PIUG: Patent Information Users Group, Inc.: A History of The International Society for Patent Information Professionals

Efforts to view and analyze patents began soon after the first patents were filed in the novel system founded in the U.S. Constitution. In the succeeding 200 plus years, classification and indexing tools have evolved from paper to digital, with searching demanding ever-higher skills. Answering the need of patent researchers and analysts for advocacy, scholarship, and professional education, leading searchers founded the Patent Information Users Group, Inc., now the pre-eminent professional organization for patent searchers in the United States. It offers formal coursework for prospective patent searchers, colloquia, and conferences where novice searchers can master their craft. Searchers, who often work in isolation, benefit from the support network and collegiality of PIUG. Patent searching is both challenging and rewarding. It is vital for individuals seeking to secure rights to intellectual property and contributes to research in many fields: history, economics, finance, management, sociology, law, medicine, and government policy. It is a career path for academic and special librarians with knowledge of the sciences behind the inventions and is a core skill for those preparing for careers in the sciences and technology fields. Skills and applications for patent knowledge receive little treatment in college curriculum, leaving it to the individual to discover the range of tools, strategies, and practical uses of patents. This article describes the developments in patent searching technology and the work of PIUG’s founders and members that led to its creation, growth, and successes in professional education, advocacy, and outreach. Keywords: PIUG, patent searchers, professional education, librarian

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

Science Inside Law: The Making of a New Patent Class in the International Patent Classification

Recent studies of patents have argued that the very materiality and techniques of legal media, such as the written patent document, are vital for the legal construction of a patentable invention. Developing the centrality placed on patent documents further, it becomes important to understand how these documents are ordered and mobilized. Patent classification answers the necessity of making the virtual nature of textual claims practicable by linking written inscription to bureaucracy. Here, the epistemological organization of documents overlaps with the grid of patent administration. How are scientific inventions represented in such a process? If we examine the process of creating a new patent category within the International Patent Classification (IPC), it becomes clear that disagreements about the substance of the novel inventive subject matter have been resolved by computer simulations of patent documents in draft classifications. The practical needs of patent examiners were the most important concerns in the making of a new category. Such a lack of epistemological mediation between the scientific and legal identities of an invention depicts a legal understanding that science is already inside patent law. From an internal legal perspective, the self-referential introduction of the new patent category may make practical sense; however it becomes problematic from a technological and scientific standpoint as the remit of the patent classification also affects other social contexts and practice

Patent Landscape of Influenza A Virus Prophylactic Vaccines and Related Technologies

Executive Summary: This report focuses on patent landscape analysis of technologies related to prophylactic vaccines targeting pandemic strains of influenza. These technologies include methods of formulating vaccine, methods of producing of viruses or viral subunits, the composition of complete vaccines, and other technologies that have the potential to aid in a global response to this pathogen. The purpose of this patent landscape study was to search, identify, and categorize patent documents that are relevant to the development of vaccines that can efficiently promote the development of protective immunity against pandemic influenza virus strains. The search strategy used keywords which the team felt would be general enough to capture (or “recall”) the majority of patent documents which were directed toward vaccines against influenza A virus. After extensive searching of patent literature databases, approximately 33,500 publications were identified and collapsed to about 3,800 INPADOC families. Relevant documents, almost half of the total, were then identified and sorted into the major categories of vaccine compositions (about 570 families), technologies which support the development of vaccines (about 750 families), and general platform technologies that could be useful but are not specific to the problems presented by pandemic influenza strains (about 560 families). The first two categories, vaccines and supporting technologies, were further divided into particular subcategories to allow an interested reader to rapidly select documents relevant to the particular technology in which he or she is focused. This sorting process increased the precision of the result set. The two major categories (vaccines and supporting technologies) were subjected to a range of analytics in order to extract as much information as possible from the dataset. First, patent landscape maps were generated to assess the accuracy of the sorting procedure and to reveal the relationships between the various technologies that are involved in creating an effective vaccine. Then, filings trends are analyzed for the datasets. The country of origin for the technologies was determined, and the range of distribution to other jurisdictions was assessed. Filings were also analyzed by year, by assignee, and by inventor. Finally, the various patent classification systems were mapped to find which particular classes tend to hold influenza vaccine-related technologies. Besides the keywords developed during the searches and the landscape map generation, the classifications represent an alternate way for further researchers to identify emerging influenza technologies. The analysis included creation of a map of keywords, as shown above, describing the relationship of the various technologies involved in the development of prophylactic influenza A vaccines. The map has regions corresponding to live attenuated virus vaccines, subunit vaccines composed of split viruses or isolated viral polypeptides, and plasmids used in DNA vaccines. Important technologies listed on the map include the use of reverse genetics to create reassortant viruses, the growth of viruses in modified cell lines as opposed to the traditional methods using eggs, the production of recombinant viral antigens in various host cells, and the use of genetically-modified plants to produce virus-like particles. Another major finding was that the number of patent documents related to influenza being published has been steadily increasing in the last decade, as shown in the figure below. Until the mid-1990s, there were only a few influenza patent documents being published each year. The number of publications increased noticeably when TRIPS took effect, resulting in publication of patent applications. However, since 2006 the number of vaccine publications has exploded. In each of 2011 and 2012, about 100 references disclosing influenza vaccine technologies were published. Thus, interest in developing new and more efficacious influenza vaccines has been growing in recent years. This interest is probably being driven by recent influenza outbreaks, such as the H5N1 (bird flu) epidemic that began in the late 1990s and the 2009 H1N1 (swine flu) pandemic. The origins of the vaccine-related inventions were also analyzed. The team determined the country in which the priority application was filed, which was taken as an indication of the country where the invention was made or where the inventors intended to practice the invention. By far, most of the relevant families originated with patent applications filed in the United States. Other prominent priority countries were the China and United Kingdom, followed by Japan, Russia, and South Korea. France was a significant priority country only for supporting technologies, not for vaccines. Top assignees for these families were mostly large pharmaceutical companies, with the majority of patent families coming from Novartis, followed by GlaxoSmithKline, Pfizer, U.S. Merck (Merck, Sharpe, & Dohme), Sanofi, and AstraZeneca. Governmental and nonprofit institutes in China, Japan, Russia, South Korea and the United States also are contributing heavily to influenza vaccine research. Lastly, the jurisdictions were inventors have sought protection for their vaccine technologies were determined, and the number of patent families filing in a given country is plotted on the world map shown on page seven. The United States, Canada, Australia, Japan, South Korea and China have the highest level of filings, followed by Germany, Brazil, India, Mexico and New Zealand. However, although there are a significant number of filings in Brazil, the remainder of Central and South America has only sparse filings. Of concern, with the exception of South Africa, few other African nations have a significant number of filings. In summary, the goal of this report is to provide a knowledge resource for making informed policy decisions and for creating strategic plans concerning the assembly of efficacious vaccines against a rapidly-spreading, highly virulent influenza strain. The team has defined the current state of the art of technologies involved in the manufacture of influenza vaccines, and the important assignees, inventors, and countries have been identified. This document should reveal both the strengths and weaknesses of the current level of preparedness for responding to an emerging pandemic influenza strain. The effects of H5N1 and H1N1 epidemics have been felt across the globe in the last decade, and future epidemics are very probable in the near future, so preparations are necessary to meet this global health threat

The Monty Hyams Archive: A New Resource in Information Science History

The Monty Hyams Archive stands as an important source of information history. This project seeks to organise and investigate the contents of the Archive while providing information on standards application to the care of the Archive. Through the research methodologies of literary warrant analysis, documentary analysis, and historical research, this dissertation proposed standards for future care of the archive, inspected the documents, and evaluated their contents and assigned descriptions. Interviews and historical research were used to expand on the information found in the documents. The descriptions generated were used to discern the major themes within the Archive and to develop an argument for The Monty Hyams as a crucial information science and patent information history resource. The project resulted in the description of the Archive’s contents, a proposed framework of standards with which to care for the Archive, and a confirmation of the argument that The Monty Hyams Archive exists as an important source of information history

Patent Landscape of Helminth Vaccines and Related Technologies

Executive Summary This report focuses on patent landscape analysis of technologies related to vaccines targeting parasitic worms, also known as helminths. These technologies include methods of formulating vaccines, methods of producing of subunits, the composition of complete vaccines, and other technologies that have the potential to aid in a global response to this pathogen. The purpose of this patent landscape study was to search, identify, and categorize patent documents that are relevant to the development of vaccines that can efficiently promote the development of protective immunity against helminths. The search strategy used keywords which the team felt would be general enough to capture (or “recall”) the majority of patent documents which were directed toward vaccines against helminths. After extensive searching of patent literature databases, approximately 2847 publications were identified and collapsed to about 446 INPADOC families. Relevant patent families, almost half of the total relevant families (210 being total number of relevant families), were then identified and sorted into the categories of trematodes, cestodes, nematodes or nonspecific helminth. The 210 patent families that were divided into these four major categories were then further divided into sub categories relating to common fields of technology (e.g. DNA vaccine, vaccine formulations, methods to produce subunits) This sorting process increased the precision of the result set. The four major categories (cestodes, nematodes, trematodes, and non specific applications) as well as the overall data set of the 210 relevant family members were subjected to a range of analytics in order to extract as much information as possible from the dataset. First, patent landscape maps were generated to assess the accuracy of the sorting procedure and to reveal the relationships between the various technologies that are involved in creating an effective vaccine. Then, filings trends are analyzed for the overall dataset of the 210 relevant families as well as by the categories of trematodes, cestodes, and nematodes. The country of origin each member of the 210 relevant families was determined, and the range of distribution to other jurisdictions was assessed. Filings were also analyzed by year, by assignee. Finally, the various patent classification systems were mapped to find which particular classes tend to hold helminth vaccine-related technologies. Besides the keywords developed during the searches and the landscape map generation, the classifications represent an alternate way for further researchers to identify emerging helminth vaccine technologies. The analysis included creation of a map of keywords describing the relationship of the various technologies involved in the development of helminth vaccines. The map has regions corresponding to plasmids and other gene based technologies used in DNA vaccines for Japonicum Schistosoma. Important technologies listed on the map include the use of reverse genetics to create reassorted viruses targeted for the use in veterinary applications. Additionally, the map suggests that numerous subunits exist for use in vaccines targeting cestodes, trematodes, and nematodes. Another major finding was that the number of patent documents related to helminths being published has been steadily increasing in the last decade, as shown in the figure below. Until the early-1990s, there were only a few helminth vaccine related patent documents being published each year. The number of publications increased noticeably when TRIPS took effect, resulting in publication of patent applications. However, since 2006 the number of vaccine publications has exploded. In the years 2011 and 2012, about 23 references disclosing parasitic worm vaccine technologies were published each year. Thus, interest in developing new and more efficacious helminth vaccines has been growing in recent years. The origin of the vaccine-related inventions was also analyzed. The team determined the country in which the priority application was filed, which was taken as an indication of the country where the invention was made or where the inventors intended to practice the invention. By far, most of the relevant families originated with patent applications filed in the United States and China. Other prominent priority countries were the United Kingdom, Japan, Brazil, Australia and France. Countries with the most filings were also analyzed. Countries that were heavily targeted for patent filings included the United States, Australia, Canada, and New Zealand. Top assignees for these families were mostly large pharmaceutical companies, with the majority of patent families coming from Heska, followed by Merck & Co., Institute Pasteur, AusBiotech Biotechnology, and Biological Sciences Research Council. Lastly, the jurisdictions were inventors have sought protection for their vaccine technologies were determined, and the number of patent families filing in a given country is plotted on the world map shown (Fig. 25). The United States, Canada, Australia, Japan, New Zealand and France have the highest level of filings, followed by Germany, Brazil, India, United Kingdom and Spain. However, although there are a significant number of filings in Brazil, the remainder of Central and South America has only sparse filings. Of concern, with the exception of South Africa, few other African nations have a significant number of filings. In summary, the goal of this report is to provide a knowledge resource for making informed policy decisions and for creating strategic plans concerning the assembly of vaccines targeting highly prevalent helminth infections. The ITTI team has defined the current state of the art of technologies involved in the manufacture of helminth vaccines, and the important assignees, inventors, and countries have been identified. This document should aid in evaluating the current state of vaccines technologies targeting helminths and the potential outgrows of these technological fields. Furthermore, as this report illustrates, the steady increase in helminth patenting, expanded diversity of assignees and greater global filings, indicates that intellectual property protection does not inhibit the development of crucial innovations for this class of neglected diseases, but, on the contrary, appears to be a driver of accelerated research and development

A review of molecular representation in the age of machine learning

Funder: UCB; Id: http://dx.doi.org/10.13039/100011110Abstract: Research in chemistry increasingly requires interdisciplinary work prompted by, among other things, advances in computing, machine learning, and artificial intelligence. Everyone working with molecules, whether chemist or not, needs an understanding of the representation of molecules in a machine‐readable format, as this is central to computational chemistry. Four classes of representations are introduced: string, connection table, feature‐based, and computer‐learned representations. Three of the most significant representations are simplified molecular‐input line‐entry system (SMILES), International Chemical Identifier (InChI), and the MDL molfile, of which SMILES was the first to successfully be used in conjunction with a variational autoencoder (VAE) to yield a continuous representation of molecules. This is noteworthy because a continuous representation allows for efficient navigation of the immensely large chemical space of possible molecules. Since 2018, when the first model of this type was published, considerable effort has been put into developing novel and improved methodologies. Most, if not all, researchers in the community make their work easily accessible on GitHub, though discussion of computation time and domain of applicability is often overlooked. Herein, we present questions for consideration in future work which we believe will make chemical VAEs even more accessible. This article is categorized under: Data Science > Chemoinformatic

Similarity Methods in Chemoinformatics

promoting access to White Rose research paper

Chemical Information Bulletin

Created as a supplement for "the regular journals of the American Chemical Society," this publication contains annotated bibliographies of chemical documentation literature as well as information about meetings, conferences, awards, scholarships, and other news from the American Chemical Society (ACS) Division of Chemical Information (CINF)

Chemical Information Bulletin

Periodic supplement for "the regular journals of the American Chemical Society," containing annotated bibliographies of chemical documentation literature as well as information about meetings, conferences, awards, scholarships, and other news from the American Chemical Society (ACS) Division of Chemical Literature