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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Integr8 : Access to complete genomes and proteomes Resource Report Resource Website 50+ mentions |
Integr8 : Access to complete genomes and proteomes (RRID:SCR_007740) | data or information resource, database | The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny. | bio.tools |
is listed by: bio.tools is listed by: Debian is related to: InteroPorc has parent organization: European Bioinformatics Institute |
nif-0000-03027, biotools:intergr8 | https://bio.tools/intergr8 | SCR_007740 | Integr8 | 2026-02-14 02:06:07 | 52 | ||||||||
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TAndem Splice Site DataBase Resource Report Resource Website 1+ mentions |
TAndem Splice Site DataBase (RRID:SCR_007961) | data or information resource, database | TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. Currently, 114,554 tandem splice sites of eight species are contained in the database, 5,209 of which have EST/mRNA evidence for alternative splicing. Users can search by Transcript Accession Number and Gene Symbol, SQL Query, and Tandem Donor/Tandem Acceptor pairs. | bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-03536, biotools:tassdb | https://bio.tools/tassdb | http://helios.informatik.uni-freiburg.de/TassDB/ | SCR_007961 | TassDB | 2026-02-14 02:06:11 | 5 | |||||||
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SISYPHUS Resource Report Resource Website 1+ mentions |
SISYPHUS (RRID:SCR_007930) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A collection of manually curated protein structural alignments and their interrelationships. Each multiple alignment within the SISYPHUS database consists of structurally similar regions common to a group of proteins. These regions range from oligomeric biological units, or individual domains to fragments of different size representing either internal structural repeats or motifs common to structurally distinct proteins. The SISYPHUS multiple alignments are displayed with SPICE, a browser that provides an integrated view of protein sequences, structures and their annotations. | bio.tools |
is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:sisyphus | https://bio.tools/sisyphus | SCR_007930 | SISYPHUS | 2026-02-14 02:06:40 | 3 | |||||||
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SilkDB Resource Report Resource Website 100+ mentions |
SilkDB (RRID:SCR_007926) | 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 20,2019.A database of integrated genome resources for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biological information such as microarray expression data, ESTs and corresponding references. SilkDB will be useful for the silkworm research community as well as comparative genomics. Recently, an international collaboration has been launched to assemble a complete silkworm genome sequence, which is based on the 6� and 3� draft genome sequences created by Chinese group and Japanese group in 2004 (Mita et al., 2004; Xia et al., 2004), respectively. The genome assembly quality has been greatly improved. Base on a high density SNP genetic map, over 80% of genome sequence could be mapped on 28 chromosomes of the silkworm. The first version of SilkDB was released in 2004. Since that time, the silkworm has become a focus in insect research community and the study of silkworm has been greatly accelerated. Now, we are happy to announce the release of a new version of SilkDB, which updated all of the data, added new information of genome sequence and genes, and provides new tools to facilitate use of the genome database. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Southwest University; Chongqing; China |
THIS RESOURCE IS NO LONGER IN SERVICE | r3d100012187, biotools:silkdb | https://bio.tools/silkdb https://doi.org/10.17616/R3435Z https://doi.org/10.17616/R3435Z |
SCR_007926 | SilkDB | 2026-02-14 02:06:40 | 159 | |||||||
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SIDER Resource Report Resource Website 100+ mentions |
SIDER (RRID:SCR_004321) | SIDER | data or information resource, database | Database containing information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug-target relations. The SIDER Side Effect Resource represents an effort to aggregate dispersed public information on side effects. To our knowledge, no such resource exist in machine-readable form despite the importance of research on drugs and their effects. The creation of this resource was motivated by the many requests for data that we received related to our paper (Campillos, Kuhn et al., Science, 2008, 321(5886):263-6.) on the utilization of side effects for drug target prediction. Inclusion of side effects as readouts for drug treatment should have many applications and we hope to be able to enhance the respective research with this resource. You may browse the drugs by name, browse the side effects by name, download the current version of SIDER, or use the search interface. | medicine, drug, side effect, adverse drug reaction, drug-target, phenotype, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Allen Institute Neurowiki has parent organization: European Molecular Biology Laboratory |
PMID:20087340 | Except as otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3, Commercial use requires permission | r3d100012791, nlx_33359, OMICS_01588, biotools:sider | https://bio.tools/sider https://doi.org/10.17616/R3J226 |
SCR_004321 | Side Effect Resource, SIDER: Side Effect Resource | 2026-02-14 02:05:51 | 372 | |||||
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SGD Resource Report Resource Website 1000+ mentions |
SGD (RRID:SCR_004694) | SGD, SGD LOCUS, SGD REF | data or information resource, database | A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available. | database, yeast, pathway, analysis, gene, nomenclature, predicted sequence, fungi, functional relationship, protein structure, bio.tools, FASEB list |
uses: InterMOD is used by: NIF Data Federation is used by: PhenoGO is listed by: re3data.org is listed by: OMICtools is listed by: InterMOD is listed by: bio.tools is listed by: Debian is affiliated with: InterMOD is related to: AmiGO is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: HomoloGene is related to: TXTGate is related to: PhenoGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford University; Stanford; California is parent organization of: Ascomycete Phenotype Ontology is parent organization of: SGD Gene Ontology Slim Mapper |
NHGRI 5P41HG001315-11; NHGRI 5P41HG002273-05; NHGRI 5U41HG001315-18; NHGRI 2U41HG002273-13; NHGRI 5R01HG004834-04 |
PMID:24265222 PMID:12519985 PMID:9399804 |
Free for academic use, The community can contribute to this resource, Non-commercial | nif-0000-03456, biotools:sgd, r3d100010419, OMICS_01661 | https://bio.tools/sgd https://doi.org/10.17616/R3N313 |
http://genome-www.stanford.edu/Saccharomyces/ | SCR_004694 | SGD LOCUS, Saccharomyces Genome Database, SGD REF | 2026-02-14 02:06:21 | 1920 | |||
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Pfam Resource Report Resource Website 10000+ mentions |
Pfam (RRID:SCR_004726) | data or information resource, database | A database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM). | database, clan, structure, sequence, protein family, domain, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: MobiDB is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Conserved Domain Database is related to: SUPFAM is related to: DBD: Transcription factor prediction database is related to: DOMINE: Database of Protein Interactions is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Eukaryotic Linear Motif is related to: TopoSNP is related to: GOTaxExplorer is related to: TrED is related to: ProOpDB is related to: Algal Functional Annotation Tool has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
EMBL core funds ; Howard Hughes Medical Institute ; BBSRC BB/L024136/1; Wellcome Trust 108433/Z/15/Z |
PMID:24288371 PMID:19920124 |
Acknowledgement requested, Available via FTP | biotools:pfam, OMICS_01696, r3d100012850, nlx_72111 | https://bio.tools/pfam https://doi.org/10.17616/R3QV4F |
http://pfam.sanger.ac.uk/ | SCR_004726 | Pfam Database, Protein Families Database, PFAM, Pfam protein families database | 2026-02-14 02:06:19 | 15523 | ||||
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NEWT Resource Report Resource Website 10+ mentions |
NEWT (RRID:SCR_004477) | NEWT | data or information resource, database | NEWT is the taxonomy database maintained by the UniProt group. It integrates taxonomy data compiled in the NCBI database and data specific to the UniProt Knowledgebase. Browse by hierarchy, List all, or Complete proteomes. Organisms are classified in a hierarchical tree structure. Our taxonomy database contains every node (taxon) of the tree. UniProtKB taxonomy data is manually curated: next to manually verified organism names, we provide a selection of external links, organism strains and viral host information. Species with protein sequences stored in the UniProt Knowledgebase are named according to UniProt nomenclature. We endeavour to maintain a list of manually curated species names for which protein sequence data is available. In particular, we have adopted a systematic convention for naming viral and bacterial strains and isolates. Links to external sites are chosen by the UniProt taxonomy team and show pictures and various scientific data of interest (taxonomy, biology, physiology,...). | archaea, bacteria, eukaryota, viruses, cellular organism, sequence, viroid, gold standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: NCBI Taxonomy has parent organization: UniProt |
PMID:12824428 | nlx_46189, biotools:newt | https://bio.tools/newt | http://www.ebi.ac.uk/newt/ | SCR_004477 | UniProtKB taxonomy database, UniProt Taxonomy Database, UniProt Taxonomy | 2026-02-14 02:05:48 | 23 | |||||
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Selectome: a Database of Positive Selection Resource Report Resource Website 1+ mentions |
Selectome: a Database of Positive Selection (RRID:SCR_004542) | data or information resource, database | Database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. | duplication, events, gene, animal, positive selection, speciation, p-value, speciation, duplication, selectome, phylogenetic, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Lausanne; Lausanne; Switzerland |
PMID:24225318 | nif-0000-03451, biotools:selectome | https://bio.tools/selectome | SCR_004542 | Selectome | 2026-02-14 02:06:19 | 8 | |||||||
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BioSample Database at EBI Resource Report Resource Website 10+ mentions |
BioSample Database at EBI (RRID:SCR_004856) | BioSD | data or information resource, database | Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI''''s assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information. The goals of the BioSample Database include: # recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; # minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and # supporting cross database queries by sample characteristics. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers. Accession numbers for the reference samples will be exchanged with a similar database at NCBI. The samples in the database can be queried by their attributes, such as sample types, disease names or sample providers. A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples (at) ebi.ac.uk. Current data sources: * European Nucleotide Archive (424,811 samples) * PRIDE (17,001 samples) * ArrayExpress (1,187,884 samples) * ENCODE cell lines (119 samples) * CORIELL cell lines (27,002 samples) * Thousand Genome (2,628 samples) * HapMap (1,417 samples) * IMSR (248,660 samples) | cell line, cell, nucleotide, sequencing, proteomics, peptide, protein, genomics, gene expression, biological sample, molecular, sequence, structure, cell line, topical portal, aggregator, gold standard, bio.tools |
uses: European Nucleotide Archive (ENA) uses: Proteomics Identifications (PRIDE) uses: ArrayExpress uses: ENCODE uses: Coriell Institute for Medical Research uses: 1000 Genomes: A Deep Catalog of Human Genetic Variation uses: International HapMap Project uses: International Mouse Strain Resource is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BioSample has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory; Heidelberg; Germany ; European Union FP7 HEALTH-F4-2010-241669; European Union FP7 HEALTH-F4-2007-201413 |
PMID:22096232 | The community can contribute to this resource, Acknowledgement requested | biotools:biosamples, r3d100012628, nlx_143930, OMICS_01025 | https://bio.tools/biosamples https://doi.org/10.17616/R37R3P |
SCR_004856 | BioSamples database, BioSamples, BioSamples Database at EBI, BioSample Database at the EBI, EBI BioSample Database, BioSample Database, BioSD at EBI, BioSD - BioSample Database | 2026-02-14 02:05:54 | 14 | ||||
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IBIS: Inferred Biomolecular Interactions Server Resource Report Resource Website 1+ mentions |
IBIS: Inferred Biomolecular Interactions Server (RRID:SCR_004886) | IBIS | data or information resource, database | A web server and database that organizes, analyzes and predicts interactions between proteins and other biomolecules. For a given protein sequence or structure query, it reports protein-protein, protein-small molecule, protein nucleic acids and protein-ion interactions observed in experimentally-determined structural biological assemblies. It also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation. | protein interaction, protein protein, protein small molecule, protein nucleic acid, protein ion interaction, interacting partner, binding site, homology, protein complex, structure conservation, nucleic acid, protein dna, protein rna, protein chemical, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: NCBI Structure has parent organization: NCBI |
PMID:22102591 PMID:19843613 |
OMICS_01917, biotools:ibis_ncbi, nlx_85682 | https://bio.tools/ibis_ncbi | SCR_004886 | Inferred Biomolecular Interactions Server, NCBI Inferred Biomolecular Interactions Server | 2026-02-14 02:05:51 | 5 | ||||||
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SGN Resource Report Resource Website 500+ mentions |
SGN (RRID:SCR_004933) | SGN, SGN ref | data or information resource, database | A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions. | database, clade, genomic, sequence, phenotype, pathway, genetic, taxonomy, annotation, blast, plant genome, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Sol Genomics Network - Bulk download is related to: AmiGO has parent organization: Boyce Thompson Institute for Plant Research |
USDA ; ATC Inc. Advanced Technologies Cambridge ; NSF 0116076; NSF 9872617; NSF 975866; NSF 0421634 |
PMID:20935049 PMID:16010005 |
Public, The community can contribute to this resource | r3d100012078, nlx_89764, biotools:sol_genomics_network | https://bio.tools/sol_genomics_network https://doi.org/10.17616/R3FS95 |
http://www.sgn.cornell.edu/ | SCR_004933 | SGN ref, Sol Genomics Network | 2026-02-14 02:05:51 | 993 | |||
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TRANSFAC Resource Report Resource Website 100+ mentions |
TRANSFAC (RRID:SCR_005620) | TRANSFAC | data or information resource, database | Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites. | Curated, eucaryotic, transcription, factor, genomic, binding, site, sequence, regulated, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: Gene Regulation Databases is related to: TRANSPATH is related to: Babelomics is related to: GeneTrail works with: rVista |
European Commission ; German Ministry of Education and Research |
PMID:12520026 | Free, Freely available | biotools:transfac, nif-0000-03576 | http://www.biobase-international.com/pages/index.php?id=transfac http://gene-regulation.com/pub/databases.html https://bio.tools/transfac |
SCR_005620 | 2026-02-14 02:05:57 | 261 | |||||
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IndelFR - Indel Flanking Region Database Resource Report Resource Website 1+ mentions |
IndelFR - Indel Flanking Region Database (RRID:SCR_006050) | IndelFR | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions. | indel, flanking region, protein, structural domain, domain, protein superfamily, protein structure, insertion/deletion, insertion, deletion, protein sequence, sequence, structure, protein domain, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: SCOP: Structural Classification of Proteins is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Shandong University; Shandong; China |
Independent Innovation Foundation of Shandong University 2009JC006; National Natural Science Foundation of China 30970092; National Natural Science Foundation of China 61070017; Scientific Research Reward Fund for excellent Young and Middle-Aged scientists in Shandong Province 20090451326 |
PMID:22127860 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:indelfr, nlx_151448 | https://bio.tools/indelfr | SCR_006050 | IndelFR: Indel Flanking Region Database, Indel Flanking Region Database | 2026-02-14 02:05:54 | 2 | ||||
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NRG-CING Resource Report Resource Website 1+ mentions |
NRG-CING (RRID:SCR_006079) | NRG-CING | data or information resource, database | NRG-CING presents a complete validation report for all 9,000+ wwPDB NMR entries including remediated experimental data such as chemical shifts from BMRB and restraints from NRG . These CING reports are compiled from internal analyses and those by CCPN, DSSP, PROCHECK-NMR/Aqua, ShiftX, Talos+, Vasco, Wattos, and WHAT_CHECK. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. (See website for more information on CING.) In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available. | macromolecular structure, nmr, macromolecule, restraint, chemical shift, validation report, validation, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Worldwide Protein Data Bank (wwPDB) is related to: NMR Restraints Grid is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Radboud University; Nijmegen; The Netherlands |
Netherlands Organization for Scientific Research (NWO) 700.55.443; Netherlands Bioinformatics Centre (NBIC) ; EU FP6 LSHG-CT-2005-018988; EU FP6 LHSG-CT-2004-512092; EU FP7 261572; Brussels Institute for Research and Innovation BB2B 2010-1-12; NLM LM05799 |
PMID:22139937 | Free | nlx_151486, biotools:nrg-cing | https://bio.tools/nrg-cing | SCR_006079 | 2026-02-14 02:05:59 | 1 | |||||
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UniParc Resource Report Resource Website 50+ mentions |
UniParc (RRID:SCR_005818) | data or information resource, database | Database that contains publicly available protein sequences with stable and unique identifiers (UPI) which are never removed, changed or reassigned. UniParc tracks sequence changes in the source databases and archives the history of all changes. Information other than protein sequence must be retrieved from the UniParc source databases using the database cross-references. | protein sequence, database, public protein sequence, gold standard, upi, unique protein identifier, identifier, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProt DAS is related to: WormBase is related to: FlyBase is related to: Ensembl is related to: RefSeq has parent organization: UniProt |
Public, Entries are available for download | SCR_004769, nif-0000-03610, r3d100011519, biotools:uniparc, nlx_76940 | https://bio.tools/uniparc https://doi.org/10.17616/R3X33B |
SCR_005818 | UniProt Archive | 2026-02-14 02:05:53 | 87 | |||||||
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Dr.VIS - Human Disease-Related Viral Integration Sites Resource Report Resource Website 1+ mentions |
Dr.VIS - Human Disease-Related Viral Integration Sites (RRID:SCR_005965) | Dr.VIS, Dr. VIS | data or information resource, database | Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free. | disease, virus, viral integration, viral integration site, integration site, malignant disease, chromosome region, genomic position, viral-host junction sequence, junction sequence, oncogene, chromosome, catalog, graphic interface, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Tongji University; Shanghai; China |
State Key Basic Research Program 973 2011CB910204; National Natural Science Foundation of China ; Major State Basic Research Development Program ; 863 Hi-Tech Program of China ; National Key Technology R&D Program in the 11th Five Year Plan of China ; Major State Basic Research Development Program of China |
PMID:22135288 | Open - Free to browse and download data in Dr.VIS. | nlx_151323, biotools:dr.vis | http://www.scbit.org/dbmi/drvis https://bio.tools/dr.vis |
SCR_005965 | Dr. VIS - Database of Human Disease-related Viral Integration Sites, Database of Human Disease-related Viral Integration Sites | 2026-02-14 02:06:25 | 1 | ||||
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FunTree Resource Report Resource Website 1+ mentions |
FunTree (RRID:SCR_006014) | FunTree | data or information resource, database | FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms. | enzyme function, enzyme superfamily, enzyme, sequence, structure, phylogenetic, chemical, mechanistic, functional annotation, superfamily, gold standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CATH: Protein Structure Classification is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: KEGG is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory; Heidelberg; Germany ; BBSRC ; Wellcome Trust 081989/Z/07/A; DOE contract DE-AC02-06CH11357 |
PMID:22006843 | Free | biotools:funtree, nlx_151402 | https://bio.tools/funtree | SCR_006014 | 2026-02-14 02:05:54 | 4 | |||||
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DBETH - Database for Bacterial ExoToxins for Humans Resource Report Resource Website 1+ mentions |
DBETH - Database for Bacterial ExoToxins for Humans (RRID:SCR_005908) | DBETH | data or information resource, database | Database of Bacterial ExoToxins for Human is a database of sequences, structures, interaction networks and analytical results for 229 exotoxins, from 26 different human pathogenic bacterial genus. All toxins are classified into 24 different Toxin classes. The aim of DBETH is to provide a comprehensive database for human pathogenic bacterial exotoxins. DBETH also provides a platform to its users to identify potential exotoxin like sequences through Homology based as well as Non-homology based methods. In homology based approach the users can identify potential exotoxin like sequences either running BLASTp against the toxin sequences or by running HMMER against toxin domains identified by DBETH from human pathogenic bacterial exotoxins. In Non-homology based part DBETH uses a machine learning approach to identify potential exotoxins (Toxin Prediction by Support Vector Machine based approach). | sequence, structure, interaction network, human, pathogen, bacterial genus, toxin, bacteria, exotoxin, homology, homolog, structure, sequence, domain, prediction, mechanism, activity, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CSIR - Indian Institute of Chemical Biology; Kolkata; India |
Council of Scientific and Industrial Research; New Delhi; India | PMID:22102573 | nlx_149481, biotools:dbeth | https://bio.tools/dbeth | SCR_005908 | Database for Bacterial ExoToxins for Humans | 2026-02-14 02:05:58 | 2 | |||||
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VirusMINT Resource Report Resource Website 10+ mentions |
VirusMINT (RRID:SCR_005987) | VirusMINT | data or information resource, database | A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome. | protein interaction, virus, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PSI-MI is related to: VirHostNet: Virus-Host Network is related to: MINT has parent organization: University of Rome Tor Vergata; Rome; Italy |
Papilloma virus, Human immunodeficiency virus, Epstein-Barr virus, Hepatitis B virus, Hepatitis C virus, Herpes virus, Simian virus 40 | PMID:18974184 | nif-0000-03636, OMICS_01909, biotools:virusmint, r3d100010685 | https://bio.tools/virusmint https://doi.org/10.17616/R3F890 |
SCR_005987 | 2026-02-14 02:06:25 | 16 |
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