An annotated corpus with nanomedicine and pharmacokinetic parameters

A vast amount of data on nanomedicines is being generated and published, and natural language processing (NLP) approaches can automate the extraction of unstructured text-based data. Annotated corpora are a key resource for NLP and information extraction methods which employ machine learning. Although corpora are available for pharmaceuticals, resources for nanomedicines and nanotechnology are still limited. To foster nanotechnology text mining (NanoNLP) efforts, we have constructed a corpus of annotated drug product inserts taken from the US Food and Drug Administration’s Drugs@FDA online database. In this work, we present the development of the Engineered Nanomedicine Database corpus to support the evaluation of nanomedicine entity extraction. The data were manually annotated for 21 entity mentions consisting of nanomedicine physicochemical characterization, exposure, and biologic response information of 41 Food and Drug Administration-approved nanomedicines. We evaluate the reliability of the manual annotations and demonstrate the use of the corpus by evaluating two state-of-the-art named entity extraction systems, OpenNLP and Stanford NER. The annotated corpus is available open source and, based on these results, guidelines and suggestions for future development of additional nanomedicine corpora are provided

Template Mining for Information Extraction from Digital Documents

published or submitted for publicatio

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 pathway—metabolic pathways—has 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 protein–protein 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 protein–protein 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

Primary crustal melt compositions: Insights into the controls, mechanisms and timing of generation from kinetics experiments and melt inclusions

We explore the controls, mechanisms and timing of generation of primary melts and their compositions, and show that the novel studies of melt inclusions in migmatites can provide important insights into the processes of crustal anatexis of a particular rock. Partial melting in the source region of granites is dependent on five main processes: (i) supply of heat; (ii) mineral–melt interface reactions associated with the detachment and supply of mineral components to the melt, (iii) diffusion in the melt, (iv) diffusion in minerals, and (v) recrystallization of minerals. As the kinetics of these several processes vary over several orders of magnitude, it is essential to evaluate in Nature which of these processes control the rate of melting, the composition of melts, and the extent to which residue–melt chemical equilibrium is attained under different circumstances. To shed light on these issues, we combine data from experimental and melt inclusion studies. First, data from an extensive experimental program on the kinetics of melting of crustal protoliths and diffusion in granite melt are used to set up the necessary framework that describes how primary melt compositions are established during crustal anatexis. Then, we use this reference frame and compare compositional trends from experiments with the composition of melt inclusions analyzed in particular migmatites. We show that, for the case of El Hoyazo anatectic enclaves in lavas, the composition of glassy melt inclusions provides important information on the nature and mechanisms of anatexis during the prograde suprasolidus history of these rocks, including melting temperatures and reactions, and extent of melt interconnection, melt homogenization and melt–residue equilibrium. Compositional trends in several of the rehomogenized melt inclusions in garnet from migmatites/granulites in anatectic terranes are consistent with diffusion in melt-controlled melting, though trace element compositions of melt inclusions and coexisting minerals are necessary to provide further clues on the nature of anatexis in these particular rocks.This work was supported by the National Science Foundation [grants EAR-9603199, EAR-9618867, EAR-9625517 and EAR-9404658], the Italian Consiglio Nazionale delle Ricerche, the European Commission (grant 01-LECEMA22F through contract No. ERAS-CT-2003-980409; and a H2020 Marie Skłodowska-Curie Actions under grant agreement No. 654606), the Italian Ministry of Education, University and Research (grants PRIN 2007278A22, 2010TT22SC and SIR RBSI14Y7PF), the Università degli Studi di Padova [Progetto di Ateneo CPDA107188/10 and a Piscopia—Marie Curie Fellowship under grant agreement No. 600376], the Australian Research Council (Australian Professorial Fellowship and Discovery Grants Nos. DP0342473 and DP0556700), and the National Research Foundation (South Africa; Incentives For Rated Researchers Program)

Representation and use of chemistry in the global electronic age.

We present an overview of the current state of public semantic chemistry and propose new approaches at a strategic and a detailed level. We show by example how a model for a Chemical Semantic Web can be constructed using machine-processed data and information from journal articles.This manuscript addresses questions of robotic access to data and its automatic re-use, including the role of Open Access archival of data. This is a pre-refereed preprint allowed by the publisher's (Royal Soc. Chemistry) Green policy. The author's preferred manuscript is an HTML hyperdocument with ca. 20 links to images, some of which are JPEgs and some of which are SVG (scalable vector graphics) including animations. There are also links to molecules in CML, for which the Jmol viewer is recommended. We susgeest that readers who wish to see the full glory of the manuscript, download the Zipped version and unpack on their machine. We also supply a PDF and DOC (Word) version which obviously cannot show the animations, but which may be the best palce to start, particularly for those more interested in the text

Guide to the nature and methods of analysis of the clay fraction of tephras from the South Auckland region, New Zealand.

The manual outlines some of the more common laboratory procedures available for qualitatively and quantitatively analysing the composition of the tephric clays, many of which are difficult to determine because of their short range order or 'amorphous' nature. Techniques described and assessed in terms of their rapidity and quantitativeness include XRD, IR, DTA, TEM and SEM, sodium fluoride reactivity, chemical dissolution analyses, and surface area measurements. No one technique alone produces a definitive clay fraction analysis of tephric deposits. -from Author