Introduction
Vector Surveillance and Management Ontology (VSMO) is an ontology developed in the Open Biological and Biomedical Ontologies (OBO) format. VSMO contains a large number of terms and a limited number of relationships between the terms. Software tool support is imperative for efficient exploration of the ontology and extraction of parts of interest from it. OBO-Edit is an open source tool for searching and editing any ontology written in OBO format. While OBO-Edit can be used for any ontology, it cannot accommodate for the semantics of any specific ontology because of its generic nature. This requires a user to perform a complex set of interactions with OBO-Edit for relatively simple ontology exploration tasks, which would have been straightforward if the tool used were aware of the semantics of the ontology. For instance, a person exploring the VSMO typically wants to know the vector species that transmit a pathogen of interest and the pathogens that are transmitted by a vector species of interest. OBO-Edit is not aware of the definition of a pathogen, the definition of a vector species, and the type of relationship used for specifying which pathogens are transmitted by which vector species. Therefore, the user needs to interact with OBO-Edit to supply this information for every such VSMO exploration tasks.
Motivated to address the above limitations of OBO-Edit and to facilitate a faster exploration of VSMO, we built an ontology explorertool called the VSMO-Explorer. The VSMO-Explorer is aware of some semantics of VSMO such as the definition of a pathogen, the definition of a vector and what relationship is used to specify which vector transmits which pathogen. Awareness of these semantics enables the VSMO-Explorer to perform common VSMO queries with shorter user interactions. For example the VSMO-Explorer can list the pathogens and vectors immediately after loading of an OBO file. It can answer questions such as ‘which vectors transmit a pathogen of interest?’ by just having the researcher specify the pathogen of interest. The VSMO-Explorer can save the result of these queries in formats that can be easily interpreted and shared. The tool can also extract relevant information about a selected term, such as its definition, references, and the synonyms of the term. It also performs web search on a selected term in two online resources: GoPubMed and Wikipedia. The search on GoPubMed is performed in a way similar to the Ontology Generation Tool of OBO-Edit. The search returns a set of terms related to the selected term and links to GoPubMed pages that lists related publications. The search on Wikipedia returns a set of links to Wikipedia articles to the selected term. VSMO explorer displays the search results to the user.
The VSMO-Explorer is entirely written in Java. It is designed in such a way that it can be extended with minimal effort to incorporate new semantics of VSMO and to support new VSMO specific queries. The VSMO-Explorer uses OBO-Edit’s parser for parsing OBO files. It usescomponents and libraries in OBO-Edit to perform search on GoPubMed. It also uses a library called Java Wiki Bot Framework in order to programmatically perform web-search on Wikipedia.
