Phenomic analysis software tools and databases
A key goal of biology is to understand phenotypic characteristics, such as health, disease and evolutionary fitness. Phenotypic variation is produced through a complex web of interactions between genotype and environment, and such a 'genotype–phenotype' map is inaccessible…
VertNet VertNet

VertNet

Makes biodiversity data free and available on the web. VertNet is designed to…

Makes biodiversity data free and available on the web. VertNet is designed to help people discover, capture, and publish biodiversity data. It is also the core of a collaboration between hundreds of…

PROkaryotic TRAITS PROkaryotic TRAITS

ProTraits PROkaryotic TRAITS

Describes environmental preferences of microbes, interactions with other…

Describes environmental preferences of microbes, interactions with other organisms, biochemical phenotypes, resistance to chemicals and other stressors. ProTraits recognizes 424 phenotypic traits and…

Desktop app
Highly Comparative… Highly Comparative Time-Series Analysis

hctsa Highly Comparative Time-Series Analysis

A software package for running highly comparative time-series analysis. hctsa…

A software package for running highly comparative time-series analysis. hctsa automates the selection of quantitative phenotypes from time-series data by leveraging a large and interdisciplinary…

Desktop app
WormGender WormGender

WormGender

A software package for automatic phenotyping in C. elegans included in…

A software package for automatic phenotyping in C. elegans included in QuantWorm. WormGender is designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions…

International Mouse… International Mouse Phenotyping Consortium

IMPC International Mouse Phenotyping Consortium

Provides the biomedical community with a unified point of access to mutant mice…

Provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous…

Arabidopsis thaliana… Arabidopsis thaliana Protein Interactome Database

AtPID Arabidopsis thaliana Protein Interactome Database

Depicts and integrates the information pertaining to protein-protein…

Depicts and integrates the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. AtPID…

Desktop app
phenomeImpute phenomeImpute

phenomeImpute

Imputes missing values in large-scale high-dimensional phenome data.…

Imputes missing values in large-scale high-dimensional phenome data. phenomeImpute contains four variations of K-nearest-neighbor (KNN) methods and was compared with two existing methods,…

Desktop app
Web app
PREsentation and… PREsentation and Characterization Of Growth-data

PRECOG PREsentation and Characterization Of Growth-data

Automates visualization, analysis and exploration of complex and highly…

Automates visualization, analysis and exploration of complex and highly resolved microbial growth data. PRECOG allows the user to quality control, interact with and evaluate microbial growth data…

Desktop app
MatrixConverter MatrixConverter

MatrixConverter

Helps expedite and facilitate the transformation of raw phenomic character data…

Helps expedite and facilitate the transformation of raw phenomic character data into discrete character matrices that can be used in most popular evolutionary inference programs. MatrixConverter…

Desktop app
Flynotyper Flynotyper

Flynotyper

A computational method to quantitatively assess the morphological defects in…

A computational method to quantitatively assess the morphological defects in the Drosophila eye resulting from genetic alterations affecting basic cellular and developmental processes. Flynotyper…

Plant Genomics and… Plant Genomics and Phenomics Research Data…

PGP Plant Genomics and Phenomics Research Data Repository

An infrastructure to comprehensively publish plant research data. PGP covers in…

An infrastructure to comprehensively publish plant research data. PGP covers in particular cross-domain datasets that are not being published in central repositories because of its volume or…

RIKEN Arabidopsis… RIKEN Arabidopsis Genome Encyclopedia

RARGE RIKEN Arabidopsis Genome Encyclopedia

An integrated phenotype database of Arabidopsis mutant traits using a…

An integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary. RARGE integrates the phenotypes of four Arabidopsis mutant lines (including two loss-of-function and two…

A A A OPTIMAS Data Warehouse OPTIMAS Data Warehouse

Optimas-DW OPTIMAS Data Warehouse

A comprehensive data collection for maize. Optimas-DW integrates data from…

A comprehensive data collection for maize. Optimas-DW integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. A web interface allows…

A A A Genoplante… Genoplante Information System

GnpIS Genoplante Information System

A multispecies integrative information system dedicated to plant and fungi…

A multispecies integrative information system dedicated to plant and fungi pests. GnpIS bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps,…

The Plant Science… The Plant Science Search Engine

LAILAPS The Plant Science Search Engine

An information retrieval system designed to link plant genomic data in the…

An information retrieval system designed to link plant genomic data in the context of phenotypic attributes for a detailed forward genetic research. LAILAPS comprises around 65 million indexed…

eHALOPH eHALOPH

eHALOPH

A database of salt-tolerant plants-halophytes. Records of plant species…

A database of salt-tolerant plants-halophytes. Records of plant species tolerant of salt concentrations of around 80 mM sodium chloride or more have been collected, along with data on plant type,…

TOMATOMA TOMATOMA

TOMATOMA

A tomato mutant database providing visible phenotypic data of tomato mutant…

A tomato mutant database providing visible phenotypic data of tomato mutant lines generated by ethylmethane sulfonate (EMS) treatment or gamma-ray irradiation in the genetic background of Micro-Tom,…

Deciphering the… Deciphering the Mechanisms of Developmental…

DMDD Deciphering the Mechanisms of Developmental Disorders

A research programme set up to identify genes in the mouse, which if mutated…

A research programme set up to identify genes in the mouse, which if mutated (or knocked-out) result in embryonic lethality when homozygous, and initiate the study of why disruption of their function…

A A A FlyRNAi FlyRNAi

FlyRNAi

Serves a dual role, tracking both production of reagents for RNA interference…

Serves a dual role, tracking both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. FlyRNAi is used as a platform for community availability of…

Desktop app
Limb formalization Limb formalization

Limbform Limb formalization

A database based on a functional ontology system that unambiguously centralize…

A database based on a functional ontology system that unambiguously centralize the knowledge of limb regeneration experiments in a diverse set of model organisms, enabling the unambiguous…

Desktop app
Planarian… Planarian formalization

Planform Planarian formalization

A manually curated database and software tool for planarian regenerative…

A manually curated database and software tool for planarian regenerative experiments, based on a mathematical graph formalism. Planform contains more than a thousand experiments from the main…

PhenomicDB PhenomicDB

PhenomicDB

A multi-organism phenotype-genotype database including human, mouse, fruit fly,…

A multi-organism phenotype-genotype database including human, mouse, fruit fly, C. elegans, and other model organisms. The inclusion of gene indices (NCBI Gene) and orthologues (same gene in…

Digital development Digital development

Digital development

Provides a comprehensive, curated, multidimensional database for developmental…

Provides a comprehensive, curated, multidimensional database for developmental phenotypes, cell-specific gene functions, differentiation trajectories and a multiscale model of lineage differentiation…

Organ system… Organ system heterogeneity DB

Organ system heterogeneity DB

Provides information on the phenotypic effects of 4865 human diseases, 1667…

Provides information on the phenotypic effects of 4865 human diseases, 1667 drugs and 5361 genetically modified mouse models on 26 different organ systems. Disease symptoms, drug side effects and…

INFRAFRONTIER INFRAFRONTIER

INFRAFRONTIER

It is the European Research Infrastructure for phenotyping and archiving of…

It is the European Research Infrastructure for phenotyping and archiving of model mammalian genomes. The INFRAFRONTIER Research Infrastructure provides access to first-class tools and data for…

iBeetle-Base iBeetle-Base

iBeetle-Base

Makes available annotations of RNAi phenotypes, which were gathered in a large…

Makes available annotations of RNAi phenotypes, which were gathered in a large scale RNAi screen in the red flour beetle Tribolium castaneum (iBeetle screen). In addition, it provides access to…

Phenotype-Genotype… Phenotype-Genotype Integrator

NCBI PheGenI Phenotype-Genotype Integrator

Merges NHGRI genome-wide association study (GWAS) catalog data with several…

Merges NHGRI genome-wide association study (GWAS) catalog data with several databases housed at the National Center for Biotechnology Information (NCBI), including Gene, dbGaP, OMIM, GTEx and dbSNP.…

Web app
SigniSite SigniSite

SigniSite

An online application for subgroup-free residue-level genotype-phenotype…

An online application for subgroup-free residue-level genotype-phenotype correlation. In contrast to similar methods, SigniSite does not require any pre-definition of subgroups or binary…

Mouse Phenome Project Mouse Phenome Project

MPD Mouse Phenome Project

A collaborative standardized collection of measured data on laboratory mouse…

A collaborative standardized collection of measured data on laboratory mouse strains and populations. MPD includes baseline phenotype data sets as well as studies of drug, diet, disease and aging…

European Mouse Mutant… European Mouse Mutant Archive

EMMA European Mouse Mutant Archive

A leading international network infrastructure for archiving and worldwide…

A leading international network infrastructure for archiving and worldwide provision of mouse mutant strains. The EMMA database gathers and curates extensive data on each line and presents it through…

Zebrafish Mutation… Zebrafish Mutation Project

ZMP Zebrafish Mutation Project

Aims to create a knockout allele in every protein coding gene in the zebrafish…

Aims to create a knockout allele in every protein coding gene in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing. Each allele created is…

Desktop app
PhenoNet PhenoNet

PhenoNet

An algorithm for the identification of pathways and networks associated with…

An algorithm for the identification of pathways and networks associated with different phenotypes. PhenoNet uses two types of input data: gene expression data (RMA, RPKM, FPKM, etc.) and phenotypic…

Web app
SurvNet SurvNet

SurvNet

A bioinformatics web app for identifying network-based biomarkers that most…

A bioinformatics web app for identifying network-based biomarkers that most correlate with patient survival data. SurvNet is a valuable bioinformatic tool for identifying network-based biomarkers…

Desktop app
APSampler APSampler

APSampler

A tool that allows multi-locus and multi-level association analysis of…

A tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data. APSampler was tested on a simulated data set and on a case-control MS (multiple sclerosis) study…

GenomeRNAi GenomeRNAi

GenomeRNAi

A database containing phenotypes from RNA interference (RNAi) screens in…

A database containing phenotypes from RNA interference (RNAi) screens in Drosophila and human. In addition, the database provides an updated resource of RNAi reagents and their predicted quality.…

PHENOtype comparisons… PHENOtype comparisons for DIsease and Gene Models

PhenoDigm PHENOtype comparisons for DIsease and Gene Models

An automated method to provide evidence about gene-disease associations by…

An automated method to provide evidence about gene-disease associations by analysing phenotype information. PhenoDigm integrates data from a variety of model organisms and, at the same time, uses…

Rice Mutant Database Rice Mutant Database

RMD Rice Mutant Database

An archive for collecting, managing and searching information of the T-DNA…

An archive for collecting, managing and searching information of the T-DNA insertion mutants generated by an enhancer trap system. RMD can be searched by keywords, nucleotide sequence or protein…

A A A RNAi DataBase RNAi DataBase

RNAiDB RNAi DataBase

Contains a compendium of publicly available data and provides information on…

Contains a compendium of publicly available data and provides information on experimental methods and phenotypic results, including raw data in the form of images and streaming time‐lapse movies.…

DNA Data Bank of Japan DNA Data Bank of Japan

DDBJ DNA Data Bank of Japan

Maintains and provides public archival, retrieval and analytical services for…

Maintains and provides public archival, retrieval and analytical services for biological information. The contents of the DDBJ databases are shared with the US National Center for Biotechnology…

NCBI MedGen NCBI MedGen

NCBI MedGen

Organizes information related to human medical genetics, such as attributes of…

Organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution. The core content of the record may include names, identifiers used by other…

GEneSTATION GEneSTATION

GEneSTATION

Integrates diverse types of omics data across mammals to advance understanding…

Integrates diverse types of omics data across mammals to advance understanding of the genetic basis of gestation and pregnancy-associated phenotypes and to accelerate the translation of discoveries…

Zebrafish TILLING… Zebrafish TILLING Project

Zebrafish TILLING Project

The goal of this project is to use TILLING to generate and distribute…

The goal of this project is to use TILLING to generate and distribute loss-of-function mutations in genes of interest to the zebrafish community. The zebrafish TILLING project is a joint effort of…

Desktop app
PhenoCurve Deprecated PhenoCurve

PhenoCurve

A knowledge based curve fitting algorithm, aiming to identify the complex…

A knowledge based curve fitting algorithm, aiming to identify the complex relationships between phenotypes and environments. PhenoCurve splits the whole dataset into reliable and unreliable windows…

A A A FLIGHT Deprecated FLIGHT

FLIGHT

An online resource compiling data from high-throughput Drosophila in vivo and…

An online resource compiling data from high-throughput Drosophila in vivo and in vitro RNAi screens. FLIGHT includes details of RNAi reagents and their predicted off-target effects, alongside RNAi…

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