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Prince V., Roche M. Information Retrieval in Biomedicine. Natural Language Processing for Knowledge Integration
Издательство Information Science Reference, 2009, -392 pp.

Natural language processing (NLP) is a sub-field of computational sciences which addresses the operation and management of texts, as inputs or outputs of computational devices. As such, this domain includes a large amount of distinct topics, depending which particular service is considered. Nowadays, with the Inteet spreading as a worldwide tremendous reservoir of knowledge, NLP is highly solicited by various scientific communities as a worthwhile help for the following tasks.
Human produced texts are seen as a valuable input, to be processed and transformed into representations and structures directly operable by computational systems. This type of service is highly required when human need is about a set of texts relevant for a given query (information retrieval), or when the need is to build up a machine readable structure (knowledge extraction) for further computer assisted developments. In both medicine and biology, these two aspects are crucial. Scientific literature is so abundant that only a computational setup is able to browse and filter so huge amounts of information. A plain search engine is too limited to undertake queries as complex as those which meet the researchers’ requirements. From the knowledge extraction point of view, manually constructed ontologies seldom reach more than a few concepts and relationships, because of the tremendous effort necessary to achieve such a task.
For the past decades, artificial intelligence (AI) has undertaken an important endeavor in favor of knowledge management. Its result, a set of taxonomies, i.e. knowledge classifications formalized according to a graph-based representation (sometimes simplified into a tree-based representation when hierarchical ties between knowledge items are dominant) also commonly called ontologies, are obtained at a very high cost in manpower, and human involvement. As soon as statistical techniques and new programming skills have appeared through machine leaing, the AI community has attempted to automate this task as much as possible, feeding systems with texts and producing, at the other end, an ontology or something similar to it. Naturally, human intervention, for validation, or re-orientation, was still needed. But the leaing techniques were operated on the front filtering task, the one seen as the most tedious and the most risky. Results looked promising and a few ontologies were initiated with such processes. However, they were incomplete: Wrong interpretations were numerous (noisy aspect), structures were scarce (silent aspect), and most of all, the linguistic-conceptual relationship was totally ignored. When the community acknowledged that, it tued toward NLP works and tools to reorganize its processes, and NLP skills in separating between the linguistic and conceptual properties of words were of a great help. This conjunction shyly began a few years ago, but is going stronger now, since NLP tools have improved with time.

Text Mining for Biomedicine
Section I Works at a Lexical Level: Crossroads Between NLP and Ontological Knowledge Management
Lexical Granularity for Automatic Indexing and Means to Achieve It: The Case of Swedish MeSH
Expanding Terms with Medical Ontologies to Improve a Multi-Label Text Categorization System
Using Biomedical Terminological Resources for Information Retrieval
Automatic Alignment of Medical Terminologies with General Dictionaries for an Efficient Information Retrieval
Translation of Biomedical Terms by Inferring Rewriting Rules
Lexical Enrichment of Biomedical Ontologies
Word Sense Disambiguation in Biomedical Applications: A Machine Leaing Approach
Section II Going Beyond Words: NLP Approaches Involving the Sentence Level
Information Extraction of Protein Phosphorylation from Biomedical Literature
CorTag: A Language for a Contextual Tagging of the Words Within Their Sentence
Analyzing the Text of Clinical Literature for Question Answering
Section III Pragmatics, Discourse Structures and Segment Level as the Last Stage in the NLP Offer to Biomedicine
Discourse Processing for Text Mining
A Neural Network Approach Implementing Non-Linear Relevance Feedback to Improve the Performance of Medical Information Retrieval Systems
Extracting Patient Case Profiles with Domain-Specific Semantic Categories
Section IV NLP Software for IR in Biomedicine
Identification of Sequence Variants of Genes from Biomedical Literature: The OSIRIS Approach
Verification of Uncurated Protein Annotations
A Software Tool for Biomedical Information Extraction (And Beyond)
Problems-Solving Map Extraction with Collective Intelligence Analysis and Language Engineering
Seekbio: Retrieval of Spatial Relations for System Biology
Section V Conclusion and Perspectives
Analysing Clinical Notes for Translation Research: Back to the Future
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