Developing a data identifier taxonomy

As the amount of research data management is growing, the use of identity metadata for discovering, linking and citing research data is growing too. To support the awareness of different identifier systems and comparison and selection of identifier for a particular data management environment, there is need for a knowledge base. This paper contributes towards that goal and analyzes the data management and related literatures to develop a data identifier taxonomy. The taxonomy includes four categories (domain, entity types, activities, and quality dimensions). In addition, the paper describes 14 identifiers referenced in the literature and analyzes them along the taxonomy

The Trichoptera Literature Database: a collaborative bibliographic resource for world caddisfly research

In addition to a list of valid names and synonyms, as provided by the Trichoptera World Checklist, access to the primary literature itself is essential for research in Trichoptera taxonomy and systematics. To improve access to bibliographic information, we established the Trichoptera Literature Database, http://www.trichopteralit.umn.edu, a bibliographic database of over 8,500 citations of literature on Trichoptera. In addition to compiling bibliographical information, we provided access to over 450 high quality Portable Document Format files (PDFs) of historically important, rare, or out-of-print older works as well as more current literature. To provide universal web access to this bibliographical resource, we constructed a dynamic, custom-designed, web application (PHP, Symfony framework) created to import Extensible Markup Language (XML) from the EndNote data file. The database allows the user to search by author and year of publication, displays citations in a standard bibliographic format, and provides download links to available PDF literature. Existing bibliographies of Trichoptera literature and online access to Zoological Record databases were used to accumulate citations. Protocols for scanning literature, issues regarding copyright, and procedures for uploading citations and PDFs to the database are established. We hope to create a collaborative framework of contributors by seeking regional, subject, or language organizers from the community of Trichoptera workers to assist in completing and maintaining this resource with the goal of lowering barriers to efficient access to taxonomic information

A global perspective on decadal challenges and priorities in biodiversity informatics

Biodiversity informatics is a field that is growing rapidly in data infrastructure, tools, and participation by researchers worldwide from diverse disciplines and with diverse, innovative approaches. A recent ‘decadal view’ of the field laid out a vision that was nonetheless restricted and constrained by its European focus. Our alternative decadal view is global, i.e., it sees the worldwide scope and importance of biodiversity informatics as addressing five major, global goals: (1) mobilize existing knowledge; (2) share this knowledge and the experience of its myriad deployments globally; (3) avoid ‘siloing’ and reinventing the tools of knowledge deployment; (4) tackle biodiversity informatics challenges at appropriate scales; and (5) seek solutions to difficult challenges that are strategic

Studies on Monitoring and Tracking Genetic Resources: An Executive Summary

The principles underlying fair and equitable sharing of benefits derived from the utilization of genetic resources are set out in Article 15 of the UN Convention on Biological Diversity, which stipulate that access to genetic resources is subject to the prior informed consent of the country where such resources are located and to mutually agreed terms regarding the sharing of benefits that could be derived from such access. One issue of particular concern for provider countries is how to monitor and track genetic resources once they have left the provider country and enter into use in a variety of forms. This report was commissioned to provide a detailed review of advances in DNA sequencing technologies, as those methods apply to identification of genetic resources, and the use of globally unique persistent identifiers for persistently linking to data and other forms of digital documentation that is linked to individual genetic resources. While the report was written for an audience with a mixture of technical, legal, and policy backgrounds it is relevant to the genomics community as it is an example of downstream application of genomics information

Enhancing systems biology models through semantic data integration

Studying and modelling biology at a systems level requires a large amount of data of different experimental types. Historically, each of these types is stored in its own distinct format, with its own internal structure for holding the data produced by those experiments. While the use of community data standards can reduce the need for specialised, independent formats by providing a common syntax, standards uptake is not universal and a single standard cannot yet describe all biological data. In the work described in this thesis, a variety of integrative methods have been developed to reuse and restructure already extant systems biology data. SyMBA is a simple Web interface which stores experimental metadata in a published, common format. The creation of accurate quantitative SBML models is a time-intensive manual process. Modellers need to understand both the systems they are modelling and the intricacies of the SBML format. However, the amount of relevant data for even a relatively small and well-scoped model can be overwhelming. Saint is a Web application which accesses a number of external Web services and which provides suggested annotation for SBML and CellML models. MFO was developed to formalise all of the knowledge within the multiple SBML specification documents in a manner which is both human and computationally accessible. Rule-based mediation, a form of semantic data integration, is a useful way of reusing and re-purposing heterogeneous datasets which cannot, or are not, structured according to a common standard. This method of ontology-based integration is generic and can be used in any context, but has been implemented specifically to integrate systems biology data and to enrich systems biology models through the creation of new biological annotations. The work described in this thesis is one step towards the formalisation of biological knowledge useful to systems biology. Experimental metadata has been transformed into common structures, a Web application has been created for the retrieval of data appropriate to the annotation of systems biology models and multiple data models have been formalised and made accessible to semantic integration techniques.EThOS - Electronic Theses Online ServiceBBSRCEPSRCGBUnited Kingdo