Golden
Cluster: Biological mapping projects

Cluster: Biological mapping projects

A cluster of topics related to biological mapping and biological databases.

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

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
  • Personal Genome Project - Harvard PGP, PGP Canada, PGP UK, Genom Austria, PGP China

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

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.

Cell, tissue and embryogenesis maps

Brain and nervous system

Microbiome

Microbes associated with human disease

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

Cow

  • 1000 Bull Genomes Project
  • Bovine Genome Database

Pig

  • Pig Genome Database

Animals - Undomesticated

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)

Biodiversity

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

Investors in biological mapping projects

Non-profit support

Other mapping projects



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