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