LibGuides: IB Biology: Research Data

Databases

Data analysis computer artwork - Britannica ImageQuest This page has links to research data that can be used for your Individual Project in the field of:

DNA, Amino Acid, SNPs, & Genes
Environmental Data from Satellites
Migrating Marine Mammals
Ocean Research
Ornithology - eBird Database
Paleobiology, Paleocology, and Paleomammalogy

You can find datasets from many disciplines, including environmental and social sciences, as well as government data and data provided by news organizations, in:

Google Dataset Search
IPUMS (Integrated Public Use Microdata Series)
National Center for Health Statistics

DNA, Amino Acid, SNPs, & Genes

You can find DNA sequences, amino acid sequences, SNPs (single nucleotide polymorphisms). genes, and other related databases in the links below. Most are from the National Center for Biotechnology Information, part of the U.S. National Library of Medicine.

BLAST
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

dbSNP
Database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants.

Gene
This database integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

Genetic Testing
This curriculum unit from the Northwest Association for Biomedical Research explores how bioinformatics is applied to genetic testing. Specifically, the bioinformatics tools of BLAST and Cn3D are used to investigate the genetic and molecular consequences of a mutation to the Breast Cancer Susceptibility 1 (BRCA1) gene.
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Cn3D ("see in 3D") is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez Structure database. Cn3D simultaneously displays structure, sequence, and alignment, and also has annotation and alignment editing features.

Genome
This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.

Nucleotide
The Nucleotide database is a collection of sequences from several sources, including GenBank (an annotated collection of all publicly available DNA sequences), Reference Sequence (RefSeq - a collection of sequences, including genomic DNA, transcripts, and proteins), TPA (tissue-type plasminogen activator) and PDB (Protein Data Bank).

Protein
The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt (a protein sequence database), PIR (Protein Information Resource), PRF (Protein Research Foundation database of amino acid sequences of peptides and proteins), and PDB. Protein sequences are the fundamental determinants of biological structure and function.

RCSB Protein Data Bank
This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) curates and annotates PDB data. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.

Environmental Data from Satellites

NOAA Comprehensive Large Array-data Stewardship System (CLASS)
The Comprehensive Large Array-data Stewardship System (CLASS) is NOAA's online system for managing environmental data. Under the 'SEARCH FOR DATA' heading on the right, click the '+' by Environmental Data from Geostationary Satellites' to see links to environmental data from GOES (Geostationary Operational Environmental Satellite) satellites. GOES takes the pictures of clouds used by the National Weather Service to watch out for severe storms and carries instruments to measure atmospheric temperature and moisture, to monitor the particles and fields around the spacecraft, to help search and rescue operations, and to echo remote data collection platforms (e.g. buoys).

Migrating Marine Animals

Oceans of Data Institute (ODI)
ODI (a division of Education Development Center (EDC)) provides students access to data collected by migrating marine animals, Earth-orbiting satellites, and drifting buoys, as well as a set of data analysis tools that can be used to take measurements and look for patterns in these complex data sets.

Ocean Tracks
Ocean Tracks provides access to authentic data collected by migrating marine animals, drifting buoys, and satellites, along with tools that allow you to display and analyze these data to investigate current and important scientific questions about animal interactions with the ocean environment. The Ocean Tracks website was created by EDC's Oceans of Data Institute and Stanford University.

Tagging of Pelagic Predators (TOPP)
oceanographic datasets, to marine life observation. By combining data from a diverse number of highly migratory species, and overlaying them with oceanographic data, it is possible to glimpse the processes that influence how open ocean ecosystems work.

Paleobiology, Paleocology, and Paleomammalogy

Neomap (Neogene Mammal Mapping Portal)
A common access portal for two different, free-standing databases in the field of paleomammalogy. These two linked datasets provide point-occurrence data for all published late Oligocene through Holocene mammals in the USA, and for many Quaternary localities in Canada.
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Search for, retrieve, and analyze data from the MIOMAP (Miocene Mammal Mapping Project) and FAUNMAP (Quaternary Faunal Mapping Project) databases, either separately or in concert.
Neotoma Paleoecology Database
An online hub for data, research, education, and discussion about paleoenvironments. Users can find information efficiently by searching the database on spatial, temporal, and metadata criteria; interactively browse and visualize live data and metadata; get data and information in a variety of useful formats (e.g., downloads, reports, graphics).
The Paleobiology Database
A public resource for paleontological data, providing global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data.

Ornithology - eBird Database

The Cornell Lab of Ornithology is a leader in the study, appreciation, and conservation of birds. Through their programs they aim to advance the understanding of nature and to engage people of all ages in learning about birds and protecting the planet. They host the eBird databse, in collaboration with organizations, regional experts, and users ("eBirders") all over the world.

eBird is the world’s largest biodiversity-related citizen science project, with more than 100 million bird sightings contributed each year by eBirders around the world. eBird data document bird distribution, abundance, habitat use, and trends through checklist data collected within a simple, scientific framework. Birders enter when, where, and how they went birding, and then fill out a checklist of all the birds seen and heard during the outing. Access this database by creating an account with a username and password. eBird includes population data from The Great Backyard Bird Count, maps of citizen-created bird habitat from Habitat Network. bird songs and calls from Macaulay Library, nest camera data from NestWatch, and sightings at bird feeders from Project FeederWatch. These citizen science projects at the Cornell Lab of Ornithology provide a way for people to learn about birds, habitat, science, and conservation while contributing to real scientific studies.

Great Backyard Bird Count
Participants are asked to count birds for as little as 15 minutes (or as long as they wish) on one or more days of the four-day event and report their sightings online at birdcount.org. Each checklist submitted during the GBBC helps researchers at the Cornell Lab of Ornithology and the National Audubon Society learn more about how birds are doing, and how to protect them and the environment we share.Citizen scientists count for as little as 15 minutes in their own backyards to help Audubon expand their understanding of birds

Macaulay Library
An extensive scientific archive of natural history audio, video, and photographs. Although the Macaulay Library is best known for its collection of bird songs and calls, the collection also includes amphibians, fishes, and mammals, and the library preserves recordings of each species’ behavior and natural history.

NestWatch
Volunteers help scientists at the Cornell Lab of Ornithology by collecting data on the successes and failures of nesting birds by tracking nests, clutches, broods, and fledglings. NestWatch is a nationwide monitoring program designed to track status and trends in the reproductive biology of birds, including when nesting occurs, number of eggs laid, how many eggs hatch, and how many hatchlings survive.

Project FeederWatch
Project FeederWatch is a winter-long survey of birds that visit feeders at backyards, nature centers, community areas, and other locales in North America. FeederWatchers periodically count the birds they see at their feeders from November through early April and send their counts to Project FeederWatch. This data helps scientists at the Cornell Lab of Ornithology track broad-scale movements of winter bird populations and long-term trends in bird distribution and abundance.

Another resource available on the Cornell Lab of Ornithology website:

BirdSleuth
BirdSleuth is the K-12 education program of the Cornell Lab of Ornithology. They take an inquiry-based approach to science curriculum that engages kids in scientific study and real data collection through the Cornell Lab of Ornithology’s citizen-science projects. Look through BirdSleuth's science curriculum resources for teachers for Internal Assessment project ideas.

Ocean Research

NOAA Data in the Classroom
NOAA Data in the Classroom makes data from several federal environmental agencies available online for use in studying El Niño, sea level, water quality, ocean acidification, and coral bleaching.

Northwest Association of Networked Ocean Observing Systems (NANOOS)
NANOOS ) is the Pacific Northwest regional ocean observing system of IOOS (Integrated Ocean Observing System). NANOOS has data on fisheries, shellfish, ocean acidification, climate change, and harmful algal blooms.

NANOOS Visualization System (NVS)
NVS is the data portal for NANOOS. It provides easy access to a wide range of data and visualizations for observations and forecasts.

SOCCOM portal for all ARGO data
The Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) program at Princeton University maintains a portal for data from all ARGO ocean drifter data collectors worldwide. ARGO is an international program the will deploy some 3000 profiling drifters in the world oceans for purposes of examining the global scale of circulation and air-sea interaction, with the goal of improving climate models and predictions.

Global Tropical Moored Buoy Array
The Global Tropical Moored Buoy Array program designs, develops and sustains moored buoy observing systems in the tropics for climate research and forecasting through collaborative multi-national efforts. You can find real-time and historical data from tropical Pacific, Atlantic, and Indian Oceans, as well as data displays and information about climate variations like El Niño and La Niña.

University of Washington Ocean Drifter Data
UW data from their ocean drifter data collectors. These floats have been deployed as the beginning step in the US ARGO program. ARGO is an international program for deploying profiling drifters in the world oceans.

Google Dataset Search

Google Dataset Search
The Dataset Search platform trawls the millions of open data repositories on the web for desired datasets, looking on publisher sites, digital libraries, and on author's personal web pages, and more. Google relies on dataset publishers to correctly label their datasets with the appropriate information, such as who created the dataset, when it was published, how the data was collected, what the terms are for using the data, etc.

Google's Dataset Search platform enables users to find datasets stored across the Web through a simple keyword search. The tool surfaces information about datasets hosted in thousands of repositories across the Web, making these datasets universally accessible and useful.

Google believes that this project will have the additional benefits of a) creating a data sharing ecosystem that will encourage data publishers to follow best practices for data storage and publication and b) giving scientists a way to show the impact of their work through citation of datasets that they have produced.

As more dataset repositories use schema.org and similar standards to describe their datasets, the variety and coverage of datasets that users find in Dataset Search, will continue to grow.

IPUMS

IPUMS (Integrated Public Use Microdata Series)
IPUMS provides census and survey data from around the world integrated across time and space. IPUMS integration and documentation makes it easy to study change, conduct comparative research, merge information across data types, and analyze individuals within family and community contexts. Data and services available free of charge. Hosted by the University of Minnesota.

National Center for Health Statistics

Public-Use Data Files - National Center for Health Statistics (NCHS)
Downloadable public-use data files through the Centers for Disease Control and Prevention’s (CDC) FTP file server. Users of this service have access to data sets, documentation, and questionnaires from NCHS surveys and data collection systems. Downloading instructions are available in “readme” files.

Datasets that can be accessed on this page include:

National Health and Nutrition Examination Survey (NHANES)
National Health Care Surveys
National Vital Statistics System (NVSS)
National Survey of Family Growth (NSFG)
National Health Interview Survey (NHIS)
National Immunization Survey (NIS)
Longitudinal Studies of Aging (LSOA)
State and Local Area Integrated Telephone Survey (SLAITS)