics in type 1 diabetes clinical trials. The T1D-RAID program is not currently accepting applications. The T1D-PTP program currently supports two contracts, which are separate from each other and from the T1D-RAID NCI contract resources, to assist in preclinical development of therapeutics for T1D: * Agents to be tested for Preclinical Efficacy in Prevention or Reversal of Type 1 Diabetes in Rodent Models. Type 1 Diabetes Preclinical Testing Program (T1D-PTP) (NOT-DK-09-006) * Needs for Preclinical Efficacy Testing of Promising Agents to Prevent or Reverse Diabetic Complications (NOT-DK-09-009) The T1D-RAID and T1D-PTP are programs intended to remove the most common barriers to progress in identification and development of new therapies for Type 1 Diabetes. The common goal of these programs is to support and provide for the preclinical work necessary to obtain proof of principle establishing that a new molecule or novel approach will be a viable candidate for expanded clinical evaluation.testing, therapeutic, clinical, drug, preclinical, therapy, drug development, high-throughput screening, animal model, formulation, pharmacology, toxicologySCR_006861( Type 1 Diabetes Preclinical Testing Program , RRID:SCR_006861)NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases Type 1 diabetesNIDDKrelated to: Type 1 Diabetes - Rapid Access to Intervention Development , NIDDK Information Network, submitted by: NIDDK Information NetworkLast checked downnlx_152741
Swami: The Next Generation Biology WorkbenchResource, service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. The NGBW is designed to be an organic tool that evolves with the needs of the Biomedical research and education communities. The Next Generation Biology Workbench (NGBW) is now available for public use, in its production release.SCR_007217(Swami: The Next Generation Biology Workbench, RRID:SCR_007217)University of California at San Diego; California; USA IBM Corporation, Microsoft Research, NIGMSLast checked downnlx_14257http://www.ngbw.org/
BovMap DatabaseResource, service resource, data or information resource, data repository, storage service resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing.genetic, bovine, cattle, chromosome, clone, cosmid, cow, cytogenetic, dna, genome, homology, locus, meiotic, phene, polymorphism, sequence, map, geneSCR_008145(BovMap Database, RRID:SCR_008145)INRA - French National Institute for Agricultural Research; Paris; France European UnionLast checked downnif-0000-20968
Candidate Genes to Inherited DiseasesResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases.function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data setSCR_008190(Candidate Genes to Inherited Diseases, RRID:SCR_008190) EMBL - Bork Group , European Molecular Biology Laboratory related to: Gene Ontology, listed by: 3DVC, Gene Ontology ToolsPMID:16115313Last checked downnif-0000-21162http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/
MAP-O-MATResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. The server uses publicly available genotype data for over 15,000 markers. It facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps. The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly.general human genetics databases, automated, distance, dna, genotype, human, linkage, map, mapping, marker, polymorphic, position, verificationSCR_008197(MAP-O-MAT, RRID:SCR_008197)Rutgers University; New Jersey; USA Last checked downnif-0000-21251http://compgen.rutgers.edu/mapomat/
PROTOTYPE - Suspected Overlap Among OBO Foundry Candidate OntologiesResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Service that determines the Suspected Overlap Among OBO Foundry Candidate Ontologies.SCR_008834(PROTOTYPE - Suspected Overlap Among OBO Foundry Candidate Ontologies, RRID:SCR_008834)National Center for Biomedical Ontology Last checked downnlx_144632
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