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Physical & Life Science Resource Guide: Websites

This guide will help you to study the physical and life sciences and prepare you for a career in the medical or research field. It will also help you understand the science behind life forms from the smallest of atoms to humans to the largest of animals.

Websites

General Life Sciences Data

  • Data.gov
    Open Federal, state, and local data from the United States government.
  • Dryad
    Repository of research data underlying scientific and medical publications, predominantly from peer-reviewed journal articles.
  • Figshare
    General repository for research outputs, including data sets, media, papers, posters, and groups of files.
  • NIH Data Sharing Repositories
    List of NIH-supported data repositories and resources that aggregate information about biomedical data. Each entry has a brief description of the repository and links to data submission and access policies.
  • re3data.org
    Global registry of research data repositories.

Ecology & Evolutionary Biology Data

  • Avian Knowledge Network (AKN)
    A partnership of people, institutions, and government agencies that supports the conservation of birds and their habitats by improving access to and use of data and tools. Data available on bird-monitoring, banding, and citizen-based bird-surveillance.
  • Catalog of Life
    Single integrated species checklist and taxonomic hierarchy. The Catalog holds essential information on the names, relationships, and distributions of over 1.6 million species.
  • Data Basin
    Provides free access to biological, physical, and socioeconomic geospatial data and maps, along with tools to create custom visualizations, drawings, and analysis.
  • Global Biodiversity Information Facility (GBIF)
    GBIF facilitates free and open access to biodiversity data, enabling anyone to discover, use, or publish data about all types of life on Earth.
  • Integrated Taxonomic Information System (ITIS)
    Authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. Full database or specific taxonomic group data available for download.
  • Knowledge Network for Biocomplexity (KNB)
    International repository for ecological and environmental data. Data originate from field stations, laboratories, research sites, and individual researchers around the world.
  • Long Term Ecological Research (LTER) Data Portal
    The Long Term Ecological Research (LTER) Network is a collaborative of researchers and graduate students who focus on long-term ecological processes at 26 LTER sites around the United States, Antarctica, and islands in the Caribbean and Pacific. The LTER Data Portal contains ecological data packages contributed by past and present LTER sites.
  • MorphoBank
    It provides collaborative tools for researchers to upload images and morphological data, and use that information to produce, edit, illustrate and annotate phylogenetic matrices. Also a repository for data associated with peer-reviewed publications.
  • NCBI Taxonomy
    National Center for Biotechnology Information (NCBI) database of names and classification for all organisms represented in NCBI sequence databases.
  • TreeBASE
    Repository of phylogenetic information, specifically user-submitted trees and the data used to generate them. Data in TreeBASE are available to the public if they have been used in a peer-reviewed publication.

Molecular Biology, Cell Biology & Biochemistry Data

Collections

Sequence Data

  • Nucleotide
    Collection of sequences from multiple sources, including GenBank, RefSeq, and Protein Data Bank (PDB). Searching Nucleotide will yield results from each of its component databases, which can also be searched separately. [NCBI database]
  • SRA: Sequence Read Archive
    Repository for raw sequencing data from next-generation sequencing technologies. [NCBI database]
  • UniProt
    Universal Protein Resource (UniProt), a collaboration between the European Bioinformatics Institute, the SIB Swiss Institute of Bioinformatics and Protein Information Resource, provides high-quality, freely accessible protein sequence and functional information.

Gene & Expression Data

  • BioProject
    Collection of genomics, functional genomics, and genetic studies with links to their datasets. [NCBI database]
  • dbGAP: Database of Genotypes and Phenotypes
    Archive and distribution center for results of studies that investigate the interaction of genotype and phenotype, including GWAS and molecular diagnostic assays. [NCBI database]
  • Gene
    Database of genes from a wide range of species, with a focus on genomes that have been completely sequenced. [NCBI database]

Structure

  • Cambridge Structural Database 
    Current; the Cambridge Structural Database (WebCSD) consists of the bibliographic, chemical, and crystallographic (single crystal and powder diffraction) records for organic molecules and metal-organic compounds whose 3-D structures have been determined using x-diffraction and/or neutron diffraction. Almost all records have three-dimensional coordinate data for at least non-hydrogen atoms. The crystal structure data comes from open literature or direct deposits by researchers. Search by substructure, reduced cell, similarity, or text/numeric.
  • Nucleic Acid Database
    Archive of structural information about nucleic acids.
  • PDB: Protein Data Bank
    Worldwide repository for information about 3D structures of biological macromolecules. Provides tools for structure visualization.

Model Organisms

  • Plant Model Organism Databases
    Collected by Plant Metabolic Network
  • BioCyc
    Collection of 2988 Pathway/Genome Databases (PGDBs), each describing the genome and metabolic pathways of a single organism. (Click on "Change organism database" in upper right to get started)
  • FlyBase
    Database of Drosophila genes and genomes.
  • MGI: Mouse Genome Informatics
    Database of laboratory mouse genetic, genomic and biologic data.
  • ZFIN: The Zebrafish Model Organism Database
    Database of zebrafish genetic, genomic and developmental data.
  • TAIR: The Arabidopsis Information Resource 
    The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.

Plant Data & Other Resources

  • TAIR: The Arabidopsis Information Resource 
    The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.
  • Grameme
    Comparative grass genomics (rice, maize, sorghum, barley, oats, wheat, rye)
  • Phytozome
    Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute. Families of related genes representing the modern descendants of ancestral genes are constructed at key phylogenetic nodes. These families allow easy access to clade-specific orthology/paralogy relationships as well as insights into clade-specific novelties and expansions. As of release v11, Phytozome provides access to sixty-five sequenced and annotated green plant genomes.
  • Plant Metabolic Network
    It provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analysis about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism in plants.
  • Plant Model Organism Databases
    Collected by Plant Metabolic Network
  • re3data - Plant Sciences
    Research Data Repositories tagged with "Plant Sciences"

 

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