RESUMO
Research data management (RDM) is needed to assist experimental advances and data collection in the chemical sciences. Many funders require RDM because experiments are often paid for by taxpayers and the resulting data should be deposited sustainably for posterity. However, paper notebooks are still common in laboratories and research data is often stored in proprietary and/or dead-end file formats without experimental context. Data must mature beyond a mere supplement to a research paper. Electronic lab notebooks (ELN) and laboratory information management systems (LIMS) allow researchers to manage data better and they simplify research and publication. Thus, an agreement is needed on minimum information standards for data handling to support structured approaches to data reporting. As digitalization becomes part of curricular teaching, future generations of digital native chemists will embrace RDM and ELN as an organic part of their research.
Assuntos
Gerenciamento de Dados , LaboratóriosRESUMO
With the move toward global, Internet enabled science there is an inherent need to capture, store, aggregate and search scientific data across a large corpus of heterogeneous data silos. As a result, standards development is needed to create an infrastructure capable of representing the diverse nature of scientific data. This paper describes a fundamental data model for scientific data that can be applied to data currently stored in any format, and an associated ontology that affords semantic representation of the structure of scientific data (and its metadata), upon which discipline specific semantics can be applied. Application of this data model to experimental and computational chemistry data are presented, implemented using JavaScript Object Notation for Linked Data. Full examples are available at the project website (Chalk in SciData: a scientific data model. http://stuchalk.github.io/scidata/, 2016).
RESUMO
BACKGROUND: A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. RESULTS: The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. CONCLUSION: The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers.
RESUMO
It is well known that the toxicity of zinc (Zn) varies with water chemistry and that its bioavailability is controlled by ligand interactions and competing ions. Zn toxicity in freshwaters with varying water chemistry has been well characterized; however, far less attention has been paid to the toxicity of Zn in estuarine and marine systems. We performed experiments using two euryhaline species of killifish, Fundulus heteroclitus and Kryptolebias marmoratus, to investigate the effects of changing salinity on acute toxicity of Zn. Larvae (7- to 8-days old) of each species were exposed to various concentrations of Zn for 96 h at salinities ranging from 0 to 36 ppt and survival was monitored. As salinity increased, Zn toxicity decreased in both fish species, and at salinities above 10 ppt, K. marmoratus larvae were generally more sensitive to Zn than were those of F. heteroclitus. The protection of salinity against Zn toxicity in F. heteroclitus was further investigated to determine the role of Ca(2+). Increased Ca(2+) in freshwater protected against Zn toxicity to the same extent as did saline waters with an equal Ca(2+) concentration up to â¼200 mg/L Ca for F. heteroclitus and â¼400 mg/L Ca for K. marmoratus. These results suggest that these two species may have differing Ca(2+) requirements and/or rates of Ca(2+) uptake in water of intermediate to full-strength salinity (â¼200-400 mg/L Ca(2+)) and thus differ in their sensitivity to Zn. The overall goal of this study was to better understand Zn toxicity in waters of different salinity and to generate data on acute Zn toxicity from multiple species over a range of salinities, ultimately for use in development of estuarine and marine biotic ligand models.
