Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences

Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information

Collaborative e-science architecture for Reaction Kinetics research community

This paper presents a novel collaborative e-science architecture (CeSA) to address two challenging issues in e-science that arise from the management of heterogeneous distributed environments: (i) how to provide individual scientists an integrated environment to collaborate with each other in distributed, loosely coupled research communities where each member might be using a disparate range of tools; and (ii) how to provide easy access to a range of computationally intensive resources from a desktop. The Reaction Kinetics research community was used to capture the requirements and in the evaluation of the proposed architecture. The result demonstrated the feasibility of the approach and the potential benefits of the CeSA

Enabling e-Research in combustion research community

Abstract This paper proposes an application of the Collaborative e-Science Architecture (CeSA) to enable e-Research in combustion research community. A major problem of the community is that data required for constructing modelling might already exist but scattered and improperly evaluated. That makes the collection of data for constructing models difficult and time-consuming. The decentralised P2P collaborative environment of the CeSA is well suited to solve this distributed problem. It opens up access to scattered data and turns them to valuable resources. Other issues of the community addressed here are the needs for computational resources, storages and interoperability amongst different data formats can also be addressed by the use of Grid environment in the CeSA

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB

Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Internet based molecular collaborative and publishing tools

The scientific electronic publishing model has hitherto been an Internet based delivery of electronic articles that are essentially replicas of their paper counterparts. They contain little in the way of added semantics that may better expose the science, assist the peer review process and facilitate follow on collaborations, even though the enabling technologies have been around for some time and are mature. This thesis will examine the evolution of chemical electronic publishing over the past 15 years. It will illustrate, which the help of two frameworks, how publishers should be exploiting technologies to improve the semantics of chemical journal articles, namely their value added features and relationships with other chemical resources on the Web. The first framework is an early exemplar of structured and scalable electronic publishing where a Web content management system and a molecular database are integrated. It employs a test bed of articles from several RSC journals and supporting molecular coordinate and connectivity information. The value of converting 3D molecular expressions in chemical file formats, such as the MOL file, into more generic 3D graphics formats, such as Web3D, is assessed. This exemplar highlights the use of metadata management for bidirectional hyperlink maintenance in electronic publishing. The second framework repurposes this metadata management concept into a Semantic Web application called SemanticEye. SemanticEye demonstrates how relationships between chemical electronic articles and other chemical resources are established. It adapts the successful semantic model used for digital music metadata management by popular applications such as iTunes. Globally unique identifiers enable relationships to be established between articles and other resources on the Web and SemanticEye implements two: the Document Object Identifier (DOI) for articles and the IUPAC International Chemical Identifier (InChI) for molecules. SemanticEye’s potential as a framework for seeding collaborations between researchers, who have hitherto never met, is explored using FOAF, the friend-of-a-friend Semantic Web standard for social networks