Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

RADIOLOGY OF THE MONTH: Pulmonary Langerhans Cell Histiocytosis (PLCH)

PURPOSE

Obtaining a tissue sample diagnostic of pulmonary Langerhans cell histiocytosis (PLCH) by transbronchial biopsy is notoriously difficult. The condition's appearance on computed tomography is well described and singularly characteristic, perhaps adequate for definitive diagnosis. We propose an approach to diagnosis of these patients.

METHODS

Radiology case report of PLCH in a middle-aged female smoker with two week history of nonproductive cough, low grade fevers, and fatigue.

RESULTS

Computed tomography (CT) provided the diagnosis of PLCH. Transbronchial biopsies failed to provide a definitive diagnosis.

CONCLUSIONS

Utility of transbronchial biopsy in diagnosis of PLCH is limited. Patients who present with signs, symptoms and high resolution computed tomography typical of PLCH do not require a correlation by tissue diagnosis. If cancer is suspected, a wedge biopsy should be performed for tissue diagnosis.

Lower airway colonization and inflammatory response in COPD: a focus on Haemophilus influenzae

Bacterial infection of the lower respiratory tract in chronic obstructive pulmonary disease (COPD) patients is common both in stable patients and during acute exacerbations. The most frequent bacteria detected in COPD patients is Haemophilus influenzae, and it appears this organism is uniquely adapted to exploit immune deficiencies associated with COPD and to establish persistent infection in the lower respiratory tract. The presence of bacteria in the lower respiratory tract in stable COPD is termed colonization; however, there is increasing evidence that this is not an innocuous phenomenon but is associated with airway inflammation, increased symptoms, and increased risk for exacerbations. In this review, we discuss host immunity that offers protection against H. influenzae and how disturbance of these mechanisms, combined with pathogen mechanisms of immune evasion, promote persistence of H. influenzae in the lower airways in COPD. In addition, we examine the role of H. influenzae in COPD exacerbations, as well as interactions between H. influenzae and respiratory virus infections, and review the role of treatments and their effect on COPD outcomes. This review focuses predominantly on data derived from human studies but will refer to animal studies where they contribute to understanding the disease in humans.

Oesophageal ruptures and perforations--a review

Oesophageal ruptures or tears carry a high mortality if they are not recognized and if therapy is delayed. This is so particularly for cases of spontaneous rupture of the oesophagus which carry a higher mortality and morbidity than do cases of iatrogenic injuries. With the widespread use of fibreoptic oesophagogastroscopy, which has been accompanied by the therapeutic manipulation of strictures and tumours, the number of iatrogenic perforations has increased substantially. We report our experience with 23 oesophageal perforations or ruptures that were seen over a 15-year period. The results of both the surgical and the conservative management of such lesions were excellent and were based on the clinical condition of the patient and on the extent of the extravasation of contrast media. Our results show that not all cases of oesophageal perforations require immediate surgical exploration and that the results of surgical treatment are excellent if the diagnosis is made early.

Treatment of medullary carcinoma of the thyroid with I-131

We present a patient with radioiodine concentration in pulmonary metastases presumably arising from medullary carcinoma of the thyroid. Transient symptomatic improvement occurred after treatment with a large dose of sodium iodide (I-131). Although radioiodine concentration in medullary carcinoma of the thyroid is rare, the findings in this patient and in other recent reports suggest that an attempt should be made to determine whether a medullary carcinoma concentrates radioiodine. If so, I-131 treatment might be beneficial.

Phase I clinical investigation of 1,4-dihydroxy-5,8-bis (( (2-[(2-hydroxyethyl)amino]ethyl) amino))-9,10-anthracenedione dihydrochloride (NSC 301739), a new anthracenedione

1,4-Dihydroxy-5,8-bis(( (2-[(2-hydroxyethyl)amino]ethyl)-amino))-9,10-anthracenedione dihydrochloride is a new anthracenedione derivative that was evaluated in a Phase I clinical trial. The schedule of administration consisted of a single i.v. injection, repeated at 4-week intervals. Twenty-five patients received a total of 41 courses of the drug in a dose range of 1.2 to 14 mg/sq m. Leukopenia and thrombocytopenia were dose limiting but were of short duration and rapidly reversible. Mild degrees of phlebitis were observed in 10% of courses, and a green discoloration of the urine was noted with doses of greater than or equal to 10 mg/sq m. One patient with adenocarcinoma of the lung experienced a partial response of his tumor secondary to the drug. Phase II studies of 1,4-dihydroxy-5,8-bis(( (2-[(2-hydroxyethyl)amino]ethyl)amino))-9,10-anthracenedione dihydrochloride are planned at a starting dose of 12 mg/sq m as a single dose repeated at 21- to 28-day intervals.