CORAAL – Towards Deep Exploitation of Textual Resources in Life Sciences

Abstract

Abstract. Prominent biomedical literature search tools like ScienceDirect, PubMed Central or MEDLINE allow for efficient retrieval of resources based on key words. Due to vast amounts of data available in life sciences, key word search is not always sufficient, though. One would often welcome more intelligent search for knowledge, i.e., for concepts and their mutual relations. This is, however, still a major challenge, since getting the necessary machine-readable knowledge manually is virtually impossible in large scale, while its automatic extraction is not particularly reliable. We have researched a novel framework actually enabling practical exploitation of automatically extracted knowledge, though. On the top of the framework, we implemented CORAAL, a prototype for knowledge-based biomedical literature search. This paper describes its essential principles, innovative capabilities and current results.

Semantic Web search based on ontological conjunctive queries

“…We now discuss related work on Semantic Web search (see especially [28] for a recent survey), which can roughly be divided into (1) approaches that are based on structured query languages, such as [17,30,35,38,45,46,50], and (2) approaches for naive users, requiring no familiarity with structured query languages. In this category, we distinguish keyword-based approaches, such as [13,33,34,40,51,52,55], where queries consist of lists of keywords, and natural-language-based approaches, such as [16,23,29,32,42,43], where users can express queries in natural language.…”

Semantic search on the Web

“…approaches based on structured query languages, such as [6,12,17,20,25,26,28]; 2. approaches for naive users, where no familiarity with ad-hoc query languages is required. In turn, these approaches can be divided into:…”

“…More recent approaches based on structured languages are [20,25,28]. In particular, [28] introduces ONTOSEARCH2, which is a search and query engine for ontologies on the Semantic Web.…”

“…It stores a copy of the ontologies in a tractable description logic and allows SPARQL queries to be evaluated on both the structures and instances of ontologies. The Coraal system [25] is a knowledge-based search engine for biomedical literature. Coraal uses NLP-based heuristics to process texts and build RDF triples from them.…”

Semantic Web Search Based on Ontological Conjunctive Queries

“…We now discuss related work on Semantic Web search (see especially [28] for a recent survey), which can roughly be divided into (1) approaches that are based on structured query languages, such as [17,30,35,38,45,46,50], and (2) approaches for naive users, requiring no familiarity with structured query languages. In this category, we distinguish keyword-based approaches, such as [13,33,34,40,51,52,55], where queries consist of lists of keywords, and natural-language-based approaches, such as [16,23,29,32,42,43], where users can express queries in natural language.…”