The taxonomic name resolution service : an online tool for automated standardization of plant names

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 14 (2013): 16, doi:10.1186/1471-2105-14-16.The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ webcite and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/ webcite.BJE was supported by NSF grant DBI 0850373 and TR by CSIRO Marine and Atmospheric Research, Australia,. BB and BJE acknowledge early financial support from Conservation International and TEAM who funded the development of early prototypes of taxonomic name resolution. The iPlant Collaborative (http://www.iplantcollaborative.org) is funded by a grant from the National Science Foundation (#DBI-0735191)

Evaluating Parsers with Dependency Constraints

Many syntactic parsers now score over 90% on English in-domain evaluation, but the remaining errors have been challenging to address and difficult to quantify. Standard parsing metrics provide a consistent basis for comparison between parsers, but do not illuminate what errors remain to be addressed. This thesis develops a constraint-based evaluation for dependency and Combinatory Categorial Grammar (CCG) parsers to address this deficiency. We examine the constrained and cascading impact, representing the direct and indirect effects of errors on parsing accuracy. This identifies errors that are the underlying source of problems in parses, compared to those which are a consequence of those problems. Kummerfeld et al. (2012) propose a static post-parsing analysis to categorise groups of errors into abstract classes, but this cannot account for cascading changes resulting from repairing errors, or limitations which may prevent the parser from applying a repair. In contrast, our technique is based on enforcing the presence of certain dependencies during parsing, whilst allowing the parser to choose the remainder of the analysis according to its grammar and model. We draw constraints for this process from gold-standard annotated corpora, grouping them into abstract error classes such as NP attachment, PP attachment, and clause attachment. By applying constraints from each error class in turn, we can examine how parsers respond when forced to correctly analyse each class. We show how to apply dependency constraints in three parsers: the graph-based MSTParser (McDonald and Pereira, 2006) and the transition-based ZPar (Zhang and Clark, 2011b) dependency parsers, and the C&C CCG parser (Clark and Curran, 2007b). Each is widely-used and influential in the field, and each generates some form of predicate-argument dependencies. We compare the parsers, identifying common sources of error, and differences in the distribution of errors between constrained and cascaded impact. Our work allows us to contrast the implementations of each parser, and how they respond to constraint application. Using our analysis, we experiment with new features for dependency parsing, which encode the frequency of proposed arcs in large-scale corpora derived from scanned books. These features are inspired by and extend on the work of Bansal and Klein (2011). We target these features at the most notable errors, and show how they address some, but not all of the difficult attachments across newswire and web text. CCG parsing is particularly challenging, as different derivations do not always generate different dependencies. We develop dependency hashing to address semantically redundant parses in n-best CCG parsing, and demonstrate its necessity and effectiveness. Dependency hashing substantially improves the diversity of n-best CCG parses, and improves a CCG reranker when used for creating training and test data. We show the intricacies of applying constraints to C&C, and describe instances where applying constraints causes the parser to produce a worse analysis. These results illustrate how algorithms which are relatively straightforward for constituency and dependency parsers are non-trivial to implement in CCG. This work has explored dependencies as constraints in dependency and CCG parsing. We have shown how dependency hashing can efficiently eliminate semantically redundant CCG n-best parses, and presented a new evaluation framework based on enforcing the presence of dependencies in the output of the parser. By otherwise allowing the parser to proceed as it would have, we avoid the assumptions inherent in other work. We hope this work will provide insights into the remaining errors in parsing, and target efforts to address those errors, creating better syntactic analysis for downstream applications

Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach

<p>Abstract</p> <p>Background</p> <p>Incorrectly annotated sequence data are becoming more commonplace as databases increasingly rely on automated techniques for annotation. Hence, there is an urgent need for computational methods for checking consistency of such annotations against independent sources of evidence and detecting potential annotation errors. We show how a machine learning approach designed to automatically predict a protein's Gene Ontology (GO) functional class can be employed to identify potential gene annotation errors.</p> <p>Results</p> <p>In a set of 211 previously annotated mouse protein kinases, we found that 201 of the GO annotations returned by AmiGO appear to be <it>inconsistent </it>with the UniProt functions assigned to their human counterparts. In contrast, 97% of the predicted annotations generated using a machine learning approach were <it>consistent </it>with the UniProt annotations of the human counterparts, as well as with available annotations for these mouse protein kinases in the Mouse Kinome database.</p> <p>Conclusion</p> <p>We conjecture that most of our predicted annotations are, therefore, correct and suggest that the machine learning approach developed here could be routinely used to detect potential errors in GO annotations generated by high-throughput gene annotation projects.</p> <p>Editors Note : Authors from the original publication (Okazaki et al.: <it>Nature </it>2002, <b>420</b>:563–73) have provided their response to Andorf et al, directly following the correspondence.</p

Transcriptomics in Toxicogenomics, Part II : Preprocessing and Differential Expression Analysis for High Quality Data

Preprocessing of transcriptomics data plays a pivotal role in the development of toxicogenomics-driven tools for chemical toxicity assessment. The generation and exploitation of large volumes of molecular profiles, following an appropriate experimental design, allows the employment of toxicogenomics (TGx) approaches for a thorough characterisation of the mechanism of action (MOA) of different compounds. To date, a plethora of data preprocessing methodologies have been suggested. However, in most cases, building the optimal analytical workflow is not straightforward. A careful selection of the right tools must be carried out, since it will affect the downstream analyses and modelling approaches. Transcriptomics data preprocessing spans across multiple steps such as quality check, filtering, normalization, batch effect detection and correction. Currently, there is a lack of standard guidelines for data preprocessing in the TGx field. Defining the optimal tools and procedures to be employed in the transcriptomics data preprocessing will lead to the generation of homogeneous and unbiased data, allowing the development of more reliable, robust and accurate predictive models. In this review, we outline methods for the preprocessing of three main transcriptomic technologies including microarray, bulk RNA-Sequencing (RNA-Seq), and single cell RNA-Sequencing (scRNA-Seq). Moreover, we discuss the most common methods for the identification of differentially expressed genes and to perform a functional enrichment analysis. This review is the second part of a three-article series on Transcriptomics in Toxicogenomics.Peer reviewe

Bayesian reverse-engineering considered as a research strategy for cognitive science

Bayesian reverse-engineering is a research strategy for developing three-level explanations of behavior and cognition. Starting from a computational-level analysis of behavior and cognition as optimal probabilistic inference, Bayesian reverse-engineers apply numerous tweaks and heuristics to formulate testable hypotheses at the algorithmic and implementational levels. In so doing, they exploit recent technological advances in Bayesian artificial intelligence, machine learning, and statistics, but also consider established principles from cognitive psychology and neuroscience. Although these tweaks and heuristics are highly pragmatic in character and are often deployed unsystematically, Bayesian reverse-engineering avoids several important worries that have been raised about the explanatory credentials of Bayesian cognitive science: the worry that the lower levels of analysis are being ignored altogether; the challenge that the mathematical models being developed are unfalsifiable; and the charge that the terms ‘optimal’ and ‘rational’ have lost their customary normative force. But while Bayesian reverse-engineering is therefore a viable and productive research strategy, it is also no fool-proof recipe for explanatory success