Text Mining System Research Articles

ITextMine: integrated text-mining system for large-scale knowledge extraction from the literature.

Numerous efforts have been made for developing text-mining tools to extract information from biomedical text automatically. They have assisted in many biological tasks, such as database curation and hypothesis generation. Text-mining tools are usually different from each other in terms of programming language, system dependency and input/output format. There are few previous works that concern the integration of different text-mining tools and their results from large-scale text processing. In this paper, we describe the iTextMine system with an automated workflow to run multiple text-mining tools on large-scale text for knowledge extraction. We employ parallel processing with dockerized text-mining tools with a standardized JSON output format and implement a text alignment algorithm to solve the text discrepancy for result integration. iTextMine presently integrates four relation extraction tools, which have been used to process all the Medline abstracts and PMC open access full-length articles. The website allows users to browse the text evidence and view integrated results for knowledge discovery through a network view. We demonstrate the utilities of iTextMine with two use cases involving the gene PTEN and breast cancer and the gene SATB1.

EGARD: Extracting associations between genomic anomalies and drug responses from text.

Tumor molecular profiling plays an integral role in identifying genomic anomalies which may help in personalizing cancer treatments, improving patient outcomes and minimizing risks associated with different therapies. However, critical information regarding the evidence of clinical utility of such anomalies is largely buried in biomedical literature. It is becoming prohibitive for biocurators, clinical researchers and oncologists to keep up with the rapidly growing volume and breadth of information, especially those that describe therapeutic implications of biomarkers and therefore relevant for treatment selection. In an effort to improve and speed up the process of manually reviewing and extracting relevant information from literature, we have developed a natural language processing (NLP)-based text mining (TM) system called eGARD (extracting Genomic Anomalies association with Response to Drugs). This system relies on the syntactic nature of sentences coupled with various textual features to extract relations between genomic anomalies and drug response from MEDLINE abstracts. Our system achieved high precision, recall and F-measure of up to 0.95, 0.86 and 0.90, respectively, on annotated evaluation datasets created in-house and obtained externally from PharmGKB. Additionally, the system extracted information that helps determine the confidence level of extraction to support prioritization of curation. Such a system will enable clinical researchers to explore the use of published markers to stratify patients upfront for ‘best-fit’ therapies and readily generate hypotheses for new clinical trials.

Constructing Genetic Networks using Biomedical Literature and Rare Event Classification

Text mining has become an important tool in bioinformatics research with the massive growth in the biomedical literature over the past decade. Mining the biomedical literature has resulted in an incredible number of computational algorithms that assist many bioinformatics researchers. In this paper, we present a text mining system called Gene Interaction Rare Event Miner (GIREM) that constructs gene-gene-interaction networks for human genome using information extracted from biomedical literature. GIREM identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature. For a given gene g, GIREM first extracts the set of genes found within the abstracts of biomedical literature associated with g. GIREM aims at enhancing biological text mining approaches by identifying the semantic relationship between each co-occurrence of a pair of genes in abstracts using the syntactic structures of sentences and linguistics theories. It uses a supervised learning algorithm, weighted logistic regression to label pairs of genes to related or un-related classes, and to reflect the population proportion using smaller samples. We evaluated GIREM by comparing it experimentally with other well-known approaches and a protein-protein interactions database. Results showed marked improvement.

MPTM: A tool for mining protein post-translational modifications from literature.

Due to the importance of post-translational modifications (PTMs) in human health and diseases, PTMs are regularly reported in the biomedical literature. However, the continuing and rapid pace of expansion of this literature brings a huge challenge for researchers and database curators. Therefore, there is a pressing need to aid them in identifying relevant PTM information more efficiently by using a text mining system. So far, only a few web servers are available for mining information of a very limited number of PTMs, which are based on simple pattern matching or pre-defined rules. In our work, in order to help researchers and database curators easily find and retrieve PTM information from available text, we have developed a text mining tool called MPTM, which extracts and organizes valuable knowledge about 11 common PTMs from abstracts in PubMed by using relations extracted from dependency parse trees and a heuristic algorithm. It is the first web server that provides literature mining service for hydroxylation, myristoylation and GPI-anchor. The tool is also used to find new publications on PTMs from PubMed and uncovers potential PTM information by large-scale text analysis. MPTM analyzes text sentences to identify protein names including substrates and protein-interacting enzymes, and automatically associates them with the UniProtKB protein entry. To facilitate further investigation, it also retrieves PTM-related information, such as human diseases, Gene Ontology terms and organisms from the input text and related databases. In addition, an online database (MPTMDB) with extracted PTM information and a local MPTM Lite package are provided on the MPTM website. MPTM is freely available online at http://bioinformatics.ustc.edu.cn/mptm/ and the source codes are hosted on GitHub: https://github.com/USTC-HILAB/MPTM .

Evaluating a Bilingual Text-Mining System With a Taxonomy of Key Words and Hierarchical Visualization for Understanding Learner-Generated Text

This study evaluated a bilingual text-mining system, which incorporated a bilingual taxonomy of key words and provided hierarchical visualization, for understanding learner-generated text in the learning management systems through automatic identification and counting of matching key words. A class of 27 in-service teachers studied a course “e-Learning in primary mathematics” was asked to reflect “what is e-Learning” before and after the course. Their concept of “e-Learning” was investigated by counting the matching key words using the text-mining system and a content analysis of learner-generated text using a rubric, respectively. The correlations of the results using these two methods were .823 and .840 in the preteaching and postteaching reflections. This text-mining system has the potential as a supporting tool for teachers to gain a general understanding of learner-generated text using the hierarchical visualization for supporting pedagogical decision-making, which can be applied to massive open online courses with a large enrolment of learners.

WebGIVI: a web-based gene enrichment analysis and visualization tool

BackgroundA major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task.ResultsWe have developed WebGIVI, an interactive web-based visualization tool (http://raven.anr.udel.edu/webgivi/) to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports uploading and visualization of any two-column tab separated data.ConclusionsWebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI. The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php.

Subjective Text Mining for Arabic Social Media

The need for designing Arabic text mining systems for the use on social media posts is increasingly becoming a significant and attractive research area. It serves and enhances the knowledge needed in various domains. The main focus of this paper is to propose a novel framework combining sentiment analysis with subjective analysis on Arabic social media posts to determine whether people are interested or not interested in a defined subject. For those purposes, text classification methods—including preprocessing and machine learning mechanisms—are applied. Essentially, the performance of the framework is tested using Twitter as a data source, where possible volunteers on a certain subject are identified based on their posted tweets along with their subject-related information. Twitter is considered because of its popularity and its rich content from online microblogging services. The results obtained are very promising with an accuracy of 89%, thereby encouraging further research.

An Effective Preprocessing Step Algorithm in Text Mining Application

Text mining was a process of mining the significant information from the text documents. Any text mining system was created its process by preprocessing step; which involve tokenization, stop words removal, stemming and finally creating term frequency and inverse document frequency matrix (TF-IDF matrix). These steps provide the highest time consuming stage in knowledge discovery. The proposed method tries to build effective preprocessing step to even win area of memory space and time requirements. That by proposed a method for improved stop words removal algorithm and improved stemming algorithm based porter stemming algorithm. The proposed method is tested in two levels, first level uses only vector space model which based on used traditional stop words removal and with traditional porter stemming and the second level uses vector space model with combined features of improved stop words removal algorithm and improved stemming algorithm. The results show that using second level as effective preprocessing step for text mining application achieves good performance from reducing storage space used in memory about 10% and the processing time become faster which achieves good performance to build the final TF-IDF matrix.

EGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality.

UniProt Knowledgebase (UniProtKB) is a publicly available database with access to a vast amount of protein sequence and functional information. To widen the scope of the publications associated with a protein entry, UniProt has introduced the computationally mapped additional bibliography section, which includes literature collected from external sources. In this article, we describe a text mining system, eGenPub, which selects articles that are ‘about’ specific proteins and allows automatic identification of additional bibliography for given UniProt protein entries. Focusing on plant proteins initially, eGenPub utilizes a gene normalization tool called pGenN, and a trained support vector machine model, which achieves a precision of 95.3%, to predict whether an article, based on its abstract, should be linked to a given UniProt entry. We have conducted a full-scale PubMed processing using eGenPub for eight common plant species. Altogether, 9025 articles are identified as relevant bibliography for 4752 UniProt entries, among which 5252 are additional papers not in the existing publication section. These newly computationally mapped additional bibliography via eGenPub is being integrated in the UniProt production pipeline, and can be accessed via the UniProtKB protein entry publication view.

Text mining electronic hospital records to automatically classify admissions against disease: Measuring the impact of linking data sources

ObjectiveText and data mining play an important role in obtaining insights from Health and Hospital Information Systems. This paper presents a text mining system for detecting admissions marked as positive for several diseases: Lung Cancer, Breast Cancer, Colon Cancer, Secondary Malignant Neoplasm of Respiratory and Digestive Organs, Multiple Myeloma and Malignant Plasma Cell Neoplasms, Pneumonia, and Pulmonary Embolism. We specifically examine the effect of linking multiple data sources on text classification performance. MethodsSupport Vector Machine classifiers are built for eight data source combinations, and evaluated using the metrics of Precision, Recall and F-Score. Sub-sampling techniques are used to address unbalanced datasets of medical records. We use radiology reports as an initial data source and add other sources, such as pathology reports and patient and hospital admission data, in order to assess the research question regarding the impact of the value of multiple data sources. Statistical significance is measured using the Wilcoxon signed-rank test.A second set of experiments explores aspects of the system in greater depth, focusing on Lung Cancer. We explore the impact of feature selection; analyse the learning curve; examine the effect of restricting admissions to only those containing reports from all data sources; and examine the impact of reducing the sub-sampling. These experiments provide better understanding of how to best apply text classification in the context of imbalanced data of variable completeness. ResultsRadiology questions plus patient and hospital admission data contribute valuable information for detecting most of the diseases, significantly improving performance when added to radiology reports alone or to the combination of radiology and pathology reports. ConclusionOverall, linking data sources significantly improved classification performance for all the diseases examined. However, there is no single approach that suits all scenarios; the choice of the most effective combination of data sources depends on the specific disease to be classified.

Improving chemical disease relation extraction with rich features and weakly labeled data

BackgroundDue to the importance of identifying relations between chemicals and diseases for new drug discovery and improving chemical safety, there has been a growing interest in developing automatic relation extraction systems for capturing these relations from the rich and rapid-growing biomedical literature. In this work we aim to build on current advances in named entity recognition and a recent BioCreative effort to further improve the state of the art in biomedical relation extraction, in particular for the chemical-induced disease (CID) relations.ResultsWe propose a rich-feature approach with Support Vector Machine to aid in the extraction of CIDs from PubMed articles. Our feature vector includes novel statistical features, linguistic knowledge, and domain resources. We also incorporate the output of a rule-based system as features, thus combining the advantages of rule- and machine learning-based systems. Furthermore, we augment our approach with automatically generated labeled text from an existing knowledge base to improve performance without additional cost for corpus construction. To evaluate our system, we perform experiments on the human-annotated BioCreative V benchmarking dataset and compare with previous results. When trained using only BioCreative V training and development sets, our system achieves an F-score of 57.51 %, which already compares favorably to previous methods. Our system performance was further improved to 61.01 % in F-score when augmented with additional automatically generated weakly labeled data.ConclusionsOur text-mining approach demonstrates state-of-the-art performance in disease-chemical relation extraction. More importantly, this work exemplifies the use of (freely available) curated document-level annotations in existing biomedical databases, which are largely overlooked in text-mining system development.

Identifying and Profiling Key Sellers in Cyber Carding Community: AZSecure Text Mining System

The past few years have witnessed millions of credit/debit cards flowing through the underground economy and ultimately causing significant financial loss. Examining key underground economy sellers has both practical and academic significance for cybercrime forensics and criminology research. Drawing on social media analytics, we have developed the AZSecure text mining system for identifying and profiling key sellers. The system identifies sellers using sentiment analysis of customer reviews and profiles sellers using topic modeling of advertisements. We evaluated the AZSecure system on eight international underground economy forums. The system significantly outperformed all benchmark machine-learning methods on identifying advertisement threads, classifying customer review sentiments, and profiling seller characteristics, with an average F-measure of about 80 percent to 90 percent. In our case study, we identified the famous carder, Rescator, who was affiliated with the Target breach, and captured important seller characteristics in terms of product type, payment options, and contact channels. Our research leverages social media analytics to probe into the underground economy in order to help law enforcement target key sellers and prevent future fraud. It also contributes to our understanding of the use of information technology in detecting deception in online systems.

A Comparative Study of Japanese and Korean "sleep" Frame Verb

We have tried to build a text-mining system to extract cultural elements by using SEJONG Corpus and BCCWJ. In this paper, we examine cultural elements of Japanese and Korean "sleep" frame verb and try to find out the differences of each language based on the analysis of the result of co-occurrence rates(t-scores). Both belonging to the same "sleep" frame("The sleeper stays in an altered state of consciousness with greatly reduced external awareness.", the definition of the frame-https://framenet.icsi.berkeley.edu-), each language shows several differences. The very noteworthy finding is that Japanese "neru" shows the very unique core lexical element of "sleeper", ‘old man’ and from the usages of "neru", it means "posture change" rather than "state change", which both English and Korean mainly mean. 本研究は独自的に開発された「日·韓文化要素抽出システム」(CEMS)を使って取り出したそれぞれの言語の文化要素を比較·対照することで両言語の特徴を浮彫りにするためのものである。CEMSは一つの単語と共起する単語との頻度差を数値化(t-score)してくれるもので、単語と単語の間の関連性を視覚的に表してくれるものである。本研究では特に‘sleep"フレームに属する両言語の動詞をCEMSに入れて得られた検索結果を分析することでいくつかの言語的な現象を見いだすことができたのである。同じく＇sleep＇フレーム("The sleeper stays in an altered state of consciousness with greatly reduced external awareness.", フレームの定義-https://framenet.icsi.berkeley.edu-)に属するものの、日本語の「寝る」はコアー語彙要素の＇sleeper＇から特徴的な文化要素である「老人」(t-sore: 11.98)が見つかれ、それと関連する語彙が多数見られたのである。また、英語と韓国語が＇sleep＇フレームの定義に沿った意味(「状態変化)で使われた用例が大多数を占めているのに対して、日本語の「寝る」が使われた用例からは工藤(2002)の指摘する「姿勢変化」の意味がより強いことが分かったのである。

Generating Drug-Gene Association for Vibrio Cholerae using Ontological Profile Similarity

Objective: The measure of biomedical literature has been expanding quickly in the most recent decade. Text mining systems can analysis this vast scale information, shed light onto complex medication instruments and concentrate connection data that can bolster computational polypharmacology. The key idea of the paper is to find the drug candidate for the disease cholera, which is caused due to the organism Vibrio cholerae. Method: The technique estimates the Pointwise Mutual Information (PMI) among protein name obtained from the UniprotKB and the Medical Subject Headings that contain drug terms. Based on the PMI scores, gene/protein profiles and drug are produced and candidate drug-gene/protein associations are constructed when evaluating the relevancy of their profiles. Findings: The association between protein and drug is found and the drug candidates are proposed. Applications: The similar technique can be applied to find the drug candidate for various diseases which reduces the drug release cost in the market.

Geoparsing history: Locating commodities in ten million pages of nineteenth-century sources

ABSTRACTIn the Trading Consequences project, historians, computational linguists, and computer scientists collaborated to develop a text mining system that extracts information from a vast amount of digitized published English-language sources from the “long nineteenth century” (1789 to 1914). The project focused on identifying relationships within the texts between commodities, geographical locations, and dates. The authors explain the methodology, uses, and the limitations of applying digital humanities techniques to historical research, and they argue that interdisciplinary approaches are critically important in addressing the technical challenges that arise. Collaborative teamwork of the kind described here has considerable potential to produce further advances in the large-scale analysis of historical documents.

DiMeX: A Text Mining System for Mutation-Disease Association Extraction.

The number of published articles describing associations between mutations and diseases is increasing at a fast pace. There is a pressing need to gather such mutation-disease associations into public knowledge bases, but manual curation slows down the growth of such databases. We have addressed this problem by developing a text-mining system (DiMeX) to extract mutation to disease associations from publication abstracts. DiMeX consists of a series of natural language processing modules that preprocess input text and apply syntactic and semantic patterns to extract mutation-disease associations. DiMeX achieves high precision and recall with F-scores of 0.88, 0.91 and 0.89 when evaluated on three different datasets for mutation-disease associations. DiMeX includes a separate component that extracts mutation mentions in text and associates them with genes. This component has been also evaluated on different datasets and shown to achieve state-of-the-art performance. The results indicate that our system outperforms the existing mutation-disease association tools, addressing the low precision problems suffered by most approaches. DiMeX was applied on a large set of abstracts from Medline to extract mutation-disease associations, as well as other relevant information including patient/cohort size and population data. The results are stored in a database that can be queried and downloaded at http://biotm.cis.udel.edu/dimex/. We conclude that this high-throughput text-mining approach has the potential to significantly assist researchers and curators to enrich mutation databases.

Comprehensive Map of Molecules Implicated in Obesity.

Obesity is a global epidemic affecting over 1.5 billion people and is one of the risk factors for several diseases such as type 2 diabetes mellitus and hypertension. We have constructed a comprehensive map of the molecules reported to be implicated in obesity. A deep curation strategy was complemented by a novel semi-automated text mining system in order to screen 1,000 full-length research articles and over 90,000 abstracts that are relevant to obesity. We obtain a scale free network of 804 nodes and 971 edges, composed of 510 proteins, 115 genes, 62 complexes, 23 RNA molecules, 83 simple molecules, 3 phenotype and 3 drugs in “bow-tie” architecture. We classify this network into 5 modules and identify new links between the recently discovered fat mass and obesity associated FTO gene with well studied examples such as insulin and leptin. We further built an automated docking pipeline to dock orlistat as well as other drugs against the 24,000 proteins in the human structural proteome to explain the therapeutics and side effects at a network level. Based upon our experiments, we propose that therapeutic effect comes through the binding of one drug with several molecules in target network, and the binding propensity is both statistically significant and different in comparison with any other part of human structural proteome.

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

BackgroundIn recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required.Development and Testing of the OntologyHere we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar.Results and SignificanceOur tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.

Overview of the interactive task in BioCreative V.

Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing pre-designed tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development of the interactive task, from planning to execution and discuss major findings for the systems tested.Database URL: http://www.biocreative.org

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.

Text mining in the biomedical sciences is rapidly transitioning from small-scale evaluation to large-scale application. In this article, we argue that text-mining technologies have become essential tools in real-world biomedical research. We describe four large scale applications of text mining, as showcased during a recent panel discussion at the BioCreative V Challenge Workshop. We draw on these applications as case studies to characterize common requirements for successfully applying text-mining techniques to practical biocuration needs. We note that system ‘accuracy’ remains a challenge and identify several additional common difficulties and potential research directions including (i) the ‘scalability’ issue due to the increasing need of mining information from millions of full-text articles, (ii) the ‘interoperability’ issue of integrating various text-mining systems into existing curation workflows and (iii) the ‘reusability’ issue on the difficulty of applying trained systems to text genres that are not seen previously during development. We then describe related efforts within the text-mining community, with a special focus on the BioCreative series of challenge workshops. We believe that focusing on the near-term challenges identified in this work will amplify the opportunities afforded by the continued adoption of text-mining tools. Finally, in order to sustain the curation ecosystem and have text-mining systems adopted for practical benefits, we call for increased collaboration between text-mining researchers and various stakeholders, including researchers, publishers and biocurators.