An ontology is a formal representation of a domain modeling the entities in the domain and their relations. When a domain is represented by multiple ontologies, there is need for creating mappings among these ontologies in order to facilitate the integration of data annotated with these ontologies and reasoning across ontologies. The objective of this paper is to recapitulate our experience in aligning large anatomical ontologies and to reflect on some of the issues and challenges encountered along the way. The four anatomical ontologies under investigation are the Foundational Model of Anatomy, GALEN, the Adult Mouse Anatomical Dictionary and the NCI Thesaurus. Their underlying representation formalisms are all different. Our approach to aligning concepts (directly) is automatic, rule-based, and operates at the schema level, generating mostly point-to-point mappings. It uses a combination of domain-specific lexical techniques and structural and semantic techniques (to validate the mappings suggested lexically). It also takes advantage of domain-specific knowledge (lexical knowledge from external resources such as the Unified Medical Language System, as well as knowledge augmentation and inference techniques). In addition to point-to-point mapping of concepts, we present the alignment of relationships and the mapping of concepts group-to-group. We have also successfully tested an indirect alignment through a domain-specific reference ontology. We present an evaluation of our techniques, both against a gold standard established manually and against a generic schema matching system. The advantages and limitations of our approach are analyzed and discussed throughout the paper.

With the emergence of tools for collaborative ontology engineering, more and more data about the creation process behind collaborative construction of ontologies is becoming available. Today, collaborative ontology engineering tools such as Collaborative Protégé offer rich and structured logs of changes, thereby opening up new challenges and opportunities to study and analyze the creation of collaboratively constructed ontologies. While there exists a plethora of visualization tools for ontologies, they have primarily been built to visualize aspects of the final product (the ontology) and not the collaborative processes behind construction (e.g. the changes made by contributors over time). To the best of our knowledge, there exists no ontology visualization tool today that focuses primarily on visualizing the history behind collaboratively constructed ontologies. Since the ontology engineering processes can influence the quality of the final ontology, we believe that visualizing process data represents an important stepping-stone towards better understanding of managing the collaborative construction of ontologies in the future. In this , we present a tool - - which taps into structured change logs provided by tools such as Collaborative Protégé to visualize various pragmatic aspects of collaborative ontology engineering. The tool is aimed at managers and leaders of collaborative ontology engineering projects to help them in monitoring progress, in exploring issues and problems, and in tracking quality-related issues such as overrides and coordination among contributors. The paper makes the following contributions: (i) we present , a tool for visualizing the creation process behind collaboratively constructed ontologies (ii) we illustrate the functionality and generality of the tool by applying it to structured logs of changes of two large collaborative ontology-engineering projects and (iii) we conduct a heuristic evaluation of the tool with domain experts to uncover early design challenges and opportunities for improvement. Finally, we hope that this work sparks a new line of research on visualization tools for collaborative ontology engineering projects.