DALSO: domain ALS ontology

Amyotrophic lateral sclerosis (ALS) is an incurable, rapidly progressive neurodegenerative disease. During the course of ALS, virtually all skeletal muscles are gradually affected, including the respiratory muscles, and the disease is usually fatal within 2 – 5 years of symptom onset. Unequivocal and conclusive tests for ALS do not exist, its disease etiology is still unknown, and therapeutic options are limited. This paper presents the ALS domain ontology (DALSO), model containing formalized, semantic descriptions of a wide range of modeled disease related notions such as patient demographics, clinical findings and history, disease clinical features and diagnostic classifications, risk factors, genetics and pathophysiological mechanisms of motor neuron degeneration. The DALSO′s aim and information scope, design assumption, structure and implementation details are also described. DALSO covers the broad range of significant biomedical concepts ranging from clinical to molecular feature of the modeled disease, it represents a comprehensive, structured knowledge source for the ALS disease domain. To the best of authors′ knowledge, the DALSO is the first attempt to develop a formal, computational model representing knowledge of this fatal motor neuron disease. It provides the means for integrating and annotating clinical and research data, not only at the generic domain knowledge level, but also at the level of individual patient case studies. The DALSO is expressed in OWL2 language, contains 910 classes, is consistent and free of logical errors. Its syntactic correctness was validated by the Fact++ reasoner. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was supported by the grant JPND/01/2015 funded by the Polish National Center of Research and Development in frames of EU Joint Program of Neurodegenerative Research (JPND) ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics commitee of Akdeniz University, Antalya, Turkey gave ethical approval of this work; Ethics commitee of Hannover University Medical School, Germany gave ethical approval of this work; Ethics commitee of Jena University Hospital, Germany gave ethical approval of this work; Ethics commitee of University Hospital of Lisbon, Portugal gave ethical approval of this work; Ethics commitee of Medical University of Warsaw, Poland gave ethical approval of this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced are availale at https://als.ibib.waw.pl/DAlsO.zip