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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ASTRAL Compendium for Sequence and Structure Analysis Resource Report Resource Website 10+ mentions |
ASTRAL Compendium for Sequence and Structure Analysis (RRID:SCR_001886) | ASTRAL | software resource, data storage software, data or information resource, data processing software, software application, database | It provides databases and tools useful for analyzing protein structures and their sequences. It is partially derived from, and augments the SCOP: Structural Classification of Proteins database, a database created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. Most of the resources provided here depend upon the coordinate files maintained and distributed by the Protein Data Bank. Sponsors: This work is supported by grants from the NIH (1-P50-GM62412, 1-K22-HG00056) and the Searle Scholars Program (01-L-116), and by the US Department of Energy under contract DE-AC03-76SF00098. | gene, amino acid, homology, protein sequence, protein structure | has parent organization: University of California at Berkeley; Berkeley; USA | PMID:10592239 | Free, Available for download, Freely available | nif-0000-02580 | SCR_001886 | ASTRAL Compendium for Sequence and Structure Analysis, The ASTRAL Compendium for Sequence and Structure Analysis | 2026-08-06 09:25:31 | 27 | ||||||
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Aspergillus Genomes Resource Report Resource Website |
Aspergillus Genomes (RRID:SCR_001880) | Aspergillus Genomes | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | A resource for viewing annotated genes arising from various Aspergillus sequencing and annotation projects, resulting from the merging of Central Aspergillus Data REpository (CADRE) and The Aspergillus Website, which took place in June 2008. The principal role of CADRE is to aid the Aspergillus research community by managing Aspergillus genome data and by providing visualization tools, ranging from relatively simple annotation displays to more complex data integration displays. In contrast, The Aspergillus Website provides a range of information to the medical community (i.e., clinicians, patients and scientists) regarding the genus Aspergillus and the diseases, such as Aspergillosis, that it can cause. CADRE has been implemented using the Ensembl v22 suite. This suite comprises: * a database schema, which has been devised for storing annotated eukaryotic genomes. The schema is implemented with the MySQL relational database management system. * several specialized programming modules for building interfaces (i.e., BioPerl and Ensembl API modules). * a series of programs (i.e., Perl CGI scripts using the API modules) for viewing genomic data within a web browser., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genome, eukaryotic genome, gene, gene annotation, aspergillosis, aspergillus, pathway, annotation, sequence, metabolic pathway, genomics, clinical, strain, dna, peptide, blast | Fungal Research Trust | PMID:19039001 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02577, r3d100011253 | https://doi.org/10.17616/R3005P | SCR_001880 | 2026-08-06 09:25:32 | 0 | ||||||
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DAVID Resource Report Resource Website 10000+ mentions |
DAVID (RRID:SCR_001881) | DAVID | software resource, data access protocol, web service, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis. | functional domain, annotation, motif, protein, ontology enrichment, gene, high-throughput, functional classification, functional annotation, clustering, genome, pathway, gene-disease association, interaction, functional domain, motif, visualization, FASEB list |
is listed by: OMICtools is listed by: 3DVC is listed by: LabWorm is listed by: SoftCite is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG has parent organization: NCI-Frederick |
NIAID NO1-CO-56000; NCI |
PMID:19131956 PMID:12734009 PMID:35325185 PMID:22543366 PMID:17980028 PMID:17576678 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30408, nif-0000-10451, OMICS_02220, SCR_003033 | http://david.abcc.ncifcrf.gov/ | SCR_001881 | DAVID Bioinformatics Resources, Visualization and Integrated Discovery Bioinformatics Resources, Database for Annotation Visualization and Integrated Discovery, The Database for Annotation, The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources | 2026-08-06 09:25:29 | 18488 | ||||
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GATK Resource Report Resource Website 10000+ mentions |
GATK (RRID:SCR_001876) | GATK | software resource, software library, data analysis software, software toolkit, data processing software, software application | A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation resequencing, bio.tools |
is used by: Halvade Somatic is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SnpEff is related to: GATK HaplotypeCaller is related to: GATK VariantFiltration has parent organization: Broad Institute |
PMID:21478889 | Free, Available for download, Freely available | nlx_154324, OMICS_00286, biotools:gatk | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit, https://bio.tools/gatk | SCR_001876 | Genome Analysis ToolKit | 2026-08-06 09:25:32 | 16663 | |||||
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University of Utah Genetic Science Learning Center - Learn Genetics Resource Report Resource Website 1+ mentions |
University of Utah Genetic Science Learning Center - Learn Genetics (RRID:SCR_001910) | Learn.Genetics, Learn Genetics | training resource, data or information resource, slide, training material, narrative resource, video resource | Educational resources that provide accurate and unbiased information about topics in genetics, bioscience and health for global and local audiences. They are jargon-free, target multiple learning styles, and often convey concepts through animation and interactivity. The Genetic Science Learning Center is a science and health education program located in the midst of the bioscience research being carried out at the University of Utah. Our mission is making science easy for everyone to understand. * Two websites, available free of charge to Internet users worldwide: ** Learn.Genetics delivers educational materials on genetics, bioscience and health topics. They are designed to be used by students, teachers and members of the public. The materials meet selected US education standards for science and health. ** Teach.Genetics provides resources for K-12 teachers, higher education faculty, and public educators. These include PDF-based Print-and-Go™ activities, unit plans and other supporting resources. The materials are designed to support and extend the materials on Learn.Genetics. *Professional development programs that update K-16 teachers' expertise in bioscience and health topics as well as prepare them to implement the materials on our websites. * Community programs that engage with diverse communities in discussions about genetics and health, and in developing culturally and linguistically-appropriate educational materials. Some topics in genetics and bioscience research are controversial. The Center does not take sides in political or ethical controversies. Rather, our goal is to provide comprehensive information that promotes a lively discussion of these topics, so that individuals can arrive at their own informed decisions. | gene, dna, protein, education, genetics, science, bioscience, health, teacher, student, public, professional development, k-12, undergraduate, lesson plan, heredity, genetic trait, cell, molecule, stem cell, cloning, gene therapy, transgenic mouse, epigentics, addiction, genetic variation |
has parent organization: University of Utah; Utah; USA is parent organization of: New Science of Addiction: Genetics and the Brain |
NIH Office of the Director R25OD021903 | You are granted a revocable license to download and print hard copy versions of the material contained on the site for your personal, Educational and noncommercial use, Provided you do not modify or delete any copyright or other notice that appears on the material you download or print. | nif-0000-10482 | http://learns.genetics.utah.edu/ | SCR_001910 | University of Utah Genetic Science Learning Center, Genetic Science Learning Center - Learn.Genetics, Genetic Science Learning Center, Genetic Science Learning Center - Learn Genetics | 2026-08-06 09:25:31 | 9 | |||||
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Arabidopsis thaliana Protein Interactome Database Resource Report Resource Website 1+ mentions |
Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) | AtPID | storage service resource, service resource, data repository, data or information resource, database | Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. | gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotype |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Northeast Forest University; Harbin; China |
National Basic Research Program of China 2010CB945400; National Basic Research Program of China 2007CB108800; National High Technology Research and Development Program of China 2006AA02Z313; National High Technology Research and Development Program of China 2006AA10Z129; National Natural Science Foundation of China 30870575; National Natural Science Foundation of China 30730078; Science and Technology Commission of Shanghai Municipality 06DZ22923 |
PMID:21036873 PMID:17962307 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01898, nif-0000-02585 | http://atpid.biosino.org/ | SCR_001896 | AtPID Database | 2026-08-06 09:25:29 | 8 | ||||
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Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, web service, software resource | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK074967; NIDDK DK062434 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root, https://bio.tools/cistrome | SCR_000242 | Galaxy Cistrome | 2026-08-06 09:25:08 | 16 | |||||
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GenNav Resource Report Resource Website 1+ mentions |
GenNav (RRID:SCR_000147) | GenNav | data access protocol, web service, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG. | image, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: National Library of Medicine |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149123 | SCR_000147 | 2026-08-06 09:25:07 | 1 | ||||||||
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Biometric Research Branch: ArrayTools Resource Report Resource Website 1+ mentions |
Biometric Research Branch: ArrayTools (RRID:SCR_000778) | software resource, data analysis software, software toolkit, data processing software, data visualization software, software application | A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in. | visualization, statistic, analysis, dna, microarray, gene, expression, c, java, excel |
is listed by: OMICtools has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30199 | SCR_000778 | BRB ArrayTools | 2026-08-06 09:25:16 | 6 | ||||||||
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Computational Cancer Genomics Group Resource Report Resource Website 1+ mentions |
Computational Cancer Genomics Group (RRID:SCR_000772) | software resource, data analysis software, data or information resource, data processing software, software application, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB). | eukaryotic, expression, function, gene, analyzer, annotation, biological, clustering, computational, data, genome, in vitro, mapping, messengerrna, molecular, mpss, mrna, one-dimensional, organism, promoter, sage, sequence, snp, software, tag, technology, tool, transcription, transcriptome | has parent organization: SIB Swiss Institute of Bioinformatics | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25561 | SCR_000772 | CCG | 2026-08-06 09:25:17 | 3 | ||||||||
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Cystic Fibrosis Mutation Database Resource Report Resource Website 10+ mentions |
Cystic Fibrosis Mutation Database (RRID:SCR_000685) | CFTR1, CFMDB | storage service resource, service resource, data repository, data or information resource, database | Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world. | Gene, genetic, amino acid, clinical, cystic fibrosis, mutation, phenotype, genotype-phenotype, genotype, dna sequence, mouse, sequence, genetic variation, polymorphism, translation, function, sequence variation, metadata standard, cftr2, FASEB list | is related to: CFTR2 | Cystic fibrosis | Free, Freely available | nif-0000-21105, r3d100012093 | https://doi.org/10.17616/R38356 | SCR_000685 | 2026-08-06 09:25:14 | 42 | ||||||
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MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, software application | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Japan Society for the Promotion of Science ; NHGRI HG006039; NHGRI HG002096; Burroughs-Wellcome Fund ; NIGMS R01GM126567; NSF ABI 1661218; NIGMS R35GM139504 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-08-06 09:25:15 | 2763 | ||||
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Understanding Human Disease Through Mouse Genetics Resource Report Resource Website 10+ mentions |
Understanding Human Disease Through Mouse Genetics (RRID:SCR_000785) | EUMORPHIA | portal, training resource, group, data or information resource | A portal documenting a project for the development of novel approaches in phenotyping, mutagenesis and informatics to improve the characterization of mouse models for understanding human molecular physiology and pathology. EUMORPHIA has developed a new robust primary screening platform for determining the phenotype of mice: EMPReSS - European Mouse Phenotyping Resource for Standardised Screens. The project is also focused on training new young scientists by funding them to work in a variety of laboratories to gain a broader swathe of techniques. The project has also identified the need for more trained mouse pathologists. To address this, they are setting up training courses in pathology and working at a European level to establish more training. | european, european union, mouse, gene, phenotype, model, physiology, molecular, informatics, mutagenesis |
is related to: European Mouse Phenotyping Resource of Standardised Screens is related to: Europhenome Mouse Phenotyping Resource has parent organization: University of Strasbourg; Strasbourg; France |
European Union under FP5 from October 2002 until March 2006 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30502 | http://www.eumorphia.org | SCR_000785 | European Union Mouse Research for Public Health and Industrial Applications | 2026-08-06 09:25:16 | 12 | |||||
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wANNOVAR Resource Report Resource Website 10+ mentions |
wANNOVAR (RRID:SCR_000565) | wANNOVAR | production service resource, analysis service resource, data analysis service, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotate, function, genetic variant, high-throughput sequencing, single nucleotide variant, gene, variant, allele frequency, mutation, annotation, genome, insertion, deletion |
is listed by: OMICtools is related to: ANNOVAR has parent organization: University of Southern California; Los Angeles; USA |
PMID:22717648 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00194 | SCR_000565 | 2026-08-06 09:25:12 | 21 | |||||||
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OnEx - Ontology Evolution Explorer Resource Report Resource Website 1+ mentions |
OnEx - Ontology Evolution Explorer (RRID:SCR_000602) | OnEx | web application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released | ontology, gene, protein, function, process, component, ontology or annotation browser, evolution, trend, annotation, version |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: NCI Thesaurus is related to: OBO has parent organization: University of Leipzig; Saxony; Germany |
BMBF 01AK803E; DFG |
PMID:19678926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02273, nlx_149129 | http://www.izbi.de/onex, http://aprilia.izbi.uni-leipzig.de:8080/onex/ | SCR_000602 | Ontology Evolution Explorer (OnEx), Ontology Evolution Explorer | 2026-08-06 09:25:13 | 1 | ||||
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MAIA Resource Report Resource Website 100+ mentions |
MAIA (RRID:SCR_007153) | MAIA | data analysis software, software application, software resource, data processing software | Software package of programs for complex segregation analysis in animal pedigrees. | gene, genetic, genomic, segregation, analysis, animal, pedigree |
is listed by: Genetic Analysis Software has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Free, Non-commercial, Change of source code requires permission | nlx_154435 | SCR_007153 | 2026-08-06 09:26:48 | 349 | ||||||||
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BioMANTA Resource Report Resource Website 1+ mentions |
BioMANTA (RRID:SCR_007177) | BioMANTA | research forum portal, ontology, software resource, topical portal, controlled vocabulary, disease-related portal, data or information resource, portal | This project encompasses development of novel biological network analysis methods and infrastructure for querying biological data in a semantically-enabled format, and aims to create a semantic interactome model. Research within the BioMANTA project will focus on computational modelling and analysis, primarily using Semantic Web technologies and Machine Learning methods, of large-scale protein-protein interaction and compound activity networks across a wide variety of species. A range of information such as kinetic activity, tissue expression, and subcellular localization and disease state attributes will be included in the resulting data model. Protein interactions are a fundamental component of biological processes. Many proteins are functional only in multimeric complexes, or require interaction partners to achieve their correct localisation or function. For this reason, the study of protein-protein interaction (PPI) networks has become an area of growing interest in computational biology. Through the use of Semantic Web technologies such as Resource Description Framework (RDF) and Web Ontology Language (OWL), interaction data is modelled to create a knowledge representation in which meaning is vested in the ontology rather than instances of data. Stochastic and computational intelligence methods are applied to this data to infer high coverage networks. Semantic inferencing is used to infer previously unknown and meaningful pathways. Major project components: - The BioMANTA Ontology:- An OWL DL ontology incorporating the PSI-MI Ontology, the NCBI Taxonomy, and elements of BioPax ontology and Gene Ontology (describing subcellular localisation). This allows us to re-use existing ontologies, thereby reducing overheads associated with knowledge acquisition in the ontology development process. We are able to integrate existing public data that contain annotation in these formats. - Data conversion & semantic protein integration:- A set of software components that convert protein-protein databases (DIP, MPact, IntAct, etc.) from PSI-MI XML to RDF compliant with the BioMANTA ontology. These software allow us to make these protein-protein interaction datasets (and more generally, any PSI-MI XML data) semantically available for querying and inference within BioMANTA. - A RDF triple store based on RDF Molecules and the MapReduce architecture:- A proof-of-concept RDF triple store using RDF molecules and Hadoop scale-out architectures. Regular RDF graphs are deconstructed into RDF molecules, which are distributed over distributed compute nodes in the MapReduce architecture, and are subsequently combined to form equivalent RDF graphs. Such an approach makes the distributed SPARQL querying and reasoning on RDF triple stores possible. - A quantitative framework to integrate networks extracted from independent data sources (gene expression, subcellular localization, and ortholog mapping):- The model is multi-layer, with a first layer based on Decision Trees where each Decision tree is built on each dataset independently. The tree nodes are cut using Shannon''s entropy (mutual information); the decision of these independent trees is integrated using logistic regression, and the parameters are optimised using maximum likelihood. Sponsors: This resource is supported by the Pfizer Global Research and Development, the Institute for Molecular Bioscience (IMB), and the University of Queensland, Australia. | biological, network, model, analysis, semantic, interactome, biological, data, development, computational, process, protein, biology, ontology, knowledge, molecule, rdf, framework, subcellular, localization, gene, expression, ortholog, mapping, dataset | has parent organization: University of Queensland; Brisbane; Australia | nif-0000-30183 | SCR_007177 | The Modelling and Analysis of Biological Network Activity | 2026-08-06 09:26:46 | 2 | ||||||||
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HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism Resource Report Resource Website 50+ mentions |
HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) | HumanCyc | software resource, service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version. | enzyme, function, functional, gene, genome, genomic, human, human genome, metabolic, metabolism, mitochondrion, nucleotide, pathway, position, reaction, sequence, metabolomics, gene expression, bioreaction, metabolic pathway, nutrition, FASEB list |
is listed by: BioCyc is related to: Pathway Commons is related to: ConsensusPathDB is related to: BioCyc is related to: Pathway Tools has parent organization: Stanford Research Institute International |
Pharmaceutical company ; NIGMS GM092729 |
PMID:15642094 | Public | r3d100011286, nif-0000-21206 | https://doi.org/10.17616/R3ZS72 | SCR_007050 | 2026-08-06 09:26:44 | 60 | |||||
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Malaria Parasite Metabolic Pathways Resource Report Resource Website 10+ mentions |
Malaria Parasite Metabolic Pathways (RRID:SCR_007072) | Malaria Parasite Metabolic Pathways | image collection, data set, data or information resource | Data set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database. | enzyme, gene, genome, map, metabolic, mosquito, parasite, pathway, plasmodium falciparum, protein, reaction, sequence, metabolic pathway, chemical structure, cell-cell interaction, transport, morphology, mitochondria, apicoplast | has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel | Malaria | UNDP/World Bank/WHO Special Programme ; NIAID ; European Union ; 6th FP- BioMalPar Network of Excellence on Biology and Pathology of the Malaria Parasite |
nif-0000-21249 | SCR_007072 | 2026-08-06 09:26:45 | 20 | |||||||
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VBASE2 Resource Report Resource Website 50+ mentions |
VBASE2 (RRID:SCR_007082) | VBASE2 | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences. Based on the properties of the source sequences, V genes are classified into 3 different classes: * Class 1: genomic and rearranged evidence * Class 2: genomic evidence only * Class 3: rearranged evidence only This allows careful sequence quality validation by the user. References to other immunological databases ( KABAT, IMGT/LIGM and VBASE ) are given to provide all public annotation data for each V gene. The VBASE2 database can be accessed either by the Direct Query interface or by the DNAPLOT Query interface. The Sequences given by the user are aligned with DNAPLOT against the VBASE2 database. Direct Query allows to enter sequence IDs and names (Field 1), choose species, locus, V gene family and class (Field 2) or search for 100% sequences (Field 3). At the DNAPLOT Query, the sequences given by the user are aligned with DNAPLOT against the VBASE2 database. The DNAPLOT program offers V gene nucleotide sequence alignment referring to the IMGT V gene unique numbering. The Quick Search can be used either for Direct Query to search for sequence IDs and V gene names or for DNAPLOT Query for up to 5 sequences. The new Fab Analysis allows you to align Fab, scFab, scAb or scFv sequences with DNAPLOT against the VBASE2 database, where both heavy and light chain are analyzed. | v gene sequence, v gene, gene, dna, sequence, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: European Nucleotide Archive (ENA) is related to: Ensembl |
BMBF 031U110A/031U210A | PMID:15608286 | Acknowledgement requested | nlx_25238, biotools:germ-line_v_genes | https://bio.tools/germ-line_v_genes | SCR_007082 | VBASE2: the integrative germ-line V gene database | 2026-08-06 09:26:44 | 72 |
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