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…
WormNet
Web

WormNet

Hosts a network-assisted hypothesis-generating server for C. elegans. WormNet…

Hosts a network-assisted hypothesis-generating server for C. elegans. WormNet includes a base gene network, which substantially improved predictions of RNAi phenotypes. The server generates various…

PhenoLink
Web

PhenoLink

Links phenotype to omics data sets using well-established as well new…

Links phenotype to omics data sets using well-established as well new techniques. PhenoLink imputes missing values and preprocesses input data (i) to decrease inherent noise in the data and (ii) to…

SeedCounter
Desktop
Mobile

SeedCounter

Calculates the number and the size of seeds thank to a white paper sheet of…

Calculates the number and the size of seeds thank to a white paper sheet of standard size as a background. SeedCounter automates evaluation of phenotypic parameters of grains using mobile devices…

AraPheno
Data

AraPheno

Provides a central repository of population-scale phenotypes for A. thaliana…

Provides a central repository of population-scale phenotypes for A. thaliana inbred lines. AraPheno includes various features to easily access, download and visualize the phenotypic data. This will…

VertNet
Data

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…

ProTraits
Data

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…

hctsa
Desktop

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…

WormGender
Desktop

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…

IMPC
Data

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…

AtPID
Data

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…

Phenoplasm
Data

Phenoplasm Phenotype database for Plasmodium

Facilitates systematic views of known experimental-genetic data across…

Facilitates systematic views of known experimental-genetic data across Plasmodium species. PhenoPlasm contains phenotypes for Plasmodium parasites. It provides a simple interface to link…

phenomeImpute
Desktop

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,…

PRECOG
Desktop
Web

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…

MatrixConverter
Desktop

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…

Flynotyper
Desktop

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…

PGP
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…

RARGE
Data

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…

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Optimas-DW
Data

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…

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GnpIS
Data

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,…

LAILAPS
Data

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
Data

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
Data

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,…

DMDD
Data

DMDD Deciphering the Mechanisms of Developmental Disorders

A free online database of image and phenotype data for embryonic lethal…

A free online database of image and phenotype data for embryonic lethal knockout mice. The data sheds new light on genes that are critical for embryo development and survival. High-resolution 3D…

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FlyRNAi
Data

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…

Limbform
Desktop

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…

Planform
Desktop

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
Data

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…
Data

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…
Data

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
Data

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
Data

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…

NCBI PheGenI
Data

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.…

SigniSite
Web

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…

MPD
Data

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…

EMMA
Data

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…

ZMP
Data

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…

Zebrafish…
Data

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…

PhenoNet
Desktop

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…

SurvNet
Web

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…

APSampler
Desktop

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
Data

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.…

PhenoDigm
Data

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…

RMD
Data

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…

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RNAiDB
Data

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.…

DDBJ
Data

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
Data

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…

Phenowiki
Data

Phenowiki

Enables representation and sharing of empirical information about phenotypes…

Enables representation and sharing of empirical information about phenotypes important to neuropsychiatric research. Phenowiki tabulates empirical findings about heritabilities and measurement…

PhenoCurve
Desktop

PhenoCurve

Aims to identify the complex relationships between phenotypes and environments.…

Aims to identify the complex relationships between phenotypes and environments. PhenoCurve splits the whole dataset into reliable and unreliable windows based on curve fitting, and then optimizes the…

GEneSTATION
Data

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…

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FLIGHT
Data

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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