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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: Sep 14, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
ASAPResource, service resource, data or information resource, data repository, storage service resource, databaseDatabase and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points.gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis serviceSCR_001849(ASAP, RRID:SCR_001849)University of Wisconsin-Madison; Wisconsin; USA NIGMS, USDArelated to: AmiGO, used by: NIF Data FederationPMID:12519969Last checked downnif-0000-02571https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
VMDResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett''''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs.microbial genome sequence, genome, genome sequence, genome model, gene, image, oomycete, fungus, bacteria, phytophthora sojae, phytophthora ramorum, hyaloperonospora arabidopsidis, plantSCR_004905(VMD, RRID:SCR_004905)Virginia Polytechnic Institute and State University; Virginia; USA NSF, USDA Cooperative State Research Education and Extension Servicerelated to: AmiGO, used by: NIF Data FederationPMID:16381891Last checked downnlx_87328http://phytophthora.vbi.vt.edu
Songbird Brain Transcriptome DatabaseResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase containing cDNA clone information of the brains of songbirds. These clones are annotated with behavioral information, as well as links to information of homologous genes of other species. The database includes over 91,000 zebra finch brain cDNAs (2009) sequenced by Duke, ESTIMA, and Rockefeller research groups. The project is a collaborative effort of the Jarvis Laboratory of Duke University, Duke Bioinformatics, and The Genomics group of RIKEN, with Erich D. Jarvis as P.I. and Kazuhiro Wada as Co-P.I. Microarrays with the cDNAs in this database are available at Duke http://mgm.duke.edu/genome/dna_micro/core/spotted.htm and through the NIH Neurosciences Microarray Consortium http://arrayconsortium.tgen.org/np2/public/overview.jspbrain, songbird, microarray, cdna, cdna clone, clone, behavior, homologous gene, annotation, homologueSCR_006182(Songbird Brain Transcriptome Database, RRID:SCR_006182)Duke University School of Medicine; North Carolina; USA Human Fronteir Science Program, Japanese Ministry of Education Culture Sports Science and Technology MEXT, Klingenstein Foundation, NIDCD, NSF, Packard Foundation, RIKEN, Waterman award, Whitehall Foundationrelated to: NIH Neuroscience Microarray Consortium, AmiGOPMID:17018643Last checked downnlx_151729
NCBIResource, portal, data or information resourceA portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.biomedical, genomic, molecular biology, health, disease, database, computational biologySCR_006472(NCBI, RRID:SCR_006472)National Library of Medicine related to: AmiGO, NCBI Viral Genomes, Clone DB, PubReader, OMIA - Online Mendelian Inheritance in Animals, European Nucleotide Archive, used by: NIF Data Federation, listed by: NIDDK Information NetworkLast checked downnif-0000-00139http://www.ncbi.nih.gov/
MeGOResource, ontology, data or information resource, controlled vocabularyA Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up.phage, plasmid, protein family, mobile genetic element, oboSCR_000110(MeGO, RRID:SCR_000110)A Classification of Mobile genetic Elements related to: OBO, AmiGO, Gene Ontology, listed by: BioPortalLast checked upnlx_156939
Candida Genome DatabaseResource, service resource, data or information resource, data repository, storage service resource, databaseDatabase of genetic and molecular biological information about Candida albicans, a yeast that is an opportunistic pathogen of humans, and about other Candida-related species, such as Candida glabrata. It contains information about genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to a DNA sequence also have Locus Pages. The Locus Page is the central clearinghouse for all information specific to that gene and tools for its analysis, including: * gene name, synonyms, and systematic name * Gene Ontology (GO) annotations * descriptions of the gene and gene product * phenotype of mutations in the gene * chromosomal and contig coordinates * interactive graphical chromosome map and browsing tool * tools for retrieval and analysis of the gene and protein sequences * a curated collection of literature CGD also provides a Gene Ontology, GO, to all its users. GO is a collaborative project involving CGD and other model organism databases to provide controlled vocabularies that are used to describe the molecular function and cellular location of gene products and the biological process in which they are involved. The three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. The development of the ontologies is ongoing in order to incorporate new information. Data submissions are welcome.protein, chromosome, classification, gene, genome, candidiasis, thrush, yeast, yeast gene, yeast genome, candida albicans, candida glabrata, data analysis service, biological role, molecular function, subcellular localization, chromosome sequenceSCR_002036(Candida Genome Database, RRID:SCR_002036)Stanford University School of Medicine; California; USA NIDCRrelated to: AmiGO, ASPGD, Gene Ontology, used by: NIF Data FederationPMID:19808938Last checked upnif-0000-02634
ASPGDResource, service resource, data or information resource, data repository, storage service resource, databaseDatabase of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.function, gene, gene name, annotation, aspergillus, aspergillus nidulans, chromosome, community, dna, genome, genomic, localization, orthology, phenotype, protein, protein-coding genes, s. cerevisiae, sequence, allele, data analysis serviceSCR_002047(ASPGD, RRID:SCR_002047) Broad Institute , Stanford University School of Medicine; California; USA NIAIDrelated to: Candida Genome Database, AmiGO, used by: NIF Data FederationPMID:19773420Last checked upnif-0000-12244http://www.aspergillusgenome.org/
ECOResource, ontology, data or information resource, controlled vocabularyA controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenanceSCR_002477(ECO, RRID:SCR_002477) Google Code , University of Maryland School of Medicine; Maryland; USA NIGMSrelated to: AmiGO, Gene Ontology, listed by: BioPortalLast checked upnlx_155860http://code.google.com/p/evidenceontology/, http://bioportal.bioontology.org/ontologies/ECO
EcoCycResource, data or information resource, databaseDatabase for the bacterium Escherichia coli K-12 MG1655, the EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.genome, metabolic pathway, transcription, transporters, escherichia coli, transcriptional regulation, metabolism, pathwaySCR_002433(EcoCyc, RRID:SCR_002433)Stanford Research Institute International NCRR, NIGMSrelated to: MultiFun, BioCyc, BioCyc, AmiGO, NCBI BioSystems Database, Pathway Tools, used by: NIF Data Federation, uses: Pathway Tools, listed by: OMICtools, BioCycReferences (2)Last checked upnif-0000-02783, OMICS_01645
Zebra Model Organism Database (ZFIN)Resource, service resource, data or information resource, data repository, storage service resource, databaseZFIN is a Model Organism Database that serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. ZFIN includes (i) access to images with associated curated data, (ii) gene expression and phenotype data, (iii) zebrafish models of human diseases, (iv) genomic features and molecular details, (v) a genome browser, (vi) transcripts, (vii) antibodies and (viii) a community wiki for protocols and antibodies. ZFIN welcomes direct data submissions. If you would like to make your unpublished expression or phenotype data available to the community, you can submit this data to ZFIN using Phenote program or contact zfinadmn@zfin.org for additional options and support. Additionally, data is downloadable as text files and available in the data mining platform zebrafishmine (zebrafishmine.org).expression, gene, anatomy, development, disease, genomic, model, molecular, mutant, neuronal, organism, phenotype, physiological, synteny, zebrafish, gene expression, genome sequence, molecular neuroanatomy resource, genotype, anatomical structure, publication, genome, image collection, gold standardSCR_002560(Zebra Model Organism Database (ZFIN), RRID:SCR_002560)University of Oregon; Oregon; USA NHGRIrelated to: AmiGO, Phenoscape Knowledgebase, MONARCH Disease Models View, Bgee: a dataBase for Gene Expression Evolution, NIH Data Sharing Repositories, HomoloGene, Zebrafish International Resource Center, Integrated Manually Extracted Annotation, used by: NIF Data Federation, Monarch Initiative, Resource Identification Portal, Morpholino Database, Integrated Animals, uses: InterMOD, recommended by: Resource Identification Portal, listed by: OMICtools, InterMOD, re3data.orgReferences (3)Last checked upnif-0000-21427, OMICS_01666http://zfin.org/ZFIN/misc_html/tips.html#newrecord, https://wiki.zfin.org/display/general/ZFIN+Data+Submissions
NCBI ProteinResource, data or information resource, databaseDatabase of protein sequences related to biological structure and function from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, Protein Information Resource (PIR), Protein Research Foundation (PRF), and Protein Data Bank (PDB).amino acid sequence, nucleotide, dna sequence, protein, sequence, sequence data, structure, function, dna, nucleotide sequence, genomics, protein binding, gold standardSCR_003257(NCBI Protein, RRID:SCR_003257)NCBI related to: AmiGO, GenBank, RefSeq, TPA, UniProtKB, PIR, Protein Research Foundation, Research Collaboratory for Structural Bioinformatics Protein Data Bank, BioExtract, DIG IT - Database of Immunoglobulins and Integrated Tools, used by: NIF Data Federation, listed by: re3data.orgLast checked upnif-0000-03178http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein
UniProtKBResource, data or information resource, databaseA central repository for the collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway.protein, annotation, amino acid sequence, taxonomy, proteomeSCR_004426(UniProtKB, RRID:SCR_004426)Universal Protein Resource related to: ESTHER, PIRSF, AmiGO, UniSave, ProRepeat, UniProt Chordata protein annotation program, neXtProt, TopFIND, UniPathway, NCBI Protein, Biomine, Gene Ontology, Monarch Initiative, UniProt DAS, FunTree, ConceptWiki, InterProScan, used by: NIF Data Federation, PINT, uses: UniportKBLast checked upnlx_53981
GeneDB LmajorResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.genome, gene, rna gene, rna, pseudogene, protein-coding, function, host-pathogen interaction, interaction, proteolytic enzyme, glycoconjugate, sequence annotationSCR_004613(GeneDB Lmajor, RRID:SCR_004613)GeneDB Wellcome Trustrelated to: AmiGO, TriTrypDB, used by: NIF Data FederationPMID:16020728Last checked upnlx_60997
GeneDB TbruceiResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase of the most recent sequence updates and annotations for the T. brucei genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. T. brucei possesses a two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split into three classes of chromosomes according to their size on pulsed-field gel electrophoresis, 11 pairs of megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and minichromosomes (50-100 kb). The T. brucei genome contains a ~0.5Mb segmental duplication affecting chromosomes 4 and 8, which is responsible for some 75 gene duplicates unique to this species. A comparative chromosome map of the duplicons can be accessed here (PubmedID 18036214). Protozoan parasites within the species Trypanosoma brucei are the etiological agent of human sleeping sickness and Nagana in animals. Infections are limited to patches of sub-Saharan Africa where insects vectors of the Glossina genus are endemic. The most recent estimates indicate between 50,000 - 70,000 human cases currently exist, with 17 000 new cases each year (WHO Factsheet, 2006). In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.blast, sequence, annotation, genomeSCR_004786(GeneDB Tbrucei, RRID:SCR_004786)GeneDB Wellcome Trustrelated to: AmiGO, TriTrypDB, used by: NIF Data FederationPMID:16020726Last checked upnlx_78417
SGNResource, data or information resource, databaseA 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 genomeSCR_004933(SGN, RRID:SCR_004933)Boyce Thompson Institute for Plant Research ATC Inc. Advanced Technologies Cambridge, NSF, USDArelated to: Sol Genomics Network - Bulk download, AmiGO, used by: NIF Data FederationReferences (2)Last checked upnlx_89764http://www.sgn.cornell.edu/
go-db-perlResource, software resourceSoftware resource that extends the functionality of go-perl (on which it depends) with GO Database access functionality. go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools. Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI and DBD Perl modules. Full installation instructions are included in the download. go-db-perl is in use both to drive AmiGO and internally within Ensembl. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblesoftware library, database, gene ontology, database or data warehouseSCR_005721(go-db-perl, RRID:SCR_005721) Gene Ontology , Comprehensive Perl Archive Network related to: AmiGO, go-moose, Ensembl, go-perl, listed by: Gene Ontology ToolsLast checked upnlx_149180
GO-ModuleResource, analysis service resource, data analysis service, service resource, production service resourceGO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online toolfunctional similarity, visualization, other analysis, reduce the dimensionality of go enrichment results, produce interpretable biomodules of significant go terms, gene ontology, ontology or annotation visualization, annotationSCR_005813(GO-Module, RRID:SCR_005813)University of Illinois at Chicago; Illinois; USA Cancer Research Foundation, NCI, NCRR, NIH, NLMrelated to: Gene Ontology, AmiGO, listed by: Gene Ontology ToolsPMID:21421553Last checked upnlx_149322
Mouse Genome Informatics (MGI)Resource, data or information resource, databaseAn international database for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Its primary mission is to facilitate the use of the mouse as a model system for understanding human biology and disease. MGI creates and maintains an integrated representation of mouse genetic, genomic, expression, and phenotype data and develops definitive reference data set and consensus data views. MGI also synthesizes comparative genomic data between the mouse and other mammals, maintains a set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides extensive technical support for database users. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.molecular neuroanatomy resource, human health, human disease, animal model, gene expression, phenotype, genotype, gene, pathway, orthology, tumor, strain, single nucleotide polymorphism, recombinase, function, blast, image, pathology, model, data analysis service, genome, genetics, gold standardSCR_006460(Mouse Genome Informatics (MGI), RRID:SCR_006460)Jackson Laboratory NCI, NHGRI, NICHDrelated to: MONARCH Disease Models View, MouseCyc, AmiGO, Gene Expression Database, Bgee: a dataBase for Gene Expression Evolution, HomoloGene, Rat Gene Symbol Tracker, Enhancer Trap Line Browser, Integrated Brain Gene Expression, MalaCards, Gene Ontology, BioMart Project, NIH Data Sharing Repositories, RIKEN integrated database of mammals, JAX Neuroscience Mutagenesis Facility, PhenoGO, used by: NIF Data Federation, Resource Identification Portal, Monarch Initiative, PhenoGO, Integrated Animals, Cytokine Registry, uses: InterMOD, recommended by: Resource Identification Portal, listed by: 3DVC, re3data.org, OMICtools, NIH Data Sharing Repositories, InterMOD, affiliated with: InterMODReferences (2)Last checked upnif-0000-00096, OMICS_01656http://www.informatics.jax.org/batch, http://www.informatics.jax.org/submit.shtml
GeneDB PfalciparumResource, data or information resource, databaseDatabase of the most recent sequence updates and annotations for the P. falciparum genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Plasmodium research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. The P. falciparum 3D7 nuclear genome is 23.3 Mb in size, with a karyotype of 14 chromosomes. The G+C content is approximately 19%. The P. falciparum genome is undergoing re-annotation. This process started in October 2007 with a weeklong workshop co-organized by staff from the Wellcome Trust Sanger Intistute and the EuPathDB team. Ongoing curation and sequence checking is being carried out by the Pathogen Genomics group. Plasmodium falciparum is the most deadly of the five Plasmodium species that cause human malaria. Malaria has a massive impact on human health; it is the worlds second biggest killer after tuberculosis. Around 300 million clinical cases occur each year resulting in between 1.5 - 2.7 million deaths annually, the majority in sub-saharan Africa. It is estimated that 3,000 children under the age of five years fall victim to malaria each day. Around 40% of the worlds population are at risk. In collaboration with EuPathDB, genomic sequence data and annotations are regularly deposited on PlasmoDB where they can be integrated with other datasets and queried using customized queries.SCR_006567(GeneDB Pfalciparum, RRID:SCR_006567)GeneDB Wellcome Trustrelated to: AmiGO, ApiDB PlasmoDB, used by: NIF Data FederationPMID:12368864Last checked upnlx_13809
Pseudomonas Genome DatabaseResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download.gene, genome, annotation, localization, prokaryote, pseudomonas aeruginosa, sequence, subcellular, cystic fibrosis, ortholog, annotation, dna sequence, intergenic dna, protein sequenceSCR_006590(Pseudomonas Genome Database, RRID:SCR_006590)Simon Fraser University; British Columbia; Canada , University of British Columbia; British Columbia; Canada Cystic Fibrosis Foundation Therapeutics Increlated to: AmiGO, used by: NIF Data FederationPMID:18978025Last checked upnif-0000-03369
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