World Patent Information 46 (2016) 21e31
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World Patent Information journal homepage: www.elsevier.com/locate/worpatin
Example of open-source OPS (Open Patent Services) for patent education and information using the computational tool Patent2Net Renato Ribeiro Nogueira Ferraz a, b, *, Luc Quoniam b, David Reymond c, ^ nio Maccari b Emerson Anto a b c
Graduate Program in Management of Health System (PMPA-GSS), Universidade Nove de Julho (UNINOVE), Sao Paulo, SP, Brazil Graduate Program in Management (PPGA), UNINOVE, Sao Paulo, SP, Brazil Interactions, Milieux, M edias, I3M, EA3820, Universit e de Toulon, France
a r t i c l e i n f o
a b s t r a c t
Article history: Received 12 June 2015 Received in revised form 3 May 2016 Accepted 10 May 2016
This paper discusses the use of Patent2Net, an open source software for extracting and making available information on patents related to dengue fever, a neglected disease of high interest to Brazil. Only ten of 1427 dengue-related patents retrieved in the European worldwide database were filed by Brazilian institutions, showing low contribution of technological research in Brazil regarding this disease. The results enable the creation of new indicators, promoting social responsibility in research, since it is expected that scientific research will produce not only high-impact bibliographic production, but also technological products that can effectively further the search for solutions to problems. © 2016 Elsevier Ltd. All rights reserved.
Keywords: Health management Patents Data mining Patent2Net Dengue Neglected diseases
1. Introduction For emerging countries like Brazil, research into patents is of great value. It has been estimated that approximately only 5% of inventions are protected by in force patents, and the protection is mostly in developed countries, whereas the remaining 95% of inventions can be freely replicated, because they are in the public domain [1]. As patent applications are usually published 18 months after the application date, it is possible to identify patent applications of interest by searching different databases. The technical knowledge described in published patent applications can be used to improve upon the described technology or inspire new technology. One obstacle, however, in accessing patent publications via the Internet is that they are usually stored in the deep web. Consequently, surface web research using generic search engines are often unable to locate patent publications or retrieve them in an organized way to enable their evaluation. To facilitate retrieval, specific search engines such as Google Patent Search (www.google.
dio C, 1º. Andar Agua * Corresponding author. Av. Francisco Matarazzo, 612, pre ~o Paulo, SP, CEP 05001-100, Brazil. Branca, Sa E-mail address:
[email protected] (R.R.N. Ferraz). http://dx.doi.org/10.1016/j.wpi.2016.05.002 0172-2190/© 2016 Elsevier Ltd. All rights reserved.
com/patents), Patentscope (http://www.wipo.int/patentscope/en/) and Espacenet (http://worldwide.espacenet.com/) can be used. Despite the existence of a number of databases that enable fulltext searching on millions of patent documents, the objective of conducting a targeted and organized assessment of the content of these documents has proven to be a rather arduous task. Thus, computational tools that can gather patent publications in a local storage and enable preliminary analysis of the content as well as organizing them so that the user can identify what he needs quickly and directly, are essential for enabling further studies of these documents. Some examples of such tools, which use copies of patent databases or web crawlers, are: Intellixir (http://www. intellixir.com/), Matheo Patent (http://www.matheo-software. com/en/), and Patent Inspiration (http://www.patentinspiration. com/), all of which are paid software programs. There are also the open-source Lens software (https://www.lens.org/lens/), and the more recent Patent2net software suite (http://patent2net.vlab4u. info/), also free. Obviously, the high cost of paid software is a major obstacle for the dissemination and use of patent information for students, small and medium sized companies, and emerging and developing countries. A web crawler is a computational tool that surfs the Internet
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Fig. 1. Enlarged print screen of home page with access links containing the results of the analysis of patent applications in respect of various topics provided by Patent2net (the complete print screen is shown in the lower left corner). Source:http://patent2net.vlab4u.info.
automatically, extracting the data in a process known as web scraping. Once the data has been harvested, filtered and cleaned, a data mining and/or text mining process is used to process volumes of information that could not be located using common browsers. This process enables the user to identify significant correlations, patterns and recurring trends in large data sets, such as patent databases, using complex statistical and mathematical techniques [2]. The use of web crawlers for data mining in patent databases is common. Several papers have proposed methods for their use [3,4], and the literature also contains a description of the processes needed for their execution [3,5,6]. Patent2Net (P2N) is an open-source software suite for academic use (education and research) developed at the University of Toulon [7]. It gathers bibliographic data and full-text patents from the European Patent Organization's Espacenet worldwide database. The decision to use Espacenet as the search database rather than, for example, Patentscope, was due to the Application Programming
Interface (API) that Espacenet offers. In general terms, API refers to the set standards and computational routines that allow other applications, such as web crawlers, to use several of its features without necessarily getting involved in complex computer details, but only if one uses the functions for which the software was originally designed. When this function relates to data mining, the release of the API is essential [8]. P2N streamlines the data mining and is quite effective when taking into account the volume and variety of information, and the speed with which it is retrieved. Thus, the use of P2N, which in turn, interacts directly with Espacenet in the search for available patent information, is absolutely legal and transparent, and is an example of an open-source Open Patent Service (OPS) for education and academic research. According to Kallas [9], the OPS is a real and strategic approach to the dissemination of information, helping to make the results of scientific research on any issue more transparent. The results obtained from OPS can relate to technical areas
Fig. 2. Enlarged section of print screen of page with access links containing the results of the analysis of dengue related patent publications collected by Patent2net. Source:http://patent2net.vlab4u.info.
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Fig. 3. Geo-location map of countries in which the highest number of dengue related patent applications have been filed (excluding PCT procedures). Source:http://patent2net.vlab4u.info.
of high importance for a developing nation like Brazil, such as nanotechnology, the handling of rare earths, energy efficiency, biodiversity and neglected diseases. Neglected diseases (ND) are a group of clinical conditions with high prevalence, especially in populations with inadequate socioeconomic conditions. They affect mostly children and contribute to the increase in infant mortality [10], as well as negatively influencing the productive capacity of adults [11]. NDs reflect the social inequality of a country which, in turn, is directly related to precarious local health conditions [12,13]. These diseases are so named because they are not the focus of scientific research, especially research financed by multinational companies in the pharmaceutical industry whose main goal is to develop profitable new drugs. Investments in research for diagnostic methods and the treatment of these diseases is lacking, outdated, and of questionable effectiveness. Investments on the development of vaccines and other preventive methods is also particularly low [13,14]. Despite the fact that NDs have historically been seen as being confined to developing countries, the numbers of individuals affected is increasing in developed countries too, alerting the need for increased global investments in research in this field [15]. Since 2010, Brazil has been considered the developing country with the highest number of ND cases. According to the World Health Organization (WHO) the top ten NDs of interest in Brazil are as follows: Chagas' disease, schistosomiasis, leprosy, leishmaniasis, onchocerciasis, lymphatic filariasis, trachoma, soil-transmitted helminths, rabies and dengue [13,16]. The ND considered to be of the most importance in Brazil is dengue because of the rampant increase in the number of cases in recent years affecting not only individuals living in poor and rural areas, but also those in urban areas of all social classes. To date, there are no vaccines to prevent infection by the dengue virus. The disease epidemic in the country has various serologies and that can lead to the death of the patient [17]. Dengue fever has reached pandemic proportions worldwide,
and is present in more than 120 countries, affecting more than three billion people [16e18]. In the last five decades, the number of cases has increased approximately thirty-fold [19], and there are around seventy million new cases each year, resulting in the occupation of more than half a million-hospital beds [17]. Its main vector, the mosquito Aedes aegypti, is present in urban and rural areas of most cities, being naturally selected to survive in the conditions presented by these environments [20]. Perhaps the factor of most concern is the absence of effective treatments, and the lack of prevention methods for this disease. There are very few methods for controlling the reproduction of vectors, which reflects the paucity of research on a topic of such importance [21]. In short, research into dengue in Brazil and elsewhere has not advanced in keeping with the increasing number of cases of the disease. Despite the considerable bibliographic production on dengue available in the main databases, the technical and technological production, which is only available in curricular and patent databases, seem fairly rudimentary. Although 15,696 scientific papers were published prior to 2013 by Brazilian researchers whose core competence is dengue, only 2,81,278 technology products and processes or techniques had been registered in the Lattes Platform (national mandatory database of scientist curricula) by the same researchers up to that date, demonstrating the low return to society provided by research on dengue in Brazil [22,23]. A core competency is understood as the specialization of a scientist who, based on certain criteria relating to research productivity, is considered to be among the group of most qualified researchers to leverage research on a particular subject [24]. Further, our search of patent publications as described below revealed only 10 patent publications that were filed by Brazilian researchers. In light of these findings, the main purpose of this paper is to present the use of a software suite for patent mining, in order to facilitate consultation and dissemination of technical information to the public. The goal of this analysis is to emphasize the reinvestment of open-source technical patent information for the
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Fig. 4. A: Enlarged print screen of page with interface for analysis of dengue related patent publications, highlighting three patents filed in the United States, and demonstrating the possibility of selecting patent publications according to the country where they were filed, being that 319/1427 are patent publications filed in the United States (the complete print screen is located in the top left corner). B: Enlarged print screen of page with interface for analysis of dengue related patent publications, highlighting three patents filed by Brazilian inventors, demonstrating the possibility of selection according to inventor country. Ten out of 1427 patent publications were filed by Brazilians (the complete print screen is located in top left corner). C: Enlarged print screen of page with interface for analysis of dengue related patent publications, highlighting three patents filed by Brazilian companies. Same objective as Fig. 4B demonstrating the possibility of selection according to the company named as patent applicant (10 out of 1427 patent publications name a Brazilian organization as a patent applicant - the complete print screen is located in top left corner). D: Enlarged print screen of page with interface for analysis of dengue related patent publications, highlighting three patent publications with publication kind code “B”, demonstrating the possibility of selecting according to the publication kind code of a patent publication. Only 37 out of 1427 patent publications were retrieved with a patent publication kind code of “B” (the complete print screen is located in the top left corner). Source:http://patent2net.vlab4u.info.
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Fig. 4. (continued).
benefit of applied research that will benefit the population. 2. Methods The computational databases related to the operation of P2N are
summarized below. The focus of this paper is to present the functionality of the tool for extracting, organizing and presenting the contents of dengue-related patent documents available via Espacenet. The technical presentation of the tool, which was originally developed in Python language, has therefore been left out of this
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Fig. 5. (continued).
text. The tool, which is freely available, can be downloaded by anyone interested in replicating the results presented here, as well as those wishing to perform new searches on any topic of interest. The link is given in the previous section of this paper. In general, P2N sequentially executes various computational modules. Initially, the user must create their own account in the Espacenet database. This will activate the web crawler on the users' database. Once the application has been logged into the database, an alphanumeric key is obtained to allow data mining (the API key, the free API key, or the pay mode from Open Patent Service, depending on the end user's requirements). The program gathers bibliographic data and full text of patents corresponding to the search criteria, and presents the text in a format that enables them to be analyzed. P2N therefore leads to the creation of various networks based on the patents retrieved, for example, networks of
interaction between inventors and the companies filing patent applications, between patent applicants and the countries in which the patent applications are filed, between subject matter and patent classifications, and so on. This analysis should be done using the free software Gephi. Downgraded networks are provided for web communication using gexf. js JavaScript support. The data processing ends with the creation of several files in html format that can be sent to a web server and made available for web consultation. These files also represent a front-end feature of the application. The main patent bibliographic data are exported in json format. The layout and basic UI elements use HTML5, CSS3 and JavaScript to enable visualization of the content, using the popular Data-Driven Documents (D3. js) library [26]. The first data presentation tool used is the DataTable library, which exploits json files to present the patent
Fig. 5. A: Use of a PivotTable to create a line graph showing the increase in the number of patent applications filed that relate to dengue. B: Use of a PivotTable to create an area chart to visualize dengue-related patent publications by country. C: Use of a PivotTable in heatmap format to arrange dengue-related patent publications by patent application date and by country in which the patent applications were filed. D: Use of a PivotTable to track the number of backward citations of each dengue-related patent according to its publication kind code. E: Use of a PivotTable to create a bar graph that allows the user to check the number of dengue-related patent publications filed, according to the assigned patent classification. Source:http://patent2net.vlab4u.info.
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Fig. 6. A: Network of dengue-related patent publications according to their International patent classification. B: Network of inventors of dengue-related patent publications. C: Network of patent applicants that have filed dengue-related patent applications. D: Network of classifications and countries that have filed dengue-related patents. Source:http://patent2net.vlab4u.info.
documents gathered in the form of interactive tables. The P2N tools also use a pivot table.1 The four main strategic benefits of the P2N solution are as follows. C It is free of charge and open source.
1 Pivot table, common Microsoft Excel facility, well known in data mining, it provides counts, identifies apparitions or crossed apparitions of entities such as inventors, applicants, IPC, dates, countries. Pivot table is also known as Pivot Grid, Pivot Chart, Cross-Tab implementation. P2N provide drag'n'drop implementation using the PivotTable.js library developed by N. Kruchten, see http://nicolas. kruchten.com/pivottable) and Three.js, (originally developed by R. Cabello, http:// threejs.org), which allows GPU-accelerated data rendering using WebGL.
C The use of external computational libraries or packages (readily available, free of charge, open source) for specific analysis2 facilitating programming in order to prepare the patent format outputs for the desired library. C These external facilities are selected on the basis they allow the results to be displayed on a common web browser. Thus the P2N results do not need any package installation to be transmitted (on a copy/paste basis) to any computer using any operating system (Windows, Linux, Mac OS).
2 For instance Gephi (networks), data table (displaying or searching), textometry with Iramuteq (text mining of abstracts, descriptions, claims), mind maps of the International Patent Classification (IPC) system, connection with Wikipedia.
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Fig. 6. (continued).
C These external facilities are selected on the basis they allow the end user to interact with the results, enabling better customization and exploration of the results. This aspect is very difficult to show/explain in paper-based articles like this one. The points listed above enable quick and easy programming, with the software working in conjunction with the respective software of the included libraries; they enable the capability to be extended to include new libraries, and maximize the possibilities of contributions and the dissemination of the results, patent use and culture. 3. Results and discussion Fig. 1 shows an enlarged section of the print screen of the home
page with the results of the analysis of patent publications in respect of various subject matter already performed with the P2N prior to the preparation of this work. It can be seen that patent publications on entrepreneurship, kidney stones, masculinity, dengue, among others, have been extracted and processed by the tool, and are available for consultation. To do this, the user simply accesses the page by clicking on the link shown at the bottom of Fig. 1, then clicking on the subject of interest. The user is then directed to the screen shown in Fig. 2, which in this case, shows the links on treatment of patents with dengue, which is the focus of this research. The data were collected on 05 march 2016. The bottom of Fig. 2 shows seven links to access the results of patent publications that include in the title or abstract the word “dengue”. The first enables access to the evaluation interface of the number of patent publications based on multiple determinants (see Fig. 4AeD), and a pivot table that allows the cited determinants to
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be crossed, in order to observe the relationships between them (see Fig. 5AeE). The second enables access to the geo-location map of countries in which patent applications have been filed (see Fig. 3). The third, fourth and fifth links provide access to various network connections between these determinants, built by the tool itself (see Fig. 6AeD). Sixth and seventh links have the same functions as the first and second, nevertheless allowing the evaluation of family patents. Fig. 3 shows the geographical distribution of dengue-related patent publications, using a scaled color scheme, which is explained in the key at the bottom of the figure. The country in which the highest number of patent applications have been filed is the United States, followed by China, Australia, Canada, Japan, Mexico, South Africa and some European and Asian countries. Patent2Net counts patent applications without any regard to patent family, then these numbers included here do not necessarily reflect the true filing pattern across countries as a patent family could for example have many patent applications that are related to each other and are all within the same patent family. The P2N family capability is intended to provide such function in a second step analysis. Future P2N version will exclude INPADOC families in the primary responses sets. Fig. 4AeD shows the print screens from one of the search interfaces created by Patent2net. At this point, it is important to note that the links presented as sources at the bottom of the figures allow access only to the dynamic interface for evaluation of the results. There are no direct links to the figures, as these are only examples to illustrate the present research. It is possible to select the patent publications (1427 in total), based on each indicator shown at the top of the screen. Fig. 4A shows the selection of patent publications by the country where they were filed, highlighting the United States (US) with a total of 319/1427 patent publications. It is interesting to note that regardless of the indicator used for the selection, other indicators related to the selected patents are also available, such as the title of the patent publication, the inventor's name, the applicant's company and country, the international patent classification, the date of the application, the number of citations it has, and its legal status, among other aspects. Fig. 4B shows that while no dengue related patent publications from Brazil were retrieved as of 05 March 2016, ten of the 1427 existing patent publications were filed by Brazilian inventors. Fig. 4C, in turn, shows that only 10 Brazilian companies in total are named as patent applicants across the 1427 results retrieved. It is interesting to note that although Brazil is one of the countries with the highest number of dengue cases in the world [27], our study retrieved a negligible number of Brazilian patent publications on the subject (less than 1% of the total). Thus, in spite of the vast literature on dengue being published by Brazilian researchers [28], any technology arising from the research may not be captured in Brazilian patent applications or the database used in our study did not capture all relevant Brazilian patent publications. Finally, regarding the demonstrations related to the first search interface, Fig. 4D shows the selection of patent publications according to their publication kind code. The publication kind code (e.g. “A”. “B”, “U” etc.) can indicate the type of intellectual property right as well as the stage of publication [25]. These publication kind codes cannot, however, be thought of as indicators of current patent legal status. Legal patent status is very complex and it depends on a very thorough understanding of the patent rules that determine the legal status of patent publications which is beyond the scope of this paper. Fig. 5AeE shows the print screens obtained during the handling of a second analysis interface of dengue related patent publications, provided by Patent2Net, which consists of a pivot table, where the
user can choose the form of representation of the results (line charts, bars and area heatmap, among others) and decide which data will be crossed for analysis in both the X axis and Y axis. Fig. 5A shows a line graph with the quantitative increase in patent applications relating to dengue filed since 1966, identifying peaks in 2000 and 2004, and a steady increase since 2006. For the creation of the area chart shown in Fig. 5B, the country in which the patent was filed was used as an indicator, enabling the prevalence of patent publications worldwide, including China and the United States, to be identified. Fig. 5C shows a heatmap showing the number of patent publications retrieved according to country in which the patent applications were filed as the Y axis and the patent application date as the X axis. As can be seen from Fig. 5C, a total of 319 US patent publications, 213 Chinese patent publications and 93 Australian patent publications were retrieved. Fig. 5D demonstrates the plotting of the number of patent publications that were cited by the 1427 patent publications retrieved (as the Y axis) against different publication kind codes (as the X axis). Finally, Fig. 5E shows a bar graph based on the number of patent publications that have been classified under each of the noted International patent subclasses. The examples provided in Fig. 5eE shows only some data matching possibilities, since any indicator may be entered alone or in combination for both of the axes, according to the user's creativity and analytical interest. Without exhausting the possibilities of analysis, Fig. 6AeD shows some networks automatically made available by Patent2Net after the analyses. As the central focus of this research was not to carry out a qualitative analysis of these networks, this evaluation has been removed, and will be addressed in a future project. We include Fig. 6AeD to illustrate the network related features of Patent2Net. Fig. 6A shows a network established between the International patent classifications of the retrieved patent publications, highlighting the relationship between the technology represented by the code C07K14 (“Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof”) and other technologies, that may help to answer the following question: what specific issues actively bring about new patent applications? Fig. 6B, in turn, shows a network on the basis of the inventors of the retrieved patent publications, highlighting the relationship between the inventor “Santiago Glay Chinea” and other inventors, that may help to answer the following question: who are the key inventors of technology products focused on dengue? Fig. 6C which shows a network based on the patent applicants of the retrieved patent publications, highlighting the relationship between the applicant “Singapore University” and other applicants, may help to answer the following question: which organizations sponsor the development of technological products, processes or techniques that can somehow fight dengue? Finally, Fig. 6D shows a multi-network that makes concomitant use of indicators related to the technology described in patent application and the applicants, highlighting the relationship between the technology represented by code C12N15 (“Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor”) and applicants. This network may help to answer the following question: which companies are seeking to patent each type of technology? 4. Conclusion and implications This study demonstrates that the Patent2Net crawler, as a tool for using the Open Patent Service, was effective in extracting,
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evaluating, organizing and making available bibliographic data on dengue-related patent publications, based on patent applications available in the Espacenet database. On the 1427 dengue related patent publications retrieved only 10 were filed by Brazilian institutions. This observation may be due to the low level of Brazilian technological research being incorporated into patent applications concerning this important neglected disease. The small number of Brazilian patent publications may also however be due to limitations associated with the source of patent publications used in this study. It is possible that not all Brazilian patent publications were available from the Espacenet database at the time of the study. The Patent2Net tool can be used to raise awareness about scientific research that may only have been described in patent publications which can help to advance further socially responsible research into a neglected disease such as dengue. The “social responsibility” of research can be assessed by whether researchers have contributed effectively to the advancement of research into a neglected disease such as dengue that is of high national importance for a country like Brazil. Production indicators that enable the social impacts of a line of research to be measured are as important as indicators that measure the quality of bibliographic production on a subject [28e30]. Given that this effect can only be measured through the technical and technological output of these scientists, it is interesting to note that these data cannot be identified in common bibliographic databases. However, it can be extracted from the curricula of these researchers in the Lattes database [22], or patent databases, as demonstrated by our study using Patent2Net. One of the main limitations of this study is the fact that only 90 million patents available in the Espacenet database were evaluated in the data mining process. Thus, some dengue-related patent publications may not have been included in our patent data collection. New tools that mine data in all patent databases are still needed. However, given that most databases do not allow automatic crawling, our task would have been impossible to achieve. The results provided by P2N allowed us to perform an organized and thorough bibliographic examination of dengue-related patent publications through dynamic interfaces, and not just static reports, enabling us to evaluate the evolution of the filing of these patent publications in recent decades and the main inventors of technological products for the diagnosis and treatment of dengue. The results also enabled the evaluation of organizations that fund dengue research, the main trends in product patenting related to business and the countries where these patents are filed. Also, and essentially, the tool helped us to identify freely available patent publications, enabling Brazilian research scientists to use the knowledge described in these documents for the advancement of science and technology with the proviso that the use does not potentially infringe the patent rights of others. The data presented in this paper are the author's own contribution using P2N. The data resulting from this trial can be easily replicated. The approach described here can be used to evaluate patent publications on any subject, according to the interest of each researcher, student or business. As this web crawler is made freely available, it helps countries like Brazil to achieve new levels of scientific and technological development, especially with regard to a neglected disease of such importance as dengue, which is a matter of high importance for the country. References ^a, S.L.R. Gomes, in: A patente na universidade: sigilo, transpare ^ncia e [1] F.C. Corre informaça ~o, 2007. Salvador, http://repositorios.questoesemrede.uff. direito a
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