Building an allergens ontology and maintaining it using machine learning techniques

Comprehensive Ontology of Fibroproliferative Diseases: Protocol for a Semantic Technology Study

BACKGROUND

Fibroproliferative or fibrotic diseases (FDs), which represent a significant proportion of age-related pathologies and account for over 40% of mortality in developed nations, are often underrepresented in focused research. Typically, these conditions are studied individually, such as chronic obstructive pulmonary disease or idiopathic pulmonary fibrosis (IPF), rather than as a collective entity, thereby limiting the holistic understanding and development of effective treatments. To address this, we propose creating and publicizing a comprehensive fibroproliferative disease ontology (FDO) to unify the understanding of FDs.

OBJECTIVE

This paper aims to delineate the study protocol for the creation of the FDO, foster transparency and high quality standards during its development, and subsequently promote its use once it becomes publicly available.

METHODS

We aim to establish an ontology encapsulating the broad spectrum of FDs, constructed in the Web Ontology Language format using the Protégé ontology editor, adhering to ontology development life cycle principles. The modeling process will leverage Protégé in accordance with a methodologically defined process, involving targeted scoping reviews of MEDLINE and PubMed information, expert knowledge, and an ontology development process. A hybrid top-down and bottom-up strategy will guide the identification of core concepts and relations, conducted by a team of domain experts based on systematic iterations of scientific literature reviews.

RESULTS

The result will be an exhaustive FDO accommodating a wide variety of crucial biomedical concepts, augmented with synonyms, definitions, and references. The FDO aims to encapsulate diverse perspectives on the FD domain, including those of clinicians, health informaticians, medical researchers, and public health experts.

CONCLUSIONS

The FDO is expected to stimulate broader and more in-depth FD research by enabling reasoning, inference, and the identification of relationships between concepts for application in multiple contexts, such as developing specialized software, fostering research communities, and enhancing domain comprehension. A common vocabulary and understanding of relationships among medical professionals could potentially expedite scientific progress and the discovery of innovative solutions. The publicly available FDO will form the foundation for future research, technological advancements, and public health initiatives.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

PRR1-10.2196/48645.

Allergen databases: current status and perspectives

An increasing number of studies on allergenic molecules have been published during the past 20 years, and the number of proteins reported as allergens is close to 1500 (http://www.allergome.org). Collecting, organizing, and displaying data reported in the scientific literature is becoming the major commitment of Web-based databases that organize this knowledge in heterogeneous ways. This heterogeneity prevents the databases from being connected to each other, something that has been done in several other biomedical fields. This review reports on the current status of allergen databases and available tools to study the allergenicity of new compounds. An analysis of what has been done by applying bioinformatics in other medical fields is presented. Suggestions on how to create a common platform in which experimental, clinical, and epidemiologic data could be merged are offered. The model of the Allergome platform and its modules and tools (eg, InterAll, ReTiME, RefArray, and AllergomeBlaster) are used to exemplify interconnectivity and data integration.