Searching the RRID Resource Information Network
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Speech Language Disorders Database Resource Report Resource Website |
Speech Language Disorders Database (RRID:SCR_003655) | SLDB | data or information resource, data set | Curated lists of genes associated to speech / language phenotypes and structural or functional abnormalities observed in patient populations. Entrez ID gene information, as well as gene expression profiles from the Allen Brain Atlas are available. You can also download expression data for a given gene in JSON or XML format. | gene, speech, language, phenotype, locus, structure, function, gene expression |
is related to: Allen Human Brain Atlas has parent organization: Boston University; Massachusetts; USA |
Speech disorder, Language disorder | nlx_157808 | SCR_003655 | Speech/Language Disorders Database, Speech / Language Disorders Database | 2026-02-14 02:07:49 | 0 | |||||||
|
Linked Neuron Data Resource Report Resource Website |
Linked Neuron Data (RRID:SCR_003658) | LND | data or information resource, data set | Neuroscience data and knowledge from multiple scales and multiple data sources that has been extracted, linked, and organized to support comprehensive understanding of the brain. The core is the CAS Brain Knowledge base, a very large scale brain knowledge base based on automatic knowledge extraction and integration from various data and knowledge sources. The LND platform provides services for neuron data and knowledge extraction, representation, integration, visualization, semantic search and reasoning over the linked neuron data. Currently, LND extracts and integrates semantic data and knowledge from the following resources: PubMed, INCF-CUMBO, Allen Reference Atlas, NIF, NeuroLex, MeSH, DBPedia/Wikipedia, etc. | neuron, brain, neuroscience, protein, gene, neurotransmitter |
is related to: Common Upper Mammalian Brain Ontology is related to: Neuroscience Information Framework is related to: PubMed is related to: NeuroLex is related to: MeSH is related to: DBpedia is related to: Allen Mouse Brain Reference Atlas is related to: Allen Institute for Brain Science has parent organization: Chinese Academy of Sciences; Beijing; China |
nlx_157812 | SCR_003658 | Linked Neuron Data (LND) | 2026-02-14 02:07:29 | 0 | ||||||||
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Sol Genomics Network - Bulk download Resource Report Resource Website |
Sol Genomics Network - Bulk download (RRID:SCR_007161) | data or information resource, data set | Allows users to download Unigene or BAC information using a list of identifiers or complete datasets with FTP., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, dataset, unigene, gene, bac, genomics, clone, array spot, unigene id, bac ends |
is related to: SGN has parent organization: Boyce Thompson Institute for Plant Research |
NSF 0820612; USDA CSREES |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30227 | SCR_007161 | SGN bulk download | 2026-02-14 02:07:54 | 0 | |||||||
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SpliceDB Resource Report Resource Website 1+ mentions |
SpliceDB (RRID:SCR_006262) | SpliceDB | data or information resource, data set | Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs. | gene, expressed sequence tag, splice, canonical, non-canonical, splice site, sequence, data set, splice site sequence |
is listed by: OMICtools is listed by: 3DVC is related to: GenBank has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11125105 PMID:11058137 |
nlx_151853, OMICS_01892 | http://linux1.softberry.com/berry.phtml?topic=splicedb | http://genomic.sanger.ac.uk/spldb/SpliceDB.htm | SCR_006262 | SpliceDB: canonical and non-canonical splice site sequences in mammalian genes | 2026-02-14 02:07:52 | 2 | |||||
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Berkeley Drosophila Genome Project Resource Report Resource Website 100+ mentions |
Berkeley Drosophila Genome Project (RRID:SCR_013094) | BDGP, BDGP EST, BDGP INS | data or information resource, database | Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs. | drosophila genome, cdna, est, transposon insertions, genomic sequencing, gene, FASEB list |
is related to: Bgee: dataBase for Gene Expression Evolution is related to: OpenFlyData.org has parent organization: University of California at Berkeley; Berkeley; USA is parent organization of: Patterns of Gene Expression in Drosophila Embryogenesis |
NHGRI ; NIGMS |
PMID:21177961 | nif-0000-02867 | http://www.bdgp.org/ | SCR_013094 | 2026-02-14 02:07:17 | 463 | ||||||
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Orphanet Resource Report Resource Website 100+ mentions |
Orphanet (RRID:SCR_006628) | Orphanet | data or information resource, portal | European website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Reference portal for rare diseases and orphan drugs to help improve diagnosis, care and treatment of patients with rare diseases. | drug, clinical, diagnostic, test, rare, disease, molecule, gene, orphan, drug |
is used by: NIF Data Federation is used by: HmtPhenome is listed by: OMICtools is related to: Disease core ontology applied to Rare Diseases is related to: phenomeNET has parent organization: National Institute of Health and Medical Research; Rennes; France is parent organization of: Orphanet Rare Disease Ontology |
National Institute of Health and Medical Research ; Rennes ; France ; French Directorate General for Health ; European Union |
Free, Freely available | nif-0000-21306, grid.458406.b, Wikidata: Q1515833 | https://ror.org/03d3kf570 | SCR_006628 | 2026-02-14 02:05:06 | 404 | ||||||
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Consensus CDS Resource Report Resource Website 100+ mentions |
Consensus CDS (RRID:SCR_006729) | CCDS | data or information resource, database | Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly. | human genome sequence, human protein, mouse genome sequence, mouse protein, protein coding region, gene, genome sequence, genome, sequence, gene annotation, protein, gold standard |
is listed by: OMICtools is related to: Entrez Gene is related to: HomoloGene is related to: MapViewer is related to: VEGA has parent organization: NCBI has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: University of California at Santa Cruz; California; USA |
PMID:24217909 PMID:22434842 PMID:19498102 |
The community can contribute to this resource, Acknowledgement requested | nif-0000-02645, OMICS_01535 | http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi | SCR_006729 | CCDS Database, NCBI Consensus CDS protein set, NCBI CCDS Database | 2026-02-14 02:06:27 | 230 | |||||
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SysZNF - C2H2 Zinc Finger genes Resource Report Resource Website |
SysZNF - C2H2 Zinc Finger genes (RRID:SCR_007056) | SysZNF | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. SysZNF is an information resource for C2H2 Zinc Finger genes in humans and mice. C2H2 Zinc Finger genes (C2H2-ZNF) constitute the largest class of transcription factors in humans and mouse. C2H2 zinc finger proteins primarily bind to DNA. In most cases, they attach to regions near certain genes and turn the genes on and off as needed. The researches on these genes show light on the evolution of gene regulation systems and development. Therefore, we develop SysZNF (Systematical information resource of Zinc Finger genes) to collect the information related to C2H2 Zinc Finger genes. The aim of SysZNF was to provide a user-friendly interface for rendering the information (DNA, Expression, Protein, Reference and so on) of each C2H2-ZNF (e.g., ZNF10) and to enable a comprehensive analysis of C2H2-ZNF. This project was supported by the Proteome-Center at Rostock University (PCRU) who conceives the concept of the database and Key laboratory of Systems biology at the Shanghai Institute for Biological Sciences (SIBS) who implemented the database. It is maintained jointly by PCRU and SIBS. | zinc finger protein, zinc finger, cysteine, histidine, zinc ion, gene |
has parent organization: University of Rostock; Mecklenburg-Vorpommern; Germany has parent organization: Chinese Academy of Sciences; Beijing; China |
BMBF 2007DFA31040; Chinese Academy of Sciences CHN07/38 |
PMID:18974185 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03530 | SCR_007056 | SysZNF: the C2H2 Zinc Finger Gene Database, SysZNF: the Zinc Finger gene database | 2026-02-14 02:06:35 | 0 | |||||
|
MyHits Resource Report Resource Website 10+ mentions |
MyHits (RRID:SCR_006757) | data or information resource, database | Database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. | protein, domain, motif, sequence, predictor, markov, model, gene, expression, mysql, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:17545200 | Free | nif-0000-02962, biotools:myhits | https://bio.tools/myhits | SCR_006757 | MyHit | 2026-02-14 02:06:34 | 39 | ||||||
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Arabidopsis Gene Regulatory Information Server Resource Report Resource Website 10+ mentions |
Arabidopsis Gene Regulatory Information Server (RRID:SCR_006928) | AGRIS | data or information resource, database | An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB). | gene regulatory, gene, arabidopsis thaliana, promoter sequence, target gene, transcription factor, FASEB list |
is listed by: OMICtools has parent organization: Ohio State University; Ohio; USA |
NSF | PMID:21059685 PMID:16524982 PMID:12820902 |
Free, Acknowledgement requested | OMICS_00548, nif-0000-02540 | SCR_006928 | 2026-02-14 02:06:35 | 49 | ||||||
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EMBRYS Resource Report Resource Website 1+ mentions |
EMBRYS (RRID:SCR_006689) | EMBRYS | data or information resource, database | Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System. | Gene, expression, pattern, mapped, whole mount, mouse, embryo, ICR strain, mid gestational stage, transcription, factor, cofactor, data |
uses: RIKEN uses: MGC uses: PANTHER |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japanese Ministry of Health Labor and Welfare |
Free, Freely available | nlx_153839 | http://embrys.jp/embrys/html/MainMenu.html | SCR_006689 | Embryonic Gene Expression Database for Biomedical Research Source, Embryonic gene expression Database as a Biomedical Research Source | 2026-02-14 02:05:56 | 8 | |||||
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UniSTS Resource Report Resource Website 10+ mentions |
UniSTS (RRID:SCR_006843) | UniSTS | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. Chromosome maps are labeled by name of the originating organism, the map title, total markers, total UniSTSs and links to view maps as well as research documents available through PubMed, another NCBI database. The search functions within UniSTS allow the user to search by gene marker, chromosome, gene symbol and gene description terms to locate markers on specified genes. A representation of the UniSTS datasets is available by ftp. NOTE: All data from this resource have been moved to the Probe database, http://www.ncbi.nlm.nih.gov/probe. You can retrieve all UniSTS records by searching the probe database using the search term unists(properties). (use brackets insead of parenthesis). Additionally, legacy data remain on the NCBI FTP Site in the UniSTS Repository (ftp://ftp.ncbi.nih.gov/pub/ProbeDB/legacy_unists). | marker, primer sequence, mapping, sequence tagged site, genomic position, gene, sequence, nucleotide, nucleotide sequence, chromosome, gold standard |
is listed by: re3data.org is related to: NCBI Probe has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03614 | SCR_006843 | UniSTS: Integrating Markers and Maps, NCBI UniSTS, Entrez UniSTS | 2026-02-14 02:06:01 | 40 | |||||||
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AthaMap Resource Report Resource Website 10+ mentions |
AthaMap (RRID:SCR_006717) | data or information resource, database | Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. | gene, arabidopsis thaliana, binding site, genome, transcription factor, small rna binding site, small rna, rna, microrna, cis-regulatory element, post-transcriptional regulation, FASEB list |
is listed by: OMICtools is listed by: bio.tools has parent organization: Technical University of Braunschweig; Braunschweig; Germany |
PMID:22800758 PMID:21177332 PMID:18842622 PMID:17148485 PMID:16922688 PMID:15980498 PMID:14681436 |
Free, Freely available | nif-0000-02583, biotools:athamap, OMICS_00549, nif-0000-20814, SCR_013106 | https://bio.tools/athamap | SCR_006717 | Arabidopsis thaliana Map | 2026-02-14 02:06:34 | 48 | ||||||
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Biomolecular Object Network Databank Resource Report Resource Website 10+ mentions |
Biomolecular Object Network Databank (RRID:SCR_007433) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.BOND, which requires registration of a free account, is a resource used to perform cross-database searches of available sequence, interaction, complex and pathway information. BOND integrates a range of component databases including GenBank and BIND, the Biomolecular Interaction Network Database. BOND contains 70+ million biological sequences, 33,000 structures, 38,000 GO terms, and over 200,000 human curated interactions contained in BIND, and is open access. BOND serves the interests of the developing global interactome effort encompassing the genomic, proteomic and metabolomic research communities. BOND is the first open access search resource to integrate sequence and interaction information. BOND integrates BLAST functionality, and contains a well-documented API. BOND also stores annotation links for sequences, including links to Genome Ontology descriptions, MedLine abstracts, taxon identifiers, associated structures, redundant sequences, sequence neighbors, conserved domains, data base cross-references, Online Mendalian Inheritance in Man identifiers, LocusLink identifiers and complete genomes. BIND on BOND The Biomolecular Interaction Network Database (BIND), a component database of BOND, is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature. BIND is an interaction database with three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions.Interactions A BIND record represents an interaction between two or more objects that is believed to occur in a living organism. A biological object can be a protein, DNA, RNA, ligand, molecular complex, gene, photon or an unclassified biological entity. BIND records are created for interactions which have been shown experimentally and published in at least one peer-reviewed journal. A record also references any papers with experimental evidence that support or dispute the associated interaction. Interactions are the basic units of BIND and can be linked together to form molecular complexes or pathways. The BIND interaction viewer is a tool to visualize and analyze molecular interactions, complexes and pathways. The BIND interaction viewer uses Ontoglyphs to display information about a protein via attributes such as molecular function, biological process and sub-cellular localization. Ontoglyphs allow to graphically and interactively explore interaction networks, by visualizing interactions in the context of 34 functional, 25 binding specificity and 24 sub-cellular localization Ontoglyphs categories. We will continue to provide an open access version of BOND, providing its subscribers with free, unlimited access to a core content set. But we are confident you will soon want to upgrade to BONDplus. | gene, genes, genome, annotation, binding specificity, biological process, complex, dna, genomes, genomic, human, interaction, interactome, ligand, metabolomic, molecular, molecular complex, molecular function, molecular interaction, mouse, ontoglyphs, ontology terms, pathway, photon, protein, protein-protein interactions, proteomic, rna, sequence, structure, sub-cellular localization, taxonomy, unclassified biological entity | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00571 | SCR_007433 | BOND | 2026-02-14 02:06:28 | 17 | |||||||||
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5S Ribosomal RNA Database Resource Report Resource Website 1+ mentions |
5S Ribosomal RNA Database (RRID:SCR_007545) | 5S Ribosomal RNA Database | data or information resource, database | A database on nucleotide sequences of 5S rRNAs and their genes. The database contains 1985 primary structures of 5S rRNA and 5S rDNA, and was last updated in 2002, according to the website. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. The multiple sequence alignments of 5S ribosomal RNAs can be downloaded in TAB-delimited and FASTA formats. | eubacteria, eukaryote, archaebacteria, mitochondrion, model rna molecule, nucleotide sequence database, ribosome, plastid, ribosomal rna, sequence alignment, rna-protein interaction, rna, rna structure, 5s rrna, gene, 5s rdna, mitochondria, sequence, alignment | has parent organization: Polish Academy of Sciences Warsaw; Warsaw; Poland | Deutsche Agentur fur Raumfahrtangelegenheiten GmbH ; Fonds der Chemischen Industrie e.V. ; Polish State Committee for Scientific Research ; DFG |
PMID:10592212 | nif-0000-02526 | http://rose.man/poznan. pl/5SData/index.html | SCR_007545 | 2026-02-14 02:06:36 | 6 | ||||||
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MIPS Ustilago maydis Database Resource Report Resource Website 1+ mentions |
MIPS Ustilago maydis Database (RRID:SCR_007563) | data or information resource, database | The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite. | drug, environment, filamentous, functional, fungal, fungal genome databases, fungus, gene, genetic, basidiomycete, cell, codon, culture, dikaryotic, diploid, genome, genomic, germinate, haploid, host, human, infection, maize, mating, meiotic, model, molecular, morphogenesis, network, orf, pathogen, pathologist, phytopathogen, phytopathogenesis, plant, protein, recombination, sequence, signal, spore, strain, structure, teliospore, teosinte, tissue, tumor, ustilago maydis, virulence, yeast | nif-0000-21276 | SCR_007563 | MUMDB | 2026-02-14 02:06:04 | 9 | ||||||||||
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GOA Resource Report Resource Website 500+ mentions |
GOA (RRID:SCR_007691) | GOA, GOA REF | data or information resource, database | An annotation program which aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). It is a central dataset for other major multi-species databases, such as Ensembl and NCBI. Because of the multi-species nature of the UniProtKB, UniProtKB-GOA assists in the curation of 200,000 species. This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. Gene Association Files can be accessed from the Downloads section of the website. | gene ontology, chicken proteome, cow proteome, human proteome, xref, gene, gene association, gold standard |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is related to: FlyMine is related to: UniProt DAS is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures has parent organization: European Bioinformatics Institute |
Public, Available to the research community, All UniProtKB-GOA Gene Association Files are released approximately every four weeks | nif-0000-02916 | SCR_007691 | UniProtKB-GOA, Gene Ontology Annotation (UniProtKB-GOA) Database, GOA - Gene Ontology Annotation, Gene Ontology Annotation, GO Annotation at EBI | 2026-02-14 02:06:01 | 570 | |||||||
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SYSTERS Resource Report Resource Website 1+ mentions |
SYSTERS (RRID:SCR_007955) | data or information resource, database | SYSTERS is a database of protein sequences grouped into homologous families and superfamilies. The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a superfamily. The sequence data underlying SYSTERS release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ENSEMBL, TAIR, SGD and GeneDB), in addition to the comprehensive Swiss-Prot/TrEMBL databases. To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server. Furthermore, users can retrieve pre-processed analyses of families like multiple alignments and phylogenetic trees. New query options comprise a batch retrieval tool for functional inference about families based on automatic keyword extraction from sequence annotations. A new access point, PhyloMatrix, allows the retrieval of phylogenetic profiles of SYSTERS families across organisms with completely sequenced genomes. Gene, Human, Vertebrate, Genome, Human ORFs | family, gene, genome, human, human orfs, protein, superfamily, vertebrate | has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany | nif-0000-03528 | SCR_007955 | SYSTERS | 2026-02-14 02:06:10 | 7 | |||||||||
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ARNIE Resource Report Resource Website |
ARNIE (RRID:SCR_000514) | ARNIE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided. | network, orthologue, paralogue, gene, orthologue, protein interaction, protein, blast, extracellular, expression profiling, interaction network, ligand, interaction, signaling |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
MRC ; Wellcome Trust |
PMID:20802085 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01529 | SCR_000514 | AVEXIS Receptor Network with Integrated Expression | 2026-02-14 02:06:00 | 0 | |||||
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Lifespan Observations Database Resource Report Resource Website 1+ mentions |
Lifespan Observations Database (RRID:SCR_001609) | Lifespan Observations Database | data or information resource, database | Database that collects published lifespan data across multiple species. The entire database is available for download in various formats including XML, YAML and CSV. | lifespan, phenotype, intervention, gene, compound, publication |
is used by: NIF Data Federation is used by: Aging Portal is related to: MONARCH Initiative has parent organization: Sageweb |
Aging | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153873 | http://sageweb.org/lifespandb | SCR_001609 | Sageweb Lifespan Observation Database | 2026-02-14 02:06:05 | 1 |
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