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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Human Genome Epidemiology Network Resource Report Resource Website 10+ mentions |
Human Genome Epidemiology Network (RRID:SCR_013117) | data or information resource, organization portal, portal | Human Genome Epidemiology Network, or HuGENet, is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. Its goals include: establishing an information exchange that promotes global collaboration in developing peer-reviewed information on the relationship between human genomic variation and health and on the quality of genetic tests for screening and prevention; providing training and technical assistance to researchers and practitioners interested in assessing the role of human genomic variation on population health and how such information can be used in practice; developing an updated and accessible knowledge base on the World Wide Web; and promoting the use of this knowledge base by health care providers, researchers, industry, government, and the public for making decisions involving the use of genetic information for disease prevention and health promotion. HuGENet collaborators come from multiple disciplines such as epidemiology, genetics, clinical medicine, policy, public health, education, and biomedical sciences. Currently, there are 4 HuGENet Coordinating Centers for the implementation of HuGENet activities: CDC''s Office of Public Health Genomics, Atlanta, Georgia; HuGENet UK Coordinating Center, Cambridge, UK; University of Ioannina, Greece; University of Ottawa , Ottawa, Canada. HuGENet includes: HuGE e-Journal Club: The HuGE e-Journal Club is an electronic discussion forum where new human genome epidemiologic (HuGE) findings, published in the scientific literature in the CDC''s Office of Public Health Genomics Weekly Update, will be abstracted, summarized, presented, and discussed via a newly created HuGENet listserv. HuGE Reviews: A HuGE Review identifies human genetic variations at one or more loci, and describes what is known about the frequency of these variants in different populations, identifies diseases that these variants are associated with and summarizes the magnitude of risks and associated risk factors, and evaluates associated genetic tests. Reviews point to gaps in existing epidemiologic and clinical knowledge, thus stimulating further research in these areas. HuGE Fact Sheets: HuGE Fact Sheets summarize information about a particular gene, its variants, and associated diseases. HuGE Case Studies: An on-line presentation designed to sharpen your epidemiological skills and enhance your knowledge on genomic variation and human diseases. Its purpose is to train health professionals in the practical application of human genome epidemiology (HuGE), which translates gene discoveries to disease prevention by integrating population-based data on gene-disease relationships and interventions. Students will acquire conceptual and practical tools for critically evaluating the growing scientific literature in specific disease areas. HUGENet Publications: Articles related to the HuGENet movement written by our HuGENet collaborators. HuGE Navigator: An integrated, searchable knowledge base of genetic associations and human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. HuGE Workshops: HuGENet has sponsored meetings and workshops with national and international partners since 2001. Available are detailed summaries, agendas or the ability to download speaker slides. HuGE Book: Human Genome Epidemiology: A Scientific Foundation for Using Genetic Information to Improve Health and Prevent Disease. (The findings and conclusions in this book are those of the author(s) and do not necessarily represent the views of the funding agency.) HuGENet Collaborators: HuGENet is interested in establishing collaborations with individuals and organizations working on population based research involving genetic information. HuGE Funding: Funding opportunities for specific population-based genetic epidemiology research projects are available. Research initiatives whose aims include assessing the prevalence of human genetic variation, the association between genetic variants and human diseases, the measurement of gene-gene or gene-environment interaction, and the evaluation of genetic tests for screening and prevention are compiled to create a posted listing. Additional information and application details can be found by clicking on the respective links. | epidemiology, gene, genetic, genetic variants, genome, articles, collaboration, disease, disease prevention, genomics, health promotion, human, human diseases | has parent organization: Centers for Disease Control and Prevention | nif-0000-00574 | SCR_013117 | HuGENet | 2026-09-05 06:30:47 | 25 | |||||||||
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BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded. | red flour beetle, tribolium castaneum, sequence data, gene, mutant, genetic marker, expressed sequence tag, genome, blast, model organism, insect, developmental biology, genomics, genetics, entomology, development, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: RefSeq has parent organization: Kansas State University; Kansas; USA |
NCRR P20 RR16475 | PMID:18362917 PMID:17090595 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02599, biotools:beetlebase, r3d100010921 | https://bio.tools/beetlebase, https://doi.org/10.17616/R3G61K | http://bioinformatics.k-state.edu/BeetleBase/, http://www.bioinformatics.ksu.edu/BeetleBase/ | SCR_001955 | 2026-09-05 06:29:54 | 82 | ||||
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University of Bergen Computational Biology Unit Resource Report Resource Website 1+ mentions |
University of Bergen Computational Biology Unit (RRID:SCR_002970) | UiB CBU | data or information resource, department portal, organization portal, portal | An inter-department center that conducts bioinformatics research and expands the interface between bioinformatics and experimental biological and biomedical research. The unit is closely associated with the the Bioinformatics group at the Department of Informatics (II) and has tight links with the Sars Centre for Marine Molecular biology (SARS) and the Department of Molecular Biology (MBI). Six research groups are currently associated with CBU with projects that include sequence and structure analysis, molecular evolution, genome annotation and genomics data analysis. CBU also provides services and contributes to bioinformatics education primarily through training courses. | computational, biology, bioinformatics, analysis, structure, molecular, evolution, genome, annotation, functional genomic, programming, rna, dna, molecular biology, protein modelling, integrated genomics, evolutionary genomics | has parent organization: University of Bergen; Bergen; Norway | Research Council of Norway ; FUGE programme |
nif-0000-30147 | http://www.cbu.uib.no | SCR_002970 | UiB Computational Biology Unit | 2026-09-05 06:29:56 | 1 | ||||||
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COnsensus-DEgenerate Hybride Oligonucleotide Primers Resource Report Resource Website 1+ mentions |
COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | fractionation, gel, 3', amplification, clone, dna, genome, homolog, human, hybrid, molecule, oligonucleotide, pcr, plant, primer, protein, sequence, transcriptase-methyltransferase |
is related to: OMICtools has parent organization: University of Washington; Seattle; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25557 | SCR_002875 | CODEHOP | 2026-09-05 06:29:55 | 8 | ||||||||
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National Swine Resource and Research Center Resource Report Resource Website 50+ mentions |
National Swine Resource and Research Center (RRID:SCR_006855) | NSRRC | biomaterial supply resource, cell repository, material resource, organism supplier | Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. | RIN, Resource Information Network, pig, fetal fibroblast, live animal, tissue, fibroblast, fetus, genetically modified pig, biomaterial manufacture, genome, genotyping, genetics, reproduction, breeding, health monitoring, cryopreservation, phenotyping, consulting, RRID Community Authority |
is used by: Integrated Animals is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: One Mind Biospecimen Bank Listing has parent organization: University of Missouri; Missouri; USA |
NHLBI ; NIAID ; NIH Office of the Director U42 OD011140 |
Public, To investigators, Application required | nif-0000-12086 | SCR_006855 | National Swine Resource Research Center | 2026-09-05 06:30:00 | 79 | ||||||
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MycoCosm Resource Report Resource Website 100+ mentions |
MycoCosm (RRID:SCR_005312) | MycoCosm | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Fungal genomics database and interactive analytical tools that integrates all fungal genomes for diverse fungi that are important for energy and environment, the focus of the JGI Fungal program. It integrates genomics data from the DOE JGI and its users and promotes user community participation in data submission, annotation and analysis. Over 100 newly sequenced and annotated fungal genomes from JGI and elsewhere are available to the public through MycoCosm, and new annotated genomes are being added to this resource upon completion of annotation. MycoCosm offers web-based genome analysis tools for fungal biologists to ''navigate'' through sequenced genomes and explore them in the context of ''genome-centric'' and ''comparative views''. | gene, genome, geneome map, jgi, fungus, genomics, energy, environment, annotation, FASEB list |
is listed by: OMICtools is related to: 1000 Fungal Genome Project has parent organization: DOE Joint Genome Institute |
DOE | PMID:24297253 PMID:22110030 |
Public, Acknowledgement requested, The community can contribute to this resource | OMICS_01657, nlx_144366, r3d100011751 | https://doi.org/10.17616/R3QQ0J | http://jgi.doe.gov/fungi | SCR_005312 | MycoCosm - the fungal genomics resource | 2026-09-05 06:29:58 | 254 | |||
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LAST Resource Report Resource Website 100+ mentions |
LAST (RRID:SCR_006119) | LAST | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence alignment, align, vertebrate, genome, sequence, alignment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: RecountDB has parent organization: National Institute of Advanced Industrial Science and Technology |
National Genome Research Network ; INTEuropean Union Systems Institute ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:21209072 PMID:20144198 PMID:20110255 DOI:10.1093/nar/gkq010 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151594, OMICS_15813, biotools:last | https://bio.tools/last, https://sources.debian.org/src/last-align/ | SCR_006119 | 2026-09-05 06:29:59 | 403 | |||||
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FaceBase Resource Report Resource Website 50+ mentions |
FaceBase (RRID:SCR_005998) | FaceBase | community building portal, data or information resource, disease-related portal, portal, research forum portal, topical portal | A web portal that provides access to data, tools and materials that will aid in craniofacial research. Included is access to genomic and imaging based data sets from a variety of species, including zebrafish, human and mouse. | microct, dna microarray, craniofacial, genome, imaging, FASEB list, DRKB |
has parent organization: University of Pittsburgh; Pennsylvania; USA is parent organization of: 3D Facial Norms Database is parent organization of: OCDM - Ontology of Craniofacial Development and Malformation is parent organization of: FaceBase Biorepository is parent organization of: FishFace - An atlas of zebrafish craniofacial development |
NIH DE034163 | Open and restricted access. Open-access data is available on the FaceBase website to any interested user and does not require any formal registration. Open-access data will be limited to summary-level human data (ex: averaged facial measures), And all non-human data. In contrast, All individual-level human data (ex: demographic descriptors, Phenotypic measures, 3D images) will fall under the restricted category and will require the requestor to fill out the Data Access Request form. | nlx_151372 | SCR_005998 | FaceBase - A Resource For Craniofacial Researchers | 2026-09-05 06:29:59 | 83 | ||||||
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ISCA Consortium Resource Report Resource Website 50+ mentions |
ISCA Consortium (RRID:SCR_006168) | ISCA Consortium, ISCA | community building portal, consortium, data or information resource, database, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 22, 2022. A rapidly growing group of clinical cytogenetics and molecular genetics laboratories committed to improving quality of patient care related to clinical genetic testing using new molecular cytogenetic technologies including array comparative genomic hybridization (aCGH) and quantitative SNP analysis by microarrays or bead chip technology. They improve clinical care by providing a large publicly available database and forum where clinicians and researchers can share knowledge to expedite the understanding of copy number variation (CNV) in an abnormal population. The ISCA database contains whole genome array data from a subset of the ISCA Consortium clinical diagnostic laboratories. Array analysis was carried out on individuals with phenotypes including intellectual disability, autism, and developmental delay. Efforts of the Consortium include: # Clinical Utility: The ISCA Consortium has made recommendations regarding the appropriate clinical indications for cytogenetic array testing (Miller et al. AJHG 2010, PMID: 20466091). Currently, discussions are focused on pediatric applications for children with unexplained developmental delay, intellectual disability, autism and other developmental disabilities. A separate committee has been developed to address appropriate cancer genetic applications (http://www.urmc.rochester.edu/ccmc/). # Evidence-based standards for cytogenomic array design: The Consortium will develop recommendations for standards for the design, resolution and content of cytogenomic arrays using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics (cytogenetics and molecular genetics), genomics and bioinformatics. This design is intended to be platform and vendor-neutral (common denominator is genome sequence coordinates), and is a dynamic process with input from the broader genetics community and evidence-based review by the expert panel (which will evolve into a Standing Committee with international representation). # Public Database for clinical and research community: It is essential that publicly available databases be created and maintained for cytogenetic array data generated in clinical testing laboratories. The ISCA data will be held in dbGaP and dbVar at NCBI/NIH and curated by a committee of clinical genetics laboratory experts. The very high quality of copy number data (i.e., deletions and duplications) coming from clinical laboratories combined with expert curation will produce an invaluable resource to the clinical and research communities. # Standards for interpretation of cytogenetic array results: Using the ISCA Database, along with other genomic and genetics databases, the Consortium will develop recommendations for the interpretation and reporting of pathogenic vs. benign copy number changes as well as imbalances of unknown clinical significance. | clinical, cytogenetics, molecular genetics, genetic testing, molecular cytogenetic technology, array comparative genomic hybridization, quantitative snp analysis, microarray, bead chip, genome, array, phenotype, copy number, deletion, duplication, copy number variation, FASEB list |
is related to: Database of Genomic Variants Archive (DGVa) is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: UCSC Genome Browser |
Intellectual disability, Developmental delay, Etc., Autism | This resource is no longer in service | nlx_151670 | SCR_006168 | ISCA Consortium and Public Database, International Standards for Cytogenomic Arrays (ISCA) Consortium, International Standards For Cytogenomic Arrays Consortium | 2026-09-05 06:29:59 | 78 | ||||||
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Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | 2026-09-05 06:30:00 | 1104 | |||||
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Candidate Genes to Inherited Diseases Resource Report Resource Website 1+ mentions |
Candidate Genes to Inherited Diseases (RRID:SCR_008190) | G2D | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases. | function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data set, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Molecular Biology Laboratory has parent organization: EMBL - Bork Group |
PMID:16115313 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21162, biotools:g2d | http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/, https://bio.tools/g2d | SCR_008190 | G2D - Candidate Genes to Inherited Diseases, Genes2Diseases | 2026-09-05 06:30:02 | 2 | |||||
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AGI Resource Report Resource Website 10+ mentions |
AGI (RRID:SCR_007203) | AGI | data or information resource, disease-related portal, portal, research forum portal, topical portal | Their primary focus is in the area of structural, evolutionary and functional genomics of crop plants. AGI is divided into 5 Centers each lead by a Center Leader and a senior Manager (BAC Library Construction Center, BAC/EST Resource Center, Sequencing & Physical Mapping Center (including: production sequencing and fingerprinting, and sequence finishing), Bioinformatics Center and the Evolutionary and Functional Genomics Center). AGI is housed in the state of the art Thomas W. Keating Bioresearch Building on the northeast part of campus near the Medical School. AGI currently employees about 30 scientists and is primarily funded through federal grants, private contracts, and the Bud Antle Endowed Chair in Plant Molecular Genetics. Sponsors: AGI is supported by Bio5, Plant Sciences, National Science Foundation, National Institues oh Health, and USDA. | genomics, structural, evolutionary, functional, genome, crop, plant, bac, est, resource, physical, sequencing, fingerprinting, bioinformatics, evoluntionary | has parent organization: University of Arizona; Arizona; USA | nif-0000-30120 | SCR_007203 | Arizona Genomics Institute, The Arizona Genomics Institute | 2026-09-05 06:30:01 | 18 | ||||||||
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Frey Lab Resource Report Resource Website 1+ mentions |
Frey Lab (RRID:SCR_008859) | Frey Lab | data or information resource, laboratory portal, organization portal, portal, topical portal | The Frey Lab develops techniques that use large scale datasets to derive predictive models of how genes and many other genomic features act in combination to produce genetic messages that control cellular activities. We have most recently focused on how organisms use alternative splicing to generate a tremendous level of biological complexity that cannot be explained by gene expression alone (Nature, 2010). Some of the tools, software and databases provided by the Frey Lab are affinity propagation, splicing prediction, PTMClust - A Post-translational Modification Refinement Algorithm, the ''epitome'': A new model of patterns, transformation invariant clustering and subspaces, learning flexible sprites from images and videos, phase unwrapping by loopy belief propagation, useful Matlab scripts, bioinformatics links, and SeedSearcher: A motif finder. | gene, genetic message, affinity propagation, alternative splicing prediction, motif, tool, software, database, flobject analysis, signal processing, graphical model, inference algorithm, computational vision, alternative splicing, transcriptome, genome, gene function prediction, gene function, computational biology, message passing | has parent organization: University of Toronto; Ontario; Canada | nlx_149187 | SCR_008859 | U of T Frey Lab, University of Toronto - Frey Lab, Frey Lab - Probabilistic and Statistical Inference Group University of Toronto | 2026-09-05 06:30:02 | 1 | ||||||||
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Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | data or information resource, database | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi | SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-09-05 06:32:03 | 545 | |||||
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HOMD Resource Report Resource Website 100+ mentions |
HOMD (RRID:SCR_012770) | HOMD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on April 14,2022. Database of comprehensive information on the approximately 600 prokaryote species that are present in the human oral cavity. The majority of these species are uncultivated and unnamed, recognized primarily by their 16S rRNA sequences. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference entity. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Full and partial oral bacterial genome sequences determined as part of this project and the Human Microbiome Project, are being added to the HOMD as they become available. HOMD offers easy to use tools for viewing all publicly available oral bacterial genomes. Data is also downloadable. | taxon, genome, 16s rna, sequence, actinobacteria, bacteroidetes, chlamydiae, chloroflexi, euryarchaeota, firmicutes, fusobacteria, proteobacteria, spirochaetes, sr1, synergistetes, tenericutes, tm7, nomenclature, naming scheme, human, FASEB list | has parent organization: Forsyth Institute | NIDCR ; ARRA ; DOE contract U01 DE016937; DOE DE016937; DOE DE015847; DOE DE017106 |
PMID:20624719 PMID:20656903 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_22198, r3d100012898 | SCR_012770 | Human Oral Microbiome Database | 2026-09-05 06:32:02 | 137 | |||||
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Ensembl Protists Resource Report Resource Website 10+ mentions |
Ensembl Protists (RRID:SCR_013154) | data or information resource, database | The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Protists, which houses protists species. Sponsors: EnsembProtists is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute. | database, genome, protist, software, specie, taxonomic | has parent organization: Ensembl | r3d100011200, nif-0000-33712 | SCR_013154 | EnsemblProtists | 2026-09-05 06:32:04 | 48 | |||||||||
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GiardiaDB Resource Report Resource Website 100+ mentions |
GiardiaDB (RRID:SCR_013377) | data or information resource, database | GiardiaDB is a resource for information on Giardia lamblia. It contains gene information, including genomic attributes, protein expression patterns, evolution, and EST sequence information. The website provides tools for BLASTing, sequence retrieval, graphic visualization, and PubMed information. | genome, giardia lamblia, protein expression, FASEB list | nif-0000-02908, r3d100012458 | SCR_013377 | GiardiaDB | 2026-09-05 06:32:06 | 108 | ||||||||||
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Cube-DB Resource Report Resource Website 1+ mentions |
Cube-DB (RRID:SCR_013233) | Cube-DB | data or information resource, database | Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera). | protein, functional divergence, vertebrate, genome, ortholog, protein sequence, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Bioinformatics Institute; Singapore; Singapore |
PMID:22139934 | nlx_149432, biotools:cube-db | https://bio.tools/cube-db | SCR_013233 | Cube-DB: Detection of Functional Divergence in Human Protein Families | 2026-09-05 06:32:05 | 3 | ||||||
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Planteome Resource Report Resource Website 10+ mentions |
Planteome (RRID:SCR_014411) | data or information resource, database | An international collaborative effort to develop and enrich new and existing reference ontologies for plants, improve ontology use and cross-references, and to develop data annotation standards. Users can search for ontology terms and bioentities and submit the ontology-related term requests by visiting the following GitHub request trackers. | database, ontology, plant, genome | NSF IOS:1340112 | Available to the research community, Only registered users of the GitHub website are allowed to submit requests and make suggestions or comments | SCR_014411 | 2026-09-05 06:32:10 | 28 | ||||||||||
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Baylor College of Medicine Human Genome Sequencing Center Resource Report Resource Website 50+ mentions |
Baylor College of Medicine Human Genome Sequencing Center (RRID:SCR_013605) | BCM-HGSC | analysis service resource, production service resource, service resource | Center for high-throughput DNA sequence generation and the accompanying analysis. The sequence data generated by the center's machines are analyzed in a complex bioinformatics pipeline, and the data are deposited regularly in the public databases at the National Center for Biotechnology Information (NCBI). | next-generation sequencing, genetic variation, genome, dna sequence, FASEB list |
has parent organization: Baylor University; Texas; USA is parent organization of: Mercury is parent organization of: xAtlas |
NIH Office of the Director R24 OD011173 | nif-0000-10162 | SCR_013605 | Human Genome Sequencing Center, BCM HGSC | 2026-09-05 06:32:08 | 65 |
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