15 research outputs found
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
Robust and Collective Entity Disambiguation through Semantic Embeddings
Entity disambiguation is the task of mapping ambiguous terms in natural-language text to its entities in a knowledge base. It finds its application in the extraction of structured data in RDF (Resource Description Framework) from textual documents, but equally so in facilitating artificial intelligence applications, such as Seman-tic Search, Reasoning and Question & Answering. We propose a new collective, graph-based disambiguation algorithm utilizing semantic entity and document embeddings for robust entity disam-biguation. Robust thereby refers to the property of achieving better than state-of-the-art results over a wide range of very different data sets. Our approach is also able to abstain if no appropriate entity can be found for a specific surface form. Our evaluation shows, that our approach achieves significantly (>5%) better results than all other publicly available disambiguation algorithms on 7 of 9 datasets without data set specific tuning. Moreover, we discuss the influence of the quality of the knowledge base on the disambigua-tion accuracy and indicate that our algorithm achieves better results than non-publicly available state-of-the-art algorithms