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

mARC: Memory by Association and Reinforcement of Contexts

This paper introduces the memory by Association and Reinforcement of Contexts (mARC). mARC is a novel data modeling technology rooted in the second quantization formulation of quantum mechanics. It is an all-purpose incremental and unsupervised data storage and retrieval system which can be applied to all types of signal or data, structured or unstructured, textual or not. mARC can be applied to a wide range of information clas-sification and retrieval problems like e-Discovery or contextual navigation. It can also for-mulated in the artificial life framework a.k.a Conway "Game Of Life" Theory. In contrast to Conway approach, the objects evolve in a massively multidimensional space. In order to start evaluating the potential of mARC we have built a mARC-based Internet search en-gine demonstrator with contextual functionality. We compare the behavior of the mARC demonstrator with Google search both in terms of performance and relevance. In the study we find that the mARC search engine demonstrator outperforms Google search by an order of magnitude in response time while providing more relevant results for some classes of queries

Facilitating Technology Transfer by Patent Knowledge Graph

Technologies are one of the most important driving forces of our societal development and realizing the value of technologies heavily depends on the transfer of technologies. Given the importance of technologies and technology transfer, an increasingly large amount of money has been invested to encourage technological innovation and technology transfer worldwide. However, while numerous innovative technologies are invented, most of them remain latent and un-transferred. The comprehension of technical documents and the identification of appropriate technologies for given needs are challenging problems in technology transfer due to information asymmetry and information overload problems. There is a lack of common knowledge base that can reveal the technical details of technical documents and assist with the identification of suitable technologies. To bridge this gap, this research proposes to construct knowledge graph for facilitating technology transfer. A case study is conducted to show the construction of a patent knowledge graph and to illustrate its benefit to finding relevant patents, the most common and important form of technologies