Combining NLP and Semantics for Mining Software Technologies from Research Publications

The natural language processing (NLP) community has developed a variety of methods for extracting and disambiguating information from research publications. However, they usually focus only on standard research entities such as authors, affiliations, venues, references and keywords. We propose a novel approach, which combines NLP and semantic technologies for generating from the text of research publications an OWL ontology describing software technologies used or introduced by researchers, such as applications, systems, frameworks, programming languages, and formats. The method was tested on a sample of 300 publications in the Semantic Web field, yielding promising results

TechMiner: Extracting Technologies from Academic Publications

In recent years we have seen the emergence of a variety of scholarly datasets. Typically these capture ‘standard’ scholarly entities and their connections, such as authors, affiliations, venues, publications, citations, and others. However, as the repositories grow and the technology improves, researchers are adding new entities to these repositories to develop a richer model of the scholarly domain. In this paper, we introduce TechMiner, a new approach, which combines NLP, machine learning and semantic technologies, for mining technologies from research publications and generating an OWL ontology describing their relationships with other research entities. The resulting knowledge base can support a number of tasks, such as: richer semantic search, which can exploit the technology dimension to support better retrieval of publications; richer expert search; monitoring the emergence and impact of new technologies, both within and across scientific fields; studying the scholarly dynamics associated with the emergence of new technologies; and others. TechMiner was evaluated on a manually annotated gold standard and the results indicate that it significantly outperforms alternative NLP approaches and that its semantic features improve performance significantly with respect to both recall and precision

A prior case study of natural language processing on different domain

In the present state of digital world, computer machine do not understand the human’s ordinary language. This is the great barrier between humans and digital systems. Hence, researchers found an advanced technology that provides information to the users from the digital machine. However, natural language processing (i.e. NLP) is a branch of AI that has significant implication on the ways that computer machine and humans can interact. NLP has become an essential technology in bridging the communication gap between humans and digital data. Thus, this study provides the necessity of the NLP in the current computing world along with different approaches and their applications. It also, highlights the key challenges in the development of new NLP model

Knowledge-based best of breed approach for automated detection of clinical events based on German free text digital hospital discharge letters

OBJECTIVES: The secondary use of medical data contained in electronic medical records, such as hospital discharge letters, is a valuable resource for the improvement of clinical care (e.g. in terms of medication safety) or for research purposes. However, the automated processing and analysis of medical free text still poses a huge challenge to available natural language processing (NLP) systems. The aim of this study was to implement a knowledge-based best of breed approach, combining a terminology server with integrated ontology, a NLP pipeline and a rules engine. METHODS: We tested the performance of this approach in a use case. The clinical event of interest was the particular drug-disease interaction "proton-pump inhibitor [PPI] use and osteoporosis". Cases were to be identified based on free text digital discharge letters as source of information. Automated detection was validated against a gold standard. RESULTS: Precision of recognition of osteoporosis was 94.19%, and recall was 97.45%. PPIs were detected with 100% precision and 97.97% recall. The F-score for the detection of the given drug-disease-interaction was 96,13%. CONCLUSION: We could show that our approach of combining a NLP pipeline, a terminology server, and a rules engine for the purpose of automated detection of clinical events such as drug-disease interactions from free text digital hospital discharge letters was effective. There is huge potential for the implementation in clinical and research contexts, as this approach enables analyses of very high numbers of medical free text documents within a short time period

Natural language processing

Beginning with the basic issues of NLP, this chapter aims to chart the major research activities in this area since the last ARIST Chapter in 1996 (Haas, 1996), including: (i) natural language text processing systems - text summarization, information extraction, information retrieval, etc., including domain-specific applications; (ii) natural language interfaces; (iii) NLP in the context of www and digital libraries ; and (iv) evaluation of NLP systems

Combining machine learning and semantic web: A systematic mapping study

In line with the general trend in artificial intelligence research to create intelligent systems that combine learning and symbolic components, a new sub-area has emerged that focuses on combining Machine Learning components with techniques developed by the Semantic Web community - Semantic Web Machine Learning (SWeML). Due to its rapid growth and impact on several communities in thepast two decades, there is a need to better understand the space of these SWeML Systems, their characteristics, and trends. Yet, surveys that adopt principled and unbiased approaches are missing. To fill this gap, we performed a systematic study and analyzed nearly 500 papers published in the past decade in this area, where we focused on evaluating architectural and application-specific features. Our analysis identified a rapidly growing interest in SWeML Systems, with a high impact on several application domains and tasks. Catalysts for this rapid growth are the increased application of deep learning and knowledge graph technologies. By leveraging the in-depth understanding of this area acquired through this study, a further key contribution of this article is a classification system for SWeML Systems that we publish as ontology.</p

TeknoAssistant : a domain specific tech mining approach for technical problem-solving support

This paper presents TeknoAssistant, a domain-specific tech mining method for building a problem-solution conceptual network aimed at helping technicians from a particular field to find alternative tools and pathways to implement when confronted with a problem. We evaluate our approach using Natural Language Processing field, and propose a 2-g text mining process adapted for analyzing scientific publications. We rely on a combination of custom indicators with Stanford OpenIE SAO extractor to build a Bernoulli Naive Bayes classifier which is trained by using domain-specific vocabulary provided by the TeknoAssistant user. The 2-g contained in the abstracts of a scientific publication dataset are classified in either "problem", "solution" or "none" categories, and a problem-solution network is built, based on the co-occurrence of problems and solutions in the abstracts. We propose a combination of clustering technique, visualization and Social Network Analysis indicators for guiding a hypothetical user in a domain-specific problem solving process

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed

BioC: a minimalist approach to interoperability for biomedical text processing

A vast amount of scientific information is encoded in natural language text, and the quantity of such text has become so great that it is no longer economically feasible to have a human as the first step in the search process. Natural language processing and text mining tools have become essential to facilitate the search for and extraction of information from text. This has led to vigorous research efforts to create useful tools and to create humanly labeled text corpora, which can be used to improve such tools. To encourage combining these efforts into larger, more powerful and more capable systems, a common interchange format to represent, store and exchange the data in a simple manner between different language processing systems and text mining tools is highly desirable. Here we propose a simple extensible mark-up language format to share text documents and annotations. The proposed annotation approach allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or diseases and relationships between named entities. In addition, we provide simple code to hold this data, read it from and write it back to extensible mark-up language files and perform some sample processing. We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge.net/. Database URL: http://bioc.sourceforge.net