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

State-of-the-art on evolution and reactivity

This report starts by, in Chapter 1, outlining aspects of querying and updating resources on the Web and on the Semantic Web, including the development of query and update languages to be carried out within the Rewerse project. From this outline, it becomes clear that several existing research areas and topics are of interest for this work in Rewerse. In the remainder of this report we further present state of the art surveys in a selection of such areas and topics. More precisely: in Chapter 2 we give an overview of logics for reasoning about state change and updates; Chapter 3 is devoted to briefly describing existing update languages for the Web, and also for updating logic programs; in Chapter 4 event-condition-action rules, both in the context of active database systems and in the context of semistructured data, are surveyed; in Chapter 5 we give an overview of some relevant rule-based agents frameworks

Wildfire monitoring using satellite images, ontologies and linked geospatial data

Advances in remote sensing technologies have allowed us to send an ever-increasing number of satellites in orbit around Earth. As a result, Earth Observation data archives have been constantly increasing in size in the last few years, and have become a valuable source of data for many scientific and application domains. When Earth Observation data is coupled with other data sources many pioneering applications can be developed. In this paper we show how Earth Observation data, ontologies, and linked geospatial data can be combined for the development of a wildfire monitoring service that goes beyond applications currently deployed in various Earth Observation data centers. The service has been developed in the context of European project TELEIOS that faces the challenges of extracting knowledge from Earth Observation data head-on, capturing this knowledge by semantic annotation encoded using Earth Observation ontologies, and combining these annotations with linked geospatial data to allow the development of interesting applications

Decentralized provenance-aware publishing with nanopublications

Publication and archival of scientific results is still commonly considered the responsability of classical publishing companies. Classical forms of publishing, however, which center around printed narrative articles, no longer seem well-suited in the digital age. In particular, there exist currently no efficient, reliable, and agreed-upon methods for publishing scientific datasets, which have become increasingly important for science. In this article, we propose to design scientific data publishing as a web-based bottom-up process, without top-down control of central authorities such as publishing companies. Based on a novel combination of existing concepts and technologies, we present a server network to decentrally store and archive data in the form of nanopublications, an RDF-based format to represent scientific data. We show how this approach allows researchers to publish, retrieve, verify, and recombine datasets of nanopublications in a reliable and trustworthy manner, and we argue that this architecture could be used as a low-level data publication layer to serve the Semantic Web in general. Our evaluation of the current network shows that this system is efficient and reliable

QUAL : A Provenance-Aware Quality Model

The research described here is supported by the award made by the RCUK Digital Economy program to the dot.rural Digital Economy Hub; award reference: EP/G066051/1.Peer reviewedPostprin

Streaming the Web: Reasoning over dynamic data.

In the last few years a new research area, called stream reasoning, emerged to bridge the gap between reasoning and stream processing. While current reasoning approaches are designed to work on mainly static data, the Web is, on the other hand, extremely dynamic: information is frequently changed and updated, and new data is continuously generated from a huge number of sources, often at high rate. In other words, fresh information is constantly made available in the form of streams of new data and updates. Despite some promising investigations in the area, stream reasoning is still in its infancy, both from the perspective of models and theories development, and from the perspective of systems and tools design and implementation. The aim of this paper is threefold: (i) we identify the requirements coming from different application scenarios, and we isolate the problems they pose; (ii) we survey existing approaches and proposals in the area of stream reasoning, highlighting their strengths and limitations; (iii) we draw a research agenda to guide the future research and development of stream reasoning. In doing so, we also analyze related research fields to extract algorithms, models, techniques, and solutions that could be useful in the area of stream reasoning. © 2014 Elsevier B.V. All rights reserved

10042 Abstracts Collection -- Semantic Challenges in Sensor Networks

From 24.01. to 29.01.2010, the Dagstuhl Seminar 10042 ``Semantic Challenges in Sensor Networks \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Analyzing Tag Semantics Across Collaborative Tagging Systems

The objective of our group was to exploit state-of-the-art Information Retrieval methods for finding associations and dependencies between tags, capturing and representing differences in tagging behavior and vocabulary of various folksonomies, with the overall aim to better understand the semantics of tags and the tagging process. Therefore we analyze the semantic content of tags in the Flickr and Delicious folksonomies. We find that: tag context similarity leads to meaningful results in Flickr, despite its narrow folksonomy character; the comparison of tags across Flickr and Delicious shows little semantic overlap, being tags in Flickr associated more to visual aspects rather than technological as it seems to be in Delicious; there are regions in the tag-tag space, provided with the cosine similarity metric, that are characterized by high density; the order of tags inside a post has a semantic relevance

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

BACKGROUND: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. RESULTS: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. CONCLUSION: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are