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List of databases

This is a living document to survey basic information about specific Natural History databases. The purpose of this list is to act as reference for getting a superficial view of databases offering data.

Arctos

  • Link: Arctos
  • About: This site, used by the UCB Museum of Vertebrate Zoology, houses data from dozens of universities and museums about mammal, bird, reptile, amphibian, fish, microorganism, and other types of specimens.
  • Type of data offered: Data is offered as specimen information (weight, size, sample types, etc) or as observation information (mostly hand-written or transcribed field notes)
  • How to access data: Use the "search" function and its GUI to search by many different filters, including species name, locality (map capabilities too!), collector, etc.

GBIF

  • Link: GBIF
  • About: Aggregator site that unites many the dataset from over 40,000 other datasets.
  • Type of data offered: It appears as though every type of dataset is offered, but it is unclear how it is able to unite this data.
  • How to access data: In addition to being able to search by research type, for example occurance or species. There is a API where you can be more specific.

iDigBio

  • Link: IDIGBio
  • About: The Integrated Digitized Biocollections (iDigBio) is a collection of data and images for millions of biological specimens.
  • Type of data offered: Taxonomical, Geographical, Physiological data in CSV and Darwin Core Archive file format along with images of various species.
  • How to access data: The data is publically available and an account is not required to access the data. The search portal can be used to search for a specific species by name or attribute.

MorphoSource

  • Link: MorphoSource
  • About: A site hosted by Duke University Research Computing containing collections of 3D images and media regarding physical objects, most commonly biological specimen.
  • Type of data offered: 3D media sorted by specimen taxonomy, common file formats include STL and PLY. Each specimen includes a description of the project the specimen was used in and a brief physical description of the specimen itself.
  • How to access data: The data is publicly available, but an account is required to access the data. The search engine allows a user to browse by Institution, Taxonomy, Bibliography, and Project.

MoveBank

  • Link: MoveBank
  • About: help animal tracking researchers to manage, share, protect, analyze, and archive their data.
  • Type of data offered: Animal activities in csv.
  • How to access data: Search the datasets or authors or just browsing the data repository and click the download link.

BHL

  • Link: BHL
  • About: The Biodiversity Heritage Library (BHL) is the world’s largest open access digital library for biodiversity literature and archives. BHL is revolutionizing global research by providing free, worldwide access to knowledge about life on Earth.
  • Type of data offered: Can be downloaded as MODS XML, BibTex and tab-delimited text file.
  • How to access data: Click “Download Contents” while viewing a book and select ways to download resources when you click on the drop-down menu for “Download Contents”.

Vertnet

  • Link: Vertnet
  • About: VertNet is a NSF-funded collaborative project that makes biodiversity data free and available on the web. VertNet is an engine for training current and future professionals to use and build upon best practices in data quality, curation, research, and data publishing.
  • Type of data offered: Data were converted into CSV text files and compressed into .zip files. VertNet generates a metadata** file that describes the contents contained within each zipped dataset. And finally, bundle up the metadata and the dataset and upload them to CyVerse.
  • How to access data: All resources produced for and by VertNet are free and open to download. You can find them in the "Resources" >> "DATASETS, TOOLS & CODE" section.

The Paleobiology Database

  • Link: The Paleobiology Database
  • About: A public database of paleontological data that anyone can use, maintained by an international non-governmental group of paleontologists.
  • Type of data offered: CSV, TSV, JSON, RIS
  • How to access data: You can download by clicking "download data" on their home page. It allows you to download data of all types from the Paleobiology Database. Use the various fields and selectors to specify which information you are looking for, and the form will generate a URL that will retrieve that specific set of records using the data service API. You can also use one or more of the sections below to select a set of records and choose output options. If you close a section, you remove those parameters from the download URL until the section is opened again.

Neotoma

  • Link: Neotoma
  • About: Neotoma Paleoecology Database and Community is an online hub for data, research, education, and discussion about paleoenvironments.
  • Type of data offered:
  • How to access data: 1 Download a complete database snapshot in Microsoft Access or SQL Server format. 2 Click Explore Database to learn more about searching, exploring, and downloading Neotoma holdings via an in interactive web application. 3 Click Get Pending Data to find data that have been sent to Neotoma but not incorporated yet into its relational database. Files here include new author submissions not yet processed by Neotoma data stewards as well as miscellaneous datasets that don’t yet fit into the Neotoma database structure

Barcode of Life

  • Link: Barcode of Life
  • About: The Barcode of Life database contains taxonomical, geographical, and sequencing data that can be used to identify organisms down to the species level.
  • Type of data offered: Geographic, Taxonomic, and DNA Sequencing data in DWC, XML, TSV, FASTA, or TRACE file formats.
  • How to access data: The database is publically available and does not require an account to access the data. The search portal can be utilized to access data about an organism, and the identification portal can be used to identify an organism by its DNA sequence. An API is also available to pull data from the database.

Bird Sound Database

  • Link: Bird Sounds
  • About: Xeno-Canto is a website that shares bird sounds from around the world. It offers a collection of bird recording data which people/researchers/bird-lovers can access, use, and/or contribute to.
  • Type of data offered: This database offers the bird recordings of different birds in different parts of the world. The recordings also offer sonograms so that you can take a look at the graph presenting the distributing the sound-energy wavelengths. If you access "All Recordings", you are also supplied with the birds' scientific name, length, and type of call (aka a "call" or a "song"). There is also information on who recorded the sounds, where and when they recorded it, and various other remarks by the recorder.
  • How to access data: If you want to see/hear the bird recordings of birds in a specific region, you can drag a box around a the region on their map, and it'll help you locate the birds in those areas. You can also access all the recordings that they have by clicking on "Explore" -> "All Recordings". Clicking the play button on the avaliabe files will allow you to hear the bird sounds.

DataOne

  • Link: DataOne
  • About: The foundation of new innovative environmental science for access to well-described and easily discovered Earth observational data, such as weather, forest types, floral resource, etc.
  • Type of data offered: Depending on your search, XML, csv, octet stream (application file), etc. are available.
  • How to access data: After you search a keyword, you can download the files. You can also use their API.

Google Earth Engine

  • Link: Google Earth Engine
  • About: Earth Engine hosts satellite imagery and is a tool that allows for analysis of geospatial datasets, which are made available for global-scale data mining. Images of Earth may go back more than 40 years and are ingested on a daily basis.
  • Type of data offered: satellite imagery, geospatial
  • How to access data: First, request access by signing up. Once accepted, browse the data catalog and find a dataset that you're interested in!

Globi

  • Link: Globi
  • About: Globi offers data about species interactions. Data is usually found in (organism) eats/is eaten by/interacts with/etc (another organism). With an experimental but exciting GUI, this database makes it relatively easy to find information about species interactions.
  • Type of data offered: 2-point data: relationships between taxa, broadly.
  • How to access data: Use the search engine on the landing page or the "Browse" feature, which is much more graphic.

KNB

  • Link: KNB
  • About: an international repository intended to facilitate ecological and environmental research
  • Type of data offered: Depending on your search, EML, XML, csv, octet stream, Microsoft etc. are available.
  • How to access data: After you search a keyword, you can download the files. API
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