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

A Linked Data Approach to Sharing Workflows and Workflow Results

A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users

Semantic process mining tools: core building blocks

Process mining aims at discovering new knowledge based on information hidden in event logs. Two important enablers for such analysis are powerful process mining techniques and the omnipresence of event logs in today's information systems. Most information systems supporting (structured) business processes (e.g. ERP, CRM, and workflow systems) record events in some form (e.g. transaction logs, audit trails, and database tables). Process mining techniques use event logs for all kinds of analysis, e.g., auditing, performance analysis, process discovery, etc. Although current process mining techniques/tools are quite mature, the analysis they support is somewhat limited because it is purely based on labels in logs. This means that these techniques cannot benefit from the actual semantics behind these labels which could cater for more accurate and robust analysis techniques. Existing analysis techniques are purely syntax oriented, i.e., much time is spent on filtering, translating, interpreting, and modifying event logs given a particular question. This paper presents the core building blocks necessary to enable semantic process mining techniques/tools. Although the approach is highly generic, we focus on a particular process mining technique and show how this technique can be extended and implemented in the ProM framework tool

MORMED: towards a multilingual social networking platform facilitating medicine 2.0

The broad adoption of Web 2.0 tools has signalled a new era of "Medicine 2.0" in the field of medical informatics. The support for collaboration within online communities and the sharing of information in social networks offers the opportunity for new communication channels among patients, medical experts, and researchers. This paper introduces MORMED, a novel multilingual social networking and content management platform that exemplifies the Medicine 2.0 paradigm, and aims to achieve knowledge commonality by promoting sociality, while also transcending language barriers through automated translation. The MORMED platform will be piloted in a community interested in the treatment of rare diseases (Lupus or Antiphospholipid Syndrome)

XML in Motion from Genome to Drug

Information technology (IT) has emerged as a central to the solution of contemporary genomics and drug discovery problems. Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution. As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics tools. Organizing these data into knowledgeable databases and developing appropriate software tools for analyzing the same are going to be major challenges. XML (eXtensible Markup Language) forms the backbone of biological data representation and exchange over the internet, enabling researchers to aggregate data from various heterogeneous data resources. The present article covers a comprehensive idea of the integration of XML on particular type of biological databases mainly dealing with sequence-structure-function relationship and its application towards drug discovery. This e-medical science approach should be applied to other scientific domains and the latest trend in semantic web applications is also highlighted

Organisational challenges of the semantic web in digital libraries: A Norwegian case study

This is the post-print version of the Article. The official published version can be accessed from the link below - Copyright @ 2009 Emerald Group Publishing LimitedPurpose – The purpose of this paper is to examine from a socio-technical point of view the impact of semantic web technology on the strategic, organisational and technological levels. The semantic web initiative holds great promise for the future for digital libraries. There is, however, a considerable gap in semantic web research between the contributions in the technological field and research in the organisational field. Design/methodology/approach – A comprehensive case study of the National Library of Norway (NL) is conducted, building on two major sources of information: the documentation of the digitising project of the NL; and interviews with nine different stakeholders at three levels of NL's organisation during June to August 2007. Top managers are interviewed on strategy, middle managers and librarians are interviewed regarding organisational issues and ICT professionals are interviewed on technology issues. Findings – The findings indicate that the highest impact will be at the organisational level. This is mainly because inter-organisational and cross-organisational structures have to be established to address the problems of ontology engineering, and a development framework for ontology engineering in digital libraries must be examined. Originality/value – ICT professionals and library practitioners should be more mindful of organisational issues when planning and executing semantic web projects in digital libraries. In particular, practitioners should be aware that the ontology engineering process and the semantic meta-data production will affect the entire organisation. For public digital libraries this probably will also call for a more open policy towards user groups to properly manage the process of ontology engineering

Knowledge Discovery in Online Repositories: A Text Mining Approach

Before the advent of the Internet, the newspapers were the prominent instrument of mobilization for independence and political struggles. Since independence in Nigeria, the political class has adopted newspapers as a medium of Political Competition and Communication. Consequently, most political information exists in unstructured form and hence the need to tap into it using text mining algorithm. This paper implements a text mining algorithm on some unstructured data format in some newspapers. The algorithm involves the following natural language processing techniques: tokenization, text filtering and refinement. As a follow-up to the natural language techniques, association rule mining technique of data mining is used to extract knowledge using the Modified Generating Association Rules based on Weighting scheme (GARW). The main contributions of the technique are that it integrates information retrieval scheme (Term Frequency Inverse Document Frequency) (for keyword/feature selection that automatically selects the most discriminative keywords for use in association rules generation) with Data Mining technique for association rules discovery. The program is applied to Pre-Election information gotten from the website of the Nigerian Guardian newspaper. The extracted association rules contained important features and described the informative news included in the documents collection when related to the concluded 2007 presidential election. The system presented useful information that could help sanitize the polity as well as protect the nascent democracy

Towards Exascale Scientific Metadata Management

Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability of metadata that describe the scientific datasets. Existing workflow engines have been capturing a limited form of metadata to provide provenance information about the identity and lineage of the data. However, much of the data produced by simulations, experiments, and analyses still need to be annotated manually in an ad hoc manner by domain scientists. Systematic and transparent acquisition of rich metadata becomes a crucial prerequisite to sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and domain-agnostic metadata management infrastructure that can meet the demands of extreme-scale science is notable by its absence. To address this gap in scientific data management research and practice, we present our vision for an integrated approach that (1) automatically captures and manipulates information-rich metadata while the data is being produced or analyzed and (2) stores metadata within each dataset to permeate metadata-oblivious processes and to query metadata through established and standardized data access interfaces. We motivate the need for the proposed integrated approach using applications from plasma physics, climate modeling and neuroscience, and then discuss research challenges and possible solutions