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ChemSpectra, a web-based software to visualize and analyze spectroscopic data, integrating solutions for infrared spectroscopy (IR), mass spectrometry (MS), and one-dimensional 1H and 13C NMR (proton and carbon nuclear magnetic resonance) spectroscopy, is described. ChemSpectra serves as web-based tool for the analysis of the most often used types of one-dimensional spectroscopic data in synthetic (organic) chemistry research. It was developed to support in particular processes for the use of open file formats which enable the work according to the FAIR data principles. The software can deal with the open file formats JCAMP-DX (IR, MS, NMR) and mzML (MS) proposing these data file types to gain interoperable data. ChemSpectra can be extended to read also other formats as exemplified by selected proprietary mass spectrometry data files of type RAW and NMR spectra files of type FID. The JavaScript-based editor can be integrated with other software, as demonstrated by integration into the Chemotion electronic lab notebook (ELN) and Chemotion repository, demonstrating the implementation into a digital work environment that offers additional functionality and sustainable research data management options. ChemSpectra supports different functions for working with spectroscopic data such as zoom functions, peak picking and automatic peak detection according to a default or manually defined threshold. NMR specific functions include the definition of a reference signal, the integration of signals, coupling constant calculation and multiplicity assignment. Embedded into a web application such as an ELN or a repository, the editor can also be used to generate an association of spectra to a sample and a file management. The file management supports the storage of the original spectra along with the last edited version and an automatically generated image of the spectra in png format. To maximize the benefit of the spectra editor for e.g. ELN users, an automated procedure for the transfer of the detected or manually chosen signals to the ELN was implemented. ChemSpectra is released under the AGPL license to encourage its re-use and further developments by the community. [ABSTRACT FROM AUTHOR]

We developed ChemScanner, a software that can be used for the extraction of chemical information from ChemDraw binary (CDX) or ChemDraw XML-based (CDXML) files and to retrieve the ChemDraw scheme from DOC, DOCX or XML documents. This can facilitate the reuse of chemical information embedded into diverse documents used as standard storage and communication instrument in chemical sciences (e.g. for student's theses, PhD theses, or publications). The extracted information is processed to reactions, molecules, as well as additional text and values and can be accessed via the ChemScanner UI. ChemScanner supports the export to Excel and CML, the direct import of the extracted data to the Open Source ELN Chemotion or the use via "copy and paste" of selected information. The software was designed with a focus on the processing of documents with embedded molecular structure information as CDX or CDXML as these are the most common file formats for chemical drawings. The project aims to support the chemists in their efforts to re-use chemistry research data by providing them missing tools for an automated assembly of reaction data. [ABSTRACT FROM AUTHOR]

The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user's data but also in conventional external sources as provided by SciFinder and PubChem. The presented development makes allowance for the growing dependency of scientific activity on the availability of digital information by providing Open Source instruments to record and reuse research data. The current version of the ELN has been using for over half of a year in our chemistry research group, serves as a common infrastructure for chemistry research and enables chemistry researchers to build their own databases of digital information as a prerequisite for the detailed, systematic investigation and evaluation of chemical reactions and mechanisms. [ABSTRACT FROM AUTHOR]