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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Histone Systematic Mutation Database Resource Report Resource Website |
Histone Systematic Mutation Database (RRID:SCR_012015) | HistoneHits | data or information resource, database | A database for histone mutations and their phenotypes. | is listed by: OMICtools | PMID:19218532 | OMICS_01839 | SCR_012015 | SciCrunch Registry | 2026-10-17 01:33:31 | 0 | |||||||||
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DBCAT Resource Report Resource Website 10+ mentions |
DBCAT (RRID:SCR_012014) | DBCAT | data or information resource, database | A database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells. | is listed by: OMICtools | Cancer | PMID:21214365 | OMICS_01837 | SCR_012014 | SciCrunch Registry | 2026-10-17 01:34:13 | 48 | ||||||||
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CRAVAT Resource Report Resource Website 10+ mentions |
CRAVAT (RRID:SCR_012776) | CRAVAT | analysis service resource, data analysis service, production service resource, service resource | A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis. |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
Cancer | NCI CA 152432; NSF DBI 0845275; NCI 1U01CA180956-01 |
OMICS_00147 | SCR_012776 | SciCrunch Registry | cancer-related analysis of variants toolkit | 2026-10-17 01:34:13 | 30 | |||||||
|
APPRIS Resource Report Resource Website 50+ mentions |
APPRIS (RRID:SCR_012019) | APPRIS | data or information resource, database | A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. | isoform, function, annotation, splice, reference sequence, structure, conservation, transcript, FASEB list |
is listed by: OMICtools has parent organization: Spanish National Cancer Research Center |
PMID:23161672 | Free | OMICS_01881 | SCR_012019 | SciCrunch Registry | APPRIS - A system for annotating alternative splice isoforms | 2026-10-17 01:33:32 | 97 | ||||||
|
Japanese Single Nucleotide Polymorphisms Resource Report Resource Website 10+ mentions |
Japanese Single Nucleotide Polymorphisms (RRID:SCR_013076) | data or information resource, database | JSNP is a database of Japanese Single Nucleotide Polymorphisms. It includes BLAST capability, keyword search, mapping information, and other tools that allow users to gather information on SNP's. SNPs are the most common form of DNA sequence variation. They are useful polymorphic markers to investigate genes susceptible to diseases or those related to drug responsiveness. Furthermore, a small subset of SNPs directly influences to the quality and/or quantity of the gene product, and increase a risk to certain diseases and to severe side effect by drugs. Through a discovery of a large number of SNPs, we would like to contribute to identification of disease-related genes and also to establish a diagnostic method to avoid drug side-effect. | FASEB list | has parent organization: University of Tokyo; Tokyo; Japan | nif-0000-03063 | SCR_013076 | SciCrunch Registry | JSNP | 2026-10-17 01:35:08 | 42 | |||||||||
|
MIT-BIH polysomnographic Resource Report Resource Website 1+ mentions |
MIT-BIH polysomnographic (RRID:SCR_013078) | data or information resource, database | MIT-BIH Polysomnographic Database is a collection of recordings of multiple physiologic signals during sleep. Subjects were monitored in Boston''s Beth Israel Hospital Sleep Laboratory for evaluation of chronic obstructive sleep apnea syndrome, and to test the effects of constant positive airway pressure (CPAP), a standard therapeutic intervention that usually prevents or substantially reduces airway obstruction in these subjects. The database contains over 80 hours'' worth of four-, six-, and seven-channel polysomnographic recordings, each with an ECG signal annotated beat-by-beat, and EEG and respiration signals annotated with respect to sleep stages and apnea | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | nlx_45862 | SCR_013078 | SciCrunch Registry | MIT-BIH polysomnographic | 2026-10-17 01:33:34 | 1 | ||||||||||
|
Interactive Fly Resource Report Resource Website 1+ mentions |
Interactive Fly (RRID:SCR_012784) | Interactive Fly | data or information resource, database | The InterActive Fly is an online database of Drosophilia development and metazoan evolution. It contains information on biochemical pathways, organs, images, a cis-decoder, and EvoPrinter, a machine that allows users to identify Evolutionarily Resilient DNA Sequences. | has parent organization: National Institute of Neurological Disorders and Stroke | nif-0000-03030 | SCR_012784 | SciCrunch Registry | Interactive Fly: A cyberspace guide to Drosophila development and metazoan evolution | 2026-10-17 01:35:06 | 7 | |||||||||
|
The Node Resource Report Resource Website 1+ mentions |
The Node (RRID:SCR_013071) | blog, data or information resource, narrative resource | The Node: a community site for development biologists | nlx_84212 | SCR_013071 | SciCrunch Registry | The Node | 2026-10-17 01:34:14 | 4 | |||||||||||
|
FusionDB Resource Report Resource Website 1+ mentions |
FusionDB (RRID:SCR_013314) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. FusionDB is a database of bacterial and archaeal gene fusion events - also known as Rosetta stones. Gene-fusion events are not the only resource to determine functional links between two proteins. Similar phylogenetic profiles and conserved chromosomal co-localization can also be used as an indicator for such interactions. | archaeal gene fusion, bacterial gene fusion, rosetta stone | has parent organization: French National Center for Scientific Research | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02861 | http://igs-server.cnrs-mrs.fr/FusionDB/ | SCR_013314 | SciCrunch Registry | FusionDB | 2026-10-17 01:35:12 | 4 | |||||||
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Colon CFR Resource Report Resource Website 1+ mentions |
Colon CFR (RRID:SCR_013162) | Colon CFR | data or information resource, database | It is an international research infrastructure for investigators interested in conducting population and clinic-based interdisciplinary studies on the genetic and molecular epidemiology of colon cancer and its behavioral implications. A central goal of the C-CFR is the translation of this research to the clinical and prevention setting for the benefit of Registry participants and the general public. The C-CFR has information and biospecimens contributed by greater than 11,300 families across the spectrum of risk for colon cancers and from population-based or relative controls. Of particular interest are: identification and characterization of cancer susceptibility genes definition of gene-gene and gene-environment interactions in cancer etiology translational, preventive, and behavioral implications of research findings Special features include: population-based and clinic-based ascertainment systematic collection of validated family history epidemiologic risk factor data clinical and follow-up data biospecimens (including tumor blocks and EBV transformed cell lines) ongoing molecular characterization of the participating families Goals: to contribute to the development of public health measures for the general population by increasing knowledge on genetic factors affecting cancer susceptibility and modification by environmental and lifestyle factors to protect those with increased susceptibility from developing cancer to provide life-prolonging treatment to genetically susceptible individuals Objectives: to establish a comprehensive research resource infrastructure to assist with the implementation of collaborative, interdisciplinary research protocols in the genetic epidemiology of cancer to identify, characterize, and follow-up a cohort of individuals and their family members, spanning the spectrum of cancer risk to identify diverse genetically susceptible populations that could benefit from enrollment in preventive and therapeutic interventions to develop an adaptive and evolving informatics model to support ongoing and future research consortia Sponsor. This study was supported by National Cancer Institute Grants R01 CA47147, R01 CA47305, and R01 CA69664. | has parent organization: National Cancer Institute | nif-0000-30482 | SCR_013162 | SciCrunch Registry | Colon Cancer Family Registry, The Colon Cancer Family Registry | 2026-10-17 01:33:34 | 7 | |||||||||
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Austrailasian Biospecimen Network Resource Report Resource Website |
Austrailasian Biospecimen Network (RRID:SCR_013161) | biomaterial supply resource, material resource, tissue bank | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 32,2023. | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_67092 | SCR_013161 | SciCrunch Registry | 2026-10-17 01:35:09 | 0 | |||||||||||
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MACiE Resource Report Resource Website 1+ mentions |
MACiE (RRID:SCR_013296) | MACiE | data or information resource, database | MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project on enzyme reaction mechanisms. MACiE currently contains 223 fully annotated enzyme reaction mechanisms, which comprise 218 EC numbers (161 EC sub-subclasses) and 310 distinct CATH codes. It is a joint effortbetween the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute. | bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:macie, nif-0000-03093 | https://bio.tools/macie | SCR_013296 | SciCrunch Registry | The MACiE Database, Annotation and Classification in Enzymes, Mechanism | 2026-10-17 01:33:33 | 8 | |||||||
|
HIV-1, Human Protein Interaction Database Resource Report Resource Website |
HIV-1, Human Protein Interaction Database (RRID:SCR_013214) | data or information resource, database | The Division of Acquired Immunodeficiency Syndrome (DAIDS) of the National Institute of Allergy and Infectious Diseases (NIAID) has initiated a project, in collaboration with Southern Research Institute and the National Center for Biotechnology Information (NCBI), designed to compile a comprehensive database of the described interactions between HIV-1 and cellular proteins. The goal of this project is to provide scientists in the field of HIV/AIDS research a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. This database has been designed to track the following information for each protein-protein interaction identified in the literature: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * National Library of Medicine (NLM) PubMed identification numbers (PMIDs) for all journal articles describing the interaction. | gold standard | has parent organization: NCBI | PMID:18927109 PMID:19025396 PMID:19262354 |
nlx_39873 | SCR_013214 | SciCrunch Registry | HIV-1 Protein Interaction Database | 2026-10-17 01:33:33 | 0 | ||||||||
|
ENA Sequence Search Resource Report Resource Website 1+ mentions |
ENA Sequence Search (RRID:SCR_013170) | ENA Sequence Search | analysis service resource, data analysis service, production service resource, service resource | A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity. | nucleotide sequencing |
is listed by: OMICtools has parent organization: European Nucleotide Archive (ENA) |
OMICS_00993 | SCR_013170 | SciCrunch Registry | 2026-10-17 01:35:10 | 7 | |||||||||
|
LIGand Attachment SITE Database Resource Report Resource Website 1+ mentions |
LIGand Attachment SITE Database (RRID:SCR_013172) | data or information resource, database | A gold-standard dataset of biologically relevant binding sites in protein structures. It consists of proteins with one unbound structure and at least one structure of the protein-ligand complex. Both a redundant and a non-redundant (sequence identity lower than 25) version is available. Quaternary structures proposed by PQS (2) are used for all structures in the dataset. The availability of both unbound and bound structures for each protein guarantees that our dataset can be used to benchmark binding site prediction methods, in conditions that mimic cases where the binding site is truly unknown. In cases where several different bound structures are available for a given protein, all are used to define the binding sites. |
has parent organization: University of Toronto; Ontario; Canada has parent organization: King's College London; London; United Kingdom |
nif-0000-03083 | SCR_013172 | SciCrunch Registry | LigASite | 2026-10-17 01:33:34 | 2 | ||||||||||
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DBAli. A Database of Structure Alignments. Resource Report Resource Website |
DBAli. A Database of Structure Alignments. (RRID:SCR_013418) | data or information resource, database | DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. It is not currently being updated; however, updates should resume in the near future. All pairwise structural comparisons in DBAli have been obtained using the MAMMOTH program developed in the group of Prof. Angel R. Ortiz. All multiple structure alignments in DBAli have been obtained using the SALIGN command in MODELLER developed in the group of Prof. Andrej Sali. | protein, protein structure comparison | nif-0000-02725 | SCR_013418 | SciCrunch Registry | DBAli | 2026-10-17 01:35:14 | 0 | ||||||||||
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DomIns: A Web Resource for Domain Insertions in Known Protein Structures Resource Report Resource Website 1+ mentions |
DomIns: A Web Resource for Domain Insertions in Known Protein Structures (RRID:SCR_013417) | data or information resource, database | DomIns is a web resource aimed at providing comprehensive information on domain insertions in proteins of known structure. We have followed the definition of protein domains as in the SCOP (Structural Classification of Proteins) database in order to identify insertions. We have considered only the major five classes (All-alpha, All-beta, alpha/beta, alpha+beta and Small Proteins), the fold and the superfamily level of SCOP hierarchy for identifying insertions. Apart from browsing insertions in whole PDB, we also provide an option to browse insertions in a pre-computed list of non-redundant PDB chains provided by PDB_Select with a sequence identity threshold of 90%. | domain insertion of protein, protein domain, protein structure | nif-0000-02760 | SCR_013417 | SciCrunch Registry | DomIns | 2026-10-17 01:33:34 | 1 | ||||||||||
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KNOTTIN database Resource Report Resource Website 10+ mentions |
KNOTTIN database (RRID:SCR_013263) | KNOTTIN Database | data or information resource, database | The KNOTTIN database provides standardized data on the knottin structural family (also referred to as the Inhibitor Cystine Knot (ICK) motif/family/fold). Knottins are intriguing miniproteins with strong potential in drug design. This knot is achieved when one disulfide bridge crosses the macrocycle formed by the two other disulfides and the interconnecting backbone. | nif-0000-03074 | SCR_013263 | SciCrunch Registry | 2026-10-17 01:34:14 | 12 | |||||||||||
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H-InvDB Resource Report Resource Website 10+ mentions |
H-InvDB (RRID:SCR_013265) | H-InvDB, H-InvDB cDNA, H-InvDB locus | data or information resource, database | H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. This database is produced by the Genome Information Integration Project (2005-) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs. | human gene, human genome, transcripts, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: National Institute of Advanced Industrial Science and Technology |
nif-0000-02936, biotools:h-invdb | https://bio.tools/h-invdb | SCR_013265 | SciCrunch Registry | H-Invitational Database, H-InvDB cDNA, H-InvDB locus, H-InvDB: Annotated Human Gene Database | 2026-10-17 01:35:11 | 25 | |||||||
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ExTopoDB Resource Report Resource Website 1+ mentions |
ExTopoDB (RRID:SCR_013143) | ExTopoDB | data or information resource, database | A publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains experimental information about the topology of 2143 transmembrane proteins. This information was collected from studies in the literature that reported the use of biochemical methods for the determination of the topology of transmembrane proteins. Each record contains unique information about the given protein, such as its sequence, cross-references to many publicly available databases worldwide, the protein''s name and organism source. The web interface of the database offers the user the ability to submit advanced queries for text search within ExTopoDB''s protein entries and there is also an interface for running BLAST against the database. Furthermore, the results of topology prediction using the HMM-TM algorithm are included for each protein in the database (unconstrained prediction) and we also incorporated the experimental information about the topology of the proteins in the HMM-TM prediction procedure, producing more reliable topology models (constrained prediction). | transmembrane protein, protein structure, topological model, blast, transmembrane, protein, model |
is listed by: 3DVC has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:20601677 | Public | nlx_151724 | SCR_013143 | SciCrunch Registry | 2026-10-17 01:34:14 | 2 |
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