Query the Database

There are a number of ways to query and retrieve information from the database. This page allows for the retrieval of cached queries, i.e. query results that have been saved as static files for easy retrieval.

Below you can query based on labels, which are an effective way to group data and sample metadata based on a particular category. From there, you can filter results based on columns.

Query based on labels

Labels are used to organize all the data in the graph database. Here you can filter data based on labels denoting different physical entities, dataset types, habitats, and select sites. For most data-related queries, you probably want to use one of the dataset type labels.

In the query output tables, each row represents a node, and each column (except for the first "node labels" column, which lists all the labels on each node) represents a property. Properties ending in "__" have been mostly standardized throughout the graph database, and are therefore very useful for harmonizing data from different sources.

A full list of label and standardized property definitions can be downloaded here. For a more comprehensive overview of the graph database structure, which may aid in understanding the query output, see the more detailed overview here.

Filtering the results

If you select one label, you'll get all the nodes associated with that one label. When running a live query (in development), if you select multiple labels, you'll get nodes that have all of those labels (which may not be many). When retrieving cached queries, which are built on a semi-regular schedule but give instant results, then you can only select one label at a time when running queries. The live querying will remove that restriction, but for now, you can still further refine your results by filtering the output table. For smaller output files, this can be done within the browser as follows:

  1. Choose a label and run the query by clicking "Cached query."
  2. Click "Display table" (bottom of page).
  3. Search for specific keywords either within the full table (top right search box) or within a specific column (search boxes under each column). This will filter the table to show only the rows with that particular keyword.
  4. Under "Download the table below as" (above the displayed table), choose either "Excel" or "CSV." Even though the browser will only display a few rows at a time, the download will include the entire table, minus any rows you eliminated by keyword filtering.

Choose one of the following labels (scroll down for the full list of options*; color codes are given in the explanatory text):

*Minor note: In this menu, all labels are included except the Sequence label (as these refer to individual contigs, which are too numerous to be practically put into a table) and the Data label (which includes too many results to practically list them all within one table, although all non-Sequence nodes with the Data label are included under their respective discipline-specific labels). If you would like to access Sequence data broken down into individual contigs, or if you would like to access all nodes with the Data label simultaneously, please contact us.