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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Candida Genome Database Resource Report Resource Website 100+ mentions |
Candida Genome Database (RRID:SCR_002036) | CGD, CGD LOCUS, CGD REF | storage service resource, data repository, service resource, database, data or information resource | Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome. | protein, chromosome, classification, gene, genome, candidiasis, thrush, yeast, yeast gene, yeast genome, candida albicans, candida glabrata, data analysis service, biological role, molecular function, subcellular localization, chromosome sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: ASPGD is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
NIDCR DE015873 | PMID:19808938 | Free, Available for download, Freely available | nif-0000-02634, biotools:cgd, r3d100010617 | https://bio.tools/cgd | SCR_002036 | 2026-08-04 09:40:32 | 472 | |||||
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Aspergillus Genomes Resource Report Resource Website |
Aspergillus Genomes (RRID:SCR_001880) | Aspergillus Genomes | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | 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 | 2026-08-04 09:40:29 | 0 | ||||||
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DAVID Resource Report Resource Website 10000+ mentions |
DAVID (RRID:SCR_001881) | DAVID | web service, software resource, data access protocol, database, data or information resource | 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 | 2026-08-04 09:40:29 | 18488 | ||||
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Human Genome Variation Society Resource Report Resource Website 100+ mentions |
Human Genome Variation Society (RRID:SCR_012989) | HGVS | portal, journal article, training resource, knowledge environment, community building portal, meeting resource, data or information resource | The Society aims to foster discovery and characterization of genomic variations including population distribution and phenotypic associations. We promote collection, documentation and free distribution of genomic variation information and associated clinical variations and endeavor to foster the development of the necessary methodology and informatics. Mission Statement To enhance human health through identification and characterization of changes in the genome that lead to susceptibility to illness. To this end, to collate the genomic information necessary for molecular diagnosis, research on basic mechanisms and design of treatments of human ailments. Society Journal Human Mutation is the Society journal. Members will receive a reduced subscription to the journal if they choose to subscribe. Meetings The Society holds two scientific meetings per year. One as a satellite to either the HUGO (Human Genome Organization) annual meeting or the ESHG (European Society of Human Genetics) annual meeting and one meeting is a satellite to the ASHG (American Society of Human Genetics annual meeting. The meetings are a forum for scientists to exchange ideas and form collaborations. Prominent speakers in the field are invited as well as a call for abstracts at large. The meetings are designed to update and increase knowledge of human genome variation and generally attract a stimulating and interesting collection of abstracts in all fields of human genome variation making it an ideal forum to share information and results. Past themes include: copy number variation, pathogenic or not?, pharmacogenomics, new DNA sequencing technologies, and genotype to pheontype relationships. We invite members and non-members alike to attend these meetings. The Society holds the Annual General Meeting of the members after the scientific meeting that is a satellite of the ASHG. Exhibitor''s booths The Society usually takes out an Exhibitor''s booth at the American & European Societies of Human Genetics annual meetings and sometimes the HUGO HGM meeting. GUIDELINES & RECOMMENDATIONS Members of the Society have formulated Guidelines & Recommendations on a number of topics, but especially for nomenclature of gene variations and guidelines on variation databases. | genetic variation, genome, homo sapiens genome, human, mutation, nomenclature, phenotypic associations, population distribution |
is related to: INFEVERS is parent organization of: HGVS Locus Specific Mutation Databases is parent organization of: Human Genome Variation Society: Databases and Other Tools is parent organization of: Nomenclature for the description of sequence variants is parent organization of: Blood Group Antigen Gene Mutation Database |
nif-0000-23953 | SCR_012989 | 2026-08-04 09:43:07 | 291 | |||||||||
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Human Genome Project Information Resource Report Resource Website 50+ mentions |
Human Genome Project Information (RRID:SCR_013028) | portal, funding resource, video resource, topical portal, training material, narrative resource, slide, data or information resource | This resource gives information about the U.S. Human Genome Project, which was was a 13-year effort to to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. The primary project goals were to: - identify all the approximately 20,000-25,000 genes in human DNA, - determine the sequences of the 3 billion chemical base pairs that make up human DNA, - store this information in databases, - improve tools for data analysis, - transfer related technologies to the private sector, and - address the ethical, legal, and social issues (ELSI) that may arise from the project. To help achieve these goals, researchers also studied the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse. These parallel studies helped to develop technology and interpret human gene function. Sponsors: The DOE Human Genome Program and the NIH National Human Genome Research Institute (NHGRI) together sponsored the U.S. Human Genome Project. | escherichia coli, fruit fly, function, gene, genome, genetic, bacterium, base pair, biological, dna, human, mouse, sequence, FASEB list |
has parent organization: National Institutes of Health has parent organization: United States Department of Energy |
nif-0000-10252 | SCR_013028 | HGP | 2026-08-04 09:43:07 | 59 | |||||||||
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Genotype-Tissue Expression Resource Report Resource Website 500+ mentions |
Genotype-Tissue Expression (RRID:SCR_013042) | GTEx | portal, storage service resource, biobank, data repository, service resource, material storage repository, data or information resource | Project to study human gene expression and regulation in multiple tissues, providing valuable insights into mechanisms of gene regulation and its disease related perturbations. Genetic variation between individuals will be examined for correlation with differences in gene expression level to identify regions of the genome that influence whether and how much a gene is expressed. Includes initiatives: Novel Statistical Methods for Human Gene Expression Quantitative Trait Loci (eQTL) Analysis ,Laboratory, Data Analysis, and Coordinating Center (LDACC), caHUB Acquisition of Normal Tissues in Support of GTEx Project. | gene expression, regulation, genetic variation, genotype, tissue, tissue bank, database, genome, disease, inherited disease, FASEB list |
is recommended by: National Library of Medicine is listed by: OMICtools |
NIH Common Fund | OMICS_00271 | https://gtexportal.org/home/ | SCR_013042 | GTEx, Genotype-Tissue Expression, Genotype-Tissue Expression (GTEx) | 2026-08-04 09:43:07 | 545 | ||||||
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eQTL Visualization Tool Resource Report Resource Website 1+ mentions |
eQTL Visualization Tool (RRID:SCR_013413) | data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics. | experiment, explore, expression, genome, genetic, genetical, cis, computational, data, database, genomic, grafical, interface, linkage, mine, pqtl type, p-value, repository, tissue, tissue type, trans, visualization, visualize | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10222 | SCR_013413 | eQTLexplorer | 2026-08-04 09:43:12 | 1 | |||||||||
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DOLOP: A Database of Bacterial Lipoproteins Resource Report Resource Website 10+ mentions |
DOLOP: A Database of Bacterial Lipoproteins (RRID:SCR_013487) | storage service resource, data repository, service resource, database, data or information resource | DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins. | figure, functional, algorithm, analysis, bacterial, biosynthetic, classification, genome, lipid, lipoprotein, modification, molecular, molecule, pathogenesis, predictive, primary, prokaryote, query, sequence, signal | has parent organization: University of Cambridge; Cambridge; United Kingdom | nif-0000-21124 | SCR_013487 | DOLOP | 2026-08-04 09:43:13 | 16 | |||||||||
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PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | simulation software, data processing software, data analysis software, software resource, software application | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-08-04 09:43:09 | 4151 | |||||
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REPCLASS Resource Report Resource Website 10+ mentions |
REPCLASS (RRID:SCR_014654) | data processing software, data analysis software, software resource, sequence analysis software, software application | Tool for the classification of known transposable elements in eukaryotic genomes. It can be combined with ab initio repeat finding in order to recover contrasting transposable element landscapes between species. | transposable element, eukaryotic genome, eukaryote, genome, ab initio, repeat, software, source code, sequence analysis software, data analysis software | DOI:10.1093/gbe/evp023 | Available for download | SCR_014654 | 2026-08-04 09:43:31 | 10 | ||||||||||
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Cscan Resource Report Resource Website 1+ mentions |
Cscan (RRID:SCR_006756) | Cscan | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Data resource that includes a large collection of genome-wide ChIP-Seq experiments performed on transcription factors (TFs), histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression. | regulator, gene, genome-wide chip-seq, chip-seq, gene, genome | is listed by: OMICtools | PMID:22669907 | Free | OMICS_00529 | SCR_006756 | 2026-08-04 09:41:40 | 4 | |||||||
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ENCODE Resource Report Resource Website 1000+ mentions |
ENCODE (RRID:SCR_006793) | data analysis service, analysis service resource, storage service resource, production service resource, service resource, data repository, database, data or information resource | Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome. | Encyclopedia, DNA, element, functional, human, genome, protein, RNA, level, regulatory, gene, active, disease, analysis |
uses: Segway - a way to segment the genome is used by: BioSample Database at EBI is used by: VizHub is used by: GEMINI is used by: Deep Blue Epigenomic Data Server is recommended by: National Library of Medicine is listed by: OMICtools is affiliated with: GENCODE is related to: Factorbook is related to: UCSC Genome Browser is related to: modENCODE is related to: UCSC Genome Browser is related to: Encode is related to: Broad Institute Genomics Platform has parent organization: University of California at Santa Cruz; California; USA |
NHGRI | PMID:21526222 | Free, Freely available | nif-0000-02797, r3d100013051, SCR_017493, OMICS_00532 | http://encodeproject.org/ENCODE/, https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements, https://www.encodeproject.org/, https://doi.org/10.17616/R31NJMKB | SCR_006793 | ENCODE - Encyclopedia of DNA Elements, ENCODE + Epigenomics Roadmap Combined Data Browser, Encyclopedia of DNA Elements, Encyclopedia of DNA Elements (ENCODE) | 2026-08-04 09:41:42 | 3681 | |||||
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1000 Genomes: A Deep Catalog of Human Genetic Variation Resource Report Resource Website 5000+ mentions |
1000 Genomes: A Deep Catalog of Human Genetic Variation (RRID:SCR_006828) | 1000 Genomes | portal, data set, consortium, organization portal, database, data or information resource | International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes | genetic variation, gene, next-generation sequencing, sequence, alignment, genome, single-nucleotide polymorphism, structural variant, haplotype, genome-wide association study, pharmacology, genetics, biomarker, consortium, data sharing, genotype, phenotype, FASEB list |
uses: NHGRI Sample Repository for Human Genetic Research is used by: BioSample Database at EBI is listed by: OMICtools is listed by: re3data.org is listed by: Consortia-pedia is related to: MOSAIK is related to: ART is related to: SNAP - SNP Annotation and Proxy Search has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: Harvard Medical School; Massachusetts; USA has parent organization: Broad Institute has parent organization: NCBI has parent organization: European Bioinformatics Institute has parent organization: National Human Genome Research Institute |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom ; Beijing Genomics Institute; Shenzhen; China ; NHGRI ; 454 Life Sciences Roche ; Life Technologies ; Illumina |
Free, Public, Restrictions apply, Http://www.1000genomes.org/data#DataAccess | r3d100010180, nlx_143819, OMICS_00261 | https://doi.org/10.17616/R3CP4M | SCR_006828 | International 1000 Genomes Project, 1000 Genomes Project | 2026-08-04 09:41:42 | 5486 | |||||
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FunNet - Transcriptional Networks Analysis Resource Report Resource Website 10+ mentions |
FunNet - Transcriptional Networks Analysis (RRID:SCR_006968) | FunNet | data analysis service, data processing software, analysis service resource, software resource, software application, production service resource, service resource | Functional Analysis of Transcriptional Networks (FunNet) is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes. FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can be downloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | genome, transcriptional interaction, microarray, gene expression, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: KEGG has parent organization: Cordelier Research Center |
PMID:18208606 | Free for academic use, GNU General Public License, v2 | nlx_149243 | SCR_006968 | Functional Analysis of Transcriptional Networks, Functional Analysis of Transcriptional Networks (FunNet) | 2026-08-04 09:41:43 | 16 | ||||||
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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 | data analysis service, analysis service resource, software resource, production service resource, service resource, database, data or information resource | 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 | 2026-08-04 09:41:45 | 60 | |||||
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TriTrypDB Resource Report Resource Website 500+ mentions |
TriTrypDB (RRID:SCR_007043) | TriTrypDB | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource, database, data or information resource | An integrated genomic and functional genomic database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ''''User Comments'''' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate. TriTrypDB provides programmatic access to its searches, via REST Web Services. The result of a web service request is a list of records (genes, ESTs, etc) in either XML or JSON format. REST services can be executed in a browser by typing a specific URL. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI). | kinetoplastid parasite, pathogen, genome, gene chromosome, annotation, trypanosomatidae, parasite, blast, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: GeneDB is related to: GeneDB Lmajor is related to: GeneDB Tbrucei has parent organization: Eukaryotic Pathogen Database Resources |
Bill and Melinda Gates Foundation 50097; Wellcome Trust WT085822MA; Wellcome Trust WT085775/Z/08/Z |
PMID:19843604 | Public - please cite. Much of the data in TriTrypDB is provided by independent researchers. Please cite them if you use their data. | nlx_152064, biotools:tritrypdb, r3d100011479 | https://bio.tools/tritrypdb, https://doi.org/10.17616/R3J05N | SCR_007043 | 2026-08-04 09:41:45 | 670 | |||||
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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 | data set, data or information resource, image collection | 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 | 2026-08-04 09:41:45 | 20 | |||||||
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YeTFaSCo Resource Report Resource Website 10+ mentions |
YeTFaSCo (RRID:SCR_006893) | YeTFaSCo | data analysis service, analysis service resource, storage service resource, production service resource, service resource, data repository, database, data or information resource | Collection of all available transcription factor (TF) specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. The specificities are evaluated for quality using several metrics. With this website, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have similar motifs to one you have found, and download the collection of motifs. Submissions are welcome. | transcription factor, binding site, sequence, yeast, motif, gene, genome, protein, protein complex |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Graduate Scholarship awards ; Canadian Institutes of Health Research Operating Grant MOP-490425; Canadian Institutes of Health Research Operating Grant MOP-86705 |
PMID:22102575 | Acknowledgement requested | nlx_151611, OMICS_01861 | SCR_006893 | Yeast Transcription Factor Specificity Compendium, YeTFaSCo: The Yeast Transcription Factor Specificity Compendium | 2026-08-04 09:41:44 | 34 | |||||
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National Institute of Mental Health (NIMH) Human Genetics Initiative Resource Report Resource Website |
National Institute of Mental Health (NIMH) Human Genetics Initiative (RRID:SCR_007436) | software resource, database, data or information resource | The Connectivity Map aims to generate a detailed map that links gene patterns associated with disease to corresponding patterns produced by drug candidates and a variety of genetic manipulations. The Connectivity Map is the most comprehensive effort yet for using genomics in a drug-discovery framework. It allows researchers to screen compounds against genome-wide disease signatures, rather than a pre-selected set of target genes. Drugs are paired with diseases using sophisticated pattern-matching methods with a high level of resolution and specificity. To build a Connectivity Map, the Broad Institute brings together molecular biologists, genomics specialists, computational scientists, pharmacologists, chemists and chemical biologists, as well as expertise from across the breadth and depth of medicine.Connectivity map is a large public database of signatures of drugs and genes, and pattern-matching tools to detect similarities among these signatures.The parent site for the Broad Institute at MIT has a software library of software applications developed for use in genetic analysis. | gene, genome, small molecule | has parent organization: Broad Institute | NIMH | nif-0000-00629 | SCR_007436 | NIMH Human Genetics Initiative | 2026-08-04 09:41:51 | 0 | ||||||||
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GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database Resource Report Resource Website 1+ mentions |
GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database (RRID:SCR_007440) | GEISHA | experimental protocol, storage service resource, narrative resource, data repository, service resource, atlas, database, data or information resource | Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA. | expression data, expression pattern, gene, gene expression, genome, chicken, chicken embryo, genomic, in situ hybridization, mapping, microarray, microrna, model organism, oligo, probe, stage, image, molecular neuroanatomy resource, embryo, embryonic chicken | has parent organization: University of Arizona; Arizona; USA | NIH ; NICHD R01HD044767 |
nif-0000-01251, r3d100012509 | https://doi.org/10.17616/R3RB6B | SCR_007440 | Gallus Expression in Situ Hybridization Analysis, GEISHA - Gallus Expression in Situ Hybridization Analysis | 2026-08-04 09:41:51 | 2 |
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