1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

Do you see what I mean?

Visualizers, like logicians, have long been concerned with meaning. Generalizing from MacEachren's overview of cartography, visualizers have to think about how people extract meaning from pictures (psychophysics), what people understand from a picture (cognition), how pictures are imbued with meaning (semiotics), and how in some cases that meaning arises within a social and/or cultural context. If we think of the communication acts carried out in the visualization process further levels of meaning are suggested. Visualization begins when someone has data that they wish to explore and interpret; the data are encoded as input to a visualization system, which may in its turn interact with other systems to produce a representation. This is communicated back to the user(s), who have to assess this against their goals and knowledge, possibly leading to further cycles of activity. Each phase of this process involves communication between two parties. For this to succeed, those parties must share a common language with an agreed meaning. We offer the following three steps, in increasing order of formality: terminology (jargon), taxonomy (vocabulary), and ontology. Our argument in this article is that it's time to begin synthesizing the fragments and views into a level 3 model, an ontology of visualization. We also address why this should happen, what is already in place, how such an ontology might be constructed, and why now

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

The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

Collaboration in the Semantic Grid: a Basis for e-Learning

The CoAKTinG project aims to advance the state of the art in collaborative mediated spaces for the Semantic Grid. This paper presents an overview of the hypertext and knowledge based tools which have been deployed to augment existing collaborative environments, and the ontology which is used to exchange structure, promote enhanced process tracking, and aid navigation of resources before, after, and while a collaboration occurs. While the primary focus of the project has been supporting e-Science, this paper also explores the similarities and application of CoAKTinG technologies as part of a human-centred design approach to e-Learning