Annotation

About: Annotation is a research topic. Over the lifetime, 6719 publications have been published within this topic receiving 203463 citations. The topic is also known as: note & markup.

Ontologies of Linguistic Annotation: Survey and perspectives

Abstract: This paper announces the release of the Ontologies of Linguistic Annotation (OLiA). The OLiA ontologies represent a repository of annotation terminology for various linguistic phenomena on a great band-width of languages. This paper summarizes the results of five years of research, it describes recent developments and directions for further research.

The Annotation Scheme of the Turkish Discourse Bank and an Evaluation of Inconsistent Annotations

Abstract: In this paper, we report on the annotation procedures we developed for annotating the Turkish Discourse Bank (TDB), an effort that extends the Penn Discourse Tree Bank (PDTB) annotation style by using it for annotating Turkish discourse. After a brief introduction to the TDB, we describe the annotation cycle and the annotation scheme we developed, defining which parts of the scheme are an extension of the PDTB and which parts are different. We provide inter-coder reliability calculations on the first and second arguments of some connectives and discuss the most important sources of disagreement among annotators.

P2RP: a web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes

Abstract: Regulatory proteins (RPs) such as transcription factors (TFs) and two-component system (TCS) proteins control how prokaryotic cells respond to changes in their external and/or internal state. Identification and annotation of TFs and TCSs is non-trivial, and between-genome comparisons are often confounded by different standards in annotation. There is a need for user-friendly, fast and convenient tools to allow researchers to overcome the inherent variability in annotation between genome sequences. We have developed the web-server P2RP (Predicted Prokaryotic Regulatory Proteins), which enables users to identify and annotate TFs and TCS proteins within their sequences of interest. Users can input amino acid or genomic DNA sequences, and predicted proteins therein are scanned for the possession of DNA-binding domains and/or TCS domains. RPs identified in this manner are categorised into families, unambiguously annotated, and a detailed description of their features generated, using an integrated software pipeline. P2RP results can then be outputted in user-specified formats. Biologists have an increasing need for fast and intuitively usable tools, which is why P2RP has been developed as an interactive system. As well as assisting experimental biologists to interrogate novel sequence data, it is hoped that P2RP will be built into genome annotation pipelines and re-annotation processes, to increase the consistency of RP annotation in public genomic sequences. P2RP is the first publicly available tool for predicting and analysing RP proteins in users’ sequences. The server is freely available and can be accessed along with documentation at http://www.p2rp.org .

Systems and methods for construction, maintenance, and improvement of knowledge representations

Abstract: In one aspect, the present disclosure relates to a method which, in one example embodiment, can include reading text data corresponding to messages, creating semantic annotations to the text data to generate one or more annotated messages, and aggregating the annotated messages and storing information associated with the aggregated annotated messages in a message store. The method can further include performing, based on information from the message store and associated with the one or more messages, one or more global analytics functions that include: identifying an annotation error in the semantic annotations created using the trained statistical language model, updating the respective semantic annotation to correct the annotation error, and back-propagating corrected data corresponding to the updated semantic annotation into training data for further language model training.

Text-mining assisted regulatory annotation

Abstract: Decoding transcriptional regulatory networks and the genomic cis-regulatory logic implemented in their control nodes is a fundamental challenge in genome biology. High-throughput computational and experimental analyses of regulatory networks and sequences rely heavily on positive control data from prior small-scale experiments, but the vast majority of previously discovered regulatory data remains locked in the biomedical literature. We develop text-mining strategies to identify relevant publications and extract sequence information to assist the regulatory annotation process. Using a vector space model to identify Medline abstracts from papers likely to have high cis-regulatory content, we demonstrate that document relevance ranking can assist the curation of transcriptional regulatory networks and estimate that, minimally, 30,000 papers harbor unannotated cis-regulatory data. In addition, we show that DNA sequences can be extracted from primary text with high cis-regulatory content and mapped to genome sequences as a means of identifying the location, organism and target gene information that is critical to the cis-regulatory annotation process. Our results demonstrate that text-mining technologies can be successfully integrated with genome annotation systems, thereby increasing the availability of annotated cis-regulatory data needed to catalyze advances in the field of gene regulation.