AKS: Highlighting of Relevant Biomedical Information

Biological entities (genes, proteins, chemical substances, diseases, etc.) appear highlighted in the text in different colors according to their type. Thus, going through large lists of documents becomes an easier process and you only have to select the highlighted elements and skip the rest.

Example
This example shows how the highlighting of biomedical concepts facilitates the reading of a large amount of documents and helping to acquire the relevant information in a fast and easy way.

Fig. 1. "Document detail" for document with PMID 14529400. The relevant biological concepts are highlighted as we click on the respective check box. The system also enables to sign out any searched sentence or significant term regarding the document or sentence ranking. (see suggestions for focusing

A bioentity in AKS is any concept with biological meaning. AKS classifies the bioentities in types:
• genes including gene and protein names
• unassigened genes holding those genes/proteins that cannot be assigned to any known official gene/protein name,
• diseases gathering biomedical disorders and
• chemicals collecting chemical elements, synthesis molecules, biochemical substances and drugs.

Thus, we have searched in the system for a document with PubMed ID (PMID) 14529400. This document describes some aspects about the safety of certain drugs indicated to treat inflammation and pain known as NSAID (for Non-steroidal Anti-Inflammatory Drugs). Both aspirin and Ibuprofen are commonly used NSAIDs. Unfortunately, they aren't devoid of adverse effects.

Fig 2. The highlighting of relevant information is an even more interesting feature as we review several documents.

Under the abstract we see a list of biomedical concepts. These are the biomedical data contained in the document we are looking at. We can read about many of the so-called NSAID if looking at the field of chemical category, while if taking genes into account we can see PTGS1 or COX-1, and PTGS2 or COX-2; when it comes to the disease group of bioentities, we can see disorders related to this type of drugs, finding COX in the category of unassigned genes. The system has classified COX under the consideration of "unassigned gene", since it knows it is a gene symbol but cannot determine which specific gene the text is referring to.

The text can be easily highlighted by clicking on the check boxes. Searched-for sentences or relevant terms can also be highlighted by clicking on the "Show object" image at the top left corner of the window. (see Search for specific sentences for more information on sentences search and Suggestions for focusing searches for more information regarding relevant terms)

However this feature becomes even more interesting when we have to review more than one document. Highlighting the relevant bioentities will lead us to the most significant documents (Fig. 2).