31 research outputs found

    A possible extension to the RInChI as a means of providing machine readable process data

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    The algorithmic, large-scale use and analysis of reaction databases such as Reaxys is currently hindered by the absence of widely adopted standards for publishing reaction data in machine readable formats. Crucial data such as yields of all products or stoichiometry are frequently not explicitly stated in the published papers and, hence, not reported in the database entry for those reactions, limiting their usefulness for algorithmic analysis. This paper presents a possible extension to the IUPAC RInChI standard via an auxiliary layer, termed ProcAuxInfo\textit{ProcAuxInfo}, which is a standardised, extensible form in which to report certain key reaction parameters such as declaration of all products and reactants as well as auxiliaries known in the reaction, reaction stoichiometry, amounts of substances used, conversion, yield and operating conditions. The standard is demonstrated via creation of the RInChI including the ProcAuxInfo\textit{ProcAuxInfo} layer based on three published reactions and demonstrates accurate data recoverability via reverse translation of the created strings. Implementation of this or another method of reporting process data by the publishing community would ensure that databases, such as Reaxys, would be able to abstract crucial data for big data analysis of their contents.PMJ is grateful to Peterhouse and the Cambridge Trust for scholarships

    A clustering analysis of the chemical metric space

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    Tese de mestrado Bioinformática e Biologia Computacional, Universidade de Lisboa, Faculdade de Ciências, 2018O tempo médio de vida da espécie humana tem vindo a aumentar significativamente, sendo a indústria farmacêutica responsável por parte desse sucesso. O tempo médio de produção de um fármaco situa-se entre os 10 e os 15 anos e o seu custo tem vindo a crescer anualmente. A quiminformática permite a redução destas adversidades, recorrendo a ferramentas informáticas com a capacidade de prever propriedades químicas e biológicas. Uma abordagem utilizada para esta previsão é a dos modelos Relação Estrutura-Atividade Quantitativa, que se baseia na relação entre a semelhança de estrutura de fármacos e o conhecimento das suas atividades. Na verdade, alguns modelos utilizados atualmente utilizam algoritmos de elevada complexidade, incapazes de fazer previsões para grandes quantidades de dados. Neste contexto, na elaboração do presente trabalho, foi desenvolvido um algoritmo de agrupamento que permitisse definir farmacologicamente o espaço molecular. A performance deste algoritmo foi avaliada para um conjunto de dados considerável, provenientes da base de dados ZINC, de modo a verificar diversos aspetos importantes, como por exemplo, se este seria capaz de produzir resultados que permitissem definir o espaço molecular. Com base nos resultados produzidos pelo algoritmo, foram definidos farmacologicamente os agrupamentos gerados, de acordo com regras lógicas, recorrendo a uma base de dados de atividades, nomeadamente o ChEMBL 23. Este processo permitiu a criação de uma base de dados, posteriormente utilizada na construção de uma interface gráfica de busca. Desta forma, para um composto desconhecido, será possível verificar a que agrupamento este se encontra mais próximo, extrapolando a informação de alvos a ele ligado para o novo fármaco.The average life expectancy of the human species has been growing significantly and the pharmaceutical industry is a part of this success. The average time of production of a drug is between 10 and 15 years and the cost of it has been growing annually. Cheminformatics allows the reduction of these adversities, using computer tools capable of predicting chemical and biological properties. An approach used is the Quantitative Structure Activity Relationship models. These, make use of the relationship between the similarity of drug’s structure and the knowledge of their activities. In fact, some models currently used, make use of highly complex algorithms, unable to make predictions for large amounts of data. Thus, this work had the purpose to develop a clustering algorithm that allowed to define pharmacologically the molecular space. The algorithm performance was evaluated for a considerable data set, from the ZINC database, in order to verify several important aspects, such as, the ability to produce results that allowed to define the molecular space. Based on the results produced by the algorithm, the clusters generated, according to logical rules, were pharmacologically defined using a database of activities, namely ChEMBL 23. This process allowed the creation of a database, later used in the construction of a search graphical user interface. So, for an unknown compound, it will be possible to verify which is the closest cluster, extrapolating the target information attached to it, to the new drug

    The Wooster Voice (Wooster, OH), 1980-04-25

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    This issue starts with a report on the Three Mile Island nuclear power reactor shutdown. William Baird, Vice President of Academic Affairs, gives a lecture entitled Black Students and GLCA Colleges: Why Should Each Seek the Other Out? to Wooster students.The University of Massachusetts-Amherst has become the third school to join a national boycott of Nestle, Inc. products in protest of the company\u27s marketing of infant formula in underdeveloped countries. The Ohio College Association is granted permission by the People\u27s Republic of China to send a delegation of Ohio college and university faculty and administrators on a follow-up mission to China. This edition includes a cartoon called Forecasters\u27 Roadmap of the 1980s. Ellen Johnson, Professor Emeritus of Art History at Oberlin College, is set to speak at the college on the topic of Women\u27s Artist. Additionally, the Voice reports a spike in college suicide rates.https://openworks.wooster.edu/voice1971-1980/1243/thumbnail.jp

    The Wooster Voice (Wooster, OH), 1980-04-25

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    This issue starts with a report on the Three Mile Island nuclear power reactor shutdown. William Baird, Vice President of Academic Affairs, gives a lecture entitled Black Students and GLCA Colleges: Why Should Each Seek the Other Out? to Wooster students.The University of Massachusetts-Amherst has become the third school to join a national boycott of Nestle, Inc. products in protest of the company\u27s marketing of infant formula in underdeveloped countries. The Ohio College Association is granted permission by the People\u27s Republic of China to send a delegation of Ohio college and university faculty and administrators on a follow-up mission to China. This edition includes a cartoon called Forecasters\u27 Roadmap of the 1980s. Ellen Johnson, Professor Emeritus of Art History at Oberlin College, is set to speak at the college on the topic of Women\u27s Artist. Additionally, the Voice reports a spike in college suicide rates.https://openworks.wooster.edu/voice1971-1980/1243/thumbnail.jp

    The Ticker, December 7, 1981

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    The Ticker is the student newspaper of Baruch College. It has been published continuously since 1932, when the Baruch College campus was the School of Business and Civic Administration of the City College of New York

    Paducah Daily Register, September 25, 1906

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    Las Vegas Daily Optic, 05-23-1904

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    https://digitalrepository.unm.edu/lvdo_news/1919/thumbnail.jp

    Kelowna Courier

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    Spruce regeneration on wet forest sites

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