12,227 research outputs found
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Citation and peer review of data: moving towards formal data publication
This paper discusses many of the issues associated with formally publishing data in academia, focusing primarily on the structures that need to be put in place for peer review and formal citation of datasets. Data publication is becoming increasingly important to the scientific community, as it will provide a mechanism for those who create data to receive academic credit for their work and will allow the conclusions arising from an analysis to be more readily verifiable, thus promoting transparency in the scientific process. Peer review of data will also provide a mechanism for ensuring the quality of datasets, and we provide suggestions on the types of activities one expects to see in the peer review of data. A simple taxonomy of data publication methodologies is presented and evaluated, and the paper concludes with a discussion of dataset granularity, transience and semantics, along with a recommended human-readable citation syntax
To share or not to share: Publication and quality assurance of research data outputs. A report commissioned by the Research Information Network
A study on current practices with respect to data creation, use, sharing and publication in eight research disciplines (systems biology, genomics, astronomy, chemical crystallography, rural economy and land use, classics, climate science and social and public health science). The study looked at data creation and care, motivations for sharing data, discovery, access and usability of datasets and quality assurance of data in each discipline
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Developing an open data portal for the ESA climate change initiative
We introduce the rationale for, and architecture of, the European Space Agency Climate Change Initiative (CCI) Open Data Portal (http://cci.esa.int/data/). The Open Data Portal hosts a set of richly diverse datasets â 13 âEssential Climate Variablesâ â from the CCI programme in a consistent and harmonised form and to provides a single point of access for the (>100 TB) data for broad dissemination to an international user community. These data have been produced by a range of different institutions and vary across both scientific and spatio-temporal characteristics. This heterogeneity of the data together with the range of services to be supported presented significant technical challenges.
An iterative development methodology was key to tackling these challenges: the system developed exploits a workflow which takes data that conforms to the CCI data specification, ingests it into a managed archive and uses both manual and automatically generated metadata to support data discovery, browse, and delivery services. It utilises both Earth System Grid Federation (ESGF) data nodes and the Open Geospatial Consortium Catalogue Service for the Web (OGC-CSW) interface, serving data into both the ESGF and the Global Earth Observation System of Systems (GEOSS). A key part of the system is a new vocabulary server, populated with CCI specific terms and relationships which integrates OGC-CSW and ESGF search services together, developed as part of a dialogue between domain scientists and linked data specialists. These services have enabled the development of a unified user interface for graphical search and visualisation â the CCI Open Data Portal Web Presence
Specimens as research objects: reconciliation across distributed repositories to enable metadata propagation
Botanical specimens are shared as long-term consultable research objects in a
global network of specimen repositories. Multiple specimens are generated from
a shared field collection event; generated specimens are then managed
individually in separate repositories and independently augmented with research
and management metadata which could be propagated to their duplicate peers.
Establishing a data-derived network for metadata propagation will enable the
reconciliation of closely related specimens which are currently dispersed,
unconnected and managed independently. Following a data mining exercise applied
to an aggregated dataset of 19,827,998 specimen records from 292 separate
specimen repositories, 36% or 7,102,710 specimens are assessed to participate
in duplication relationships, allowing the propagation of metadata among the
participants in these relationships, totalling: 93,044 type citations,
1,121,865 georeferences, 1,097,168 images and 2,191,179 scientific name
determinations. The results enable the creation of networks to identify which
repositories could work in collaboration. Some classes of annotation
(particularly those regarding scientific name determinations) represent units
of scientific work: appropriate management of this data would allow the
accumulation of scholarly credit to individual researchers: potential further
work in this area is discussed.Comment: 9 pages, 1 table, 3 figure
Curating E-Mails; A life-cycle approach to the management and preservation of e-mail messages
E-mail forms the backbone of communications in many modern institutions and organisations and is a valuable type of organisational, cultural, and historical record. Successful management and preservation of valuable e-mail messages and collections is therefore vital if organisational accountability is to be achieved and historical or cultural memory retained for the future. This requires attention by all stakeholders across the entire life-cycle of the e-mail records.
This instalment of the Digital Curation Manual reports on the several issues involved in managing and curating e-mail messages for both current and future use. Although there is no 'one-size-fits-all' solution, this instalment outlines a generic framework for e-mail curation and preservation, provides a summary of current approaches, and addresses the technical, organisational and cultural challenges to successful e-mail management and longer-term curation.
A text-mining system for extracting metabolic reactions from full-text articles
Background: Increasingly biological text mining research is focusing on the extraction of complex relationships
relevant to the construction and curation of biological networks and pathways. However, one important category of
pathwayâmetabolic pathwaysâhas been largely neglected.
Here we present a relatively simple method for extracting metabolic reaction information from free text that scores
different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence
and location of stemmed keywords. This method extends an approach that has proved effective in the context of the
extraction of proteinâprotein interactions.
Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our
method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the
well-known protein-protein interaction extraction task.
Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been
assumed, and that (as in the case of proteinâprotein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed
Theory and Practice of Data Citation
Citations are the cornerstone of knowledge propagation and the primary means
of assessing the quality of research, as well as directing investments in
science. Science is increasingly becoming "data-intensive", where large volumes
of data are collected and analyzed to discover complex patterns through
simulations and experiments, and most scientific reference works have been
replaced by online curated datasets. Yet, given a dataset, there is no
quantitative, consistent and established way of knowing how it has been used
over time, who contributed to its curation, what results have been yielded or
what value it has.
The development of a theory and practice of data citation is fundamental for
considering data as first-class research objects with the same relevance and
centrality of traditional scientific products. Many works in recent years have
discussed data citation from different viewpoints: illustrating why data
citation is needed, defining the principles and outlining recommendations for
data citation systems, and providing computational methods for addressing
specific issues of data citation.
The current panorama is many-faceted and an overall view that brings together
diverse aspects of this topic is still missing. Therefore, this paper aims to
describe the lay of the land for data citation, both from the theoretical (the
why and what) and the practical (the how) angle.Comment: 24 pages, 2 tables, pre-print accepted in Journal of the Association
for Information Science and Technology (JASIST), 201
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