A text-mining system for extracting metabolic reactions from full-text articles

Background: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway—metabolic pathways—has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein–protein interactions. Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein–protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed

Mining chemical information from Open patents

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is a huge amount of information available in the published literature, the vast majority of which is not available in machine-understandable formats. PatentEye, a prototype system for the extraction and semantification of chemical reactions from the patent literature has been implemented and is discussed. A total of 4444 reactions were extracted from 667 patent documents that comprised 10 weeks' worth of publications from the European Patent Office (EPO), with a precision of 78% and recall of 64% with regards to determining the identity and amount of reactants employed and an accuracy of 92% with regards to product identification. NMR spectra reported as product characterisation data are additionally captured.Peer Reviewe

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

HOLMES: A Hybrid Ontology-Learning Materials Engineering System

Designing and discovering novel materials is challenging problem in many domains such as fuel additives, composites, pharmaceuticals, and so on. At the core of all this are models that capture how the different domain-specific data, information, and knowledge regarding the structures and properties of the materials are related to one another. This dissertation explores the difficult task of developing an artificial intelligence-based knowledge modeling environment, called Hybrid Ontology-Learning Materials Engineering System (HOLMES) that can assist humans in populating a materials science and engineering ontology through automatic information extraction from journal article abstracts. While what we propose may be adapted for a generic materials engineering application, our focus in this thesis is on the needs of the pharmaceutical industry. We develop the Columbia Ontology for Pharmaceutical Engineering (COPE), which is a modification of the Purdue Ontology for Pharmaceutical Engineering. COPE serves as the basis for HOLMES. The HOLMES framework starts with journal articles that are in the Portable Document Format (PDF) and ends with the assignment of the entries in the journal articles into ontologies. While this might seem to be a simple task of information extraction, to fully extract the information such that the ontology is filled as completely and correctly as possible is not easy when considering a fully developed ontology. In the development of the information extraction tasks, we note that there are new problems that have not arisen in previous information extraction work in the literature. The first is the necessity to extract auxiliary information in the form of concepts such as actions, ideas, problem specifications, properties, etc. The second problem is in the existence of multiple labels for a single token due to the existence of the aforementioned concepts. These two problems are the focus of this dissertation. In this work, the HOLMES framework is presented as a whole, describing our successful progress as well as unsolved problems, which might help future research on this topic. The ontology is then presented to help in the identification of the relevant information that needs to be retrieved. The annotations are next developed to create the data sets necessary for the machine learning algorithms to perform. Then, the current level of information extraction for these concepts is explored and expanded. This is done through the introduction of entity feature sets that are based on previously extracted entities from the entity recognition task. And finally, the new task of handling multiple labels for tagging a single entity is also explored by the use of multiple-label algorithms used primarily in image processing

ChemicalTagger: A tool for semantic text-mining in chemistry.

BACKGROUND: The primary method for scientific communication is in the form of published scientific articles and theses which use natural language combined with domain-specific terminology. As such, they contain free owing unstructured text. Given the usefulness of data extraction from unstructured literature, we aim to show how this can be achieved for the discipline of chemistry. The highly formulaic style of writing most chemists adopt make their contributions well suited to high-throughput Natural Language Processing (NLP) approaches. RESULTS: We have developed the ChemicalTagger parser as a medium-depth, phrase-based semantic NLP tool for the language of chemical experiments. Tagging is based on a modular architecture and uses a combination of OSCAR, domain-specific regex and English taggers to identify parts-of-speech. The ANTLR grammar is used to structure this into tree-based phrases. Using a metric that allows for overlapping annotations, we achieved machine-annotator agreements of 88.9% for phrase recognition and 91.9% for phrase-type identification (Action names). CONCLUSIONS: It is possible parse to chemical experimental text using rule-based techniques in conjunction with a formal grammar parser. ChemicalTagger has been deployed for over 10,000 patents and has identified solvents from their linguistic context with >99.5% precision.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Knowledge representation and text mining in biomedical, healthcare, and political domains

Knowledge representation and text mining can be employed to discover new knowledge and develop services by using the massive amounts of text gathered by modern information systems. The applied methods should take into account the domain-specific nature of knowledge. This thesis explores knowledge representation and text mining in three application domains. Biomolecular events can be described very precisely and concisely with appropriate representation schemes. Protein–protein interactions are commonly modelled in biological databases as binary relationships, whereas the complex relationships used in text mining are rich in information. The experimental results of this thesis show that complex relationships can be reduced to binary relationships and that it is possible to reconstruct complex relationships from mixtures of linguistically similar relationships. This encourages the extraction of complex relationships from the scientific literature even if binary relationships are required by the application at hand. The experimental results on cross-validation schemes for pair-input data help to understand how existing knowledge regarding dependent instances (such those concerning protein–protein pairs) can be leveraged to improve the generalisation performance estimates of learned models. Healthcare documents and news articles contain knowledge that is more difficult to model than biomolecular events and tend to have larger vocabularies than biomedical scientific articles. This thesis describes an ontology that models patient education documents and their content in order to improve the availability and quality of such documents. The experimental results of this thesis also show that the Recall-Oriented Understudy for Gisting Evaluation measures are a viable option for the automatic evaluation of textual patient record summarisation methods and that the area under the receiver operating characteristic curve can be used in a large-scale sentiment analysis. The sentiment analysis of Reuters news corpora suggests that the Western mainstream media portrays China negatively in politics-related articles but not in general, which provides new evidence to consider in the debate over the image of China in the Western media

Easy Semantification of Bioassays

Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. We propose a solution for automatically semantifying biological assays. Our solution contrasts the problem of automated semantification as labeling versus clustering where the two methods are on opposite ends of the method complexity spectrum. Characteristically modeling our problem, we find the clustering solution significantly outperforms a deep neural network state-of-the-art labeling approach. This novel contribution is based on two factors: 1) a learning objective closely modeled after the data outperforms an alternative approach with sophisticated semantic modeling; 2) automatically semantifying biological assays achieves a high performance F1 of nearly 83%, which to our knowledge is the first reported standardized evaluation of the task offering a strong benchmark model

A two-stage deep learning approach for extracting entities and relationships from medical texts

This Work Presents A Two-Stage Deep Learning System For Named Entity Recognition (Ner) And Relation Extraction (Re) From Medical Texts. These Tasks Are A Crucial Step To Many Natural Language Understanding Applications In The Biomedical Domain. Automatic Medical Coding Of Electronic Medical Records, Automated Summarizing Of Patient Records, Automatic Cohort Identification For Clinical Studies, Text Simplification Of Health Documents For Patients, Early Detection Of Adverse Drug Reactions Or Automatic Identification Of Risk Factors Are Only A Few Examples Of The Many Possible Opportunities That The Text Analysis Can Offer In The Clinical Domain. In This Work, Our Efforts Are Primarily Directed Towards The Improvement Of The Pharmacovigilance Process By The Automatic Detection Of Drug-Drug Interactions (Ddi) From Texts. Moreover, We Deal With The Semantic Analysis Of Texts Containing Health Information For Patients. Our Two-Stage Approach Is Based On Deep Learning Architectures. Concretely, Ner Is Performed Combining A Bidirectional Long Short-Term Memory (Bi-Lstm) And A Conditional Random Field (Crf), While Re Applies A Convolutional Neural Network (Cnn). Since Our Approach Uses Very Few Language Resources, Only The Pre-Trained Word Embeddings, And Does Not Exploit Any Domain Resources (Such As Dictionaries Or Ontologies), This Can Be Easily Expandable To Support Other Languages And Clinical Applications That Require The Exploitation Of Semantic Information (Concepts And Relationships) From Texts...This work was supported by the Research Program of the Ministry of Economy and Competitiveness - Government of Spain, (DeepEMR project TIN2017-87548-C2-1-R)