Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search™

Motivation: With the tremendous growth in scientific literature, it is necessary to improve upon the standard pattern matching style of the available search engines. Semantic NLP may be the solution to this problem. Cognition Search (CSIR) is a natural language technology. It is best used by asking a simple question that might be answered in textual data being queried, such as MEDLINE. CSIR has a large English dictionary and semantic database. Cognition’s semantic map enables the search process to be based on meaning rather than statistical word pattern matching and, therefore, returns more complete and relevant results. The Cognition Search engine uses downward reasoning and synonymy which also improves recall. It improves precision through phrase parsing and word sense disambiguation.
Result: Here we have carried out several projects to "teach" the CSIR lexicon medical, biochemical and molecular biological language and acronyms from curated web-based free sources. Vocabulary from the Alliance for Cell Signaling (AfCS), the Human Genome Nomenclature Consortium (HGNC), the United Medical Language System (UMLS) Meta-thesaurus, and The International Union of Pure and Applied Chemistry (IUPAC) was introduced into the CSIR dictionary and curated. The resulting system was used to interpret MEDLINE abstracts. Meaning-based search of MEDLINE abstracts yields high precision (estimated at >90%), and high recall (estimated at >90%), where synonym information has been encoded. The present implementation can be found at http://MEDLINE.cognition.com. 
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Smart Search Engine For Information Retrieval

This project addresses the main research problem in information retrieval and semantic search. It proposes the smart search theory as new theory based on hypothesis that semantic meanings of a document can be described by a set of keywords. With two experiments designed and carried out in this project, the experiment result demonstrates positive evidence that meet the smart search theory. In the theory proposed in this project, the smart search aims to determine a set of keywords for any web documents, by which the semantic meanings of the documents can be uniquely identified. Meanwhile, the size of the set of keywords is supposed to be small enough which can be easily managed. This is the fundamental assumption for creating the smart semantic search engine. In this project, the rationale of the assumption and the theory based on it will be discussed, as well as the processes of how the theory can be applied to the keyword allocation and the data model to be generated. Then the design of the smart search engine will be proposed, in order to create a solution to the efficiency problem while searching among huge amount of increasing information published on the web. To achieve high efficiency in web searching, statistical method is proved to be an effective way and it can be interpreted from the semantic level. Based on the frequency of joint keywords, the keyword list can be generated and linked to each other to form a meaning structure. A data model is built when a proper keyword list is achieved and the model is applied to the design of the smart search engine

A differential semantic algorithm for query relevant web page recommendation

With the exponential rise in the amount of information in the World Wide Web, there is a need for a much efficient algorithm for Web Search. The traditional keyword matching as well as the standard statistical techniques is insufficient as the Web Pages they recommend are not highly relevant to the query. With the growth in Semantic Web, an algorithm which semantically computes the most relevant Web Pages is required. In this paper, a methodology which computes the semantic heterogeneity between the keywords, content words and query words for web page recommendation is incorporated. A Differential Adaptive PMI Algorithm is formulated for with varied thresholds for recommending the Web Pages based on the input query. The proposed methodology yields an accuracy of 0.87 which is much better than the existing strategies. © 2016 IEEE

Tailored semantic annotation for semantic search

This paper presents a novel method for semantic annotation and search of a target corpus using several knowledge resources (KRs). This method relies on a formal statistical framework in which KR concepts and corpus documents are homogeneously represented using statistical language models. Under this framework, we can perform all the necessary operations for an efficient and effective semantic annotation of the corpus. Firstly, we propose a coarse tailoring of the KRs w.r.t the target corpus with the main goal of reducing the ambiguity of the annotations and their computational overhead. Then, we propose the generation of concept profiles, which allow measuring the semantic overlap of the KRs as well as performing a finer tailoring of them. Finally, we propose how to semantically represent documents and queries in terms of the KRs concepts and the statistical framework to perform semantic search. Experiments have been carried out with a corpus about web resources which includes several Life Sciences catalogs and Wikipedia pages related to web resources in general (e.g., databases, tools, services, etc.). Results demonstrate that the proposed method is more effective and efficient than state-of-the-art methods relying on either context-free annotation or keyword-based search.We thank anonymous reviewers for their very useful comments and suggestions. The work was supported by the CICYT project TIN2011-24147 from the Spanish Ministry of Economy and Competitiveness (MINECO)

ENTITY EXTRACTION USING STATISTICAL METHODS USING INTERACTIVE KNOWLEDGE MINING FRAMEWORK

There are various kinds of valuable semantic information about real-world entities embedded in web pages and databases. Extracting and integrating these entity information from the Web is of great significance. Comparing to traditional information extraction problems, web entity extraction needs to solve several new challenges to fully take advantage of the unique characteristic of the Web. In this paper, we introduce our recent work on statistical extraction of structured entities, named entities, entity facts and relations from Web. We also briefly introduce iKnoweb, an interactive knowledge mining framework for entity information integration. We will use two novel web applications, Microsoft Academic Search (aka Libra) and EntityCube, as working examples

A Robust Linguistic Platform for Efficient and Domain specific Web Content Analysis

Web semantic access in specific domains calls for specialized search engines with enhanced semantic querying and indexing capacities, which pertain both to information retrieval (IR) and to information extraction (IE). A rich linguistic analysis is required either to identify the relevant semantic units to index and weight them according to linguistic specific statistical distribution, or as the basis of an information extraction process. Recent developments make Natural Language Processing (NLP) techniques reliable enough to process large collections of documents and to enrich them with semantic annotations. This paper focuses on the design and the development of a text processing platform, Ogmios, which has been developed in the ALVIS project. The Ogmios platform exploits existing NLP modules and resources, which may be tuned to specific domains and produces linguistically annotated documents. We show how the three constraints of genericity, domain semantic awareness and performance can be handled all together

Resource description framework triples entity formations using statistical language model

A method in formatting unstructured sentences from the source corpus to a specificknowledge representation such as RDF is needed. A method for RDF entity formations from aparagraph of text using statistical language model based on N-gram is introduced. Theimplementation of RDF entity formation is applied on natural language query for informationretrieval of the Islamic knowledge. 300 concepts from the English translation of Holy Quranwith 350 relationships are used as a knowledge base. We evaluate our approach on collectionof queries from the Islamic Research Foundation website with a total, 82 queries and comparethe performance against previous method used in FREyA. The result shown the proposedmethod improved 17.07% on the accuracy of the natural language formulation analysis, whichtested on search strategy. It shows the increment on recall and precision with 7% and 3%.Keywords: semantic web; N-gram; ontology; statistical mode

A Generic architecture for semantic enhanced tagging systems

The Social Web, or Web 2.0, has recently gained popularity because of its low cost and ease of use. Social tagging sites (e.g. Flickr and YouTube) offer new principles for end-users to publish and classify their content (data). Tagging systems contain free-keywords (tags) generated by end-users to annotate and categorise data. Lack of semantics is the main drawback in social tagging due to the use of unstructured vocabulary. Therefore, tagging systems suffer from shortcomings such as low precision, lack of collocation, synonymy, multilinguality, and use of shorthands. Consequently, relevant contents are not visible, and thus not retrievable while searching in tag-based systems. On the other hand, the Semantic Web, so-called Web 3.0, provides a rich semantic infrastructure. Ontologies are the key enabling technology for the Semantic Web. Ontologies can be integrated with the Social Web to overcome the lack of semantics in tagging systems. In the work presented in this thesis, we build an architecture to address a number of tagging systems drawbacks. In particular, we make use of the controlled vocabularies presented by ontologies to improve the information retrieval in tag-based systems. Based on the tags provided by the end-users, we introduce the idea of adding “system tags” from semantic, as well as social, resources. The “system tags” are comprehensive and wide-ranging in comparison with the limited “user tags”. The system tags are used to fill the gap between the user tags and the search terms used for searching in the tag-based systems. We restricted the scope of our work to tackle the following tagging systems shortcomings: - The lack of semantic relations between user tags and search terms (e.g. synonymy, hypernymy), - The lack of translation mediums between user tags and search terms (multilinguality), - The lack of context to define the emergent shorthand writing user tags. To address the first shortcoming, we use the WordNet ontology as a semantic lingual resource from where system tags are extracted. For the second shortcoming, we use the MultiWordNet ontology to recognise the cross-languages linkages between different languages. Finally, to address the third shortcoming, we use tag clusters that are obtained from the Social Web to create a context for defining the meaning of shorthand writing tags. A prototype for our architecture was implemented. In the prototype system, we built our own database to host videos that we imported from real tag-based system (YouTube). The user tags associated with these videos were also imported and stored in the database. For each user tag, our algorithm adds a number of system tags that came from either semantic ontologies (WordNet or MultiWordNet), or from tag clusters that are imported from the Flickr website. Therefore, each system tag added to annotate the imported videos has a relationship with one of the user tags on that video. The relationship might be one of the following: synonymy, hypernymy, similar term, related term, translation, or clustering relation. To evaluate the suitability of our proposed system tags, we developed an online environment where participants submit search terms and retrieve two groups of videos to be evaluated. Each group is produced from one distinct type of tags; user tags or system tags. The videos in the two groups are produced from the same database and are evaluated by the same participants in order to have a consistent and reliable evaluation. Since the user tags are used nowadays for searching the real tag-based systems, we consider its efficiency as a criterion (reference) to which we compare the efficiency of the new system tags. In order to compare the relevancy between the search terms and each group of retrieved videos, we carried out a statistical approach. According to Wilcoxon Signed-Rank test, there was no significant difference between using either system tags or user tags. The findings revealed that the use of the system tags in the search is as efficient as the use of the user tags; both types of tags produce different results, but at the same level of relevance to the submitted search terms