Home > Public Domain Data > Dusting off the spatial data hidden in museum collections

Dusting off the spatial data hidden in museum collections

This installment of Spatial Reserves is authored by:  Shelley James and Molly Phillips. iDigBio, Florida Museum of Natural History.   We thank these authors very much for their contribution!

If you’ve ever had a need to document where a plant or animal species occurs today, or 100 years ago, perhaps the 1 billion biological specimens housed in natural history collections across the USA, and 5 billion around the world can help!  Each of these specimens imparts knowledge about their existence in time at a specific location.  Fish, fossils, birds, skeletons, mushrooms, skins – all with a date and location of collection.  The data, found on the labels attached to the specimens, in field notebooks and catalogues, is being transcribed by museum professionals and citizen scientists alike, revealing information about the world’s living organisms dating back to the 1600’s, some with very accurate spatial data, others much less so depending on the geographic knowledge of the collector at the time.  iDigBio – Integrated Digitized Biocollections – a project supported by the US National Science Foundation – is collaborating with biological collections across the globe to help combine and mobilize voucher specimen data for research, education, and environmental management uses.

All of this biodiversity data is in a format known as Darwin Core, a standardized set of descriptors enabling biological data from different sources to be combined, indexed, and shared.  The iDigBio data Portal allows open access to this aggregated data, allowing filtering for types of organisms, a spatial region using latitude-longitude co-ordinates, polygons or place descriptions, and many other options.  The data is delivered dynamically, and can be downloaded for use.  Currently about 50% of the biological records in iDigBio (over 30 million records) have a geopoint and error, and georeferencing is something the collections community continues to work on in order to improve this valuable dataset.  Any tools or improvements to data the geospatial community can provide would be a great help as iDigBio expands beyond 65 million specimen records, and we invite you to join the conversation by participating in the iDigBio Georeferencing Working Group.


Pigeons and doves from around the world.  The iDigBio Portal maps the distribution of species and provides specimen record details “on the fly” as filters are applied by the user.  The dataset can be downloaded, or data can be accessed through the iDigBio API.



  1. John Gallo
    September 12, 2016 at 4:35 pm

    Thanks! What is the relationshipo between iDigBio and GBIF? Do the data freely interchange between both? Or at least one way? Thanks.

    • josephkerski
      September 13, 2016 at 1:03 am

      Hi John:

      Thanks for your comment.

      I have asked the authors, and they say the following:

      The way that biodiversity datasets are published and shared (using Darwin Core Standards) means that data aggregators such as iDigBio and GBIF independently retrieve (and ingest) datasets. Most commonly this is through an Integrated Publishing Toolkit (IPT – http://www.gbif.org/ipt). Because of the close relationship iDigBio has with some collections, we provide IPT services which allow biological collections to also publish data for use by GBIF and other aggregators. Some datasets of vouchered biological specimens may be available through GBIF but not, as yet, available through iDigBio, and vice versa due to data accessibility and the process of data ingestion. What are the differences then between GBIF and iDigBio? iDigBio only shares vouchered specimen collections (whereas GBIF also hosts observational and checklist data), iDigBio shares more data fields than GBIF due to our database infrastructure, has a user-friendly portal for easy data visualization, and has many images of specimens not available through GBIF. Ultimately, a researcher may need to use several data aggregators to retrieve all pertinent data for a particular project, and the features and foci of the different aggregator portals will appeal to different users.

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