The BioLink SIG workshop at ISMB2004

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The availability of massive sets of unstructured data has opened up new opportunities for businesses to gain meaningful insights into what is currently happening in their organization and market place. Unfortunately, unstructured data is often challenging to work with, as it requires specialized toolsets, techniques, knowledge and skills to engage with the data. This study used a systematic review (SLR) process to explore the current and conversant state of affairs in the field of text mining (TM) techniques that exist for the processing of natural language in unstructured text datasets across a broad expanse of applications and domains. A comprehensive literature search yielded 1022 eligible articles from five prominent bibliographic databases, narrowed down to 89 articles for review. Information related to TM techniques, the TM process, applications, challenges and recommendations for the improvement of TM results were extracted and synthesized. Eighteen TM techniques were identified and used to complete a variety of tasks such as data pre-processing, information retrieval, information extraction, text classification, clustering, topic modeling, text summarization and sentiment analysis or opinion mining. No single TM technique may be suitable for all text representation and extraction requirements. Therefore, context and applicability are key factors for TM technique selection.KeywordsText miningText mining techniquesUnstructured dataKnowledge discovery

BackgroundBioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information extraction (IE) systems that incorporate natural language processing (NLP) techniques have thus been developed for use in the biomedical field. A key IE task in this field is the extraction of biomedical relations, such as protein-protein and gene-disease interactions. However, most biomedical relation extraction systems usually ignore adverbial and prepositional phrases and words identifying location, manner, timing, and condition, which are essential for describing biomedical relations. Semantic role labeling (SRL) is a natural language processing technique that identifies the semantic roles of these words or phrases in sentences and expresses them as predicate-argument structures. We construct a biomedical SRL system called BIOSMILE that uses a maximum entropy (ME) machine-learning model to extract biomedical relations. BIOSMILE is trained on BioProp, our semi-automatic, annotated biomedical proposition bank. Currently, we are focusing on 30 biomedical verbs that are frequently used or considered important for describing molecular events.ResultsTo evaluate the performance of BIOSMILE, we conducted two experiments to (1) compare the performance of SRL systems trained on newswire and biomedical corpora; and (2) examine the effects of using biomedical-specific features. The experimental results show that using BioProp improves the F-score of the SRL system by 21.45% over an SRL system that uses a newswire corpus. It is noteworthy that adding automatically generated template features improves the overall F-score by a further 0.52%. Specifically, ArgM-LOC, ArgM-MNR, and Arg2 achieve statistically significant performance improvements of 3.33%, 2.27%, and 1.44%, respectively.ConclusionWe demonstrate the necessity of using a biomedical proposition bank for training SRL systems in the biomedical domain. Besides the different characteristics of biomedical and newswire sentences, factors such as cross-domain framesets and verb usage variations also influence the performance of SRL systems. For argument classification, we find that NE (named entity) features indicating if the target node matches with NEs are not effective, since NEs may match with a node of the parsing tree that does not have semantic role labels in the training set. We therefore incorporate templates composed of specific words, NE types, and POS tags into the SRL system. As a result, the classification accuracy for adjunct arguments, which is especially important for biomedical SRL, is improved significantly.

IntroductionSince the Coronavirus disease 2019 (COVID-19), public safety measures, including social distancing and school closures, have been implemented, precipitating psychological difficulties and heightened online activities for adolescents. However, studies examining the impact of the pandemic on adolescent mental health and their coping strategies in Asian countries are limited. Further, most studies have used survey measures to capture mental health challenges so far. Accordingly, this study aimed to examine the psychological challenges South Korean adolescents experienced and their coping strategies during the pandemic using the Natural Language Processing (NLP) and Text mining (TM) technique on adolescents’ social media texts/posts.MethodsThe data were gathered from social media texts/posts such as online communities, Twitter, and personal blogs from January 1, 2019, to October 31, 2021. The 12,520,250 texts containing keywords related to adolescents’ common psychological difficulties reported during the pandemic, including self-harm, Attention-Deficit/Hyperactivity Disorders (ADHD), and insomnia, were analyzed by TM, NLP using information extraction, co-occurrence and sentiment analysis. The monthly frequency of the keywords and their associated words was also analyzed to understand the time trend.ResultsAdolescents used the word “self-harm” in their social media texts more frequently during the second wave of COVID-19 (August to September 2020). “Friends” was the most associated word with “self-harm.” While the frequency of texts with “Insomnia” stayed constant throughout the pandemic, the word “ADHD” was increasingly mentioned in social media. ADHD and insomnia were most frequently associated with ADHD medications and sleeping pills, respectively. Friends were generally associated with positive words, while parents were associated with negative words.ConclusionDuring COVID-19, Korean adolescents often expressed their psychological challenges on social media platforms. However, their coping strategies seemed less efficient to help with their difficulties, warranting strategies to support them in the prolonged pandemic era. For example, Korean adolescents shared psychological challenges such as self-harm with friends rather than their parents. They considered using medicine (e.g., sleeping pills and ADHD medication) as coping strategies for sleep and attention problems.

This Chapter discusses the application of Natural Language Processing (NLP) in the legal domain for entity identification and the generation of hierarchy-based applications. NLP techniques, such as Named Entity Recognition (NER) and information extraction, are utilized to analyse legal documents, extract key information, and understand contextual relationships. The integration of NLP facilitates tasks such as legal document summarization, contract analysis, automated document generation, and legal research, thereby enhancing the efficiency and accuracy of legal processes. The creation of hierarchical structures within documents, language translation, sentiment analysis, and compliance monitoring further contribute to the comprehensive utilization of NLP in the legal field. The abstract highlights the transformative impact of NLP in streamlining legal workflows, improving information retrieval, and ensuring compliance with evolving legal standards. Most judicial systems in the world, centered around the Supreme Court as the highest-level court, grapples with a substantial caseload, receiving over 7,500 cases annually but hearing fewer than 150. The Supreme Court's unique role in interpreting the constitutionality of laws and establishing precedents underscores its significant influence. Challenges arise from the overwhelming caseload, leading to increased use of plea bargains and potential concerns about justice. To address these issues, a proposed research initiative suggests employing machine learning and natural language processing to accelerate Supreme Court decisions, aiming to uncover pivotal aspects that greatly influence the outcomes, and enhance our comprehension on India legal system's functioning and constraints. This chapter presents a methodology for sentiment-based summarization of legal documents using Natural Language Processing (NLP) techniques. The process involves pre-processing the text, conducting sentiment analysis to label sentences as positive, negative, or neutral, and then summarizing the document while incorporating the identified sentiments. Special attention is paid to legal-specific considerations such as terminology and context.

Machine learning techniques have long been the foundations of speech processing. Bayesian classiflcation, decision trees, unsupervised clustering, the EM algorithm, maximum entropy, etc. are all part of existing speech recognition systems. The success of statistical speech recognition has led to the rise of statistical and empirical methods in natural language processing. Indeed, many of the machine learning techniques used in language processing, from statistical part-of-speech tagging to the noisy channel model for machine translation have roots in work conducted in the speech fleld. However, advances in learning theory and algorithmic machine learning approaches in recent years have led to signiflcant changes in the direction and emphasis of the statistical and learning centered research in natural language processing and made a mark on natural language and speech processing. Approaches such as memory based learning, a range of linear classiflers such as Boosting, SVMs and SNoW and others have been successfully applied to a broad range of natural language problems, and these now inspire new research in speech retrieval and recognition. We have seen an increasingly close collaboration between voice and language processing researchers in some of the shared tasks such as spontaneous speech recognition and understanding, voice data information extraction, and machine translation. The purpose of this special issue was to invite speech and language researchers to communicate with each other, and with the machine learning community on the latest machine learning advances in their work. The call for papers was met with great enthusiasm from the speech and natural language community. Thirty six submissions were received; each paper was reviewed by at least three reviewers. Only ten papers were selected re∞ecting not only some of the best work on machine learning in the areas of natural language and spoken language processing but also what we view as a collection of papers that represent current trends in these areas of research both from the perspective of

Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the final interpretation and communication of the results. The biological literature also constitutes the main information source for manual literature curation used by expert-curated databases. Following the increasing popularity of web-based applications for analyzing biological data, new text-mining and information extraction strategies are being implemented. These systems exploit existing regularities in natural language to extract biologically relevant information from electronic texts automatically. The aim of the BioCreative challenge is to promote the development of such tools and to provide insight into their performance. This review presents a general introduction to the main characteristics and applications of currently available text-mining systems for life sciences in terms of the following: the type of biological information demands being addressed; the level of information granularity of both user queries and results; and the features and methods commonly exploited by these applications. The current trend in biomedical text mining points toward an increasing diversification in terms of application types and techniques, together with integration of domain-specific resources such as ontologies. Additional descriptions of some of the systems discussed here are available on the internet .

The analysis of the text content in emails, blogs, tweets, forums and other forms of textual communication constitutes what we call text analytics. Text analytics is applicable to most industries: it can help analyze millions of emails; you can analyze customers’ comments and questions in forums; you can perform sentiment analysis using text analytics by measuring positive or negative perceptions of a company, brand, or product. Text Analytics has also been called text mining, and is a subcategory of the Natural Language Processing (NLP) field, which is one of the founding branches of Artificial Intelligence, back in the 1950s, when an interest in understanding text originally developed. Currently Text Analytics is often considered as the next step in Big Data analysis. Text Analytics has a number of subdivisions: Information Extraction, Named Entity Recognition, Semantic Web annotated domain’s representation, and many more. Several techniques are currently used and some of them have gained a lot of attention, such as Machine Learning, to show a semisupervised enhancement of systems, but they also present a number of limitations which make them not always the only or the best choice. We conclude with current and near future applications of Text Analytics.

Research and development in the area of biomedical literature analysis aims at providing life science researchers with effective means to access and exploit knowledge contained in scientific publications. Virtually all journal publications and many conference proceedings are nowadays readily available in an electronic form—for instance, as abstracts through the MEDLINE citation index or as full-text articles through PubMed Central. Nevertheless, keeping up to date with and searching for recent findings in a research domain remains a tedious task hampered by inefficient and ineffective means for access and exploitation. Biomedical text analysis aims to improve access to unstructured knowledge by alleviating searches, providing auto generated summaries of documents and topics, linking and integrating publications with structured resources, visualizing content for better understanding, and guiding researchers to novel hypotheses and into knowledge discovery. Focused research over recent years has improved fundamental solutions for biomedical text mining, such as document retrieval, named entity recognition, normalization and grounding, and extraction of relationships, with levels of accuracy that reach human annotators when considering inter annotator agreement. Consequently, more and more integrative analysis tools were put forward by the text mining community targeting a broad audience of end users: generic and task-specific search engines for life science researchers, interfaces for networks synthesis based on textual evidences, or more specialized tools searching for transcription factors, or primer sequences. This special issue of Advances in Bioinformatics presents overviews and examples of end-user-oriented biomedical text mining tools for bioinformaticians, molecular biologists, biochemists, clinicians, pharmacologists, and other researchers in life sciences. We start with A. Manconi et al. survey on “Literature retrieval and mining in bioinformatics: state of the art and challenges.” The authors introduce the major concepts that life science researchers should be familiar with getting the best out of existing text mining solutions, and survey key tools and research. In a dedicated second part of their survey, the authors address the major challenges both life science researchers and solution developers are facing at this point. The reader will find plenty of references to existing search tools, resources, and research papers. A. E. Thessen et al. focus on a particular domain, presenting an overview of “Applications of natural language processing in biodiversity science.” The authors review the application of natural processing and machine learning for biological information extraction regarding cellular processes, taxonomic names, and morphological characters. You will find detailed examples, a summary of all steps involved in information extraction, and lots of references to existing tools and resources. S. T. Ahmed et al. introduce their semantic faceted search engine, BioEve, in “A novel framework to facilitate interactive literature search.” They couple an automated extraction system with a cognitive search and navigation service, to alleviate the process of searching and browsing huge amounts of literature such as provided/delivered by MEDLINE. BioEve enables interactive query refinement and suggests concepts and entities (like genes, drugs, and diseases) to quickly filter and modify search directions, thereby achieving semantic enrichment that improves insight gains while searching literature. S. V. Landeghem et al. present their EVEX resource in “Exploring biomolecular literature with EVEX: connecting genes through events, homology, and indirect associations.” The authors extracted more than 20 million biomolecular events involving genes and proteins, such as phosphorylation and gene regulation, from MEDLINE. The online tool generates a summary on the searched gene denoting all regulated genes, binding partners, subcellular locations, and other related data linked to the searched gene. We conclude this special issue with the paper by A. Divoli et al., discussing whether “Do Peers see more in a paper than its authors.” In a meta-analysis using automatic text analysis, they address questions such as how informative an abstract is compared to the full text; and how peers and authors might view the major contributions of a paper differently. Their analyses are comparing the information content of an abstract, as written by the paper's authors, to sentences that mention the paper as a reference, written by peers. Using this strategy, A. Divoli et al. found, for example, that citing sentences contain 20% additional concepts (likely important contributions) that were not mentioned in the abstract of the paper referred to, but maybe should have been to help attract even more peers.

<italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Context:</i> User stories have been widely accepted as artifacts to capture the user requirements in agile software development. They are short pieces of texts in a semi-structured format that express requirements. Natural language processing (NLP) techniques offer a potential advantage in user story applications. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Objective:</i> Conduct a systematic literature review to capture the current state-of-the-art of NLP research on user stories. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Method:</i> The search strategy is used to obtain relevant papers from SCOPUS, ScienceDirect, IEEE Xplore, ACM Digital Library, SpringerLink, and Google Scholar. Inclusion and exclusion criteria are applied to filter the search results. We also use the forward and backward snowballing techniques to obtain more comprehensive results. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Results:</i> The search results identified 718 papers published between January 2009 to December 2020. After applying the inclusion/exclusion criteria and the snowballing technique, we identified 38 primary studies that discuss NLP techniques in user stories. Most studies used NLP techniques to extract aspects of who, what, and why from user stories. The purpose of NLP studies in user stories is broad, ranging from discovering defects, generating software artifacts, identifying the key abstraction of user stories, and tracing links between model and user stories. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Conclusion:</i> NLP can help system analysts manage user stories. Implementing NLP in user stories has many opportunities and challenges. Considering the exploration of NLP techniques and rigorous evaluation methods is required to obtain quality research. As with NLP research in general, the ability to understand a sentence’s context continues to be a challenge.

Automatic classification of text document plays a vital area of research in the field of Text Mining (TM) ever since the explosion of online text information. The sources like digital libraries, emails, blogs, etc., make the rapid evolving growth of text documents in the digital era. In general the categorization of text document includes several field of interest like Information Retrieval (IR), Machine Learning (ML) and Natural Language Processing (NLP). Hence, this paper focuses on various research attempts which employ both supervised and unsupervised ML techniques for classifying a set of text documents into pre-defined category labels.

1 IntroductionOrganizations focus on automate their processes in order to improve efficiency, reduce costs, and/or reduce human beings' errors in an easy and rapid manner. Business process management (BPM) methods provide a solution to this issue. In this context, information systems like CRM, ERP, SCM, etc. have known an increasing demand. The main problem consists of the length of the business process specifications. If new regulations appear, these specifications must be adapted. Manually extraction of visual models is time consuming. During time, a series of solutions were proposed. The literature shows a crowd of approaches that extracts data models [1], [2], [3], and process models [4], [5] from Natural Language (NL) text. This paper aims to analyze the Natural Language Processing (NLP) techniques and tools used in order to provide different types of visual representations.On the last few years, approaches based on NLP have been developed in order to automate process conversion from NL text. NLP plays an important role in NL text analysis as NLP tries to understand speech and text as humans beings would do. Colloquialism, abbreviations or typos make this task a challenging one. NLP has the origins in 1950s when Alan Turing proposed the Turing test [6], by introducing the imitation game. Since then, the literature shows a plethora of NLP tools [7], [8], [9], [10] using several machine learning techniques, our focus being on those applied on data models and process models discovery from NL text, starting with the first language parser [11] to the actual ones like NLTk [7], [8], ANTLR1, etc.Linguistic analysis is closely tied to NLP. Liddy [12] highlights 7 levels of linguistic analysis: a) Phonetic or Phonological level: how words are pronounced, b) Morphological level: prefixes, suffixes and roots analysis, c) Lexical level: word level analysis including lexical meaning and Part-Of-Speech (POS) analysis, d) Syntactic level: grammatical analysis of words in a sentence, e) Semantic level: determining the possible meanings of sentences, f) Discourse level: interpreting structure and meaning for texts larger than a sentence, g) Pragmatic level: understanding the purpose of a language.Some of the problems approached by NLP are: POS tagging, parsing, Named Entity Recognition (NER), chunking, Semantic Role Labeling (SRL). Anaphora resolution [13] refers to the interpretation of the link between the anaphor and its antecedents.The remainder of the paper is organized as follows: Section 2 briefly outlines the NLP domain, describing the levels of linguistic analysis and the main NLP approaches of analyzing NL requirements. Section 3 focuses on data and process models extraction from NL text. This section makes an introduction to Object Oriented Analysis and Business Process Modeling and analyses the existing tools that discover data and process models from text. Subsequently, Section 4 summarizes the results of this work and the conclusions are drawn in Section 5.2NLPA detailed review on NLP is given in [14] and in [15]. Jones [14] divides the history of NLP into four phases: the first starts at the beginning of the 1940s and lasts to the late 1960s, the second begins from the end of 60s and lasts to the end of 70s, the third is represented by late 80s, where the fourth phase starts in the late of 90s. Next, we will detail each phase as they were defined in [14] and [15]. First phase treated machine translation issues, while the second focused on artificial intelligence. The third phase can be called grammatico-logical phase, which is followed by the lexical phase. A fifth phase is proposed in [16] where formal theories and statistical data are combined. Since this study was published first in 1994 and then it was re-organized in 2001 we can add the sixth phase: from 2000 until present where NLP techniques are combined in order to contribute to visual models extraction.Software requirements are usually written in NL which is asymmetric and irregular [17]. …

BioCreative: Critical Assessment of Information Extraction in Biology is an international community-wide effort for evaluating text mining and information extraction systems applied to the biological domain (http://www.biocreative.org/). The Challenge Evaluations and the accompanying BioCreative Workshops bring together the text mining and biology communities to drive the development of text mining systems that can be integrated into the biocuration workflow and the knowledge discovery process. To address the current barriers in using text mining in biology, BioCreative has further been conducting user requirement analysis, user-based evaluations and fostering standard development for text mining tool re-use and integration. This DATABASE virtual issue captures the major results from the BioCreative-2012 Workshop on Interactive Text Mining in the Biocuration Workflow and is the fifth special issue devoted to BioCreative.

The rapid expansion of metal-organic framework (MOF) literature presents both a rich resource and a significant challenge for knowledge extraction. Text mining, which enables the conversion of unstructured scientific texts into structured, machine-readable data, has emerged as a key tool for accelerating data-driven research in the MOF domain. This review traces the development of text mining approaches in MOF research, from early manual curation and rule-based methods to recent breakthroughs powered by large language model (LLM)-based automation. We discuss the foundational role of natural language processing (NLP) and machine learning (ML) techniques such as named entity recognition and vector embedding models, followed by an in-depth analysis of LLM-based frameworks that enable flexible, scalable, and context-aware information extraction. Additionally, we introduce and compare their accuracy, and explore their diverse applications-including prediction of synthesizability, materials properties, and thermal stability. We conclude with a perspective on future directions for text mining in MOF research, including its integration into interactive graphical user interfaces, autonomous laboratories, multi-agent AI systems, and multi-modal LLM frameworks that can process textual, visual, and structural information in a unified way. This review aims to provide a foundational understanding for both experimental and computational researchers interested in adopting or advancing text mining methods in the MOF field.

Reviewed by: Handbook for language engineers ed. by Ali Farghaly Stuart Robinson Handbook for language engineers. Ed. by Ali Farghaly. Stanford, CA: CSLI Publications, 2002. Pp. 300. ISBN 1575863960. $25. Handbook for language engineers is a guide to the field of language processing aimed at linguists with no previous training in the area. The book contains a total of ten chapters (including the introduction). Each covers an important aspect of language processing. ‘Domain analysis and representation’ by Ali Farghaly and Bruce Hedin looks at how attention to ‘domains of discourse’ (e.g. product purchase e-mails) can improve the quality of natural language processing (NLP). ‘The language of the internet’ by Naomi S. Baron provides an overview of the language of the internet in the broadest sense, covering the unique character of natural language on the internet as well as other issues, such as coding systems (mark-up languages), search engines, and crosslinguistic issues. ‘Grammar writing, testing, and evaluation’ by Miriam Butt and Tracy Holloway King gives an overview of various aspects of grammar implementation, focusing on development, testing, evaluation, and documentation. ‘Ontologies’ by Natalya Noy discusses the role of ontologies in language [End Page 679] engineering, where the term ontology is understood to mean ‘an explicit formal specification of conceptualization’ (Thomas R. Gruber, ‘A translation approach to portable ontology specifications’, Knowledge Acquisition 5.2.199–220, 1993). ‘Text mining, corpus building, and testing’ by Karine Megerdoomian looks at the role of corpora in language engineering. She discusses the nature of corpora, touching on a wide variety of topics (corpus analysis vs. text mining, tokenization and annotation, the application of corpus linguistics, tools for corpus processing, symbolic and statistical approaches). ‘Statistical natural language processing’ by Chris Callison-Burch and Miles Osborne discusses the role of statistics in NLP, beginning with a discussion of probabilistic parsing, then moving on to modeling, estimation/learning, data, and evaluation. Matthew Stone (‘Knowledge representation for language engineering’) examines how world knowledge is represented in language processing. The discussion is broadly divided into three sections, each of which covers three layers of analysis in intelligent systems: the knowledge level, the representations-and-algorithms level, and the implementation level. In ‘Speech recognition and understanding’, Jan W. Amtrup looks at the state of the art in speech recognition and speech synthesis, focusing on some of the statistical methods that have been successfully employed in the field, such as hidden Markov models. Ali Farghaly wraps up the discussion in ‘Language engineering and the knowledge economy’ by looking at the changing economics of globalization and the place of language engineering in the new economy. The growth of the internet has created many jobs for linguists in industry and raised the profile of computational linguistics. This book should serve as an excellent guide for those interested in a practical introduction to the current state of language processing technology. Stuart Robinson Max Planck Institute for Psycholinguistics Copyright © 2006 Linguistic Society of America