Facilitating the development of controlled vocabularies for metabolomics technologies with text mining

BACKGROUND: Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources. Experimental data sets from metabolomics studies need to be integrated with one another, but also with data produced by other types of omics studies in the spirit of systems biology, hence the pressing need for vocabularies and ontologies in metabolomics. However, it is time-consuming and non trivial to construct these resources manually. RESULTS: We describe a methodology for rapid development of controlled vocabularies, a study originally motivated by the needs for vocabularies describing metabolomics technologies. We present case studies involving two controlled vocabularies (for nuclear magnetic resonance spectroscopy and gas chromatography) whose development is currently underway as part of the Metabolomics Standards Initiative. The initial vocabularies were compiled manually, providing a total of 243 and 152 terms. A total of 5,699 and 2,612 new terms were acquired automatically from the literature. The analysis of the results showed that full-text articles (especially the Materials and Methods sections) are the major source of technology-specific terms as opposed to paper abstracts. CONCLUSIONS: We suggest a text mining method for efficient corpus-based term acquisition as a way of rapidly expanding a set of controlled vocabularies with the terms used in the scientific literature. We adopted an integrative approach, combining relatively generic software and data resources for time- and cost-effective development of a text mining tool for expansion of controlled vocabularies across various domains, as a practical alternative to both manual term collection and tailor-made named entity recognition methods

A bacterial filter protects and structures the gut microbiome of an insect

Associations with symbionts within the gut lumen of hosts are particularly prone to disruption due to the constant influx of ingested food and non-symbiotic microbes, yet we know little about how partner fidelity is maintained. Here we describe for the first time the existence of a gut morphological filter capable of protecting an animal gut microbiome from disruption. The proventriculus, a valve located between the crop and midgut of insects, functions as a micro-pore filter in the Sonoran Desert turtle ant (Cephalotes rohweri), blocking the entry of bacteria and particles ⩾0.2 μm into the midgut and hindgut while allowing passage of dissolved nutrients. Initial establishment of symbiotic gut bacteria occurs within the first few hours after pupation via oral–rectal trophallaxis, before the proventricular filter develops. Cephalotes ants are remarkable for having maintained a consistent core gut microbiome over evolutionary time and this partner fidelity is likely enabled by the proventricular filtering mechanism. In addition, the structure and function of the cephalotine proventriculus offers a new perspective on organismal resistance to pathogenic microbes, structuring of gut microbial communities, and development and maintenance of host–microbe fidelity both during the animal life cycle and over evolutionary time.This work was funded by NIH grant 5K12GM000708-13. PAPR received support from NSF Grant 0604067 to DEW.Open access.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Gravity modeling of the Muertos Trough and tectonic implications (north-eastern Caribbean)

The Muertos Trough in the northeast Caribbean has been interpreted as a subduction zone from seismicity, leading to infer a possible reversal subduction polarity. However, the distribution of the seismicity is very diffuse and makes definition of the plate geometry difficult. In addition, the compressive deformational features observed in the upper crust and sandbox kinematic modeling do not necessarily suggest a subduction process. We tested the hypothesized subduction of the Caribbean plate’s interior beneath the eastern Greater Antilles island arc using gravity modeling. Gravity models simulating a subduction process yield a regional mass deficit beneath the island arc independently of the geometry and depth of the subducted slab used in the models. This mass deficit results from sinking of the less dense Caribbean slab beneath the lithospheric mantle replacing denser mantle materials and suggests that there is not a subducted Caribbean plateau beneath the island arc. The geologically more realistic gravity model which would explain the N–S shortening observed in the upper crust requires an overthrusted Caribbean slab extending at least 60 km northward from the deformation front, a progressive increase in the thrusting angle from 8 to 30 reaching a maximum depth of 22 km beneath the insular slope. This new tectonic model for the Muertos Margin, defined as a retroarc thrusting, will help to assess the seismic and tsunami hazard in the region. The use of gravity modeling has provided targets for future wide-angle seismic surveys in the Muertos Margin