AKS: Powerful search capabilities oriented to biomedical needs.

Approximately 42% of human genes are reported in different ways in PubMed. AKS automatically takes into account synonyms and solves problems that arise because of ambiguous homonyms and acronyms. This lets you can search documents that contain groups of genes, proteins, chemical substances, diseases. The AKS database currently consists of more than 1,000,000 references where human genes were detected.

Example
Synonyms, various spelling of the same search term, and the use of acronyms make it difficult to extract all the information for an entity. This example will show how AKS solves this problem thanks to its conceptual searches capability and the ambiguity resolution procedure.

Fig 1. The search with FAD provokes an "Ambiguity resolution list" in order to choose the items we are interested in. The fourth "FAD" is selected by checking on the corresponding box. (Click to Enlarge)

In this search we are looking for an acronym, FAD. AKS generates an "Ambiguity resolution list" (Fig. 1) reflecting the fact that FAD has several homonyms and yields each homonym term: there is a disease, a chemical, three genes and one "unassigned gene" related to the term FAD. In this case, we solve the ambiguity by selecting the gene FAD whose official name in HUGO (the human gene organization database) is PSEN1 (the presenilin 1) and then clicking on the select button.

FAD as presenilin-1 is contained in 1,283 documents and in 4,075 sentences as shown in the set of documents in Fig. 2. As a result of the conceptual search capability the system is able to retrieve all documents mentioning the FAD gene by any of its synonym or by its functional definition (PSEN1, AD3, S182, FAD, etc).

Fig 2. List of documents where the gene FAD appears. Sentences mentioning the gene are highlighted. The sentences shown contain some of the synonyms of PSEN1.