Showing papers on "Annotation published in 2014"

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Abstract: In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast.nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.

RefSeq: an update on mammalian reference sequences

Abstract: The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration (http://wwwncbinlmnihgov/refseq/) We report here on growth of the mammalian and human subsets, changes to NCBI’s eukaryotic annotation pipeline and modifications affecting transcript and protein records Recent changes to NCBI’s eukaryotic genome annotation pipeline provide higher throughput, and the addition of RNAseq data to the pipeline results in a significant expansion of the number of transcripts and novel exons annotated on mammalian RefSeq genomes Recent annotation changes include reporting supporting evidence for transcript records, modification of exon feature annotation and the addition of a structured report of gene and sequence attributes of biological interest We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

Abstract: Although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats they offer; few applications can process the large data sets produced by whole-genome resequencing projects. Furthermore, there is no coherent framework for the easy integration of new statistics into existing pipelines, hindering the development and application of new population genetics and genomics approaches. Here, we present PopGenome, a population genomics package for the R software environment (a de facto standard for statistical analyses). PopGenome can efficiently process genome-scale data as well as large sets of individual loci. It reads DNA alignments and single-nucleotide polymorphism (SNP) data sets in most common formats, including those used by the HapMap, 1000 human genomes, and 1001 Arabidopsis genomes projects. PopGenome also reads associated annotation files in GFF format, enabling users to easily define regions or classify SNPs based on their annotation; all analyses can also be applied to sliding windows. PopGenome offers a wide range of diverse population genetics analyses, including neutrality tests as well as statistics for population differentiation, linkage disequilibrium, and recombination. PopGenome is linked to Hudson’s MS and Ewing’s MSMS programs to assess statistical significance based on coalescent simulations. PopGenome’s integration in R facilitates effortless and reproducible downstream analyses as well as the production of publication-quality graphics. Developers can easily incorporate new analyses methods into the PopGenome framework. PopGenome and R are freely available from CRAN (http://cran.r-project.org/) for all major operating systems under the GNU General Public License.

The UCSC Genome Browser database: 2014 update

Abstract: The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser's web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation 'tracks' for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany.

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Abstract: Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan ‘BIN’ ontology, which is tailored for functional annotation of plant ‘omics’ data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan-to-GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator.

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

Abstract: We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.

A Gold Standard Dependency Corpus for English

Abstract: We present a gold standard annotation of syntactic dependencies in the English Web Treebank corpus using the Stanford Dependencies formalism. This resource addresses the lack of a gold standard dependency treebank for English, as well as the limited availability of gold standard syntactic annotations for English informal text genres. We also present experiments on the use of this resource, both for training dependency parsers and for evaluating the quality of different versions of the Stanford Parser, which includes a converter tool to produce dependency annotation from constituency trees. We show that training a dependency parser on a mix of newswire and web data leads to better performance on that type of data without hurting performance on newswire text, and therefore gold standard annotations for non-canonical text can be a valuable resource for parsing. Furthermore, the systematic annotation effort has informed both the SD formalism and its implementation in the Stanford Parser’s dependency converter. In response to the challenges encountered by annotators in the EWT corpus, the formalism has been revised and extended, and the converter has been improved.

Annotating Argument Components and Relations in Persuasive Essays

Abstract: In this paper, we present a novel approach to model arguments, their components and relations in persuasive essays in English. We propose an annotation scheme that includes the annotation of claims and premises as well as support and attack relations for capturing the structure of argumentative discourse. We further conduct a manual annotation study with three annotators on 90 persuasive essays. The obtained inter-rater agreement of αU =0 .72 for argument components and α =0 .81 for argumentative relations indicates that the proposed annotation scheme successfully guides annotators to substantial agreement. The final corpus and the annotation guidelines are freely available to encourage future research in argument recognition.

Temporal Annotation in the Clinical Domain

Abstract: This article discusses the requirements of a formal specification for the annotation of temporal information in clinical narratives. We discuss the implementation and extension of ISO-TimeML for annotating a corpus of clinical notes, known as the THYME corpus. To reflect the information task and the heavily inference-based reasoning demands in the domain, a new annotation guideline has been developed, “the THYME Guidelines to ISO-TimeML (THYME-TimeML)”. To clarify what relations merit annotation, we distinguish between linguistically-derived and inferentially-derived temporal orderings in the text. We also apply a top performing TempEval 2013 system against this new resource to measure the difficulty of adapting systems to the clinical domain. The corpus is available to the community and has been proposed for use in a SemEval 2015 task.

Deep autoencoder neural networks for gene ontology annotation predictions

Abstract: The annotation of genomic information is a major challenge in biology and bioinformatics. Existing databases of known gene functions are incomplete and prone to errors, and the bimolecular experiments needed to improve these databases are slow and costly. While computational methods are not a substitute for experimental verification, they can help in two ways: algorithms can aid in the curation of gene annotations by automatically suggesting inaccuracies, and they can predict previously-unidentified gene functions, accelerating the rate of gene function discovery. In this work, we develop an algorithm that achieves both goals using deep autoencoder neural networks. With experiments on gene annotation data from the Gene Ontology project, we show that deep autoencoder networks achieve better performance than other standard machine learning methods, including the popular truncated singular value decomposition.

Choice of transcripts and software has a large effect on variant annotation

Abstract: Variant annotation is a crucial step in the analysis of genome sequencing data. Functional annotation results can have a strong influence on the ultimate conclusions of disease studies. Incorrect or incomplete annotations can cause researchers both to overlook potentially disease-relevant DNA variants and to dilute interesting variants in a pool of false positives. Researchers are aware of these issues in general, but the extent of the dependency of final results on the choice of transcripts and software used for annotation has not been quantified in detail. This paper quantifies the extent of differences in annotation of 80 million variants from a whole-genome sequencing study. We compare results using the RefSeq and Ensembl transcript sets as the basis for variant annotation with the software Annovar, and also compare the results from two annotation software packages, Annovar and VEP (Ensembl’s Variant Effect Predictor), when using Ensembl transcripts. We found only 44% agreement in annotations for putative loss-of-function variants when using the RefSeq and Ensembl transcript sets as the basis for annotation with Annovar. The rate of matching annotations for loss-of-function and nonsynonymous variants combined was 79% and for all exonic variants it was 83%. When comparing results from Annovar and VEP using Ensembl transcripts, matching annotations were seen for only 65% of loss-of-function variants and 87% of all exonic variants, with splicing variants revealed as the category with the greatest discrepancy. Using these comparisons, we characterised the types of apparent errors made by Annovar and VEP and discuss their impact on the analysis of DNA variants in genome sequencing studies. Variant annotation is not yet a solved problem. Choice of transcript set can have a large effect on the ultimate variant annotations obtained in a whole-genome sequencing study. Choice of annotation software can also have a substantial effect. The annotation step in the analysis of a genome sequencing study must therefore be considered carefully, and a conscious choice made as to which transcript set and software are used for annotation.

An Annotation Framework for Dense Event Ordering

Abstract: Today’s event ordering research is heavily dependent on annotated corpora. Current corpora influence shared evaluations and drive algorithm development. Partly due to this dependence, most research focuses on partial orderings of a document’s events. For instance, the TempEval competitions and the TimeBank only annotate small portions of the event graph, focusing on the most salient events or on specific types of event pairs (e.g., only events in the same sentence). Deeper temporal reasoners struggle with this sparsity because the entire temporal picture is not represented. This paper proposes a new annotation process with a mechanism to force annotators to label connected graphs. It generates 10 times more relations per document than the TimeBank, and our TimeBank-Dense corpus is larger than all current corpora. We hope this process and its dense corpus encourages research on new global models with deeper reasoning.

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy

Abstract: Complete Genomics provides an open-source suite of command-line tools for the analysis of their CG-formatted mapped sequencing files. Determination of; for example, the functional impact of detected variants, requires annotation with various databases that often require command-line and/or programming experience; thus, limiting their use to the average research scientist. We have therefore implemented this CG toolkit, together with a number of annotation, visualisation and file manipulation tools in Galaxy called CGtag (Complete Genomics Toolkit and Annotation in a Cloud-based Galaxy). In order to provide research scientists with web-based, simple and accurate analytical and visualisation applications for the selection of candidate mutations from Complete Genomics data, we have implemented the open-source Complete Genomics tool set, CGATools, in Galaxy. In addition we implemented some of the most popular command-line annotation and visualisation tools to allow research scientists to select candidate pathological mutations (SNV, and indels). Furthermore, we have developed a cloud-based public Galaxy instance to host the CGtag toolkit and other associated modules. CGtag provides a user-friendly interface to all research scientists wishing to select candidate variants from CG or other next-generation sequencing platforms’ data. By using a cloud-based infrastructure, we can also assure sufficient and on-demand computation and storage resources to handle the analysis tasks. The tools are freely available for use from an NBIC/CTMM-TraIT (The Netherlands Bioinformatics Center/Center for Translational Molecular Medicine) cloud-based Galaxy instance, or can be installed to a local (production) Galaxy via the NBIC Galaxy tool shed.

IXA pipeline: Efficient and Ready to Use Multilingual NLP tools

Abstract: IXA pipeline is a modular set of Natural Language Processing tools (or pipes) which provide easy access to NLP technology. It offers robust and efficient linguistic annotation to both researchers and non-NLP experts with the aim of lowering the barriers of using NLP technology either for research purposes or for small industrial developers and SMEs. IXA pipeline can be used “as is” or exploit its modularity to pick and change different components. Given its open-source nature, it can also be modified and extended for it to work with other languages. This paper describes the general data-centric architecture of IXA pipeline and presents competitive results in several NLP annotations for English and Spanish.

Learning part-of-speech taggers with inter-annotator agreement loss

Abstract: In natural language processing (NLP) annotation projects, we use inter-annotator agreement measures and annotation guidelines to ensure consistent annotations. However, annotation guidelines often make linguistically debatable and even somewhat arbitrary decisions, and interannotator agreement is often less than perfect. While annotation projects usually specify how to deal with linguistically debatable phenomena, annotator disagreements typically still stem from these “hard” cases. This indicates that some errors are more debatable than others. In this paper, we use small samples of doublyannotated part-of-speech (POS) data for Twitter to estimate annotation reliability and show how those metrics of likely interannotator agreement can be implemented in the loss functions of POS taggers. We find that these cost-sensitive algorithms perform better across annotation projects and, more surprisingly, even on data annotated according to the same guidelines. Finally, we show that POS tagging models sensitive to inter-annotator agreement perform better on the downstream task of chunking.

Standardized description of scientific evidence using the Evidence Ontology (ECO).

Abstract: The Evidence Ontology (ECO) is a structured, controlled vocabulary for capturing evidence in biological research. ECO includes diverse terms for categorizing evidence that supports annotation assertions including experimental types, computational methods, author statements and curator inferences. Using ECO, annotation assertions can be distinguished according to the evidence they are based on such as those made by curators versus those automatically computed or those made via high-throughput data review versus single test experiments. Originally created for capturing evidence associated with Gene Ontology annotations, ECO is now used in other capacities by many additional annotation resources including UniProt, Mouse Genome Informatics, Saccharomyces Genome Database, PomBase, the Protein Information Resource and others. Information on the development and use of ECO can be found at http://evidenceontology.org. The ontology is freely available under Creative Commons license (CC BY-SA 3.0), and can be downloaded in both Open Biological Ontologies and Web Ontology Language formats at http://code.google.com/p/evidenceontology. Also at this site is a tracker for user submission of term requests and questions. ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources.

The Benefits of a Model of Annotation

Abstract: Standard agreement measures for interannotator reliability are neither necessary nor sufficient to ensure a high quality corpus. In a case study of word sense annotation, conventional methods for evaluating labels from trained annotators are contrasted with a probabilistic annotation model applied to crowdsourced data. The annotation model provides far more information, including a certainty measure for each gold standard label; the crowdsourced data was collected at less than half the cost of the conventional approach.

NoSta-D Named Entity Annotation for German: Guidelines and Dataset

Abstract: We describe the annotation of a new dataset for German Named Entity Recognition (NER). The need for this dataset is motivated by licensing issues and consistency issues of existing datasets. We describe our approach to creating annotation guidelines based on linguistic and semantic considerations, and how we iteratively refined and tested them in the early stages of annotation in order to arrive at the largest publicly available dataset for German NER, consisting of over 31,000 manually annotated sentences (over 591,000 tokens) from German Wikipedia and German online news. We provide a number of statistics on the dataset, which indicate its high quality, and discuss legal aspects of distributing the data as a compilation of citations. The data is released under the permissive CC-BY license, and will be fully available for download in September 2014 after it has been used for the GermEval 2014 shared task on NER. We further provide the full annotation guidelines and links to the annotation tool used for the creation of this resource.

Large Scale Arabic Error Annotation: Guidelines and Framework

Abstract: We present annotation guidelines and a web-based annotation framework developed as part of an effort to create a manually annotated Arabic corpus of errors and corrections for various text types. Such a corpus will be invaluable for developing Arabic error correction tools, both for training models and as a gold standard for evaluating error correction algorithms. We summarize the guidelines we created. We also describe issues encountered during the training of the annotators, as well as problems that are specific to the Arabic language that arose during the annotation process. Finally, we present the annotation tool that was developed as part of this project, the annotation pipeline, and the quality of the resulting annotations.

Reflections on the penn discourse treebank, comparable corpora, and complementary annotation

Abstract: The Penn Discourse Treebank (PDTB) was released to the public in 2008. It remains the largest manually annotated corpus of discourse relations to date. Its focus on discourse relations that are either lexically-grounded in explicit discourse connectives or associated with sentential adjacency has not only facilitated its use in language technology and psycholinguistics but also has spawned the annotation of comparable corpora in other languages and genres. Given this situation, this paper has four aims: (1) to provide a comprehensive introduction to the PDTB for those who are unfamiliar with it; (2) to correct some wrong (or perhaps inadvertent) assumptions about the PDTB and its annotation that may have weakened previous results or the performance of decision procedures induced from the data; (3) to explain variations seen in the annotation of comparable resources in other languages and genres, which should allow developers of future comparable resources to recognize whether the variations are relevant to them; and (4) to enumerate and explain relationships between PDTB annotation and complementary annotation of other linguistic phenomena. The paper draws on work done by ourselves and others since the corpus was released.

A Multi-Dialect, Multi-Genre Corpus of Informal Written Arabic

Abstract: This paper presents a multi-dialect, multi-genre, human annotated corpus of dialectal Arabic. We collected utterances in five Arabic dialects: Levantine, Gulf, Egyptian, Iraqi and Maghrebi. We scraped newspaper websites for user commentary and Twitter for two distinct types of dialectal content. To the best of the authors’ knowledge, this work is the most diverse corpus of dialectal Arabic in both the source of the content and the number of dialects. Every utterance in the corpus was human annotated on Amazon’s Mechanical Turk; this stands in contrast to Al-Sabbagh and Girju (2012) where only a small subset was human annotated in order to train a classifier to automatically annotate the remainder of the corpus. We provide a discussion of the methodology used for the annotation in addition to the performance of the individual workers. We extend the Arabic dialect identification task to the Iraqi and Maghrebi dialects and improve the results of Zaidan and Callison-Burch (2011a) on Levantine, Gulf and Egyptian.

A method for increasing expressivity of Gene Ontology annotations using a compositional approach.

Abstract: The Gene Ontology project integrates data about the function of gene products across a diverse range of organisms, allowing the transfer of knowledge from model organisms to humans, and enabling computational analyses for interpretation of high-throughput experimental and clinical data. The core data structure is the annotation, an association between a gene product and a term from one of the three ontologies comprising the GO. Historically, it has not been possible to provide additional information about the context of a GO term, such as the target gene or the location of a molecular function. This has limited the specificity of knowledge that can be expressed by GO annotations. The GO Consortium has introduced annotation extensions that enable manually curated GO annotations to capture additional contextual details. Extensions represent effector–target relationships such as localization dependencies, substrates of protein modifiers and regulation targets of signaling pathways and transcription factors as well as spatial and temporal aspects of processes such as cell or tissue type or developmental stage. We describe the content and structure of annotation extensions, provide examples, and summarize the current usage of annotation extensions. The additional contextual information captured by annotation extensions improves the utility of functional annotation by representing dependencies between annotations to terms in the different ontologies of GO, external ontologies, or an organism’s gene products. These enhanced annotations can also support sophisticated queries and reasoning, and will provide curated, directional links between many gene products to support pathway and network reconstruction.

Treebank Translation for Cross-Lingual Parser Induction

Abstract: Cross-lingual learning has become a popular approach to facilitate the development of resources and tools for low density languages. Its underlying idea is to make use of existing tools and annotations in resource-rich languages to create similar tools and resources for resource-poor languages. Typically, this is achieved by either projecting annotations across parallel corpora, or by transferring models from one or more source languages to a target language. In this paper, we explore a third strategy by using machine translation to create synthetic training data from the original source-side annotations. Specifically, we apply this technique to dependency parsing, using a cross-lingually unified treebank for adequate evaluation. Our approach draws on annotation projection but avoids the use of noisy source-side annotation of an unrelated parallel corpus and instead relies on manual treebank annotation in combination with statistical machine translation, which makes it possible to train fully lexicalized parsers. We show that this approach significantly outperforms delexicalized transfer parsing.% despite the error-prone translation step.

An innovative web-based collaborative platform for video annotation

Abstract: Large scale labeled datasets are of key importance for the development of automatic video analysis tools as they, from one hand, allow multi-class classifiers training and, from the other hand, support the algorithms' evaluation phase. This is widely recognized by the multimedia and computer vision communities, as witnessed by the growing number of available datasets; however, the research still lacks in annotation tools able to meet user needs, since a lot of human concentration is necessary to generate high quality ground truth data. Nevertheless, it is not feasible to collect large video ground truths, covering as much scenarios and object categories as possible, by exploiting only the effort of isolated research groups. In this paper we present a collaborative web-based platform for video ground truth annotation. It features an easy and intuitive user interface that allows plain video annotation and instant sharing/integration of the generated ground truths, in order to not only alleviate a large part of the effort and time needed, but also to increase the quality of the generated annotations. The tool has been on-line in the last four months and, at the current date, we have collected about 70,000 annotations. A comparative performance evaluation has also shown that our system outperforms existing state of the art methods in terms of annotation time, annotation quality and system's usability.

Potsdam Commentary Corpus 2.0: Annotation for Discourse Research

Abstract: We present a revised and extended version of the Potsdam Commentary Corpus, a collection of 175 German newspaper commentaries (op-ed pieces) that has been annotated with syntax trees and three layers of discourse-level information: nominal coreference,connectives and their arguments (similar to the PDTB, Prasad et al. 2008), and trees reflecting discourse structure according to Rhetorical Structure Theory (Mann/Thompson 1988). Connectives have been annotated with the help of a semi-automatic tool, Conano (Stede/Heintze 2004), which identifies most connectives and suggests arguments based on their syntactic category. The other layers have been created manually with dedicated annotation tools. The corpus is made available on the one hand as a set of original XML files produced with the annotation tools, based on identical tokenization. On the other hand, it is distributed together with the open-source linguistic database ANNIS3 (Chiarcos et al. 2008; Zeldes et al. 2009), which provides multi-layer search functionality and layer-specific visualization modules. This allows for comfortable qualitative evaluation of the correlations between annotation layers.

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt

Abstract: The Gene Ontology Consortium (GOC) is a major bioinformatics project that provides structured controlled vocabularies to classify gene product function and location. GOC members create annotations to gene products using the Gene Ontology (GO) vocabularies, thus providing an extensive, publicly available resource. The GO and its annotations to gene products are now an integral part of functional analysis, and statistical tests using GO data are becoming routine for researchers to include when publishing functional information. While many helpful articles about the GOC are available, there are certain updates to the ontology and annotation sets that sometimes go unobserved. Here we describe some of the ways in which GO can change that should be carefully considered by all users of GO as they may have a significant impact on the resulting gene product annotations, and therefore the functional description of the gene product, or the interpretation of analyses performed on GO datasets. GO annotations for gene products change for many reasons, and while these changes generally improve the accuracy of the representation of the underlying biology, they do not necessarily imply that previous annotations were incorrect. We additionally describe the quality assurance mechanisms we employ to improve the accuracy of annotations, which necessarily changes the composition of the annotation sets we provide. We use the Universal Protein Resource (UniProt) for illustrative purposes of how the GO Consortium, as a whole, manages these changes.

Automatic Annotation Suggestions and Custom Annotation Layers in WebAnno

Abstract: In this paper, we present a flexible approach to the efficient and exhaustive manual annotation of text documents. For this purpose, we extend WebAnno (Yimam et al., 2013) an open-source web-based annotation tool. 1 While it was previously limited to specific annotation layers, our extension allows adding and configuring an arbitrary number of layers through a web-based UI. These layers can be annotated separately or simultaneously, and support most types of linguistic annotations such as spans, semantic classes, dependency relations, lexical chains, and morphology. Further, we tightly integrate a generic machine learning component for automatic annotation suggestions of span annotations. In two case studies, we show that automatic annotation suggestions, combined with our split-pane UI concept, significantly reduces annotation time.

Rediscovering Annotation Projection for Cross-Lingual Parser Induction

Abstract: Previous research on annotation projection for parser induction across languages showed only limited success and often required substantial language-specific post-processing to fix inconsistencies and to lift the performance onto a useful level. Model transfer was introduced as another quite successful alternative and much research has been devoted to this paradigm recently. In this paper, we revisit annotation projection and show that the previously reported results are mainly spoiled by the flaws of evaluation with incompatible annotation schemes. Lexicalized parsers created on projected data are especially harmed by such discrepancies. However, recently developed cross-lingually harmonized annotation schemes remove this obstacle and restore the abilities of syntactic annotation projection. We demonstrate this by applying projection strategies to a number of European languages and a selection of human and machine-translated data. Our results outperform the simple direct transfer approach by a large margin and also pave the road to cross-lingual parsing without gold POS labels.

Jannovar: a java library for exome annotation.

Abstract: Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar.

Not an Interlingua, But Close: Comparison of English AMRs to Chinese and Czech

Abstract: Meaning Representations (AMRs) are rooted, directional and labeled graphs that abstract away from morpho-syntactic idiosyncrasies such as word category (verbs and nouns), word order, and function words (determiners, some prepositions). Because these syntactic idiosyncrasies account for many of the cross-lingual differences, it would be interesting to see if this representation can serve, e.g., as a useful, minimally divergent transfer layer in machine translation. To answer this question, we have translated 100 English sentences that have existing AMRs into Chinese and Czech to create AMRs for them. A cross-linguistic comparison of English to Chinese and Czech AMRs reveals both cases where the AMRs for the language pairs align well structurally and cases of linguistic divergence. We found that the level of compatibility of AMR between English and Chinese is higher than between English and Czech. We believe this kind of comparison is beneficial to further refining the annotation standards for each of the three languages and will lead to more compatible annotation guidelines between the languages.