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The application and benefits of Semantic Web Technologies (SWT) for managing, sharing, and (re-)using of research data are demonstrated in implementations in the field of Materials Science and Engineering (MSE). However, a compilation and classification are needed to fully recognize the scattered published works with its unique added values. Here, the primary use of SWT at the interface with MSE is identified using specifically created categories. This overview highlights promising opportunities for the application of SWT to MSE, such as enhancing the quality of experimental processes, enriching data with contextual information in knowledge graphs, or using ontologies to perform specific queries on semantically structured data. While interdisciplinary work between the two fields is still in its early stages, a great need is identified to facilitate access for nonexperts and develop and provide user-friendly tools and workflows. The full potential of SWT can best be achieved in the long term by the broad acceptance and active participation of the MSE community. In perspective, these technological solutions will advance the field of MSE by making data FAIR. Data-driven approaches will benefit from these data structures and their connections to catalyze knowledge generation in MSE.
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly
(2023)
Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody–antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69–99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences.
The amount of data generated worldwide is constantly increasing. These data come from a wide variety of sources and systems, are processed differently, have a multitude of formats, and are stored in an untraceable and unstructured manner, predominantly in natural language in data silos. This problem can be equally applied to the heterogeneous research data from materials science and engineering. In this domain, ways and solutions are increasingly being generated to smartly link material data together with their contextual information in a uniform and well-structured manner on platforms, thus making them discoverable, retrievable, and reusable for research and industry. Ontologies play a key role in this context. They enable the sustainable representation of expert knowledge and the semantically structured filling of databases with computer-processable data triples.
In this perspective article, we present the project initiative Materials-open-Laboratory (Mat-o-Lab) that aims to provide a collaborative environment for domain experts to digitize their research results and processes and make them fit for data-driven materials research and development. The overarching challenge is to generate connection points to further link data from other domains to harness the promised potential of big materials data and harvest new knowledge.