Building a cell and anatomy ontology of Caenorhabditis elegans

We are endowed with a rich knowledge about Caenorhabditis elegans. Its stereotyped anatomy and development has stimulated research and resulted in the accumulation of cell-based information concerning gene expression, and the role of specific cells in developmental signalling and behavioural circuits. To make the information more accessible to sophisticated queries and automated retrieval systems, WormBase has begun to construct a C. elegans cell and anatomy ontology. Here we present our strategies and progress

Integrating Genomic Knowledge Sources through an Anatomy Ontology

Modern genomic research has access to a plethora of knowledge sources. Often, it is imperative that researchers combine and integrate knowledge from multiple perspectives. Although some technology exists for connecting data and knowledge bases, these methods are only just begin-ning to be successfully applied to research in modern cell biology. In this paper, we argue that one way to integrate multiple knowledge sources is through anatomy—both generic cellular anatomy, as well as anatomic knowledge about the tissues and organs that may be studied via microarray gene expression experiments. We present two examples where we have combined a large ontology of human anatomy (the FMA) with other genomic knowledge sources: the gene ontology (GO) and the mouse genomic databases (MGD) of the Jackson Labs. These two initial examples of knowledge integration provide a proof of concept that anatomy can act as a hub through which we can usefully combine a variety of genomic knowledge and data

WormBase: a comprehensive resource for nematode research

WormBase (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base

Modularization for the Cell Ontology

One of the premises of the OBO Foundry is that development of an orthogonal set of ontologies will increase domain expert contributions and logical interoperability, and decrease maintenance workload. For these reasons, the Cell Ontology (CL) is being re-engineered. This process requires the extraction of sub-modules from existing OBO ontologies, which presents a number of practical engineering challenges. These extracted modules may be intended to cover a narrow or a broad set of species. In addition, applications and resources that make use of the Cell Ontology have particular modularization requirements, such as the ability to extract custom subsets or unions of the Cell Ontology with other OBO ontologies. These extracted modules may be intended to cover a narrow or a broad set of species, which presents unique complications.

We discuss some of these requirements, and present our progress towards a customizable simple-to-use modularization tool that leverages existing OWL-based tools and opens up their use for the CL and other ontologies

How do Ontology Mappings Change in the Life Sciences?

Mappings between related ontologies are increasingly used to support data integration and analysis tasks. Changes in the ontologies also require the adaptation of ontology mappings. So far the evolution of ontology mappings has received little attention albeit ontologies change continuously especially in the life sciences. We therefore analyze how mappings between popular life science ontologies evolve for different match algorithms. We also evaluate which semantic ontology changes primarily affect the mappings. We further investigate alternatives to predict or estimate the degree of future mapping changes based on previous ontology and mapping transitions.Comment: Keywords: mapping evolution, ontology matching, ontology evolutio

An evaluation of the performance of three semantic background knowledge sources in comparative anatomy

In this paper we evaluate the performance and usefulness of three semantic background knowledge sources for predicting synonymous anatomical terms across species boundaries. The reference sources under evaluation are UMLS, FMA-OBO and WordNet, which are applied to the anatomical ontologies of mouse and zebrafish. Our results show that the use of specialized knowledge sources leads to highly accurate predictions, verified through complete manual curation, which can be further improved by combining multiple of said sources. We argue that these three references complement each other in terms of granularity and specificity. From our results we conclude that these references can be used to create reliable ontology mappings with minimal human supervision

An ontology for carcinoma classification for clinical bioinformatics

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population