Tag: phenotype

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being develope ...

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs contai ...

Online Mendelian Inheritance in Man. It is an authoritative compendium of human genes and phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 15,000 genes. OMIM focuses on the relation ...

The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular dia ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variat ...

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...

VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrat ...

The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this in ...

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

PharmGKB is a resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relati ...

The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually an ...

The Open Targets Platform is a comprehensive and robust data integration for access to and visualisation of potential drug targets associated with disease. It brings together multiple data types and aims to assist users to identify and prioritise tar ...

The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and an ...

Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public so ...

A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims ...

LOINC is a common language (set of identifiers, names, and codes) for clinical and laboratory observations. LOINC is a catalog of measurements, including laboratory tests, clinical measures like vital signs and anthropomorphic measures, standardized ...

The Genomes Online Database provides access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing ...

PHI-Base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. PHI-base catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete ...

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB) focuses on eukaryotic pathogens and invertebrate vectors of infectious diseases, , encompassing data from prior resources devoted to parasitic species (EuPathDB), fungi (FungiD ...

The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the ...

The observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan.

dbVar is a database of human genomic structural variation where users can search, view, and download data from submitted studies. dbVar stopped supporting data from non-human organisms in 2017, however existing non-human data remains available. In ke ...

PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as w ...

PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily phenotype annotation. This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes.

OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes as well as the relationship between them, that is freely available and updated daily. The OMIM ontology contains terms used within the OMIM database.

The BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides lin ...

The Stanford HIV Drug Resistance Database (HIVDB) is an essential resource for public health officials monitoring ADR and TDR, for scientists developing new ARV drugs, and for HIV care providers managing patients with HIVDR.

MaizeGDB is the maize research community's central repository for genetics and genomics information.

HomoloGene is an automated system for the detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene takes protein sequences from differing species and compares them to one another (using blastp) an ...

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitati ...

The NCBI BioSample database stores submitter-supplied descriptive information, or metadata, about the biological materials from which data stored in NCBI’s primary data archives are derived. NCBI’s archives host data from diverse types of samples fro ...

A resource providing data on bioentities and their associated ontology terms for Plant Biology. The database provides access to ontology-based annotations of genes, phenotypes and germplasms from about 90 plant species. A number of internal and exter ...

The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also stores patient-centered data, NGS data, and variants outside of genes.

BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. Our current index is version 1.0.3 and searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model ...

Database for open data sharing of resting-state fMRI and DTI images collected from over 50 sites around the world. These data collections now contain comprehensive phentoypic information, openly available via data usage agreements.

The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.

The GeneWeaver data and analytics website is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, enviro ...

GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, ...

The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. ...

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped ...

MitoMiner is an integrated data warehouse of mammalian localisation evidence, phenotypes and diseases. This data has been integrated to allow the creation of sophisticated data mining queries spanning many different sources. It is primarily concerned ...

PhenoM (Phenomics of yeast Mutants) stores, retrieves, visualises and data mines the quantitative single-cell measurements extracted from micrographs of temperature-sensitive mutant cells. PhenoM allows users to rapidly search and retrieve raw images ...

The Legume Information System (LIS) is a collaborative, community resource to facilitate crop improvement by integrating genetic, genomic, and trait data across legume species.

ToxoDB is a free online resource that provides access to genomic and functional genomic data for Toxoplasma and related organisms. The resource contains over 30 fully sequenced and annotated genomes, with genomic sequence from multiple strains availa ...

dictyBase is a single-access database for the complete genome sequence and expression data of four Dictyostelid species providing information on research, genome and annotations. There is also a repository of plasmids and strains held at the Dicty St ...

Zfishbook is a real-time database of transposon-labeled mutants in zebrafish. This resource provides services for any size of GBT mutagenesis projects on zebrafish to encourage collaboration in the research community.

SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. Further, SNPeffect holds pe ...

MIAPPE is a reporting guideline for plant phenotyping experiments. It comprises a checklist, i.e., a list of attributes to describe an experiment so that it is understandable and replicable. It should be consulted by people recording and depositing p ...

The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents. LINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad ...

The Measurement Method Ontology is designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.

The NIDDK Central Repository stores biosamples, genetic and other data collected in designated NIDDK-funded clinical studies. The purpose of the NIDDK Central Repository is to expand the usefulness of these studies by allowing a wider research commun ...

Standard measures related to complex diseases, phenotypic traits and environmental exposures.

BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. BacDive contains entries for over 63,000 strains and provides information on their taxonomy, morph ...

FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes compara ...

An ontology of the anatomy of Drosophila melanogaster. It can be used for annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. It was originally developed by FlyBase, who continue to main ...

The Triticeae Toolbox (T3) is a repository for public wheat data generated by the Wheat Coordinated Agricultural Project (Wheat CAP). Funding is provided by the National Institute for Food and Agriculture (NIFA) and the United States Department of Ag ...

The MalaCards human disease database (http://www. malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ∼20 000 disease entries, in six global categories. It portrays a broa ...

The STrengthening the REporting of Genetic Association studies (STREGA) initiative builds on the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement and provides additions to 12 of the 22 items on the STROBE checkl ...

This is a community-curated controlled vocabulary for soybean field growth stages (Soybean Whole Plant Growth Ontology), plant structure names (Soybean Structure Ontology), development (Soybean Development Ontology) and plant traits (Soybean Trait On ...

The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biol ...

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...

Cyclebase is a database to visualize and download results from genome-wide cell-cycle-related experiments. In addition to genome annotation, Cyclebase also provides mRNA data, protein expression data, and integrated cell-cycle phenotype information f ...

The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.

Online Mendelian Inheritance in Animals is a a database of inherited disorders, other (single-locus) traits, and genes in animal species (other than human and mouse).

The PHArmacogenomic RElationships Ontology (or PHARE) proposes concepts and roles to represent relationships of pharmacogenomics interest.

Human Gene and Protein Database (HGPD) presents SDS-PAGE patterns and other informations of human genes and proteins.

GWAS Central stores genome-wide association study data. The database content comprises direct submissions received from GWAS authors and consortia in addition to actively gathered data sets from various public sources. GWAS data are discoverable from ...

TCRD is the central resource behind the Illuminating the Druggable Genome Knowledge Management Center (IDG-KMC). TCRD contains information about human targets, with special emphasis on four families of targets that are central to the NIH IDG initiati ...

The CHD7 database contains locus-specific, anonymised mutation data on both published and unpublished variants of the CHD7 gene related to the CHARGE syndrome phenotype. It can be searched for patients and their clinical phenotype or for mutations. I ...

GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists togethe ...

International Dystrophic Epidermolysis Bullosa Patient Registry (DEB Register) provides phenotypic and genotypic information on DEB and the related COL7A1 mutations. The registry is intended to aid in disease diagnosis, genetic counseling, and discov ...

Panzea provides information on the connection between phenotypes and genotypes of complex traits in maize and its wild relative, teosinte, and specifically in how rare genetic variations contribute to overall plant function.

The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools for the biology and genetics of ageing. HAGR features several databases with high-quality, manually-curated data: 1) GenAge, a database of genes associated with ageing i ...

MIMPP is a reporting guideline for the minimum information that should be reported about a mouse phenotyping procedure to enable unambiguous interpretation and comparison of the data and to allow the data to be shared through communal resources.

BacMap is a picture atlas of annotated bacterial genomes. It is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.

Orphanet Rare Diseases Ontology (ORDO) provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.

FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource (www.pombase.org). Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes ...

A database of integrated mouse data from MGI, powered by InterMine. MouseMine is member of InterMOD, a consortium of model organism databases dedicated to making cross-species data analysis easier through ongoing coordination and collaborative system ...

The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects. The JGA contains exclusive data col ...

The Leaf Senescence Database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. LSD includes data types such as leaf senescence-associated transcriptomics, phenotype and interaction data.

The Crop Ontology project is a service of the Integrated Breeding Platform to harmonize the traits measured by breeders. Crop Ontology provides trait names and standard variables that annotate precisely the trait observation made. CO is to be used fr ...

CellFinder maps validated gene and protein expression, phenotype and images related to cell types.The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells ...

GeneNet Engine is an exploratory tool to aid hypothesis and biomarker development at a systems-level for genotype-phenotype relationships. Expressed phenotypes may arise due to interactions between multiple genes in a system and effects from the surr ...

SO-Pharm is a formal ontology that represent domain knowledge in pharmacogenomics. To achieve this goal, SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e. genotype, phenotype, drug, trial representations). SO-Pharm enables to ...

This guideline describes a set of best practices when using phenotype ontologies to annotate genomic variant files using Genome Variation Format (GVF) and the Sequence Ontology.

The recent genome sequence assemblies of major cucurbit crop species, including cucumber, melon, watermelon and pumpkin have made it feasible to use advanced genomic approaches in cucurbit breeding. Under the CucCAP project (http://cuccap.org), the C ...

FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them ...

The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or t ...

PhenomeBLAST is an ontology-based tool that provides a practical implementation of cross-species alignments of phenotypes using ontologies. Both a command-line tool and a web-server are available.

The Ontology of Microbial Phenotypes (OMP) is a community ontology for annotating microbial phenotypes, including bacteria, archaea, protists, fungi, and viruses. It has been created to help with standardized capture of essential phenotypic informati ...

A structured controlled vocabulary of phenotypes of the social amoeba Dictyostelium discoideum. The Dicty Phenotype Ontology is a hierarchical controlled vocabulary used for annotating strains with phenotypes. Terms from the Dicty Phenotype Ontology ...

This repository provides several plant genomic and phenotypic datasets resulting from IPK and German Plant Phenotyping Network (DPPN) research activities. It was established in January 2015. The background of the study is in plant genetic resources, ...

A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part. The TO is part of the Planteome Project.

The GWAS Atlas is a manually curated resource of genome-wide variant-trait associations for a wide range of species.

This resource stores and distributes clinical data and biomaterials (DNA samples and cell lines) available in the NIDA Genetics Initiative. This includes blood and other biospecimens along with phenotypic data.

Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations

Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromesome, cytoband, gene and refseq p ...

Soybean Knowledge Base (SoyKB), is a comprehensive all-inclusive web resource developed for soybean translational genomics and molecular breeding. SoyKB stores information about genes/proteins, miRNAs/sRNAs, metabolites, SNPs, plant introduction (PI ...

The ontology represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was build reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clini ...

The Musa Germplasm Information System (MGIS) contains key information on Musa germplasm diversity, including passport data, botanical classification, morpho-taxonomic descriptors, molecular studies, plant photographs and GIS information on 4771 acces ...

The PhenX (consensus measures for Phenotypes and eXposures) Toolkit is a web-based catalog of recommended, standard measures of phenotypes and environmental exposures for use in biomedical research. The PhenX Toolkit offers well-established, broadly ...

RNAiDB provides access to results from RNAi interference studies in C. elegans , including images, movies, phenotypes, and graphical maps.

The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes. Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes ...

A crowdsourced collection of personal genomics data. Includes SNP genotyping, exome sequencing data, phenotypic annotation and quantified self tracking data.

Large-scale genomic data for the peanut have only become available in the last few years, with the advent of low-cost sequencing technologies. To make the data accessible to researchers and to integrate across diverse types of data, the International ...

Monitoring of insect vector populations with respect to their susceptibility to one or more insecticides is a crucial element of the strategies used for the control of arthropod-borne diseases. This management task can nowadays be achieved more effic ...

A structured controlled vocabulary of Caenorhabditis elegans phenotypes .

The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.

Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Genoplante rice insertion line library.

A structured controlled vocabulary developed and used by FlyBase, including the Drosophila phenotype ontology. It is used in annotation and classification of data related to Drosophila, including phenotypes and expression.

The Cowpea Trait Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods ...

Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.

The Flora Phenotype Ontology is a domain ontology for the description of plant characters. FLOPO contains more than 25000 phenotype and traits classes, the creation of FLOPO is data-driven: For each trait/phenotype class exists a taxon annotation in ...

The Neurobehavior Ontology (NBO) consists of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and ext ...

Ontology of Glucose Metabolism Disorder includes disease names, phenotypes and their classifications involved in Glucose Metabolism Disorder, Diabetes. It must be used with other two ontologies, in the case of Diabetes: the Ontology of Geographical R ...

An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.

EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

The Bone Dysplasia ontology provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discrimin ...

Mouse PATHology (MPATH) ontology is a structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes. This resource was developed by the Pathology Consortium of Pathbase (www.pathbase.net).

The MIQAS set of rules accompanied with the standardized XML and tab-delimited file formats will serve two goals: to encourage research groups that wish to publish a QTL paper to provide and submit the necessary information that would make meta-analy ...

Scratchpads are an online virtual research environment for biodiversity for the sharing of data and the creation of specific research networks. Sites can focus on specific taxonomic groups, the biodiversity of a biogeographic region, or any aspect of ...

The Ontology for Experimental Phenotypic Objects (OEPO) describes objects involved in phenotyping experiments (e.g. infrastructure, devices, germplasm, scientific objects) and defines a hierarchy between them according to the specificities of the ins ...

The Brassica Information Portal is a web repository for population and trait scoring information related to the Brassica breeding community. It provides information about quantitative trait loci and links curated Brassica phenotype experimental data ...

Features of Saccharomyces cerevisiae cells, cultures, or colonies that can be detected, observed, measured, or monitored.

The Agronomic Linked Data (AgroLD) is a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, which integrates data about plant species of high interest for the plant science community. AgroLD is an RD ...

An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.

A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene express ...

WormMine integrates many types of data for C. elegans and related nematodes. You can run flexible queries, export results and analyse lists of data.

This site provides access to raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results ar ...

Ontology for livestock reproductive traits and phenotypes.

The Autism DSM-ADI-R (ADAR) ontology uses SWRL rules to infer phenotypes from ADI-R items. It includes OWL class definitions representing DSM IV diagnostic criteria for autistic disorder and ASD criteria for Autism Spectrum Disorder. The goal is to c ...

MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was ...

The Phenotype Fragment Ontology, together with a processing pipeline, enable the automatic decomposition and conceptualization of phenotype descriptions for the human skeletal phenome.

MusaBase is a breeding database designed for advanced breeding methods in banana breeding. It focuses on bananas that are important food crops in Africa, such as Mchare and Matooke bananas. Data in MusaBase comes mainly from breeding programs in Ugan ...

YamBase is a database containing breeding data for Yam (genus Dioscorea). Yam species that are being used for breeding include Dioscorea rotundata, Dioscorea cayenensis (both are native to Africa and the major cultivated species), Dioscorea aleata (n ...

The MIQAS set of rules accompanied with the standardized XML and tab-delimited file formats will serve two goals: to encourage research groups that wish to publish a QTL paper to provide and submit the necessary information that would make meta-analy ...

A modified version of the Medical Subjects Headings Thesaurus (MeSH) 2014. This is an OWL representation of MeSH so that it can be integrated with other ontologies represented in OWL. It contains all terms that are in MeSH and in the MeSH concept tre ...

The LEAFDATA resource collects information from primary research articles focusing on Arabidopsis leaf growth and development. The result section of selected papers is manually annotated and organized into distinct categories. Text fragments of the m ...

The Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology (RPO) is a controlled vocabulary for phenotypic terms for primary immunodeficiency diseases (PIDs) used within the RAPID database. It is intended to facilitate global ...

Ascomycete Phenotype Ontology is a structured controlled vocabulary for the phenotypes of Ascomycete fungi.

An application ontology for the domain of Sleep Medicine.

NIF has developed a comprehensive vocabulary for annotating and searching neuroscience resources.

The AHOL ontology (Animal Health Ontology for Livestock) was built collaboratively within a network of experts in the livestock health field, in order to describe production diseases. Its structure is based on the type of disease: communicable, non c ...

ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment. ATOL aims to: provide a reference ontology of phenotypic traits of farm animals for the international scientific and e ...

DEEMY collects descriptive data on ectomycorrhizae, including extant character descriptions and definitions. Ectomycorrhizae are mutualistic structures formed by fungi and the roots of forest trees. They are predominantly found in the temperate and b ...

DDIEM Ontology for the Drug Database for Inborn Errors of Metabolism. The DDIEM database is a database of therapeutic strategies and treatments for inborn errors of metabolism. These strategies are classified by mechanism and outcome using the DDIEM ...

Synthetic data replicating 30,000 ethnically diverse hypertrophic cardiomyopathy patients: This includes clinical and biological phenotyping, co-morbidities, investigations (including ECG, ECHO), any procedures undertaken and outcomes.

The health of an individual organism results from a complex interplay between its genes and environment. Although great strides have been made in standardizing the representation of genetic information for exchange, there are no comparable standards ...

The Plant Phenotyping Experiment Ontology (PPEO) is an implementation of the Minimal Information About Plant Phenotyping Experiment (MIAPPE) Guidelines. It lists and organises all the information necessary to describe and reuse a phenotyping dataset ...

The Mungbean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as w ...

The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods a ...

A sample information file accompanying a .bed binary genotype table.

The Lentil Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as wel ...

The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well ...

The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as we ...

The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as wel ...

The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as we ...

The Groundnut Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as ...

The Banana Anatomy Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and method ...

Development of crop-specific trait ontologies including the Chickpea Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, s ...

Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops ...

Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops ...

Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops ...

Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops ...

Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops ...

Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops ...

The Face Of Fungi database allows deposition of taxonomic data, phenotypic details and other useful data. Its aim is to enhance current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fun ...

The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies.

Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops ...

The Drosophila Genetic Reference Panel (DGRP) is a population consisting of more than 200 inbred lines derived from the Raleigh, USA population. The DGRP is a living library of common polymorphisms affecting complex traits, and a community resource f ...

Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops ...

This database is a tool for describing patient information and facts such as patient health history, diagnosis, medication etc...This is supported by the i2b2 software. Datasets are gathered from a variety of sources. The i2b2 team merged with the Tr ...

Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed in the context of the ...

This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution and breeding company within the project. Reference Plant Ontologies are being de ...

The Woody Plant Ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Reference Plant Ontologies are being developed in the context o ...

METLIN represents the largest MS/MS collection of data with the database generated at multiple collision energies and in positive and negative ionization modes. The data is generated on multiple instrument types including SCIEX, Agilent, Bruker and W ...

Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops ...

TOP, a Thesaurus Of Plant characteristics, defines standards for a functional approach to plant diversity by stabilizing the terminology for concepts widely used in ecology and evolution. TOP provides names, definitions, formal units and synonyms for ...

The Cystic Fibrosis Mutation Database (CFTR1) was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers, and is maintained by the Cystic Fibrosis Centre at the Hospital for ...

The Drosophila Synthetic Population Resource (DSPR) consists of a new panel of over 1700 recombinant inbred lines (RILs) of Drosophila melanogaster, derived from two highly recombined synthetic populations, each created by intercrossing a different s ...

Crop-specific trait ontologies enhance the interoperability and effectiveness of data exchange between the data sources which adopt it, by providing standard concepts that are use to describe phenotypes stored in those sources. As one of them, the Ca ...

The National Database for Autism Research (NDAR) is an NIH-funded research data repository that aims to accelerate progress in autism spectrum disorders (ASD) research through data sharing, data harmonization, and the reporting of research results. N ...

LIAS is a global information system for Lichenized and Non-Lichenized Ascomycetes. It includes several interoperable data repositories. In recent years, the two core components ‘LIAS names’ and ‘LIAS light’ have been enlarged. LIAS light stores pheno ...