Bioinformatics

OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents

Abstract

OrganismTagger example result annotationOrganismTagger example result annotation
Motivation: Semantic tagging of organism mentions in full-text articles is an important part of literature mining and semantic enrichment solutions. Tagged organism mentions also play a pivotal role in disambiguating other entities in a text, such as proteins. A high-precision organism tagging system must be able to detect the numerous forms of organism mentions, including common names as well as the traditional taxonomic groups: genus, species and strains. In addition, such a system must resolve abbreviations and acronyms, assign the scientific name and if possible link the detected mention to the NCBI Taxonomy database for further semantic queries and literature navigation.

Results: We present the OrganismTagger, a hybrid rule-based/machine learning system to extract organism mentions from the literature. It includes tools for automatically generating lexical and ontological resources from a copy of the NCBI Taxonomy database, thereby facilitating system updates by end users. Its novel ontology-based resources can also be reused in other semantic mining and linked data tasks. Each detected organism mention is normalized to a canonical name through the resolution of acronyms and abbreviations and subsequently grounded with an NCBI Taxonomy database ID. In particular, our system combines a novel machine-learning approach with rule-based and lexical methods for detecting strain mentions in documents. On our manually annotated OT corpus, the OrganismTagger achieves a precision of 95%, a recall of 94% and a grounding accuracy of 97.5%. On the manually annotated corpus of Linnaeus-100, the results show a precision of 99%, recall of 97% and grounding accuracy of 97.4%.

Availability: The OrganismTagger, including supporting tools, resources, training data and manual annotations, as well as end user and developer documentation, is freely available under an open-source license at http://www.semanticsoftware.info/organism-tagger.

Algorithms and semantic infrastructure for mutation impact extraction and grounding

Abstract

Mutation Impact OntologyMutation Impact Ontology

Background

Mutation impact extraction is a hitherto unaccomplished task in state of the art mutation extraction systems. Protein mutations and their impacts on protein properties are hidden in scientific literature, making them poorly accessible for protein engineers and inaccessible for phenotype-prediction systems that currently depend on manually curated genomic variation databases.

Results

We present the first rule-based approach for the extraction of mutation impacts on protein properties, categorizing their directionality as positive, negative or neutral. Furthermore protein and mutation mentions are grounded to their respective UniProtKB IDs and selected protein properties, namely protein functions to concepts found in the Gene Ontology. The extracted entities are populated to an OWL-DL Mutation Impact ontology facilitating complex querying for mutation impacts using SPARQL. We illustrate retrieval of proteins and mutant sequences for a given direction of impact on specific protein properties. Moreover we provide programmatic access to the data through semantic web services using the SADI (Semantic Automated Discovery and Integration) framework.

Conclusion

We address the problem of access to legacy mutation data in unstructured form through the creation of novel mutation impact extraction methods which are evaluated on a corpus of full-text articles on haloalkane dehalogenases, tagged by domain experts. Our approaches show state of the art levels of precision and recall for Mutation Grounding and respectable level of precision but lower recall for the task of Mutant-Impact relation extraction. The system is deployed using text mining and semantic web technologies with the goal of publishing to a broad spectrum of consumers.

Ontology-Based Extraction and Summarization of Protein Mutation Impact Information

Introduction

Poster at BioNLP 2010: Ontology-Based Extraction and Summarization of Protein Mutation Impact InformationPoster at BioNLP 2010: Ontology-Based Extraction and Summarization of Protein Mutation Impact InformationNLP methods for extracting mutation information from the bibliome have become an important new research area within bio-NLP, as manually curated databases, like the Protein Mutant Database (PMD) (Kawabata et al., 1999), cannot keep up with the rapid pace of mutation research. However, while significant progress has been made with respect to mutation detection, the automated extraction of the impacts of these mutations has so far not been targeted. In this paper, we describe the first work to automatically summarize impact information from protein mutations. Our approach is based on populating an OWL-DL ontology with impact information, which can then be queried to provide structured information, including a summary.

Empowering the Enzyme Biotechnologist with Ontologies

Introduction

The FungalWeb Ontology is a knowledge representation vehicle designed to integrate information relevant to industrial applications of enzymes. The ontology integrates information from established sources and supports complex queries to the instantiated FungalWeb knowledge base. The ontology represents prototype Semantic Web technology customized to the domain of industrial enzymes with a focus on enzyme discovery, commercial enzyme products and vendors, and the industrial applications and benefits of industrial enzymes. Using a series of application scenarios we demonstrate the utility of this 'Semantic Web' infrastructure to the enzyme biotechnologist.

Ontology Design for Biomedical Text Mining

Abstract

Text Mining in biology and biomedicine requires a large amount of domain-specific knowledge. Publicly accessible resources hold much of the information needed, yet their practical integration into natural language processing (NLP) systems is fraught with manifold hurdles, especially the problem of semantic disconnectedness throughout the various resources and components. Ontologies can provide the necessary framework for a consistent semantic integration, while additionally delivering formal reasoning capabilities to NLP.

In this chapter, we address four important aspects relating to the integration of ontology and NLP: (i) An analysis of the different integration alternatives and their respective vantages; (ii) The design requirements for an ontology supporting NLP tasks; (iii) Creation and initialization of an ontology using publicly available tools and databases; and (iv) The connection of common NLP tasks with an ontology, including technical aspects of ontology deployment in a text mining framework. A concrete application example—text mining of enzyme mutations—is provided to motivate and illustrate these points.

Keywords: Text Mining, NLP, Ontology Design, Ontology Population, Ontological NLP

Enhanced Semantic Access to the Protein Engineering Literature using Ontologies Populated by Text Mining

Abstract

The biomedical literature is growing at an ever-increasing rate, which pronounces the need to support scientists with advanced, automated means of accessing knowledge. We investigate a novel approach employing description logics (DL)-based queries made to formal ontologies that have been created using the results of text mining full-text research papers. In this paradigm, an OWL-DL ontology becomes populated with instances detected through natural language processing (NLP). The generated ontology can be queried by biologists using DL reasoners or integrated into bioinformatics workflows for further automated analyses. We demonstrate the feasibility of this approach with a system targeting the protein mutation literature.

Keywords: text mining; semantic web; ontological NLP; protein mutations; automated reasoning in bioinformatics; querying OWL-DL ontologies; description logics.

Towards a Systematic Evaluation of Protein Mutation Extraction Systems

Abstract

The development of text analysis systems targeting the extraction of information about mutations from research publications is an emergent topic in biomedical research. Current systems differ in both scope and approaches, which prevents a meaningful comparison of their performance and therefore possible synergies. To overcome this "evaluation bottleneck," we developed a comprehensive framework for the systematic analysis of mutation extraction systems, precisely defining tasks and corresponding evaluation metrics that will allow a comparison of existing and future applications.

Keywords: mutation extraction systems; mutation evaluation tasks; mutation evaluation metrics

Protein Domains

Enriching Protein Structure Visualizations with Mutation Annotations Obtained by Text Mining Protein Engineering Literature

Multiple Sequence Alignment

Abstract

Protein structure visualization tools render images that allow the user to explore structural features of a protein. Context specific information relating to a particular protein or protein family is not easily integrated and must be uploaded from databases or provided through manual curation of input files. We describe a mixed natural language processing and sequence analysis based approach for the retrieval of mutation specific annotations from full text articles for rendering with protein structures.

Keywords

Text Mining, Protein Structure Annotation, Protein Function, ProSAT, Xylanase

Combining Biological Databases and Text Mining to support New Bioinformatics Applications

Alicante, Spain

Abstract

A large amount of biological knowledge today is only available from full-text research papers. Since neither manual database curators nor users can keep up with the rapidly expanding volume of scientific literature, natural language processing approaches are becoming increasingly important for bioinformatic projects.

In this paper, we go beyond simply extracting information from full-text articles by describing an architecture that supports targeted access to information from biological databases using the results derived from text mining of research papers, thereby integrating information from both sources within a biological application.

The described architecture is currently being used to extract information about protein mutations from full-text research papers. Text mining results drive the retrieval of sequence information from protein databases and the employment of algorithmic sequence analysis tools, which facilitate further data access from protein structure databases. Complex mapping of NLP derived text annotations to protein structures allows the rendering, with 3D structure visualization, of information not available in databases of mutation annotations.

The FungalWeb Ontology: Application Scenarios

Abstract

The FungalWeb Ontology aims to support the data integration needs of enzyme biotechnology from inception to product roll out. Serving as a knowledge base for decision support, the conceptualization seeks to link fungal species with enzymes, enzyme substrates, enzyme classifications, enzyme modifications, enzyme retail and applications. We demonstrate how the FungalWeb Ontology supports this remit by presenting application scenarios, conceptualizations of the ontological frame able to support these scenarios and semantic queries typical of a Biotech Manager. Queries to the knowledge base are answered with description logic (DL) and automated reasoning tools.

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