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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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VirOligo: Virus Oligonucleotide Database Resource Report Resource Website 1+ mentions |
VirOligo: Virus Oligonucleotide Database (RRID:SCR_013481) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of virus-specific oligonucloetides and their primers. It allows users to search based on virus name, PMID, VirOligoID, or taxonomy ID. The VirOligo database is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place. To this end, researchers are also exploring Virus Signature Hybridization (ViSH) and Virus Signature Amplification (ViSA), microarray-based methods for hybridization and PCR amplification. The site employs Universal PCR techniques, a PCR that amplifies DNA fragments from more than one viral species, such as family- or genus-specific PCR. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03635 | SCR_013481 | SciCrunch Registry | VirOligo | 2026-10-17 01:35:16 | 1 | ||||||||||
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Brain Coactivation Map Resource Report Resource Website |
Brain Coactivation Map (RRID:SCR_014172) | atlas, data or information resource | The Brain Coactivation Map describes all the coactivation networks in the human brain based on the meta-analysis of more than 5,400 neuroimaging articles (from NeuroSynth) containing more than 16,000 individual experiments. The map can be browsed interactively (CoactivationMap.app on GitHub) or queried from a shell using a command line tool (cmtool on GitHub). | atlas, map, coactivation network, human brain, interactive, command line |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Pasteur Institute |
Available to the research community | https://github.com/r03ert0/CoactivationMap.app, https://github.com/r03ert0/cmtool | SCR_014172 | SciCrunch Registry | 2026-10-17 01:35:19 | 0 | |||||||||
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PhenoGO Resource Report Resource Website 1+ mentions |
PhenoGO (RRID:SCR_013646) | data or information resource, database | PhenoGO is a computed database designed for high throughput mining that provides phenotypic and experimental context - such as the cell type, disease, tissue, and organ - to existing annotations between gene products and Gene Ontology (GO) terms, as specified in the Gene Ontology Annotations (GOA) for multiple model organisms. Phenotypic and Experimental (P&E) contexts to identifiers are computationally mapped to general biological ontologies, including: the Cell Ontology (CO), phenotypes from the Unified Medical Language System (UMLS), species from Taxonomy of the National Center for Biotechnology Information (NCBI) taxonomy, and specialized ontologies such as Mammalian Phenotype Ontology (MP) and Mouse Anatomy (MA). |
uses: WormBase uses: SGD uses: Gene Ontology uses: Mouse Genome Informatics (MGI) uses: FlyBase is related to: WormBase is related to: SGD is related to: Gene Ontology is related to: Mouse Genome Informatics (MGI) is related to: FlyBase has parent organization: University of Arizona; Arizona; USA |
Available to the research community, Acknowledgement requested | nlx_152722 | www.phenogo.org | SCR_013646 | SciCrunch Registry | Phenotype Context Database for Gene Ontology Annotations | 2026-10-17 01:33:35 | 2 | ||||||||
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Aminoacyl-tRNA synthetase database Resource Report Resource Website 1+ mentions |
Aminoacyl-tRNA synthetase database (RRID:SCR_013498) | data or information resource, database | The AARSs database is the collection of amino acid sequences of all published AARSs. Currently it contains 1047 primary structures of cytoplasmic and organellar AARSs from various organisms. The entries are grouped according to AARS amino acid specificity. They are based on EMBL/SWISS-PROT format. Each includes the AARS amino acid sequence, its SWISS-PROT name and the accession number, a short description of the sequence, its source (organism name with taxonomic classification) and bibliographic information. For the enzymes whose sequences were determined at the nucleotide level, the appropriate EMBL/GenBank or TIGR entries are included, and for those with already known 3D structure, the cross-references to the Brookhaven Protein Data Base are indicated. The partial sequences of AARSs are also included in the database. According to the original SWISS-PROT description, some of the entries have been marked as putative or probable. | aars, aars specificity, aminoacyl-trna synthetase, aminoacyl-trna synthetase specificity | has parent organization: Polish Academy of Sciences Poznan; Poznan; Poland | PMID:11125115 | nif-0000-02546 | SCR_013498 | SciCrunch Registry | AARS DB | 2026-10-17 01:33:36 | 1 | ||||||||
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SBM DB Resource Report Resource Website 1+ mentions |
SBM DB (RRID:SCR_013491) | SBM DB | data or information resource, database | It is a comprehensive database of Gene Expression Profiles, which enable to compare the transcriptome of various tissues, organs and experiments. mRNA expression levels of thousands of genes are measured with oligo-nucleotide DNA microarray "GeneChip". All gene expression data in this database is produced by LSBM (Laboratory for Systems Biology and Medicine) and the collaborators. SBM DB provides two different databases: A reference database for fur expression analysis (RefEXA) and LSMB GeNet, a database of various organisms, tissues, and experiences. RefEXA provides a comprehensive gene expression database of Human normal tissues, normal cultured cells and cancer cell lines with GeneChip HG-U133A, can help investigation of Human disease. LSMB provides | has parent organization: University of Tokyo; Tokyo; Japan | nif-0000-03395 | SCR_013491 | SciCrunch Registry | Systems Biology and Medicine Database | 2026-10-17 01:35:16 | 5 | |||||||||
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WormGUIDES Resource Report Resource Website 1+ mentions |
WormGUIDES (RRID:SCR_013733) | atlas, data or information resource | A worm atlas that provides an interactive 4D atlas of nuclear positions, from zygote until hatching which can be used to guide cell identification. The tools enable examination of the connectome during development from integrate knowledge of C. elegans embryogenesis to widely used resources, such as WormAtlas and WormBase. | embryogenesis, development, neural connectivity, diSPIM, 4d atlas, c elegans | has parent organization: Yale University; Connecticut; USA | NIH Office of the Director R24 OD016474 | Free, Public, Requires Java | SCR_014203 | https://orip.nih.gov/comparative-medicine/programs/invertebrate-models, http://www.wormguides.org/wormguides | SCR_013733 | SciCrunch Registry | Global Understanding in Dynamic Embryonic Systems | 2026-10-17 01:33:37 | 4 | ||||||
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LabLog Resource Report Resource Website |
LabLog (RRID:SCR_013975) | electronic laboratory notebook, software application, software resource | An ELN (electronic lab notebook) software application which can be used to document neuroscience projects and store metadata. LabLog is meant to constitute a laboratory's long term memory for project related information. To do this, project information is stored in a central laboratory database and can be easily retrieved by searching and filtering. | ELN, electronic laboratory notebook, software application, data management, lab management, neuroscience |
is listed by: Connected Researchers is related to: Connected Researchers |
Free | SCR_013975 | SciCrunch Registry | Laboratory Logbook | 2026-10-17 01:34:16 | 0 | |||||||||
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RARTF Resource Report Resource Website 1+ mentions |
RARTF (RRID:SCR_013457) | RARTF | data or information resource, database | Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available. | transcription factor, protein, gene, microarray, expression profile |
is listed by: OMICtools is related to: InterProScan |
PMID:16769687 | Free | OMICS_00562 | SCR_013457 | SciCrunch Registry | RARTF: RIKEN Arabidopsis Transcription Factor database, RIKEN Arabidopsis Transcription Factor database | 2026-10-17 01:33:36 | 2 | ||||||
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EchinoBase Resource Report Resource Website 100+ mentions |
EchinoBase (RRID:SCR_013732) | data or information resource, database | Database that provide a genomic information and comparative genomics platform on sea urchins and related echinoderms. It provide collection of information to directly support experimental work on these useful research models in cell and developmental biology. | sea urchins, echinoderms, genome, FASEB list | NIH Office of the Director P40 OD010959 | PMID:19010966 | Free, Public | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | SCR_013732 | SciCrunch Registry | SpBase, Echinoderm genomic database, Gene Library Resource for the Sea Urchin Strongylocentrotus purpuratus, Sea Urchin Genome Database, Echino Base | 2026-10-17 01:35:17 | 108 | |||||||
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labfolder Resource Report Resource Website 1+ mentions |
labfolder (RRID:SCR_013974) | electronic laboratory notebook, software application, software resource | An ELN (electronic lab notebook) software application where researchers can record and organize their data by recording, dragging, and dropping elements. Users can utilize tools and features such as image annotation, search and filter, protocol templates, and team communication. The format of the ELN is customizable and can be rearranged at any point. | ELN, electronic laboratory notebook, software application, data management, lab management, |
is listed by: Connected Researchers is related to: Connected Researchers |
Available to the research and education community, Fee for different packages (pay per user per month) | SCR_013974 | SciCrunch Registry | Labfolder, LabFolder | 2026-10-17 01:33:35 | 1 | |||||||||
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NoPdb: Nucleolar Proteome Database Resource Report Resource Website 1+ mentions |
NoPdb: Nucleolar Proteome Database (RRID:SCR_013459) | NoPDB | data or information resource, database | It archives data on more than 700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene its domain structures and relevant protein homologues across species as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of 500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints highlighted by visualization means in the NOPdb provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/ uncharacterized proteins. The NOPdb is searchable by either gene names protein sequences Gene Ontology terms or motifs or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink OMIM and PubMed). | has parent organization: University of Dundee; Scotland; United Kingdom | nif-0000-03196 | SCR_013459 | SciCrunch Registry | Nucleolar Proteome Database | 2026-10-17 01:34:15 | 7 | |||||||||
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KAVIAR Resource Report Resource Website 10+ mentions |
KAVIAR (RRID:SCR_013737) | data or information resource, database | A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants. | SNV, single nucleotide variant, database, indel, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Institute for Systems Biology; Washington; USA |
Inova Translational Medicine Institute | PMID:21965822 | Free, Public | biotools:kaviar | https://bio.tools/kaviar | SCR_013737 | SciCrunch Registry | queryable database of known variants, Known VARiants | 2026-10-17 01:33:35 | 18 | |||||
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The Soybean GBrowse Database Resource Report Resource Website 1+ mentions |
The Soybean GBrowse Database (RRID:SCR_013463) | data or information resource, database | It provides the mapping of relationships between soybean genomic features in a way that is presentable in GBrowse. It combines Perl MySQL database programming with Gbrowse to provide an integrated way of presenting soybean genomic features. The database is also searchable for listings of these relationships. | soybean, soybean gene, soybean genome | has parent organization: Southern Illinois University; Illinois; USA | nif-0000-03484 | SCR_013463 | SciCrunch Registry | The Soybean GBrowse Database | 2026-10-17 01:35:15 | 9 | |||||||||
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STRBase Resource Report Resource Website 10+ mentions |
STRBase (RRID:SCR_013465) | data or information resource, database | A database of information on short tandem repeat systems. It contains facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes. | dna typing, short tandem repeat, str, str allele, str loci, str locus | has parent organization: NIST - National Institute of Standards and Technology | PMID:11125125 | nif-0000-03501 | SCR_013465 | SciCrunch Registry | STRBase | 2026-10-17 01:33:36 | 21 | ||||||||
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National Cell Culture Center Resource Report Resource Website 1+ mentions |
National Cell Culture Center (RRID:SCR_013467) | NCCC | biomaterial supply resource, material resource, tissue bank | Provides access to large scale cell culture at reasonable cost. The Cell Culture Center has experience with the production of over 1700 cell lines. Numerous common cell lines, such as HeLa, CHO, 293, BHK, and hybridomas are routinely produced at the Center. We will adapt your cell line or custom protocol to large scale production then deliver the cells in the quantity and frequency you need. Large Scale Production Services: Mammalian cells: Suspension culture (1 to 400 liters per day), Anchorage dependent culture (1 to 200 roller bottles per batch), Purified monoclonal antibodies (10 mg to 100 grams), Non-hybridoma cell secreted proteins, Conditioned media Secreted proteins from suspension cultures can be produced in automated hollow fiber bioreactor systems. These systems may be considered after initial static culture production yields are determined. Upon determining the quantities requested by the investigator, the appropriate automated system will be used. For more information on the automated instrumentation available for the use of secreted protein production, please refer to the Biovest International web page (www.biovest.com). Working with our experienced personnel and quality controlled, state-of-the-art facilities also permits access to large quantities of cells or protein so you aren''t limited by the cell culture capacities of your own laboratory. The Center fulfills the needs of small research laboratories as well as those of larger institutions. Customers from all sectors of the research and industrial community are welcome to inquire about our services. If you''d like to inquire about using our services, use the contact infromation below. Key words: Cell, cells, culture, monoclonal, antibodies, antibody. | is listed by: One Mind Biospecimen Bank Listing | All | NIH Blueprint for Neuroscience Research | nif-0000-00566 | SCR_013467 | SciCrunch Registry | 2026-10-17 01:34:15 | 4 | ||||||||
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Human Brain Transcriptome Resource Report Resource Website 100+ mentions |
Human Brain Transcriptome (RRID:SCR_013742) | HBT | data or information resource, database | A data repository containing transcriptome and associated metadata for the developing and adult human brain. It provides genome-wide, exon-level transcriptome data from both sexes and multiple ethnicities. | human brain, transcriptome data, brain regions, FASEB list |
is related to: Spatio-temporal transcriptome of the human brain has parent organization: Yale University; Connecticut; USA |
NIMH U01MH081896 | PMID:19477152 | SCR_013742 | SciCrunch Registry | 2026-10-17 01:33:37 | 107 | ||||||||
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dcGO Resource Report Resource Website 10+ mentions |
dcGO (RRID:SCR_014392) | data or information resource, database | A database of domain-centric ontologies on functions, phenotypes, diseases and more. As a biomedical ontology resource, dcGO integrates functional, phenotypic, disease, and drug information. As a protein domain resource, it includes annotations to both the individual domains and supra-domains. Domain classifications and ontologies are organized in hierarchies, and dcGO includes the facility to browse the hierarchies: SCOP Hierarchy for browsing domains, GO Hierarchy for browsing GO terms, and BO Hierarchy for browsing other terms (mostly phenotypes). Users can mine and browse through resources. | database, mining, domain centric ontology, phenotype, human disease, drug, biomedical ontology, protein domain, hierarchy |
uses: Gene Ontology has parent organization: University of Bristol; Bristol; United Kingdom |
PMID:23161684 | Acknowledgement required, Both flat files and MySQL tables are available for download | SCR_014392 | SciCrunch Registry | 2026-10-17 01:33:35 | 27 | |||||||||
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StemCord Cord Blood Bank Resource Report Resource Website |
StemCord Cord Blood Bank (RRID:SCR_013502) | biomaterial supply resource, material resource, tissue bank | Not yet vetted by NIF curator | nlx_15565 | SCR_013502 | SciCrunch Registry | 2026-10-17 01:34:16 | 0 | ||||||||||||
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NURSA Transcriptomine Resource Report Resource Website 1+ mentions |
NURSA Transcriptomine (RRID:SCR_013746) | data or information resource, database | A database of tissue specific nuclear receptor transcriptomes based on annotated published genome wide transcriptional profiling experiments in the field of nuclear receptor signaling. Queries can include single and multiple genes, Gene Ontology terms, disease terms, and uploaded custom gene lists. | nuclear receptor signaling, transcriptome, database, nuclear receptors, transcription, genome-wide expression profiling, expression microarray |
is listed by: Nuclear Receptor Signaling Atlas is listed by: NIDDK Information Network (dkNET) |
NIDDK NURSA U19DK-62434; NCI Cancer Center P30CA125123 |
PMID:22786849 | Public | https://www.nursa.org/nursa/tools/index.jsf | SCR_013746 | SciCrunch Registry | Transcriptomine | 2026-10-17 01:34:16 | 1 | ||||||
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ArchDB - Biological Database of Protein Loops Resource Report Resource Website 1+ mentions |
ArchDB - Biological Database of Protein Loops (RRID:SCR_013472) | data or information resource, database |
ArchDB is a compilation of structural classifications of loops extracted from known protein structures. ArchDB includes 4 classifications: * ArchDB40 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 40% sequence identity. * ArchDB95 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 95% sequence identity. * ArchDB-EC is a classification of loops extracted from proteins with known enzymatic function * ArchDB-KI is a curated classification database of kinase loops EC number 2.7.X.X with functional information of residues. Futhermore, the functional annotation of residues in this database are further classified in four categories: 1. ATP interaction: for residues involved on ATP binding/interaction. 2. Substrate binding: for residues involved in substrate interaction/binding with the exception of ATP 3. Ion interaction: for residues involved in ion interaction/binding of ions needed for the catalytic mechanism 4. Catalytic: involved in reaction, the stabilization of a transition state or the activation of substrates. Additionally, three different approaches were applied to identify functional residues of the loops of the sub-classes: 1. Residues found within a cut-off distance of 6���� from an heteroatom, ligand, inhibitor, cofactor or complex partner molecule (protein or DNA), with the exception of D2O or crystallization buffer molecules. 2. Residues identified by functional information from ACTSITE and SITE records in the RCSB protein data bank. 3. Residues identified by the functional annotation collected from the literature and assigned to specific motifs of kinases. Lastly, the multiple ways to browse and query in ArchDB are: * Search by sequence: Users can search for classified loop(s) with sequence similarity to a query sequence. * Search by structure: Users can upload protein coordinates in PDB format and its loops will be extracted and compared with those from the classification. First: structural class is assigned comparing loop geometry and, second: the loop conformation is compared among the subclasses within the assigned class. * Search subclasses and/or Search Loops: A range of options are offered for subclass or loop searches. Users can query ArchDB asking for subclasses or loops with specific flanking secondary structures, length of loops or phi/psi loop conformation. Also, users can retrieve all subclasses or loops with PDB SITE annotations and contacts with co-crystallized ligands. Finally, users can search for subclasses that have SCOP, GO or EC annotations conserved at different percentage levels. * Search structures: Users can search for classified PDB structures in ArchDB with specific Sprot. Annotation/Keyword, GO annotation, SCOP and EC codes. * Specific queries for ArchDB-KI: Users can list functional subclasses or loops classified in ArchKI. :Sponsors: ArchDB is funded by grants from Fundacin Areces (Spain), Ministerio de Ciencia y Tecnologa Spain (MCYT; BIO2002-03609, BIO2001-246 and BIO2001-264), Centre de Referncia en Biotecnologia Generalitat de Catalunya (CERBA), and the Generalitat de Catalunya : :Enzyme-specific classification, :Kinase proteins, ligand, Protein residue, Protein motif, Protein loop, |
enzyme-specific classification, kinase proteins, ligand, protein loop, protein motif, protein residue, protein structure database | nif-0000-02564 | http://sbi.imim.es/archdb | SCR_013472 | SciCrunch Registry | ArchDB | 2026-10-17 01:33:34 | 9 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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