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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ConsensusPathDB Resource Report Resource Website 500+ mentions |
ConsensusPathDB (RRID:SCR_002231) | CPDB | data or information resource, database | An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered. | gene regulatory network, pathway, gene regulatory network, molecular interaction, interaction, gene regulation, protein interaction, genetic interaction, biochemical reaction, drug-target interaction, molecule, visualization, gene, protein, complex, metabolite, FASEB list |
is listed by: OMICtools is related to: BIND is related to: BioCarta Pathways is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: CORUM is related to: Database of Interacting Proteins (DIP) is related to: DrugBank is related to: HPRD - Human Protein Reference Database is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: Integrating Network Objects with Hierarchies is related to: InnateDB is related to: IntAct is related to: KEGG is related to: MINT is related to: MIPS Mammalian Protein-Protein Interaction Database is related to: MatrixDB is related to: NetPath is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDZBase is related to: Pathway Interaction Database is related to: PIG - Pathogen Interaction Gateway is related to: PINdb is related to: PharmGKB is related to: PhosphoPOINT is related to: PhosphoSitePlus: Protein Modification Site is related to: Reactome is related to: Small Molecule Pathway Database is related to: SignaLink is related to: SPIKE is related to: Therapeutic Target Database is related to: WikiPathways has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
European Union HEALTH-F4-2007-200767 | PMID:23143270 PMID:21071422 PMID:20847220 PMID:18940869 |
Free, Freely available | nif-0000-02684, OMICS_01903, r3d100012822 | https://doi.org/10.17616/R3HF8Z | SCR_002231 | ConsensusPathDB, ConsensusPathDB-human | 2026-08-03 09:31:36 | 667 | ||||
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EPILEPSIE database Resource Report Resource Website 1+ mentions |
EPILEPSIE database (RRID:SCR_003179) | data or information resource, database | A comprehensive database for human surface and intracranial EEG data that is suitable for a broad range of applications e.g. of time series analyses of brain activity. Currently, the EU database contains annotated EEG datasets from more than 200 patients with epilepsy, 50 of them with intracranial recordings with up to 122 channels. Each dataset provides EEG data for a continuous recording time of at least 96 hours (4 days) at a sample rate of up to 2500 Hz. Clinical patient information and MR imaging data supplement the EEG data. The total duration of EEG recordings included execeeds 30000 hours. The database is composed of different modalities: Binary files with EEG recording / MR imaging data and Relational database for supplementary meta data. | seizure, electroencephalography, mri, eeg recording, metadata, intracranial, surface, time series analyses, brain activity, brain, clinical, image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
Epilepsy | Excellence Initiative of the German Federal and State Governments ; European Union 211713; BMBF 01GQ0420; German Science Foundation Ti 315/4-2 |
PMID:22738131 | Free, Freely available | nlx_156892 | http://www.nitrc.org/projects/epilepsiaedb http://epilepsy-database.eu/project/ http://www.epilepsiae.eu http://epilepsy-database.eu | SCR_003179 | EPILEPSIAE Project Database, European Epilepsy Database | 2026-08-03 09:32:12 | 3 | ||||
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Recognition of Errors in Assemblies using Paired Reads Resource Report Resource Website 1+ mentions |
Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) | REAPR | software resource, software application, data processing software | Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls. | Identify, error, genome, assembly, without, reference, sequence, incorrect, scaffold, error |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
European Union ; Wellcome Trust ; JSPS KAKENHI |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-08-03 09:37:05 | 2 | |||||
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MINT Resource Report Resource Website 1000+ mentions |
MINT (RRID:SCR_001523) | MINT | data or information resource, database | A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them. | protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, ortholog, FASEB list |
uses: IntAct uses: PSI-MI is listed by: re3data.org is affiliated with: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: VirusMINT is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer has parent organization: University of Rome Tor Vergata; Rome; Italy works with: IMEx - The International Molecular Exchange Consortium |
European Union ; ENFIN ; Interaction Proteome Project ; IMEx - The International Molecular Exchange Consortium ; HUPO Proteomics Standards Initiative ; AIRC Associazione Italiana per la Ricerca sul Cancro |
PMID:22096227 PMID:24234451 PMID:19897547 PMID:18592188 PMID:18551417 PMID:18428712 PMID:17135203 PMID:11911893 |
nlx_152821, r3d100010414 | https://doi.org/10.17616/R38S3B | SCR_001523 | MINT, the Molecular INTeraction database, Molecular Interactions Database, Molecular INTeraction database, MINT - the Molecular INTeraction database | 2026-08-03 09:31:21 | 1109 | |||||
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Arabidopsis Reactome Resource Report Resource Website 1+ mentions |
Arabidopsis Reactome (RRID:SCR_002063) | data or information resource, database | Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context. | pathway, reaction, biological process |
uses: AraCyc uses: KEGG is listed by: 3DVC has parent organization: John Innes Centre; Norwich; United Kingdom |
European Union LSHG-CT-2006-037704 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20812 | SCR_002063 | Arabidopsis Reactome - a curated knowledgebase of plant biological pathways | 2026-08-03 09:31:38 | 3 | |||||||
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CancerResource Resource Report Resource Website 1+ mentions |
CancerResource (RRID:SCR_011945) | data or information resource, database | Comprehensive database of cancer relevant proteins and compound interactions supported by experimental knowledge.Knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data. | compound, drug, target gene, cancer relevant proteins, compound interactions, drug-target relationships, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | International Research Training Group IRTG ; DFG ; Federal Ministry of Education and Research BMBF ; European Union |
PMID:20952398 | Free, Freely available | biotools:cancerresource, OMICS_01576 | https://bio.tools/cancerresource | http://bioinf-data.charite.de/cancerresource/index.php?site=home | SCR_011945 | 2026-08-03 09:35:01 | 5 | ||||
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VDJbase Resource Report Resource Website 1+ mentions |
VDJbase (RRID:SCR_022599) | data or information resource, database | Open source adaptive immune receptor genotype and haplotype database. Core collection is inferred from immune receptor repertoire sequences and genomically derived material. Provides customisable reports, which allow users to study gene and allele usage in various ways. | Adaptive immune receptor genes, genotypes and haplotypes, immune receptor repertoire sequences, customisable reports, gene and allele | European Union ; NIAID R01AI127877; NIAID R01AI125567; NIAID R01AI130398 |
DOI:10.1093/nar/gkz872 | Free, Freely available | SCR_022599 | 2026-08-03 09:38:01 | 6 | |||||||||
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RNAmmer Resource Report Resource Website 100+ mentions |
RNAmmer (RRID:SCR_017075) | production service resource, data analysis service, web service, software application, standalone software, data processing software, data analysis software, analysis service resource, data access protocol, service resource, software resource | Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes. | predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNA | has parent organization: Technical University of Denmark; Lyngby; Denmark | EMBIO at the University of Oslo ; Research Council of Norway ; Danish Center for Scientific Computing ; European Union |
PMID:17452365 | Restricted | SCR_017075 | 2026-08-03 09:36:59 | 103 | ||||||||
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SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | ontology, data analysis service, production service resource, service resource, analysis service resource, controlled vocabulary, data or information resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-08-03 09:36:50 | 134 | |||||||
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Project DARE Resource Report Resource Website |
Project DARE (RRID:SCR_017538) | DARE | organization portal, portal, consortium, data or information resource, project portal | EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously. | European Union, infrastructure, workflow, connectivity, layer, methodology, integrated, data, Agile | European Union | SCR_017538 | project-dare, Delivering Agile Research Excellence on European e-Infrastructures | 2026-08-03 09:37:04 | 0 | |||||||||
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STARNET Resource Report Resource Website 1+ mentions |
STARNET (RRID:SCR_025238) | STARNET | web service, data access protocol, software resource, source code | Web interactive browser to visualize data and perform gene set enrichment analysis along with gene and SNP lookup. Web interface used to query STARNET datasets and downstream analysis which includes RNAseq from 7 tissues: blood, free internal mammary artery (MAM), atherosclerotic aortic root (AOR), subcutaneous fat (SF), visceral abdominal fat (VAF), skeletal muscle (SKLM), and liver (LIV). Paired SNP genotyping data is included and utilized for tissue expression quantitative trait loci (eQTL), CAD heritability (H2), co-expression networks and gene regulatory networks. | cross-tissue co-expression analysis, STARNET multitissue gene expression data, cardiovascular disease patients, | NHLBI R01HL125863; American Heart Association ; Swedish Research Council ; Heart Lung Foundation ; AstraZeneca ; European Union ; Federal German Ministries ; ModulMax ; NHLBI R01HL130423; NHLBI R01HL135093; NHLBI R01HL148167; New South Wales health ; NHLBI R01 HL144651; NHLBI R01 HL147883; NHLBI PO1 HL28481; NIDDK R01 DK117850; NHLBI HL138193 |
PMID:36276926 | Free, Freely available | https://github.com/skoplev/starnet | SCR_025238 | Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task | 2026-08-03 09:39:05 | 5 | ||||||
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Pathogens Portal Norway Resource Report Resource Website |
Pathogens Portal Norway (RRID:SCR_025641) | topical portal, data or information resource, portal, disease-related portal | Portal provides information about available datasets, resources, tools, and services related to pandemic preparedness in Norway. Portal gives researchers, clinicians and policymakers access to collection of biomolecular data about pathogens. | Norway, pandemic preparedness in Norway, pandemic data, pandemic, datasets, resources, tools, services, | is related to: Pathogens Portal Netherlands | European Union ; ELIXIR Norway |
Free, Freely available | SCR_025641 | 2026-08-03 09:38:49 | 0 | |||||||||
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Alzheimer Europe Resource Report Resource Website 1+ mentions |
Alzheimer Europe (RRID:SCR_003802) | AE | nonprofit organization | A non-governmental organization aimed at raising awareness of all forms of dementia by creating a common European platform through co-ordination and co-operation between Alzheimer organizations throughout Europe. Alzheimer Europe is also a source of information on all aspects of dementia. |
is related to: Greek Association of Alzheimers Disease and Related Disorders is related to: PharmaCog is related to: EMIF is parent organization of: PharmaCog |
Dementia, Alzheimer's disease | European Union | ISNI: 0000 0001 0739 010X, Wikidata: Q16827712, nlx_158313, grid.424021.1 | https://ror.org/029yy6d70 | SCR_003802 | 2026-08-01 12:02:33 | 8 | |||||||
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BibSonomy Resource Report Resource Website 1+ mentions |
BibSonomy (RRID:SCR_013756) | collaboration tool, software resource | A software application which assists in managing and sharing scientific literature. Users can collect and share publications, collaborate with other researchers, and find new resources and publications for research. | software, publications, collaboration tool, scientific literature | uses: Citation Style Language | European Union ; German Research Foundation ; Land Hessen |
DOI:10.1007/s00778-010-0208-4 | Free, Public | SCR_013756 | 2026-08-01 12:04:53 | 5 | ||||||||
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KI Biobank - TwinGene Resource Report Resource Website 10+ mentions |
KI Biobank - TwinGene (RRID:SCR_006006) | TwinGene | biomaterial supply resource, material resource | In collaboration with GenomeEUtwin, the TwinGene project investigates the importance of quantitative trait loci and environmental factors for cardiovascular disease. It is well known that genetic factors are of considerable importance for some familial lipid syndromes and that Type A Behavior pattern and increased lipid levels infer increased risk for cardiovascular disease. It is furthermore known that genetic factors are of importance levels of blood lipid biomarkers. The interplay of genetic and environmental effects for these risk factors in a normal population is less well understood and virtually unknown for the elderly. In the TwinGene project twins born before 1958 are contacted to participate. Health and medication data are collected from self-reported questionnaires, and blood sampling material is mailed to the subject who then contacts a local health care center for blood sampling and a health check-up. In the simple health check-up, height, weight, circumference of waist and hip, and blood pressure are measured. Blood is sampled for DNA extraction, serum collection and clinical chemistry tests of C-reactive protein, total cholesterol, triglycerides, HDL and LDL cholesterol, apolipo��protein A1 and B, glucose and HbA1C. The TwinGene cohort contains more than 10000 of the expected final number of 16000 individuals. Molecular genetic techniques are being used to identify Quantitative Trait Loci (QTLs) for cardiovascular disease and biomarkers in the TwinGene participants. Genome-wide linkage and association studies are ongoing. DZ twins have been genome-scanned with 1000 STS markers and a subset of 300 MZ twins have been genome-scanned with Illumina 317K SNP platform. Association of positional candidate SNPs arising from these genomscans are planned. The TwinGene project is associated with the large European collaboration denoted GenomEUtwin (www.genomeutwin.org, see below) which since 2002 has aimed at gathering genetic data on twins in Europe and setting up the infrastructure needed to enable pooling of data and joint analyses. It has been the funding source for obtaining the genome scan data. Types of samples: * EDTA whole blood * DNA * Serum Number of sample donors: 12 044 (sample collection completed) | quantitative trait loci, environmental factor, cardiovascular disease, environment, genetic, gene, lipid syndrome, lipid, health, medication, questionnaire, c-reactive protein, total cholesterol, triglyceride, hdl, ldl, cholesterol, apolipo-protein a1, apolipo-protein b, glucose, hba1c, genome-wide linkage study, genome-wide association study, genome |
is listed by: One Mind Biospecimen Bank Listing is related to: GenomEUtwin is related to: Swedish Twin Registry has parent organization: Karolisnka Biobank |
Twin | NIH ; European Union ; VR ; SSF |
nlx_151387 | http://ki.se/ki/jsp/polopoly.jsp?d=29354&a=31600&l=en | SCR_006006 | 2026-08-01 12:10:51 | 19 | ||||||
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HC2: Human-Computer Confluence Resource Report Resource Website |
HC2: Human-Computer Confluence (RRID:SCR_005549) | HC2, HCC | knowledge environment, training resource | HC2 is an EU funded project that aims to promote, support and help define future lines of research in Human Computer Confluence (HCC). HCC is the study of the intersection of HCI, Cognitive Neuroscience, VR/AR, Presence, Pervasive Computing and how they can enable new forms of sensing, perception, interaction and understanding. In a sense it is the study of the disappearing interface. HCC, Human-Computer Confluence, is an ambitious research program studying how the emerging symbiotic relation between humans and computing devices can enable radically new forms of sensing, perception, interaction, and understanding. The horizontal character of HCC makes it a fascinating and fertile interdisciplinary field, but it can also compromise its growth, with researchers scattered across disciplines and groups worldwide. To address this we are building a community of HCC researchers. There are lots of ways you can join in. Add your name to the HCC Players Map, take advantage of our Exchange Program to work with colleagues at your favorite lab, sign up for our Summer School or just follow us on Twitter and LinkedIn to see what''s happening. In order to foster interdisciplinary research and promote HCC research we have set up an Exchange Program. Students that wish to apply for financial support from our Exchange Program should follow the steps provided. The Exchange Program is open to all graduate students (Masters and PhD). A maximum of 500 Euro support will be provided per student. | human, computing, cognitive neuroscience, summer school, funding resource | has parent organization: Starlab | European Union | nlx_144641 | SCR_005549 | Human-Computer Confluence, HC Squared, Human Computer Confluence | 2026-08-01 12:10:51 | 0 | |||||||
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ABACAS Resource Report Resource Website 100+ mentions |
ABACAS (RRID:SCR_015852) | ABACAS | software resource, software application | Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account. | contiguation, primer, shotgun assembled contig, reference sequence, assembled sequence |
is listed by: Debian is listed by: OMICtools |
European Union LSHP-LT-2004-503578; Wellcome Trust Sanger Institute |
Free, Available for download | OMICS_06933 | https://sourceforge.net/projects/abacas/files/, https://sources.debian.org/src/abacas/ | SCR_015852 | ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences, Algorithm Based Automatic Contiguation of Assembled Sequences (ABACAS), Algorithm Based Automatic Contiguation of Assembled Sequences | 2026-08-01 12:10:58 | 174 | |||||
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Chernobyl Tissue Bank Resource Report Resource Website 1+ mentions |
Chernobyl Tissue Bank (RRID:SCR_010662) | CTB | biomaterial supply resource, material resource | The CTB (Chernobyl Tissue Bank) is an international cooperation that collects, stores and disseminates biological samples from tumors and normal tissues from patients for whom the aetiology of their disease is known - exposure to radioiodine in childhood following the accident at the Chernobyl power plant. The main objective of this project is to provide a research resource for both ongoing and future studies of the health consequences of the Chernobyl accident. It seeks to maximize the amount of information obtained from small pieces of tumor by providing multiple aliquots of RNA and DNA extracted from well documented pathological specimens to a number of researchers world-wide and to conserve this valuable material for future generations of scientists. It exists to promote collaborative, rather than competitive, research on a limited biological resource. Tissue is collected to an approved standard operating procedure (SOP) and is snap frozen; the presence or absence of tumor is verified by frozen section. A representative paraffin block is also obtained for each case. Where appropriate, we also collect fresh and paraffin-embedded tissue from loco-regional metastases. Currently we do not issue tissue but provide extracted nucleic acid, paraffin sections and sections from tissue microarrays from this material. The project is coordinated from Imperial College, London and works with Institutes in the Russian Federation (the Medical Radiological Research Centre in Obninsk) and Ukraine (the Institute of Endocrinology and Metabolism in Kiev) to support local scientists and clinicians to manage and run a tissue bank for those patients who have developed thyroid tumors following exposure to radiation from the Chernobyl accident. Belarus was also initially included in the project, but is currently suspended for political reasons. |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Imperial College London; London; United Kingdom |
Tumor, Normal, Exposure to radioiodine in childhood following the accident at the Chernobyl power plant | European Union ; Sasakawa Memorial Health Foundation ; NCI |
nlx_70828 | SCR_010662 | 2026-08-01 12:11:02 | 9 | ||||||||
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Connection-set algebra Resource Report Resource Website |
Connection-set algebra (RRID:SCR_017397) | CSA | software resource | Software tool for description of connectivity in small and large scale neuronal network models. It provides operators to form more complex sets of connections from simpler ones and also provides parameterization of such sets. Can be used as component of neuronal network simulators or other tools. | Connectivity, neuronal, network, model, simulator | European Union | PMID:22437992 | Free, Available for download, Freely available | SCR_017397 | Connection Set Algebra | 2026-08-01 12:06:03 | 0 | |||||||
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pyxnat Resource Report Resource Website 1+ mentions |
pyxnat (RRID:SCR_002574) | pyxnat | software library, software toolkit, software resource | Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data. | computed tomography, magnetic resonance, pet, spect, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: XNAT - The Extensible Neuroimaging Archive Toolkit |
European Union | PMID:22654752 | Free, Available for download, Freely available | nlx_155977 | https://sources.debian.org/src/python-pyxnat/ | SCR_002574 | pyxnat: XNAT in Python | 2026-08-02 09:03:22 | 1 |
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