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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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European Molecular Biology Laboratory Resource Report Resource Website 5000+ mentions |
European Molecular Biology Laboratory (RRID:SCR_004473) | EMBL | data or information resource, graduate program resource, organization portal, portal, postdoctoral program resource, training resource | Intergovernmental organisation funded by public research money from its member states in Europe. Groups and laboratories perform basic research in molecular biology and molecular medicine, training for scientists, students and visitors. Provides development of services, new instruments and methods, data and technology in its member states. | molecular, biology, medicine, data, training, service, organization, data, technology, academic |
is related to: GenBank is related to: EU-AIMS is related to: EMIF is related to: 3D-Beacons is parent organization of: EMBL - Bork Group is parent organization of: PTMcode is parent organization of: eggNOG is parent organization of: Eukaryotic Linear Motif is parent organization of: BreakDB is parent organization of: SIDER is parent organization of: DELLY is parent organization of: European Bioinformatics Institute is parent organization of: STRING is parent organization of: PEMer is parent organization of: HTSeq is parent organization of: OGEE - Online GEne Essentiality database is parent organization of: Expression Database in 4D is parent organization of: DSMM - a Database of Simulated Molecular Motions is parent organization of: FUNPEP is parent organization of: Search Tool for Interactions of Chemicals is parent organization of: AltSplice Database of Alternative Spliced Events is parent organization of: Candidate Genes to Inherited Diseases is parent organization of: Washington University Basic Local Alignment Search Tool is parent organization of: Secondary Structure Matching is parent organization of: Agadir is parent organization of: Bork Group's WU-BLAST2 Search Service at EMBL is parent organization of: FoldX is parent organization of: BioModels.net is parent organization of: CopySeq is parent organization of: miRNA is parent organization of: htseq-count is parent organization of: MOCAT is parent organization of: Human-gpDB is parent organization of: easyRNASeq is parent organization of: Transeq is parent organization of: PhenoMeNal |
nlx_46173 | SCR_004473 | European Molecular Biology Laboratory, EMBL | 2026-08-29 11:22:08 | 5410 | ||||||||
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3D-Beacons Resource Report Resource Website 1+ mentions |
3D-Beacons (RRID:SCR_022919) | software application, software resource | Software platform to provide programmatic access to experimentally determined and theoretical protein structures. Provides unified programmatic access to experimentally determined and predicted structure models. Used for open collaboration between providers of macromolecular structure models to provide model coordinates and meta information from all contributing data resources in standardised data format, on unified platform.3D Beacons API retrieves and combines data from member data providers, and returns data in JSON format according to 3D-Beacons API specification. | EMBL EBI, programmatic access, experimentally determined and theoretical protein structures, macromolecular structure models collaboration, model coordinates and meta information |
is related to: European Bioinformatics Institute is related to: European Molecular Biology Laboratory |
Free, Freely available | SCR_022919 | 3D-Beacons Network | 2026-08-29 11:31:34 | 2 | |||||||||
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GenBank Resource Report Resource Website 10000+ mentions |
GenBank (RRID:SCR_002760) | GB | data or information resource, data repository, database, service resource, storage service resource | NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP. | genetic sequence, dna sequence, human genetics, human genome, nucleotide sequence, nucleotide, dna, dna data bank, gene mapping, genetics, gold standard |
is used by: Structural Genomics Consortium is used by: xFITOM is used by: Transcriptional Regulatory Element Database is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: CINERGI is related to: High Throughput Genomic Sequences Division is related to: DNA DataBank of Japan (DDBJ) is related to: HS3D - Homo Sapiens Splice Sites Dataset is related to: Influenza Virus Resource is related to: TPA is related to: Anopheles gambiae (African malaria mosquito) genome view is related to: Nucleotide database is related to: NCBI BioSample is related to: NCBI Nucleotide is related to: SpliceDB is related to: MaizeGDB is related to: NCBI Assembly Archive Viewer is related to: DNA DataBank of Japan (DDBJ) is related to: European Molecular Biology Laboratory is related to: INSDC is related to: NCBI Protein Database is related to: TrED is related to: Xenopus Gene Collection is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: INSDC is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables has parent organization: NCBI is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: NCBI Genome Survey Sequences Database works with: OGDraw works with: A plasmid Editor works with: Webcutter works with: merge-gbk-records works with: PremierBiosoft Proteo IQ Software works with: SARS-CoV-2-Sequences works with: rentrez works with: MiMeDB |
NLM | PMID:24217914 PMID:23193287 PMID:21071399 |
Free, Freely available | nif-0000-02873, r3d100010528, OMICS_01650 | https://doi.org/10.17616/R3D31X | SCR_002760 | , Gen Bank, GenBank | 2026-08-29 11:21:31 | 64417 | ||||
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EU-AIMS Resource Report Resource Website 1+ mentions |
EU-AIMS (RRID:SCR_003861) | EU-AIMS | consortium, data or information resource, organization portal, portal | Consortium aiming to generate tools that will enhance understanding of autism spectrum disorders (ASD) and pave the way for the development of new, safe and effective treatments for use in both children and adults. For example, the team will gather samples from people bearing certain mutations associated with ASD; this will pave the way for the generation of cell lines that can be used to test treatments. Elsewhere, the researchers will advance the use of brain scans as a tool to boost ASD drug discovery and also identify which people with ASD might respond best to a given drug. The project will also create a pan-European network of clinical sites. As well as making it easier to run clinical trials, this network will create an interactive platform for those with ASD and professionals. By the end of the 5 year project they expect to provide novel validated cellular assays, animal models, new fMRI methods with dedicated analysis techniques, new PET radioligands, as well as new genetic and proteomic biomarkers for patient-segmentation or individual response prediction. They will provide a research network that can rapidly test new treatments in man. These tools should provide their EFPIA partners with an added competitive advantage in developing new drugs for ASD. | basic science, tool development, child, adult human, young human, treatment, diagnose, symptom, clinical, cell line, drug, drug discovery, neuroimaging, mutation, clinical trial, medicine |
is listed by: Consortia-pedia is related to: Roche is related to: Janssen Research and Development is related to: Pfizer Animal Genetics is related to: King's College London; London; United Kingdom is related to: Birkbeck University of London; London; United Kingdom is related to: Central Institute of Mental Health; Mannheim; Germany is related to: CEA; Gif sur Yvette; France is related to: European Molecular Biology Laboratory is related to: University College London; London; United Kingdom is related to: Pasteur Institute is related to: Karolinska Institute; Stockholm; Sweden is related to: Max-Planck-Gesellschaft is related to: Biomedical University Campus of Rome; Rome; Italy is related to: University of Basel; Basel; Switzerland is related to: Ulm University; Baden-Wurttemberg; Germany is related to: University of Cambridge; Cambridge; United Kingdom is related to: Autism Speaks is related to: GABO:mi is related to: deCODE genetics is related to: Noldus has parent organization: Roche |
Innovative Medicines Initiative ; EFPIA |
nlx_158184 | SCR_003861 | European Autism Interventions - A Multicentre Study for Developing New Medications, European Autism Interventions | 2026-08-29 11:21:40 | 2 | |||||||
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EMIF Resource Report Resource Website 50+ mentions |
EMIF (RRID:SCR_010495) | EMIF | consortium, data or information resource, organization portal, portal | A project that aims to improve access to human health data by developing a common information framework (EMIF-Platform) that allows for efficient re-use of existing health data, opening up new avenues of research for scientists. To ensure immediate applicability, the project includes two specific therapeutic research topics: the onset of Alzheimer's Disease (EMIF-AD) and metabolic complications of obesity (EMIF-Metabolics). The AD Topic aims to discover and validate biomarkers of AD onset in the preclinical and prodromal phase as well as for disease progression and identify high-risk individuals for therapeutic trials for prevention. The Metabolic Topic aims to discover and evaluate biomarkers for the risk of metabolic complications in obesity and to identify high-risk populations for intervention purposes. Collaboration between the 3 topics will ensure the development and delivery of an efficient Information Framework. This initiative has combined several data sets for neuroimaging including ADNI and several others, curating them into transmart. | metabolic complication, biomarker, tool development, data sharing, health data, preclinical, prodromal, interoperability, adult human, pediatric, young human, cell model, animal model, therapeutic target, trial design, high-risk population, metabolic, health, platform, prevention, clinical trial, disease progression |
is related to: eTRIKS is related to: Roche is related to: Janssen Research and Development is related to: Pfizer Animal Genetics is related to: Brighton Collaboration is related to: Ealing Hospital; London; United Kingdom is related to: EuroRec is related to: European Molecular Biology Laboratory is related to: PENTA-ID is related to: University of Gothenburg; Gothenburg; Sweden is related to: University of Helsinki; Helsinki; Finland is related to: National Institute of Health and Medical Research; Rennes; France is related to: University of Eastern Finland; Eastern Finland; Finland is related to: Karolinska Institute; Stockholm; Sweden is related to: King's College London; London; United Kingdom is related to: Maastricht University; Maastricht; Netherlands is related to: Max-Planck-Gesellschaft is related to: University of Tartu; Tartu; Estonia is related to: VTT Technical Research Centre of Finland is related to: University of Aveiro; Aveiro; Portugal is related to: University of Pisa; Pisa; Italy is related to: University of Leipzig; Saxony; Germany is related to: Pompeu Fabra University; Barcelona; Spain is related to: University of Antwerp; Antwerp; Belgium is related to: University College London; London; United Kingdom is related to: University of Cambridge; Cambridge; United Kingdom is related to: University of Copenhagen; Copenhagen; Denmark is related to: University of Glasgow; Glasgow; United Kingdom is related to: University of Leicester; Leicester; United Kingdom is related to: University Hospital Erlangen; Bavaria; Germany is related to: University of Manchester; Manchester; United Kingdom is related to: Sorbonne University; Paris; France is related to: VIB; Flanders; Belgium is related to: Alzheimer Europe is related to: Cambridge Cognition is related to: concentris research management is related to: Custodix is related to: Genomedics is related to: PHARMO Institute is related to: Synapse Research Management Partners is related to: Proteome Sciences is related to: Pedianet is related to: Gnubila is related to: Medical Research Council is related to: Vestische Children and Youth Clinic Dates; North Rhine-Westphalia; Germany has parent organization: University of Oxford; Oxford; United Kingdom |
EFPIA ; Innovative Medicines Initiative 115372 |
nlx_158040 | SCR_010495 | European Medical Information Framework | 2026-08-29 11:23:43 | 52 | |||||||
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MOCAT Resource Report Resource Website 10+ mentions |
MOCAT (RRID:SCR_011943) | MOCAT | software resource | Software package for analyzing metagenomics datasets. |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
OMICS_01517 | SCR_011943 | 2026-08-29 11:24:08 | 42 | ||||||||||
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European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
BBSRC ; EMBL member states ; European Union ; Industry Programme partners ; NIH ; UK Research Councils ; Wellcome Trust |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-08-29 11:21:59 | 3760 | ||||||
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Agadir Resource Report Resource Website 50+ mentions |
Agadir (RRID:SCR_008402) | algorithm | A prediction algorithm based on the helix/coil transition theory. Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed. To submit a job to Agadir, log in the calculation part using the login button in the right bottom. Then fill-in the input form and proceed to next page, etc. You will reach a final page that resumes all the input information and allows you to run the calculation. You can submit one or more peptide sequences in one-letter format. Sequences should be separated by one return character. Spaces and tabulations are automatically removed. Only standard amino acids are accepted. Agadir accepts two modifications at the N-terminus (acetylation or succynilation), and one at the C-terminus (amidation). Just choose the desired option in the input form. You can use only one set of parameters: temperature, ionic strength (calibrated for NaCl) and pH, or explore a particular range of conditions for one parameter. In the latter case the intervals between any two values are: Ionic strength 0.05 M Temperature 1 K pH 0.2 units When setting the conditions for these parameters please be aware that the allowed ranges are: Ionic strength between 0.001 and 1 M Temperature between 273 and 400 K pH between 1 and 14 Output of the prediction at the residue level is available only when submitting no more than ten peptide sequences, and without any screening of conditions. Hstaple is the Hydrophobic Staple motif, Schellman is the Shellman motif, CaH are the expecte chemical shifts of the Calpha proton, 13Ca are the alpha Carbon 13 chemical shifts, JaN is the Jalpha--nitrogen coupling. | has parent organization: European Molecular Biology Laboratory | nif-0000-30072 | SCR_008402 | Agadir | 2026-08-29 11:23:14 | 55 | ||||||||||
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Bork Group's WU-BLAST2 Search Service at EMBL Resource Report Resource Website 1+ mentions |
Bork Group's WU-BLAST2 Search Service at EMBL (RRID:SCR_008431) | data or information resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This portal let you search BLAST through the WU-BLAST2 Search Service provided by the Bork Group at EMBL. Sponsors: This resource is supported by EMBL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | has parent organization: European Molecular Biology Laboratory | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30210 | http://archive.is/dove.embl-heidelberg.de | SCR_008431 | BLAST2 | 2026-08-29 11:23:05 | 7 | ||||||||
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Expression Database in 4D Resource Report Resource Website 1+ mentions |
Expression Database in 4D (RRID:SCR_007066) | 4DXpress | data or information resource, data repository, database, service resource, storage service resource | This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The name 4DXpress stands for expression database in 4D. The 4D (four dimensions) of 4DXpress can be interpreted either as: 3 spatial dimensions plus time, or as 1. species 2. gene 3. developmental stage 4. anatomical structure. The major focus of this database lies in cross species comparison. The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. Data was integrated from several species specific expression pattern databases, such as ZFIN, BDGP, GXD, MEPD as well as directly submitted by researchers of the participating groups at EMBL. The 4DXpress database is a project within the Centre for Computational Biology at EMBL. It is developed by Yannick Haudry, Thorsten Henrich and Ivica Letunic and coordinated by Thorsten Henrich. Hugo Berube is developing the 4D ArrayExpress Data Warehouse at EBI for integrating in situ data with microarray data. | genes, anatomical structures, developmental stage, microarray data, species, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
European Molecular Biology Laboratory; Heidelberg; Germany | PMID:17916571 | nif-0000-02524, biotools:4dxpress | https://bio.tools/4dxpress | SCR_007066 | 4DXpress Database | 2026-08-29 11:23:00 | 1 | |||||
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HTSeq Resource Report Resource Website 5000+ mentions |
HTSeq (RRID:SCR_005514) | HTSeq | authoring tool, data processing software, software application, software resource, standalone software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge. | python, high-throughput sequencing assay, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
DOI:10.1093/bioinformatics/btu638 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:htseq, OMICS_01053 | https://bio.tools/htseq | http://www-huber.embl.de/users/anders/HTSeq/, https://sources.debian.org/src/python3-htseq/ | SCR_005514 | HTSeq: Analysing high-throughput sequencing data with Python | 2026-08-29 11:27:28 | 8618 | ||||
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AltSplice Database of Alternative Spliced Events Resource Report Resource Website 1+ mentions |
AltSplice Database of Alternative Spliced Events (RRID:SCR_008162) | data or information resource, database | AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations. This data is being integrated with other data that is generated by other members of the ASD consortium. The ASD project will provide the following in its three year duration: -human curated database of alternative spliced genes and their properties -a computer generated database of alternatively spliced genes and their properties -the integration of the above and newly found knowledge in a user-friendly interface and research workbench for both bioinformaticists and biologists -DNA chips that are based on the data in the above databases -the DNA chips will be used to test against predisposition for and diagnoses of human diseases ASD aims to analyse this mechanism on a genome-wide scale by creating a database that contains all alternatively spliced exons from human, and other model species. Disease causing mutations seem to induce aberrations in the process of splicing and its regulation. The ASD consortium will develop a DNA microarray (chip) that contains cDNAs of all the splicing regulatory proteins and their isoforms, as well as a chip that contains a number of disease relevant genes. We will concentrate on three models of disease (breast cancer, FTDP-17, male infertility) in which a connection between mis-splicing and a pathological state has been observed. Finally, these chips will be developed as demonstrative kits to detect predisposition for and diagnosis of such diseases. Categories: Nucleotide Sequences: Gene Structure, Introns and Exons, & Splice Sites Databases | event, exon, gene, alternative, annotation, bioinformatic, biology, breast cancer, cdna, chip, diagnosis, disease, dna, human, infertility, intron, isoform, male, microarray, mis-splicing, model, nucleotide, pathological, pattern, property, protein, regulatory, splice, splicing, structure, transcript | has parent organization: European Molecular Biology Laboratory | nif-0000-21021 | SCR_008162 | AltSplice Database of Alternative Spliced Events | 2026-08-29 11:30:17 | 3 | |||||||||
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Secondary Structure Matching Resource Report Resource Website 100+ mentions |
Secondary Structure Matching (RRID:SCR_008365) | data or information resource, database | Secondary Structure Matching (SSM) is an interactive service for comparing protein structures in 3D. SSM compares to other protein matching services, see results here. It is used as a structure search engine in PISA service (Protein Interfaces, Surfaces and Assemblies). It queries may be launched from any web site, see instructions here and it is based on the CCP4 Coordinate Library, found here. The service provides for: -pairwise comparison and 3D alignment of protein structures -multiple comparison and 3D alignment of protein structures -examination of a protein structure for similarity with the whole PDB or SCOP archives -best Ca-alignment of compared structures -download and visualization of best-superposed structures using Rasmol (Unix/Linux platforms), Rastop (MS Windows machines) and Jmol (platform-independent server-side java viewer) -linking the results to other services - PDBe Motif, OCA, SCOP, GeneCensus, FSSP, 3Dee, CATH, PDBSum, SWISS-PROT and ProtoMap. Sponsors: The project is funded by the Collaborative Computational Project Number 4 in Protein Crystallography of the Biotechnology and Biological Sciences Research Council | alignment 3d, compare, interactive, interface, matching, multiple, pairwise, protein, secondary, structure, visualization | has parent organization: European Molecular Biology Laboratory | nif-0000-25563 | SCR_008365 | SSM | 2026-08-29 11:30:23 | 166 | |||||||||
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Search Tool for Interactions of Chemicals Resource Report Resource Website 1000+ mentions |
Search Tool for Interactions of Chemicals (RRID:SCR_007947) | STITCH | data or information resource, database | Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. | drug-target relationship, chemical, chemical-protein interaction, chemical relationship, crystal structure, metabolic pathway interaction, protein, interaction, small molecule, drug, interaction network, FASEB list |
is listed by: OMICtools is related to: Integrated Molecular Interaction Database has parent organization: European Molecular Biology Laboratory |
BMBF ; European Union FP6 EMBO ; ProBioC |
PMID:22075997 PMID:19897548 PMID:18084021 |
r3d100012165, OMICS_01589, nif-0000-03499 | https://doi.org/10.17616/R3606X, https://doi.org/10.17616/R3606X | SCR_007947 | STITCH: Chemical-Protein Interactions | 2026-08-29 11:30:16 | 1054 | |||||
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eggNOG Resource Report Resource Website 1000+ mentions |
eggNOG (RRID:SCR_002456) | eggNOG | data or information resource, database | A database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). eggNOG's database currently counts 1.7 million orthologous groups in 3686 species, covering over 7.7 million proteins (built from 9.6 million proteins). (Jan 30, 2014) | orthologous gene, ortholog, gene, function, FASEB list |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
BMBF ; European Union FP6 |
PMID:24297252 PMID:22096231 |
Free, Available for download, Freely available | nif-0000-02789, OMICS_01689 | SCR_002456 | eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups, eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups), evolutionary genealogy of genes: Non-supervised Orthologous Groups | 2026-08-29 11:29:17 | 4095 | |||||
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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 | 2026-08-29 11:29:26 | 410 | |||||
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BreakDB Resource Report Resource Website |
BreakDB (RRID:SCR_003134) | BreakDB | data or information resource, data set | Data set developed to store, annotate and dsplay structural variant (SV) breakpoint events identified by PEMer and from other sources. | structural variant, breakpoint |
is related to: PEMer has parent organization: European Molecular Biology Laboratory |
PMID:19236709 | Free, Freely available | nlx_156789 | SCR_003134 | Break DB | 2026-08-29 11:31:53 | 0 | ||||||
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PEMer Resource Report Resource Website 1+ mentions |
PEMer (RRID:SCR_005263) | software resource | Software package as computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from novel genome. | structural variation, genome, next-generation sequencing, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: BreakDB has parent organization: European Molecular Biology Laboratory |
PMID:19236709 | biotools:pemer, OMICS_00320 | https://bio.tools/pemer, https://bio.tools/pemer | SCR_005263 | Paired-End Mapper | 2026-08-29 11:22:18 | 7 | |||||||
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OGEE - Online GEne Essentiality database Resource Report Resource Website 1+ mentions |
OGEE - Online GEne Essentiality database (RRID:SCR_006080) | OGEE, OGEEdb | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Online GEne Essentiality database containing genes that were tested experimentally for essentiality and their features; it also provides a set of tools to systematically explore and analyze these data. The main purpose of this project is to better understand gene essentiality by facilitating the comparisons of the differences and similarities between essential and non-essential genes. This is achieved by collecting not only experimentally tested essential and non-essential genes, but also associated gene features such as expression profiles, duplication status, conservation across species, evolutionary origins and involvement in embryonic development. We focus on large-scale experiments and complement our data with text-mining results. Genes are organized into data sets according to their sources. Genes with variable essentiality status across data sets are tagged as conditionally essential, highlighting the complex interplay between gene functions and environments. Linked tools allow the user to compare gene essentiality among different gene groups, or compare features of essential genes to non-essential genes, and visualize the results. Why is it different from existing databases? * we included both essential and non-essential genes so that we could better understand the gene essentiality by comparing the similarities and differences between the two gene sets; * we compiled a list of features for each gene, including whether they are duplicates or involved in development, the number of other homologous genes in the same genome, as well as their earliest expression stages during development. These features are keys to understand the essentiality of genes; * we also provide a set of tools to explore our data and visualize the results. For example, users can simply divide genes into two groups according to whether they are duplicates, calculate the proportion of essential genes (PE%) in each group and then visualize the results in a bar plot; or they can classify genes into multiple groups according to their earliest expression stages during evolution, compare the essentiality of genes that were expressed earlier with those were latter, and plot the results in a line chart. | genome-wide association study, essentiality, gene, essential gene, non-essential gene, growth, expression profile, duplication status, conservation, evolutionary origin, embryonic development, text-mining, gene function, environment, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
BMBF 0315450C | PMID:22075992 | Free | nlx_151488, biotools:ogee | https://bio.tools/ogee | SCR_006080 | Online GEne Essentiality database | 2026-08-29 11:22:32 | 2 | ||||
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Human-gpDB Resource Report Resource Website 1+ mentions |
Human-gpDB (RRID:SCR_006223) | Human-gpDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A publicly accessible, relational database of human G-Proteins and their interactions with human GPCRs and Effectors. Advanced data integration techniques make Human-gpDB very rich in context since all of the bioentities are linked to a rich variety of external data sources. High quality visualization methods make the networks more informative and the extraction of information easier. Human-gpDB is currently a very useful tool for drug targeting investigation. The sequences of G-Proteins and GPCRs are classified according to a hierarchy of different classes, families and sub-families, whereas the Effectors sequences are classified in families, subfamilies and types, based on extensive literature search. The classification of GPCRs follows the IUPHAR classification, while the Effectors classification is a unique feature and is based on their function. The database currently holds information about 713 human GPCRs, 36 human G-Proteins and 99 human Effectors. The collection of the information about the interactions between these molecules was done manually and the current status of Human-gpDB reveals information about 1663 connections between GPCRs and G-Proteins and 1618 connections between G-Proteins and Effectors. | g-protein coupled receptor, g-protein, effector, interaction, visualization, data integration |
has parent organization: University of Athens Biophysics and Bioinformatics Laboratory has parent organization: European Molecular Biology Laboratory |
PMID:20689020 | Public | nlx_151774 | http://schneider.embl.de/human_gpdb | SCR_006223 | Human-gpDB: A database of human GPCRs G-proteins Effectors and their interactions | 2026-08-29 11:22:34 | 1 |
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