AKS: Search for Specific Sentences

Who hasn't had the experience of having to sort through too many irrelevant documents to find a specific fact? AKS takes you directly to the sentences -where, for example, two genes appear or a gene and a disease appear- to quickly obtain the information you are looking for.

Example
It is a frequent fact that a sentence makes it all. AKS helps you to find the sentence that explains the relation about two biomedical entities or gives a clear definition of a concept. This example will show you how.

Fig. 1 displays the resulting set of sentences that contain the enzyme phenylalanine hydroxylase and the phenylketonurias (a group of metabolic diseases). Review of the five first sentences reveals the relationship between the two bioentities [sentences 1, 4 and 5].

Fig. 2 shows the result of a search for two genes/proteins, APP and APOE. The set of retrieved sentences indicates some relevant facts: APOE binds to APP [sentences 1, 2, 4 and 5] with avidity [sentence 1]. The binding is associated to certain morphological structures (plaques and monofibrils [sentences 4 and 5] ) and this is closely related to the onset of Alzheimer's disease [sentences 2, 3 and 4].

There are two important features provided in this functionality. First, AKS generates a list of sentences highlighting the biological entities (bioentities) in different colors by type (to learn more about bioentity highlighting see Highlighting of relevant biomedical information). This enables to easily review and locate the most interesting bioentities. Second, AKS has the capability to perform conceptual searches, which enables the retrieval of sentences that include all the synonyms for the searched bioentities (to learn more about conceptual search see Powerful search capabilities oriented to biomedical needs). For example, Fig 2 displays the retrieved sentences for the searched gene APOE which contain the equivalent expressions and synonyms ApoE, APO-E, "human apolipoprotein E" and "apolipoprotein E gene".

Fig 1. Result of query searching for the sentences in documents (published from december 2003 to february 2005) that contain "phenylketonurias" (a metabolic disease) and "phenylalanine hydroxylase" (an enzyme in the tyrosine metabolism). The bioentities contained in each sentence are highlighted according to the type (gene, disease or chemical substance).

Fig 2. Result of the query searching for the sentences in documents containing two genes symbols: "APP" and "APOE". As a conceptual search is done, the retrieved sentences contain not only the exact string for each gene in the query but also any of their synonyms or functional descriptions.