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

Commercial Availability, Safety, and Hazards

The importance of being able to obtain chemicals commercially, being aware of necessary laboratory precautions, and having access to hazardous-property information is essential for students and researchers. This chapter provides commercial availability links to individual chemical company catalogs and to websites that are linked to multiple commercial sources. It describes laboratory-safety information resources and provides hazardous-property information, for both individual and classes of chemicals, and includes appropriate search techniques. Information on commercial availability, safety, and hazards is interrelated in the sense that commercial chemical companies are responsible for providing Material Safety Data Sheets (MSDSs) for their products. The MSDS for a substance provides basic physical-property information, possible hazardous properties, and instructions for safe use

Similarity Methods in Chemoinformatics

promoting access to White Rose research paper

FAIR Data Model for Chemical Substances: Development Challenges, Management Strategies, and Applications

Data models for representation of chemicals are at the core of cheminformatics processing workflows. The standard triple, (structure, properties, and descriptors), traditionally formalizes a molecule and has been the dominant paradigm for several decades. While this approach is useful and widely adopted from academia, the regulatory bodies and industry have complex use cases and impose the concept of chemical substances applied for multicomponent, advanced, and nanomaterials. Chemical substance data model is an extension of the molecule representation and takes into account the practical aspects of chemical data management, emerging research challenges and discussions within academia, industry, and regulators. The substance paradigm must handle a composition of multiple components. Mandatory metadata is packed together with the experimental and theoretical data. Data model elucidation poses challenges regarding metadata, ontology utilization, and adoption of FAIR principles. We illustrate the adoption of these good practices by means of the Ambit/eNanoMapper data model, which is applied for chemical substances originating from ECHA REACH dossiers and for largest nanosafety database in Europe. The Ambit/eNanoMapper model allows development of tools for data curation, FAIRification of large collections of nanosafety data, ontology annotation, data conversion to standards such as JSON, RDF, and HDF5, and emerging linear notations for chemical substances

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

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

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)

Design, Development and Implementation of Tools in Drug Discovery

The main focus of our work is to develop, apply and assess cheminformatics tools and methods. In particular, we focus on the following three areas: Integration of open source tools with application to drug discovery, usability studies to assess the efficacy of these software tools and finally, developing novel techniques for database query. Rapid globalization in the present time has sparked a need in the scientific community to interact with each other at an economic and a fast pace. This is achieved by developing and sharing open source databases using World Wide Web. A web based open source database application has been developed to incorporate freeware from varied sources. The deployment of developed database and user interface in a university lab setting is discussed. To aid in connecting the end user and the software tools, usability studies are necessary. These studies communicate the end users’ needs and desires, resulting in a user-friendly and more powerful interactive software packages. Usability studies were conducted on developed database student application and on different drawing packages to determine their effectiveness. Developing new and interactive search engines to query publicly available databases helps researchers work more efficiently. The huge volume of data available and its heterogeneous nature presents issues related to querying, integration and presentation. In aiding the retrieval process, an innovative multi faceted classification system, called ChemFacets, is developed. This system provides dynamic categorization of large result sets retrieved from multiple databases

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