Cluster: Biological mapping projects

Human and model organisms

Most biological maps and catalogs allow comparisons between human and non-human model organisms and provide information about homologous genes or corresponding processes across different organisms. Model organisms such as yeast, fruit flies and mice are used in research as a proxy for understanding human biology because they have genes and biological processes in common with humans.

Genomics

1000 Genomes Project
100,000 Genomes Project
BioCyc - genomes and metabolic pathways, includes EcoCyc
Dictybase - Dictyostelium discoideum (amoeba)
DisGeNET
Dubai Genomics
ENCODE: Encyclopedia of DNA Elements - NHGRI project building a comprehensive parts list of functional elements in the human genome such as elements that regulate protein and RNA levels
Ensembl genome database project
Flybase
French Plan for Genomic Medicine 2025
Human Variome Project
Mouse Genome Informatics
Repbase - maintained by the Genetic Information Research Institute (GIRI), a collection of eukaryotic genome repeat sequences used for annotation of sequences
Saccharomyces Genome Database
Turkish Genome Project 
The Literature Human Gene Derived Network
PomBase - fission yeast Schizosaccharomyces pombe
Rat Genome Database
WormBase - Caenorhabditis elegans
Xenbase - Xenopus laevis and Xenopus tropicalis
Mouse Genome Database (MGD)
Gene Expression Database (GXD)
Mouse Models of Human Cancer database (MMHCdb)

Human health and disease relationships to genomics, lifestyle and environment

All of Us Research Program
Australian Genomics Health Futures Mission
Inborn Errors of Metabolism Knowledgebase (IEMbase)
Initiative on Rare and Undiagnosed Diseases (IRUD) - Japan based program aimed to improve data sharing in relation to clinical diagnostics with genetic analysis
Online Mendelian Inheritance in Man
Personal Genome Project - Harvard PGP, PGP Canada, PGP UK, Genom Austria, PGP China
UK Biobank

Phenomics and genotype-phenotype associations

Phenomics is the systematic study of measurable phenotypes or characteristics on a genome-wide scale. Ontologies are used for cataloging the biological roles of gene products using a common language. The characterization of the phenotype of organisms with gene mutations or gene knock outs is used to understand gene function. Both genotype and environment determine phenotype. Since not all genetic differences between individuals have an impact on phenotype, genotype-phenotype association projects aim to catalogue the genotypes that are associated with observable or measurable phenotypes such as disease or altered cell function.



Chemical Phenomics Initiative - chemotype-phenotype data in zebrafish for drug discovery
Consortium for Neuropsychiatric Phenomics (CNP)
The Gene Ontology (GO) resource and GO Consortium - Computational models of biological systems from genes to molecular pathways to organism for the understanding of gene function

Human Phenotype Ontology (HPO) 
The Knockout Mouse Project
International Mouse Phenotyping Consortium (IMPC)
Mouse Phenome Database
National Bio Resource Project (NBRP) Rat Phenome
Navigome
Phenome Wide Association Studies (PheWAS)
Phenoscape

Proteins and proteomics

Proteomics is the study of the full protein complement of a cell, tissue or organism. Proteomics and protein databases can be used to map differences in protein composition and shape to health and disease.

Human Proteome Folding Project
UniProt
Human Infectious Diseases HPP initiative (HID-HPP) through the Human Proteome Organization (HPO)

Cell, tissue and embryogenesis maps

Broad Bioimage Benchmark Collection
Broad Cancer Cell Line Encyclopedia
Cell Atlas Initiative

Cell Image Library
Human Cell Atlas
Human Cytome Project
Mitotic Cell Atlas
Single cell RNA sequencing map of embryogenesis in Xenopus
Single cell RNA sequencing map of embryogenesis in zebrafish
Worm Atlas (C. elegans)

Brain and nervous system

Blue Brain Project
BrainMaps

Human Brainnetome Project
Human Connectome Project

Microbiome

American Gut
Human Microbiome Project
Human Gastrointestinal Bacteria Genome Collection (HBC)

Microbes associated with human disease

Candida Genome Database

Animals - Livestock and domesticated

Functional Annotation of Animal Genomes project (FAANG)
AgBase - Resource for functional analysis of agricultural plant and animal gene products and Gene Ontology annotations

Dog

Darwin's Dogs
DogDNA
The NHGRI Dog Genome Project

Cow

1000 Bull Genomes Project
Bovine Genome Database

Pig

Pig Genome Database

Animals - Undomesticated

Chimpanzee Genome Project
AgBase - Resource for functional analysis of agricultural plant and animal gene products and Gene Ontology annotations

Plants

The Arabidopsis Information Resource (TAIR) - database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana
AgBase - Resource for functional analysis of agricultural plant and animal gene products and Gene Ontology annotations

Phenomics and genotype-phenotype associations



Australian Plant Phenomics Facility
The European Infrastructure for Multi-scale Plant Phenomics and Simulation (EMPHASIS)
International Plant Phenotyping Network
National Plant Phenomics Centre (IBERS Gogerddan, Wales, UK)
PHENOME, the French plant phenomic Infrastructure
Plant Ontology - structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data

Bacteria and archaea

Genomics

BacMap - zoomable and searchable chromosome maps for prokaryotic species (archaebacterial and eubacterial)

Viruses

Virus-Host DB

Microbiome projects (non human)

Earth Microbiome Project
Project Acari - microbiome of ticks

Biodiversity

The Barcode of Life Data System (BOLD) developed at the Centre for Biodiversity Genomics in Canada
The Biogeographic Atlas of the Southern Ocean

Earth BioGenome Project
International Barcode of Life (iBOL), a research alliance that overseeing BARCODE 500K, BIOSCAN and the Planetary Biodiversity Mission (PBM)
Map of Life (MOL)
Ocean Biogeographic Information System (OBIS)

Biological mapping companies

Chan Zuckerberg Biohub
Genomic Health

Investors in biological mapping projects

Illumina
Y Combinator
Polaris Partners
Google Ventures
Arch Venture Partners
Lightspeed Venture Partners
Sequoia Capital
IndieBio
Longitude Capital

Non-profit support

Phoenix Bioinformatics
Wellcome Trust

Other mapping projects