Atrium Quick Start Guide
Atrium is a Biodiversity Information System designed to support the research activities of the Andes to Amazon Botany Program and to make the data generated by this program available to collaborators and the general public. This guide is intended to provide a brief overview of the features and usage of Atrium.
The data in Atrium can be generally divided into three types:
Botanical Data – information regarding plant specimens (collections) including plant name (scientific and common), collector, location, plant description and images.
Bibliographic Data – a complete record of all bibliographic references related to biology and conservation in the Madre de Dios department of Peru.
GIS Data – a repository of raster and vector files which can be searched and downloaded for use in GIS applications.
While there are some overlaps among these data sets, each can be accessed primarily through the methods outlined below. The majority of the data and features are available without being logged in but there are some key features that are only available to people who are registered and logged in. Additionally, some features are restricted to people who have been granted higher levels of permissions. If you are logged in and are still unable to access necessary features, please contact Jason Best at firstname.lastname@example.org to ensure you have sufficient access permissions.
The botanical data is arranged in a hierarchy based upon plant taxonomy. The first way to access this data is to browse the taxonomy directly by selecting the Browse Taxonomy link in the main navigation menu. This will display the top level of categorization for living organisms – the Kingdoms (currently limited to Plantae and Fungi). From this point you can continue to explore the taxonomy “tree” by selecting a Kingdom, then a Division, then a Class etc. As you browse, you will see a listing of each sub-taxon name followed by a summary of what each contains. To view the contents of the sub-taxon, simply select it. At each taxon level you will also see tabs which provide further information about each taxon. These tabs are:
Summary – used for browsing and displaying a summary of each taxon.
Details – further information about the taxon including common names, morphological diagnosis, description, distribution, ecology and uses.
Collections – A listing of all collections contained within the taxon. The collection list has many features that are covered below.
References – A listing of web sites relevant to the taxon as well as search links to popular databases of botanical data.
Images – a listing of collection images.
Map View – a map displaying all the points of collections
As you browse the taxonomy, you will see a “breadcrumb” above the tabs. This breadcrumb indicates your location in the taxonomy and allows you to quickly move up the taxonomy to any rank.
The collection list provides the primary method of viewing multiple collections and accessing the data for individual collections. The list displays basic data in columns for Collector, Collector Number, Family, Genus and Species. Each of these columns can be sorted by clicking on the column heading. You view the details of each collection by clicking on the details link in the first column. Above the collection list is a filter form which allows you to view collections within the taxon which match specific values such as collector, family, genus, species, location etc.
Above and below the list are controls for moving through “pages” of collections or for displaying all collections. This is only displayed when the number of collections exceeds the page length specified in your preferences.
Below the collection list are additional options which are displayed based upon your permission levels. One option which is to export the displayed collection data to a file with comma separated values (CSV) which can be imported into Microsoft Excel or other spreadsheet programs. Another option is to add selected collections to a personal project which is discussed in further detail below. The final option is a link which allows you to create herbarium labels of the displayed collections.
When you select a collection from the collection list, the collection detail is displayed. The collection detail contains information about the determination of the collection (family, genus and species) and the person who determined the collection as well as information about the location, habitat and other data for the collection. Below the collection data, you can select the “Export Data” link to save the data in a spreadsheet format. The collection detail also has an images tab which allows you to view the images for the collection.
When you are viewing a collection, you can annotate it if you have sufficient access privileges. Below the collection data, there is a link titled “Make Determination” which you can select to begin the determination process. Note: Make sure you select “Make Determination” and not “Edit Determination”. The latter is to be used only for correcting typographic errors in past determinations. After you select the “Make Determination” link, you will see a form for changing the family, genus or species of the collection using dropdown lists to select the correct taxa. If the taxon you need does not yet exist in the dropdown list, first select the appropriate taxa until you reach the taxon rank for which the taxon does not yet exist. Then enter the name of the taxon or taxa to the right of the appropriate ranks (Ex: if the genus and species do not exist in the menus, first select the correct family, then enter the new genus name to the right of the genus rank and the new specific epithet to the right of the species rank.) The only other required fields are the name of the person making the determination and the date of determination. When you are finished, press the “Edit Determination” button to complete the process.
When you are viewing the Image tab of any taxa, you will see the image list which displays all the collection images in the selected taxon. To view an image, simply click on the image preview.
Personal projects allow you to add images and collections to separate projects that are only available to you. This features allows you to easily collect multiple images and collections from many different taxa into one project group which can then be exported in spreadsheet or field guide format. To add collections to a project, select the checkbox in the column to the left of the collections you wish to add, then select the “Save to Project” button at the bottom of the page. This will add the collections to a new project named with the current date and time. If you wish to add the collections to an existing project, select its name from the dropdown list first. When you are viewing an image list, you can follow the above process to add images to a project.
To view your projects, select the Project link in the main navigation menu. You will see a list of your projects which you can select to view and edit. Collections in projects can be exported to spreadsheet formats and used to generate herbarium labels using the links at the bottom of the project page. Images can be used to generate field guides using the link at the bottom of the project page.
The bibliographic section of Atrium contains over 2000 bibliographic entries for book, reports and other publications pertaining to biology and conservation in the Madre de Dios department of Peru. You view this data by selecting the “Biblio Search” link in the main navigation menu then entering a text string in the search form. There are many import and export options for the bibliographic data as well as a feature which allows you to store selected bibliographic entries in a personal “folder” within Atrium. Further details will be provided in the future.
This feature is not implemented on the public server yet.
Support and Comments
If you have questions or comments about this guide or the features of Atrium, please contact Jason Best at email@example.com.