Searching and visualising data in BioSamples


BioSamples home page

Figure 1 BioSamples website: home page

All the web pages in the BioSamples dataabase feature a query box in top right-hand corner, with the option to search samples or sample groups

There are also links to browse by sample or sample group, and links to documentation which includes instructions on how to submit.

Search results

Figure 2 Search results list for the term 'leukemia'
  • Query reminder: The exact search query is reproduced at the top of the results table. It is also kept in the search box, where it can easily be edited to refine the query.
  • Highlighting: Matches to the search query are highlighed in the results table, including exact matches (green), synonyms (yellow) or more specific terms (red).
  • Links to sample or group pages: Each result has a link on the left-hand side to a specific BioSamples Database web page.
  • Links to sources: Where applicable, the right-hand side of each result has link(s) to other web pages.

Sample group

Search results page (top) using 'search by Groups'

Figure 3.1  Search results page (upper section) using 'search by Groups' for the terms "chronic myelogenous leukemia", and selecting the group accession 'SAMEG14728'

On the upper section of the sample group page, notice that:

  • Search term highlighting (colour coded) persists from the initial search (including synonyms and more specific terms).
  • General information about the group is displayed first, such as publications, release dates and dates of updates.
  • Attributes that are common to all the samples in this group are also displayed here.
Figure 3.2  Search results page (lower) using 'search by Groups' for the terms "chronic myelogenous leukemia", and selecting the group accession 'SAMEG14728'
In the lower section of the sample group page, notice that:
  • For large sample groups, only some samples are shown at once. The other pages of samples can be accessed by links in the top left.
  • If there are a larger number of attributes, a horizontal scroll bar allows you to see all of them.
  • There is a search box to find particular samples of interest; if no samples are displayed, check that this has been cleared.

Single sample

Figure 4 Single sample page, resulting from a search for the sample accession "SAMEA249878"

Each sample in the BioSamples Database has a specific web page with a unique and permant URL, e.g. This can be used to refer to a specific sample in publications and other documents.

On this page you can notice the following features:

  • Search query highlighting;
  • Where attributes are linked to a controlled vocabulary or ontology, those links are displayed here;
  • The sample group(s) that this sample is part of are listed.