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

Compatibility of Breeding Techniques in Organic Systems

Introduction The rapid development of genetic engineering techniques is leading to a level of genetic disruption never experienced before. In order to safeguard organic integrity and to ensure organic food will continue to meet the highest consumer expectations in this challenging situation, IFOAM - Organics International is proposing a number of measures to be put in place to further fortify and enhance the organic sector’s available genetic resources. This position paper provides clarity and transparency on the criteria used by the organic sector as to what breeding techniques are compatible with organic systems, which techniques to exclude, and definitions on what should be considered as genetic engineering and genetically modified organisms (GMOs). We further differentiate between the criteria relevant for organic breeding as defined in the IFOAM – Organics International norms, versus the criteria for cultivars and breeds derived from nonorganic breeding programs regarding their compatibility for the use in commercial organic production and processing. The following experts are members of the IFOAM Working Group on New Plant Breeding Techniques: Michael Glos, Monika Messmer, Gebhard Rossmanith, Gunter Backes, Michael Sligh, Adrian Rodriguez-Burruezo, Heli Matilainen, Andre Leu, Louise Luttikholt, Helen Jensen, Eric Gall, Chito Medina, Krishna Prasad, Kirsten Arp

A study of patent thickets

Report analysing whether entry of UK enterprises into patenting in a technology area is affected by patent thickets in the technology area

Can Post-Grant Reviews Improve Patent System Design? A Twin Study of US and European Patents

This paper assesses the impact of adopting a post-grant review institution in the US patent system by comparing the “opposition careers” of European Patent Office (EPO) equivalents of litigated US patents to those of a control group of EPO patents. We demonstrate several novel methods of "twinning" US and European patents and investigate the implications of employing these different methods in our data analysis. We find that EPO equivalents of US litigated patent applications are more likely to be awarded EPO patent protection than are equivalents of unlitigated patents, and the opposition rate for EPO equivalents of US litigated patents is about three times higher than for equivalents of unlitigated patents. Patents attacked under European opposition are shown to be either revoked completely or narrowed in about 70 percent of all cases. For EPO equivalents of US litigated patents, the appeal rate against opposition outcomes is considerably higher than for control-group patents. Based on our estimates, we calculate a range of net welfare benefits that would accrue from adopting a post-grant review system. Our results provide strong evidence that the United States could benefit substantially from adopting an administrative post-grant patent review, provided that the post-grant mechanism is not too costly

After Heparin: Protecting Consumers From the Risks of Substandard and Counterfeit Drugs

Based on case studies, examines globalization and quality management trends in pharmaceutical manufacturing, barriers to Federal Drug Administration oversight, and the security of pharmaceutical distribution. Makes policy recommendations to ensure safety

What Patent Attorney Fee Awards Really Look Like

This Essay provides an empirical account of attorney fee awards over the last decade of patent litigation. Given the current attention in legislative proposals and on the Supreme Court’s docket to more liberal fee shifting as a check on abusive patent litigation, a fuller descriptive understanding of the current regime is of utmost importance to forming sound patent-litigation policy. Following a brief overview of judicial experience in patent cases and trends in patent-case filing, this study presents analysis of over 200 attorney fee award orders from 2003–2013

Information extraction from chemical patents

The automated extraction of semantic chemical data from the existing literature is demonstrated. For reasons of copyright, the work is focused on the patent literature, though the methods are expected to apply equally to other areas of the chemical literature. Hearst Patterns are applied to the patent literature in order to discover hyponymic relations describing chemical species. The acquired relations are manually validated to determine the precision of the determined hypernyms (85.0%) and of the asserted hyponymic relations (94.3%). It is demonstrated that the system acquires relations that are not present in the ChEBI ontology, suggesting that it could function as a valuable aid to the ChEBI curators. The relations discovered by this process are formalised using the Web Ontology Language (OWL) to enable re-use. PatentEye – an automated system for the extraction of reactions from chemical patents and their conversion to Chemical Markup Language (CML) – is presented. Chemical patents published by the European Patent Office over a ten-week period are used to demonstrate the capability of PatentEye – 4444 reactions are extracted 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 are extracted from the text using OSCAR3, which is developed to greatly increase recall. The resulting system is presented as a significant advancement towards the large-scale and automated extraction of high-quality reaction information. Extended Polymer Markup Language (EPML), a CML dialect for the description of Markush structures as they are presented in the literature, is developed. Software to exemplify and to enable substructure searching of EPML documents is presented. Further work is recommended to refine the language and code to publication-quality before they are presented to the community.Unileve

Data production methods for harmonized patent statistics : patentee name harmonization.

Patent documents are one of the most comprehensive data sources on technology development. As such, they provide a unique source of information to analyze and monitor technological performance. Patent indicators are now used by companies and by policy and government agencies alike to assess technological progress on the level of regions, countries, domains, and even specific entities such as companies, universities and individual inventors. In this paper, we develop a comprehensive method to achieve harmonization of patentee names in an automated way so that analysis at the level of patentees can be facilitated. The method has been applied to an extensive set of all patentee names found for all EPO patent applications published between 1978 and 2004 and all granted USPTO patents published between 1991 and 2003. As completeness (the extent to which the name-harmonization procedure is able to capture all name variants of the same patentee ) and accuracy (the extent to which the name-harmonization procedure correctly allocates name variants to a single, harmonized patentee name ) do not go hand in hand, priority has been given to accuracy. Before discussing in detail the methodology and its effects as applied to the EPO and USPTO patentee name list, we will first clarify the difference between patentee name harmonization and legal entity identification. In addition, we will briefly expand on the methods and approaches previously developed to address the issue of patentee name harmonization, in order to shed light on our specific contribution. Finally, future refinements and extensions are discussed.Agency; Applications; EPO; USPTO; Name harmonization; Information;

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