# A Knowledge Graph Framework for Dementia Research Data
## 3 Materials and Methods
### Terminological Extensions  
OBO covers most of the conceptualization needs, but gaps remain relevant to the implementation. To overcome this issue, we implement an application ontology that is also one of the inputs of the merging process. The primary interventions relate to phenotypic normality, as well as to the necessary assay and platform definitions missing from OBI.  
HP and MONDO thoroughly model disease states, conditions, and abnormal phenotypes, leaving out any reference to normal counterparts. To allow the categorization of instances of normal/healthy cases, we introduced a \"Phenotypic normality\" hierarchy. This new hierarchy is modeled as a sibling branch of the HP \"Phenotypic abnormality\", mirroring its hierarchy to allocate the \"normality\" concepts of interests.  
In dementia research, the utilization of neuropsychological assessments such as the Mini-Mental State Examination (MMSE) [75], the Consortium to Establish a Registry for Alzheimer's Disease (CERAD) wordlist memory test (WLT) [76], Visual Object and Space Perception (VOSP) battery [77], Trail Making Test (TMT) [78], Clock Drawing Test [79], and Controlled Oral Word Association Test (COWAT-FAS) [80] is instrumental in quantifying cognitive function domains and tracking disease progression. We have implemented the necessary concepts to cover CERAD, VOSP, and COWAT-FAS tests, with the primary classes  
\begin{table}
\begin{tabular}{c c c} \hline \hline
**Source** & **Source Identifier** & **Reference** \\ \hline Mass Spectrometry Ontology & MS & [71] \\ Mondo Disease Ontology & MONDO & [55] \\ Monarch KG & Monarch & [29] \\ Neurocognitive Integrated & NIO & [63] \\ Ontology & NPT & [62] \\ Ontology & Ontology of Biological & OBA & [72] \\ Attributes & Ontology for Biomedical & OBI & [65] \\ Investigations & Ontology for General Medical & OGMS & [73] \\ Science & Ontology of Medically & OMRSE & [74] \\ Related Social Enities & Phenotype And Trait & PATO & [58] \\ Ontology & Phenomics Integrated & PHENIO & - \\ Ontology & Protein Ontology & PR & [54] \\ Relations Ontology & RO & - \\ Reactome & Reactome & [67] \\ Scientific Evidence and & & \\ Provenance Information & SEPIO & - \\ Ontology & & \\ STRING database ingestion & STRING & [66] \\ Uber Anatomy Ontology & UBERON & [59] \\ \hline \hline \end{tabular}
\end{table}
Table 1: _Cont._allocated under the \"cognitive function assay\" branch of NPT, while also relating to the mental and cognitive functions they assess.  
The AT(N) classification system [81] is another tool of great importance for assessing the subject's biological state and understanding the intricate relationships between key biomarkers and their impact on disease evolution. AT(N) categorizes biomarkers according to their role in the disease progression, namely, Beta-amyloid deposition (A), pathologic tau (T), and neurodegeneration (N). Within each biomarker category, values can be positive or negative (+/-), derived from defined normal or abnormal cut points, resulting in the creation of eight distinct AT(N) \"biomarker profiles\" (Table 2). To provide proper terminological coverage, we have defined new classes for each biomarker profile and phenotype terms related to abnormal CSF protein concentration phenotypes related to phosphorylated tau (P-tau) and total tau (T-tau) missing from HP. Each biomarker profile is defined under the \"value specification\" class from OBI, with asserted logical axioms to associate them with the specific phenotype.