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

From stable isotope ecology to forensic isotope ecology: isotopes' tales.

Stable isotope ecology and forensic isotope ecology are not only linked by name. More often than not, knowledge and insights gained through the former serve as a springboard for application focused work of the latter. This review aims to offer a glimpse into the fascinating world of both though with more emphasis on forensic isotope ecology. To this end a selection of past and recent published work is presented and discussed to highlight both potential and limitations of isotopic analytical approaches to the detection of illegal trade in plants and animals

FlyTED: the Drosophila Testis Gene Expression Database

FlyTED, the Drosophila Testis Gene Expression Database, is a biological research database for gene expression images from the testis of the fruit fly Drosophila melanogaster. It currently contains 2762 mRNA in situ hybridization images and ancillary metadata revealing the patterns of gene expression of 817 Drosophila genes in testes of wild type flies and of seven meiotic arrest mutant strains in which spermatogenesis is defective. This database has been built by adapting a widely used digital library repository software system, EPrints (http://eprints.org/software/), and provides both web-based search and browse interfaces, and programmatic access via an SQL dump, OAI-PMH and SPARQL. FlyTED is available at http://www.fly-ted.org/

A model of provenance applied to biodiversity datasets

Nowadays, the Web has become one of the main sources of biodiversity information. An increasing number of biodiversity research institutions add new specimens and their related information to their biological collections and make this information available on the Web. However, mechanisms which are currently available provide insufficient provenance of biodiversity information. In this paper, we propose a new biodiversity provenance model extending the W3C PROV Data Model. Biodiversity data is mapped to terms from relevant ontologies, such as Dublin Core and GeoSPARQL, stored in triple stores and queried using SPARQL endpoints. Additionally, we provide a use case using our provenance model to enrich collection data

A strontium isoscape of Italy for provenance studies

We present a novel database of biological and geological 87Sr/86Sr values (n = 1920) from Italy, using literature data and newly analysed samples, for provenance purposes. We collected both bioavailable and non-bioavailable (i.e. rocks and bulk soils) data to attain a broader view of the Sr isotope variability of the Italian territory. These data were used to build isotope variability maps, namely isoscapes, through Kriging interpolations. We employed two different Kriging models, namely Ordinary Kriging and Universal Kriging, with a geolithological map of Italy categorized in isotope classes as external predictor. Model performances were evaluated through a 10-fold cross validation, yielding accurate 87Sr/86Sr predictions with root mean squared errors (RMSE) ranging between 0.0020 and 0.0024, dependent on the Kriging model and the sample class. Overall, the produced maps highlight a heterogeneous distribution of the 87Sr/86Sr across Italy, with the highest radiogenic values (>0.71) mainly localized in three areas, namely the Alps (Northern Italy), the Tuscany/Latium (Central Italy) and Calabria/Sicily (Southern Italy) magmatic/metamorphic terrains. The rest of the peninsula is characterized by values ranging between 0.707 and 0.710, mostly linked to sedimentary geological units of mixed nature. Finally, we took advantage of the case study of Fratta Polesine, to underscore the importance of choosing appropriate samples when building the local isoscape and of exploring different end-members when interpreting the local Sr isotope variability in mobility and provenance studies. Our user-friendly maps and database are freely accessible through the Geonode platform and will be updated over time to offer a state-of-the-art reference in mobility and provenance studies across the Italian landscape

Aspects of the taphonomy of the Cambrian Explosion in North Greenland

This thesis describes and elucidates the taphonomic pathways responsible for the exceptional preservation of some of the most common elements of the Sirius Passet Lagerstätte (early Cambrian), North Greenland. Investigative techniques including cathodoluminescence, are tested first on silicified molluscs from the Oligocene of Antigua, associated with a volcanic source; described in chapter 2. By describing the depositional environment of the Sirius Passet biota in detail and using a combination of analytical techniques such as SEM, EDAX, SEM-CL and elemental mapping two published papers address a number of the key research questions surrounding the unique taphonomic pathways in the Sirius Passet biota and their broader significance in understanding Cambrian ecosystems. The papers are included in the form of chapters 3 and 4 and the published versions included in the appendices. A unique, mat-dominated, tissue specific taphonomic pathway is proposed, more akin to the Proterozoic than the typical Burgess Shale Type (BST) preservation seen elsewhere in the Cambrian. This together with mouldic preservation indicates a range of taphonomic styles concomitant with the range of new biotas at the dawn of the Cambrian Explosion

Applying biogeochemistry to identify the geographic origins of insects - a model using prostephanus truncatus

"The application of geochemical screening for tracking insects and other organisms is poorly understood. We explored multi-elemental profiles of an insect pest and its food from different locations in order to identify intrinsic markers of geographic origin. ICP-AES screening was completed for soil, maize grains and Prostephanus truncatus of different geographic origin, with insects collected in the field or reared on maize under controlled conditions. Background level geochemical data are presented with concentrations of Cu, S and Sr in maize, and Al, Ba, Ca, Fe, S, Si, Sr, Ti and Zn in insects differing according to their origin, or that of their food. Cu, Fe and Zn determinations of insects were 20, 6.5 and 11.5 times the concentrations of the maize they were reared on. A Linear Discriminant Analysis (LDA) based on Al, Fe, Sr and Zn successfully assigned 78% of laboratory-reared P. truncatus and 94% of field-caught insects to their origin (68% and 75% respectively after jacknifing). There was excellent discrimination between insects reared on maize from Guanajuato and Nuevo Léon, and Guanajuato and Michoacán, good separation between Sonora and Nuevo Léon but overlap for Sonora, Guanajuato and Michoacán, and Michoacán and Nuevo Léon. The same LDA for field-caught insects gave complete separation between Michoacán and Sonora, but some overlap between Michoacán and Nuevo Léon. This robust ICP-AES technique successfully identified a combination of elements able to classify insects according to their origin. The model was restricted to elements showing a normal distribution but non-parametric tests suggest other elements may act as intrinsic markers. This shows the potential of atomic spectroscopy for remotely tracing insects and other biological materials, with applications including providing provenance data for species routinely captured for surveillance and to track natural enemies and wildlife.

United Kingdom Terrestrial Evidence Partnership of Partnerships data products: improving opportunities for re-use

The United Kingdom Terrestrial Evidence Partnership of Partnerships (UKTEPoP) schemes produce a large quantity of data, both in terms of raw observations and results from analyses. UKTEPoP schemes produce ‘data products’ that have many commonalities which provides opportunities for analyses across schemes, creating greater value than if each scheme’s data were analysed in isolation. The FAIR principles of findability, accessibility, interoperability, and reusability were used to assess the current state of UKTEPoP data products and suggest opportunities for improvements that will lead to an increase in re-use