Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

Template Mining for Information Extraction from Digital Documents

published or submitted for publicatio

Preliminary Report on Patent Literature, Search Methodology and Patent Status of Medicines on the WHO EML 2009

Over the past several decades the World Health Organization (WHO) has produced the Essential Medicines List (EML) to assist countries in deciding what medicines should be essential and available in National Essential Medicine Lists.1 WHO, through the work of regional offices, supports nations using the EML to ensure the quality, availability, and affordability of pharmaceuticals required to promote and advance public health in nations across the globe. However in some cases, access to EML pharmaceuticals might be complicated by existing patents, i.e., where issued, patent rights might pose obstacles to access and inclusion in national EMLs. Indeed, in developed and emerging economy national jurisdictions patent protection may be in effect for a not insignificant number of the WHO EML pharmaceuticals (Figure 2A). However, in developing countries, it is uncertain whether these patents have been filed or issued. Without patent data predicated on an established, reproducible protocol for accessing and assembling patent information on the EML pharmaceuticals, discussions, debates and strategic approaches to understanding and managing patents with regard to access and delivery to developing countries remain in the dark. Indeed, it is absurd to make policy and formulate strategy without solid patent information: the critical foundation for rational debate. To analyze the degree and scope of patenting of EML pharmaceuticals, WIPO (with WHO) approached the Franklin Pierce Center for Intellectual Property at the University of New Hampshire School of Law, specifically the International Technology Transfer Institute (ITTI) to generate a preliminary overview of patents appurtenant to recently added pharmaceutical updates to the EML.2 As part of this work, with inputs from WHO and WIPO, ITTI developed novel methodology and a detailed protocol for identifying EML pharmaceutical patents in national jurisdictions, with an easily reproducible yet cost effective template. Herein is described the development of such a protocol and a preliminary pool of patent information that illustrates its utility. The protocol yields data in a layered approach thereby allowing a user to quickly and effectively obtain both broad and detailed patent information for medications on the WHO EML. In addition, the protocol can be used as an initial path for targeted strategic analysis of potentially relevant patent information in national jurisdictions. In sum, the objectives for this project were: To develop a robust methodology to assess the patent status of medicines on the WHO Model List of Essential Medicines; To place in the public domain a detailed report on the present (2010) patent status of medicines that were on patent in 2003 and those medicines added to the Model List since 2003 by country and level of development; and To analyze the patent status of these Essential Medicines by the development status of countries. The report describes the development of the protocol and presents a preliminary list of EML and corresponding patents in certain jurisdictions to illustrate the utility of the approach. Results will be discussed both in terms of global access and patents, and in the context of establishing standard, systematic, protocols for periodic patent searches related to EML content. 1 WORLD HEALTH ORGANIZATION, CONTINUITY AND CHANGE IMPLEMENTING THE THIRD WHO MEDICINES STRATEGY 2008--‐2013 20 (WHO Press, 3rd ed. 2009). 2 This report covers the EML up to and including updates until 2009

The computer storage, retrieval and searching of generic structures in chemical patents : the machine-readable representation of generic structures.

The nature of the generic chemical structures found in patents is described, with a discussion of the types of statement commonly found in them. The available representations for such structures are reviewed, with particular note being given to the suitability of the representation for searching files of such structures. Requirements for the unambiguous representation of generic structures in an "ideal" storage and retrieval system are discussed. The basic principles of the theory of formal languages are reviewed, with particular consideration being given to parsing methods for context-free languages. The Grammar and parsing of computer programming languages, as an example of artificial formal languages, is discussed. Applications of formal language theory to chemistry and information work are briefly reviewed. GENSAL, a formal language for the unambiguous description of generic structures from patents, is presented. It is designed to be intelligible to a chemist or patent agent, yet sufficiently ABSTRACT formaLised to be amenabLe to computer anaLysis. DetaiLed description is given of the facilities it provides for generic structure representation, and there is discussion of its Limitations and the principLes behind its design. A connection-tabLe-based internaL representation for generic structures, caLLed an ECTR <Extended Connection TabLe Representation) is presented. It is designed to represent generic structures unambiguousLy, and to be generated automatically from structures encoded in GENSAL. It is compared to other proposed representations, and its implementation using data types of the programming Language PascaL described. An interpreter program which generates an ECTR from structures encoded in a subset of the GENSAL Language is presented. The principles of its operation are described. Possible applications of GENSAL outside the area of patent documentation are discussed, and suggestions made for further work on the development of a generic structure storage and retrieval system based on GENSAL and ECTRs

Tracing technological development trajectories: A genetic knowledge persistence-based main path approach

The aim of this paper is to propose a new method to identify main paths in a technological domain using patent citations. Previous approaches for using main path analysis have greatly improved our understanding of actual technological trajectories but nonetheless have some limitations. They have high potential to miss some dominant patents from the identified main paths; nonetheless, the high network complexity of their main paths makes qualitative tracing of trajectories problematic. The proposed method searches backward and forward paths from the high-persistence patents which are identified based on a standard genetic knowledge persistence algorithm. We tested the new method by applying it to the desalination and the solar photovoltaic domains and compared the results to output from the same domains using a prior method. The empirical results show that the proposed method overcomes the aforementioned drawbacks defining main paths that are almost 10x less complex while containing more of the relevant important knowledge than the main path networks defined by the existing method.Comment: 20 pages, 7 figure

Multiple Retrieval Models and Regression Models for Prior Art Search

This paper presents the system called PATATRAS (PATent and Article Tracking, Retrieval and AnalysiS) realized for the IP track of CLEF 2009. Our approach presents three main characteristics: 1. The usage of multiple retrieval models (KL, Okapi) and term index definitions (lemma, phrase, concept) for the three languages considered in the present track (English, French, German) producing ten different sets of ranked results. 2. The merging of the different results based on multiple regression models using an additional validation set created from the patent collection. 3. The exploitation of patent metadata and of the citation structures for creating restricted initial working sets of patents and for producing a final re-ranking regression model. As we exploit specific metadata of the patent documents and the citation relations only at the creation of initial working sets and during the final post ranking step, our architecture remains generic and easy to extend

Special Libraries, April 1940

Volume 31, Issue 4https://scholarworks.sjsu.edu/sla_sl_1940/1003/thumbnail.jp

A survey of chemical information systems

A survey of the features, functions, and characteristics of a fairly wide variety of chemical information storage and retrieval systems currently in operation is given. The types of systems (together with an identification of the specific systems) addressed within this survey are as follows: patents and bibliographies (Derwent's Patent System; IFI Comprehensive Database; PULSAR); pharmacology and toxicology (Chemfile; PAGODE; CBF; HEEDA; NAPRALERT; MAACS); the chemical information system (CAS Chemical Registry System; SANSS; MSSS; CSEARCH; GINA; NMRLIT; CRYST; XTAL; PDSM; CAISF; RTECS Search System; AQUATOX; WDROP; OHMTADS; MLAB; Chemlab); spectra (OCETH; ASTM); crystals (CRYSRC); and physical properties (DETHERM). Summary characteristics and current trends in chemical information systems development are also examined