SmartFigures Lab (beta)

What are SmartFigures?

SmartFigures display data in the context of related results published in other papers and link the data to major biological databases. As such, they offer an enhanced browsing experience by enabling users to intuitively navigate across papers through the network of related figures.

Thanks to the descriptive metadata underlying each SmartFigure, finding pertinent figures is a simple matter of searching for the names of biological entities (a gene, a protein, a cell type, etc…). Any SmartFigures featuring research on these entities will be shown in the results.

You can find an example SmartFigure here. The figure is enriched with extra information, including a summary of the key experimental entities and links to other related papers as well as to published upstream and downstream relationships of each entity.

From the SmartFigure viewer, you can cycle through the results presented in the same paper, jump straight to results of studies where the same elements were assayed or manipulated, or read the papers that presented these findings.

How do I use the search bar?

The SourceData database, which powers the SmartFigures Lab, contains thousands of figure panels from hundreds of papers. Human curators have analysed the figure panels in those papers and annotated them with the name of the biological entities under investigation, as well as the organism or cell line with which the experiment was conducted. These experimental relationships have been connected in a web of information - the SourceData knowledge graph.

The SmartFigure interface allows you to intuitively navigate through the database of relationships between biological entities. For example, you could search for genes potentially 'upstream' of p53 (i.e. genes that have been tested against the expression of p53), or for genes potentially 'downstream' of p53 (i.e. genes where p53 has been tested for its effect on their expression).

To perform a search, enter the name of the biological entity (gene, protein or small molecule), process, cell or organism in which you are interested. For example, you could search for Autophagy:

Within the results, the term you searched for will be highlighted in snippets of the paper and figure legends where it is mentioned. A thumbnail of the figures pertinent to your search will be shown for the first three results. You can click the thumbnails or the paper title to be taken to the figure in the paper.

How do I view SmartFigures?

From the SmartFigure embedded in a paper, you can open the SmartFigure interface by simply clicking the Open SmartFigure icon

The SmartFigure summarises the entities involved in an experiment (note you are viewing one or two relevant panels, not a full figure). The entities that were manipulated in the experiment are listed in red on the left (we call these 'Interventions/Perturbations'), and the entities that were measured in response to the manipulation are listed in blue on the right (we call these 'Assayed'). If you click on an entity, you will see a pop-up providing a standard identifier for this entity and a link to the relevant external database.

You are able to browse other panels in this same paper using the figure and panel browser just below the currently displayed panel.

How do I view other panels in the same paper?

You are able to browse other panels in this same paper using the figure and panel browser just below the currently displayed panel.

How do I navigate to upstream and downstream effects?

Once you have identified an entity of interest in the current paper, you can look 'upstream' or 'downstream' of that entity to see what else it might have an impact on downstream, or what might influence its expression or behaviour upstream.

Navigating upstream or downstream returns a list of papers and panels within those papers in which your entity of choice was present. If you have navigated upstream, your entity of choice will always be the Assayed (i.e. measured) entity. If you have navigated downstream, your entity will always be the Intervention (i.e. experimentally altered entity). If you see a relationship of interest, you can click on it to see the experiment in the SmartFigure view.

What is the summary view?

The SmartFigure view offers a second output in addition to the annotated panel. The metadata that has been added to the figure is displayed in a visual summary that draws out the entities involved, the experimental system and the experiment type.

How do I find related papers?

You can also browse related figures and papers - found at the bottom of the screen. These are figures and papers in which approximately the same collection of entities were tested against one another in approximately the same way. This allows you to collect highly related experiments that support or contradict one another to give you a feeling for the robustness of the current relationship you are viewing. You will notice results with red/blue labels and results with orange labels. Red/blue results are SmartFigures curated by SourceData, while orange results are papers that have been automatically processed by text-mining algorithms.

Once you have found an experiment of interest, you can open the original paper by clicking the paper's title at the top of the SmartFigure screen.