Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Mining the Medical and Patent Literature to Support Healthcare and Pharmacovigilance

Recent advancements in healthcare practices and the increasing use of information technology in the medical domain has lead to the rapid generation of free-text data in forms of scientific articles, e-health records, patents, and document inventories. This has urged the development of sophisticated information retrieval and information extraction technologies. A fundamental requirement for the automatic processing of biomedical text is the identification of information carrying units such as the concepts or named entities. In this context, this work focuses on the identification of medical disorders (such as diseases and adverse effects) which denote an important category of concepts in the medical text. Two methodologies were investigated in this regard and they are dictionary-based and machine learning-based approaches. Futhermore, the capabilities of the concept recognition techniques were systematically exploited to build a semantic search platform for the retrieval of e-health records and patents. The system facilitates conventional text search as well as semantic and ontological searches. Performance of the adapted retrieval platform for e-health records and patents was evaluated within open assessment challenges (i.e. TRECMED and TRECCHEM respectively) wherein the system was best rated in comparison to several other competing information retrieval platforms. Finally, from the medico-pharma perspective, a strategy for the identification of adverse drug events from medical case reports was developed. Qualitative evaluation as well as an expert validation of the developed system's performance showed robust results. In conclusion, this thesis presents approaches for efficient information retrieval and information extraction from various biomedical literature sources in the support of healthcare and pharmacovigilance. The applied strategies have potential to enhance the literature-searches performed by biomedical, healthcare, and patent professionals. The applied strategies have potential to enhance the literature-searches performed by biomedical, healthcare, and patent professionals. This can promote the literature-based knowledge discovery, improve the safety and effectiveness of medical practices, and drive the research and development in medical and healthcare arena

Text Mining for Chemical Compounds

Exploring the chemical and biological space covered by patent and journal publications is crucial in early- stage medicinal chemistry activities. The analysis provides understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents and journals through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. In this book, we addressed the lack of quality measurements for assessing the correctness of structural representation within and across chemical databases; lack of resources to build text-mining systems; lack of high performance systems to extract chemical compounds from journals and patents; and lack of automated systems to identify relevant compounds in patents. The consistency and ambiguity of chemical identifiers was analyzed within and between small- molecule databases in Chapter 2 and Chapter 3. In Chapter 4 and Chapter 7 we developed resources to enable the construction of chemical text-mining systems. In Chapter 5 and Chapter 6, we used community challenges (BioCreative V and BioCreative VI) and their corresponding resources to identify mentions of chemical compounds in journal abstracts and patents. In Chapter 7 we used our findings in previous chapters to extract chemical named entities from patent full text and to classify the relevancy of chemical compounds

Automatic identification of relevant chemical compounds from patents

In commercial research and development projects, public disclosure of new chemical compounds often takes place in patents. Only a small proportion of these compounds are published in journals, usually a few years after the patent. Patent authorities make available the patents but do not provide systematic continuous chemical annotations. Content databases such as Elsevier’s Reaxys provide such services mostly based on manual excerptions, which are time-consuming and costly. Automatic text-mining approaches help overcome some of the limitations of the manual process. Different text-mining approaches exist to extract chemical entities from patents. The majority of them have been developed using sub-sections of patent documents and focus on mentions of compounds. Less attention has been given to relevancy of a compound in a patent. Relevancy of a compound to a patent is based on the patent’s context. A relevant compound plays a major role within a patent. Identification of relevant compounds reduces the size of the extracted data and improves the usefulness of patent resources (e.g. supports identifying the main compounds). Annotators of databases like Reaxys only annotate relevant compounds. In this study, we design an automated system that extracts chemical entities from patents and classifies their relevance. The goldstandard set contained 18 789 chemical entity annotations. Of these, 10% were relevant compounds, 88% were irrelevant and 2% were equivocal. Our compound recognition system was based on proprietary tools. The performance (F-score) of the system on compound recognition was 84% on the development set and 86% on the test set. The relevancy classification system had an F-score of 86% on the development set and 82% on the test set. Our system can extract chemical compounds from patents and classify their relevance with high performance. This enables the extension of the Reaxys database by means of automation

Named entity recognition in chemical patents using ensemble of contextual language models

Chemical patent documents describe a broad range of applications holding key reaction and compound information, such as chemical structure, reaction formulas, and molecular properties. These informational entities should be first identified in text passages to be utilized in downstream tasks. Text mining provides means to extract relevant information from chemical patents through information extraction techniques. As part of the Information Extraction task of the Cheminformatics Elsevier Melbourne University challenge, in this work we study the effectiveness of contextualized language models to extract reaction information in chemical patents. We assess transformer architectures trained on a generic and specialised corpora to propose a new ensemble model. Our best model, based on a majority ensemble approach, achieves an exact F1-score of 92.30% and a relaxed F1-score of 96.24%. The results show that ensemble of contextualized language models can provide an effective method to extract information from chemical patents

Boosting Drug Named Entity Recognition using an Aggregate Classifier

AbstractObjectiveDrug named entity recognition (NER) is a critical step for complex biomedical NLP tasks such as the extraction of pharmacogenomic, pharmacodynamic and pharmacokinetic parameters. Large quantities of high quality training data are almost always a prerequisite for employing supervised machine-learning techniques to achieve high classification performance. However, the human labour needed to produce and maintain such resources is a significant limitation. In this study, we improve the performance of drug NER without relying exclusively on manual annotations.MethodsWe perform drug NER using either a small gold-standard corpus (120 abstracts) or no corpus at all. In our approach, we develop a voting system to combine a number of heterogeneous models, based on dictionary knowledge, gold-standard corpora and silver annotations, to enhance performance. To improve recall, we employed genetic programming to evolve 11 regular-expression patterns that capture common drug suffixes and used them as an extra means for recognition.MaterialsOur approach uses a dictionary of drug names, i.e. DrugBank, a small manually annotated corpus, i.e. the pharmacokinetic corpus, and a part of the UKPMC database, as raw biomedical text. Gold-standard and silver annotated data are used to train maximum entropy and multinomial logistic regression classifiers.ResultsAggregating drug NER methods, based on gold-standard annotations, dictionary knowledge and patterns, improved the performance on models trained on gold-standard annotations, only, achieving a maximum F-score of 95%. In addition, combining models trained on silver annotations, dictionary knowledge and patterns are shown to achieve comparable performance to models trained exclusively on gold-standard data. The main reason appears to be the morphological similarities shared among drug names.ConclusionWe conclude that gold-standard data are not a hard requirement for drug NER. Combining heterogeneous models build on dictionary knowledge can achieve similar or comparable classification performance with that of the best performing model trained on gold-standard annotations

The state-of-the-art on Intellectual Property Analytics (IPA): A literature review on artificial intelligence, machine learning and deep learning methods for analysing intellectual property (IP) data

Big data is increasingly available in all areas of manufacturing and operations, which presents an opportunity for better decision making and discovery of the next generation of innovative technologies. Recently, there have been substantial developments in the field of patent analytics, which describes the science of analysing large amounts of patent information to discover trends. We define Intellectual Property Analytics (IPA) as the data science of analysing large amount of IP information, to discover relationships, trends and patterns for decision making. In this paper, we contribute to the ongoing discussion on the use of intellectual property analytics methods, i.e artificial intelligence methods, machine learning and deep learning approaches, to analyse intellectual property data. This literature review follows a narrative approach with search strategy, where we present the state-of-the-art in intellectual property analytics by reviewing 57 recent articles. The bibliographic information of the articles are analysed, followed by a discussion of the articles divided in four main categories: knowledge management, technology management, economic value, and extraction and effective management of information. We hope research scholars and industrial users, may find this review helpful when searching for the latest research efforts pertaining to intellectual property analytics.The authors would like to acknowledge support of the Engineering and Physical Sciences Research Council (EPSRC)

Harvesting Entities from the Web Using Unique Identifiers -- IBEX

In this paper we study the prevalence of unique entity identifiers on the Web. These are, e.g., ISBNs (for books), GTINs (for commercial products), DOIs (for documents), email addresses, and others. We show how these identifiers can be harvested systematically from Web pages, and how they can be associated with human-readable names for the entities at large scale. Starting with a simple extraction of identifiers and names from Web pages, we show how we can use the properties of unique identifiers to filter out noise and clean up the extraction result on the entire corpus. The end result is a database of millions of uniquely identified entities of different types, with an accuracy of 73--96% and a very high coverage compared to existing knowledge bases. We use this database to compute novel statistics on the presence of products, people, and other entities on the Web.Comment: 30 pages, 5 figures, 9 tables. Complete technical report for A. Talaika, J. A. Biega, A. Amarilli, and F. M. Suchanek. IBEX: Harvesting Entities from the Web Using Unique Identifiers. WebDB workshop, 201