Patents in combi-space: patent challenges in combinatorial chemistry

Patent protection of inventions relating to combinatorial chemistry is attended by special challenges. The "breakthrough" nature of the field together with the always complex and often arcane chemical manipulations, apparatus, and strategies which suffuse this field make it difficult to describe the inventions adequately. It can be a challenge to communicate effectively with official authorities charged with patent examination. Extraordinary effort is called for in clarifying such inventions such that their patentability can be appreciated. The utility of some types of inventions in this field may be open to question; clear statements of at least one acceptable utility-even if only a minor utility-is beneficial. Because a principal product of many aspects of combinatorial chemistry is information, e.g., the identification of a lead compound, offshore "piracy" is a risk. Domestic claim tie-ins may improve the ability to abate such piracy. Copyright 1998 John Wiley & Sons, Inc.     

Patenting nonassociated polymeric structures (NAPS): implications for structural genomic data release

The intellectual property laws that govern patent rights should provide a reasonable balance between the competing concerns of open access and exclusivity. Open access can facilitate knowledge dissemination and collaboration in furthering science. On the other hand, exclusivity can ensure interest and financial investment in scientific research and development.In recent days, the appropriate balance between open access and exclusivity has been a focus of public debate, particularly with regard to genomic inventions and their applications. In seeking to reconcile the timing of structural genomic data release with certain efforts to secure intellectual property rights, the International Structural Genomics Organisation joins others confronting this controversy.This paper seeks to inform the discussion with an overview of the U.S. standards for patenting nonassociated polymeric structures (NAPS), which include polynucleotides or polypeptides of unknown biological significance, and their corresponding structural data. In the United States, the present ability to obtain patent rights to these discoveries appears problematic given the requirement of specific, substantial and credible utility, among other things. Without demonstrable utility, NAPS and NAPS-related data likely will not be entitled to patent protection, whether the U.S. Patent & Trademark Office rejects NAPS claims as unpatentable in the first instance, or the U.S. federal courts invalidate NAPS claims in later patent litigation. As such, the improbability of obtaining enforceable patent rights to NAPS might undermine the rationale for delaying structural genomic data release to allow for the filing of patent applications in this regard.Abbreviations: ESTs, expressed sequence tags; ISGO, International Structural Genomics Organisation; NAPS, nonassociated polymeric structures; SNPs, single nucleotide polymorphisms; USPTO, U.S. Patent & Trademark Office     

United States patents and microbes

This article reviews the current state of patent availability in the United States for microbiological inventions and the current controversy as to the patentability of microbes as products. It also sums up the practical value of American patents.     

Patenting in biotechnology: a review of the 20th Symposium of ECB8

The patenting of biotechnological inventions is practically in harmony with the general requirements of patent protection. It stands still in the foreground of interests since this is the only technical field where the living material itself may be the subject matter of patents. In consequence ethical problems have arisen first of all in the patenting of human cells and genes in which there is no agreement between R&D firms, patent offices and green movements. This has called for the elaboration of special Directives. On the other hand, patent systems are instrumental in safeguarding biodiversity. This review gives a picture of the patenting situation in biotechnology in the European Patent Office and in Hungary, the host country of the Congress. It also gives practical advice to biotechnological researchers on how to draft the applications and to observe the time limits, as well as on the necessity and possibilities of the deposit of microorganisms.     

Invisible genomes: the genomics revolution and patenting practice

In the mid-1990s, the company Human Genome Sciences submitted three potentially revolutionary patent applications to the US Patent and Trademark Office, each of which claimed the entire genome sequence of a microorganism. The patent examiners, however, objected to these applications, and after negotiation they were eventually re-written to resemble more traditional gene patents. In this paper, which is based on a study of the patent examination files, we examine the reasons why these patent applications were unsuccessful in their original form. We show that with respect to utility and novelty, the patent attorney's case built on an understanding of the genome as a computer-related invention. The patent examiners did not object to the patenting of complete genome sequences as computer-related inventions on moral grounds or in terms of the distinction between a discovery and an invention. Instead, their objections were based on classification, rules and procedure. Rather than patent examiners having a notion of a genome that should not be patented, the notion of a 'genome', and the ways in which it may be different from a 'gene', played no role in these debates. We discuss the consequences of our findings for patenting in the biosciences.     

Enabling Policy Planning and Innovation Management through Patent Information and Co-Authorship Network Analyses: A Study of Tuberculosis in Brazil

Introduction

New tools and approaches are necessary to facilitate public policy planning and foster the management of innovation in countries'' public health systems. To this end, an understanding of the integrated way in which the various actors who produce scientific knowledge and inventions in technological areas of interest operate, where they are located and how they relate to one another is of great relevance. Tuberculosis has been chosen as a model for the present study as it is a current challenge for Brazilian research and innovation.

Methodology

Publications about tuberculosis written by Brazilian authors were accessed from international databases, analyzed, processed with text searching tools and networks of coauthors were constructed and visualized. Patent applications about tuberculosis in Brazil were retrieved from the Brazilian National Institute of Industrial Property (INPI) and the European Patent Office databases, through the use of International Patent Classification and keywords and then categorized and analyzed.

Results/Conclusions

Brazilian authorship of articles about tuberculosis jumped from 1% in 1995 to 5% in 2010. Article production and patent filings of national origin have been concentrated in public universities and research institutions while the participation of private industry in the filing of Brazilian patents has remained limited. The goals of national patenting efforts have still not been reached, as up to the present none of the applications filed have been granted a patent. The analysis of all this data about TB publishing and patents clearly demonstrates the importance of maintaining the continuity of Brazil''s production development policies as well as government support for infrastructure projects to be employed in transforming the potential of research. This policy, which already exists for the promotion of new products and processes that, in addition to bringing diverse economic benefits to the country, will also contribute to effective dealing with public health problems affecting Brazil and the World.     

An assessment of emerging molecular farming activities based on patent analysis (2002∼2006)

The products of Plant Molecular Farming are recombinant proteins or their metabolic products. In this study, patent data was employed to assess industrial trend in the research and innovation process of Plant Molecular Farming within national and international context. The US Patent and Trade Organization (USPTO), the European Patent Office (EPO) issued a total of 585 patents covering Plant Molecular Farming from 2002 through 2006. By nationality, US inventors predominated as recipients of PMF patents, followed by Germany, Denmark, and Japan. The PMF patents were catagorized in five major areas of research namely pharmaceutical and nutraceuticals with 170 patents (31%) and plant expression tools and methods for alternative production systems with 169 patents (29%) were the dominating patent applications, followed by 102 patent claims associated with antibodies (17%), 71 patents of industrial molecules (12%), 48 patents of vaccines (8%), and finally 18 patents related to post-translational protein glycosylation (3%). The greatest proportion of patentees was of US origin (52%), and PMF associated patenting activities at the USPTO and EPO were dominated with 67% by private organizations. Disclaimer: The views expressed in this study do not necessarily reflect those of the European Commission.     

Bioinformatics -- a patenting view

The use of bioinformatics in the biological sciences has brought about a change in the way that biological inventions can be protected by patent laws. Using approaches developed in the fields of computer science and business, patent applicants now seek to protect certain aspects of their inventions, which include software, methods of doing business and uses of information as well as more traditional biotechnological products and processes. These approaches are useful in resolving some of the difficulties now faced in prosecuting patent applications directed to biological inventions that are claimed in more conventional terms.     

Technology Resource,Distribution, and Development Characteristics of Global Influenza Virus Vaccine: A Patent Bibliometric Analysis

Influenza virus vaccine (IVV) is a promising research domain that is closely related to global health matters, which has been acknowledged not only by scientists and technology developers, but also by policy-makers. Meanwhile, patents encompass valuable technological information and reflect the latest technological inventions as well as the innovative capability of a nation. However, little research has examined this up-and-coming research field using patent bibliometric method. Thus, this paper (a) designs the technology classification system and search strategy for the identification of IVV; and (b) presents a longitudinal analysis of the global IVV development based on the European Patent Office (EPO) patents. Bibliometric analysis is used to rank countries, institutions, inventors and technology subfields contributing to IVV technical progress. The results show that the global trends of IVV are a multi-developing feature of variety but an uneven technical resource distribution. Although the synthetic peptide vaccine is a comparatively young field, it already demonstrates the powerful vitality and the enormous development space. With the worldwide competition increasing, all nations especially China should be looking to increase devotion, enhance capability and regard effectiveness of technological innovation.     

Characteristics of genetic material with reference to patent documents

Characteristics of genetic material: plasmids, vectors, recombinant DNA and DNA fragments were, studied from 235 patent documents. These documents were from the patent offices of the Federal, Republic of Germany (38), the German Democratic Republic (15), the European Patent Office (53), Finland (43), Great Britain (65), the Soviet Union (3), and the United States of America (18). Attention was paid also to the terminology used in the patent documents. According to this study the way in which the genetic material was characterized in patent documents of different countries was quite variable, and the terminology used was sometimes confusing.     

Annotated Chemical Patent Corpus: A Gold Standard for Text Mining

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.     

Patentability of life and ethics

Patent law has relied in part on ethical considerations since its inception in Europe. Such considerations have been introduced more recently in the United States. Whereas the EU Directive on the protection on the occasion of the Human Genome Project of biotechnological inventions was intended to foster economic development in Europe, its implementation is outweighted by controversy about patenting life and commercialization of science. The confusion created must be cleared at the international level through harmonization of patent office policies preventing abusive commercial practices in the absence of inventiveness.     

Patentes fúngicas: de Pasteur a nuestros días

At the end of the 19^th century, the American Patent Office granted the patent known as “Pasteur's application”, claiming the protection of a yeast strain. Since that date, the debate around biotechnology patents, especially for those that affect living organisms or part of them, has grown exponentially.In the present article, the Patent Law is reviewed, pointing out the particular problems about fungi or parts of them. Also, some of the fungus patents are discussed from the perspective of the ethical, economical, social and environmental aspects of these kind of patents.     

Evaluation of brazilian biotechnology patent activity from 1975 to 2010

The analysis of patent activity is one methodology used for technological monitoring. In this paper, the activity of biotechnology-related patents in Brazil were analyzed through 30 International Patent Classification (IPC) codes published by the Organization for Economic Cooperation and Development (OECD). We developed a program to analyse the dynamics of the major patent applicants, countries and IPC codes extracted from the Brazilian Patent Office (INPI) database. We also identified Brazilian patent applicants who tried to expand protection abroad via the Patent Cooperation Treaty (PCT). We had access to all patents published online at the INPI from 1975 to July 2010, including 9,791 biotechnology patent applications in Brazil, and 163 PCTs published online at World Intellectual Property Organization (WIPO) from 1997 to December 2010. To our knowledge, there are no other online reports of biotechnology patents previous to the years analyzed here. Most of the biotechnology patents filed in the INPI (10.9%) concerned measuring or testing processes involving nucleic acids. The second and third places belonged to patents involving agro-technologies (recombinant DNA technology for plant cells and new flowering plants, i.e. angiosperms, or processes for obtaining them, and reproduction of flowering plants by tissue culture techniques). The majority of patents (87.2%) were filed by nonresidents, with USA being responsible for 51.7% of all biotechnology patents deposited in Brazil. Analyzing the resident applicants per region, we found a hub in the southeast region of Brazil. Among the resident applicants for biotechnology patents filed in the INPI, 43.5% were from S?o Paulo, 18.3% were from Rio de Janeiro, and 9.7% were from Minas Gerais. Pfizer, Novartis, and Sanofi were the largest applicants in Brazil, with 339, 288, and 245 biotechnology patents filed, respectively. For residents, the largest applicant was the governmental institution FIOCRUZ (Oswaldo Cruz Foundation), which filed 69 biotechnology patents within the period analyzed. The first biotechnology patent applications via PCT were submitted by Brazilians in 1997, with 3 from UFMG (university), 2 from individuals, and 1 from EMBRAPA (research institute).     

Patenting of plant varieties and plant breeding methods

This article considers the relationship between patenting and plant variety rights protection, through a detailed analysis of the recent determination by the Extended Board of Appeal of the European Patent Office that methods for breeding broccoli and tomatoes were not patentable. It concludes that the right to patent agricultural innovations is increasingly located within a political context.     

Strategic mining of cyanobacterial patents from the USPTO patent database and analysis of their scope and implications

Patent analysis with the help of the strategic mining of patents from databases is important and useful within the framework of application-oriented research and its commercialization. In the analysis reported here, we have mined cyanobacterial patents from the patent database of the United States Patent and Trademark Office (USPTO). In order to make an assessment of the commercial potentials of cyanobacteria, we conducted the patent search (from 1976 to April 2006) using certain generic terms and the 84 genera of cyanobacteria as keywords. The search was performed in two major ways – searching the abstracts and claims of the patents cumulatively and searching the entire patent documents by the mode of ‘all fields’ in USPTO. In the abstract- and claims-based search, 234 patents were obtained after the removal of overlapping patents among the keywords. An additional 31 patents were added following the ‘all fields’ search; these patents were not covered in the search that was based on abstracts and claims. The entire package of 265 patents, of which 244 were related to cyanobacteria, was then analyzed. Information derived from these patents identified five major areas of cyanobacterial utilization. Cyanobacteria have been patented as a source of a wide spectrum of products, for medical, agriculture and environmental applications, for gene-based products, for methods of cultivation and for methods of control. The chronological development in granting cyanobacterial patents was also traced. This study demonstrates that such strategic mining and analysis of patent data can be used as an index for future development.     

Antagonistic effects of Schistosoma mansoni on superimposed Hymenolepis diminuta and H. microstoma infections in mice

Patent, but not prepatent, Schistosoma mansoni infections in mice enhanced the expulsion of a superimposed infection with Hymenolepis diminuta. An antagonistic effect was also directed against a superimposed H. microstoma infection in mice harbouring patent S. mansoni infections.     

Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures

In order to bridge the gap between proteins with three-dimensional (3-D) structural information and those without 3-D structures, extensive experimental and computational efforts for structure recognition are being invested. One of the rapid and simple computational approaches for structure recognition makes use of sequence profiles with sensitive profile matching procedures to identify remotely related homologous families. While adopting this approach we used profiles that are generated from structure-based sequence alignment of homologous protein domains of known structures integrated with sequence homologues. We present an assessment of this fast and simple approach. About one year ago, using this approach, we had identified structural homologues for 315 sequence families, which were not known to have any 3-D structural information. The subsequent experimental structure determination for at least one of the members in 110 of 315 sequence families allowed a retrospective assessment of the correctness of structure recognition. We demonstrate that correct folds are detected with an accuracy of 96.4% (106/110). Most (81/106) of the associations are made correctly to the specific structural family. For 23/106, the structure associations are valid at the superfamily level. Thus, profiles of protein families of known structure when used with sensitive profile-based search procedure result in structure association of high confidence. Further assignment at the level of superfamily or family would provide clues to probable functions of new proteins. Importantly, the public availability of these profiles from us could enable one to perform genome wide structure assignment in a local machine in a fast and accurate manner.     

Trematode eggshells: Novel protein biopolymers

In the past few years recombinant DNA technology has somewhat serendipitously shed new light on the formation of trematode eggshells, with the publication of the sequences of highly expressed female-specific genes encoding protein components of the schistosome eggshell and with the isolation of DOPA-rich proteins and one of the corresponding genes from Fasciola. These proteins and other structural polypeptides with repetitive structures were the subject of a recent meeting Bioengineering for Material Applications (sponsored by the Office of Naval Research in Bethesda, USA, June 1987). In this article, based on that meeting, John Cordingley explains how the structure of trematode eggshells appears to show features common to several other biopolymers.