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Database of open-framework aluminophosphate structures.

ABSTRACT: Open-framework aluminophosphates are an important class of inorganic crystalline compounds because of their rich structural chemistry and diverse properties. We have collected 312 open-framework aluminophosphate crystal structures from published literature and established a database for these structures. For each aluminophosphate structure, we have assigned a unique index code and extracted its key chemical and crystallographic information from the original literature and the associated CIF file, such as the name, chemical formula, extra-framework species, Al/P ratio, space group, and unit cell parameters of the compound. More importantly, we have calculated the topological features for each aluminophosphate framework, including local connectivity, framework dimension, coordination sequences, vertex symbols, topology density, and the largest ring. To help experimental chemists identify their products, we have also calculated theoretical XRD peaks for all aluminophosphate structures. This database will provide important insight into understanding the structural chemistry of open-framework aluminophosphate compounds.

SUBMITTER: Zheng C

PROVIDER: S-EPMC7109073 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Database of open-framework aluminophosphate structures.

Zheng Chuting C Li Yi Y Yu Jihong J

Scientific data 20200331 1

Open-framework aluminophosphates are an important class of inorganic crystalline compounds because of their rich structural chemistry and diverse properties. We have collected 312 open-framework aluminophosphate crystal structures from published literature and established a database for these structures. For each aluminophosphate structure, we have assigned a unique index code and extracted its key chemical and crystallographic information from the original literature and the associated CIF file ...[more]

PMID: 32235834

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Project description:BackgroundResearch in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time.ResultsMolecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files.ConclusionsBy using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

Project description:BackgroundCardiotocography (CTG) is a monitoring of fetal heart rate and uterine contractions. Since 1960 it is routinely used by obstetricians to assess fetal well-being. Many attempts to introduce methods of automatic signal processing and evaluation have appeared during the last 20 years, however still no significant progress similar to that in the domain of adult heart rate variability, where open access databases are available (e.g. MIT-BIH), is visible. Based on a thorough review of the relevant publications, presented in this paper, the shortcomings of the current state are obvious. A lack of common ground for clinicians and technicians in the field hinders clinically usable progress. Our open access database of digital intrapartum cardiotocographic recordings aims to change that.DescriptionThe intrapartum CTG database consists in total of 552 intrapartum recordings, which were acquired between April 2010 and August 2012 at the obstetrics ward of the University Hospital in Brno, Czech Republic. All recordings were stored in electronic form in the OB TraceVue®;system. The recordings were selected from 9164 intrapartum recordings with clinical as well as technical considerations in mind. All recordings are at most 90 minutes long and start a maximum of 90 minutes before delivery. The time relation of CTG to delivery is known as well as the length of the second stage of labor which does not exceed 30 minutes. The majority of recordings (all but 46 cesarean sections) is - on purpose - from vaginal deliveries. All recordings have available biochemical markers as well as some more general clinical features. Full description of the database and reasoning behind selection of the parameters is presented in the paper.ConclusionA new open-access CTG database is introduced which should give the research community common ground for comparison of results on reasonably large database. We anticipate that after reading the paper, the reader will understand the context of the field from clinical and technical perspectives which will enable him/her to use the database and also understand its limitations.

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Database of open-framework aluminophosphate structures.

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Database of open-framework aluminophosphate structures.

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