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.

A Biomedical Knowledge Graph System to Propose Mechanistic Hypotheses for Real-World Environmental Health Observations: Cohort Study and Informatics Application

BACKGROUND

Knowledge graphs are a common form of knowledge representation in biomedicine and many other fields. We developed an open biomedical knowledge graph-based system termed Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP). ROBOKOP consists of both a front-end user interface and a back-end knowledge graph. The ROBOKOP user interface allows users to posit questions and explore answer subgraphs. Users can also posit questions through direct Cypher query of the underlying knowledge graph, which currently contains roughly 6 million nodes or biomedical entities and 140 million edges or predicates describing the relationship between nodes, drawn from over 30 curated data sources.

OBJECTIVE

We aimed to apply ROBOKOP to survey data on workplace exposures and immune-mediated diseases from the Environmental Polymorphisms Registry (EPR) within the National Institute of Environmental Health Sciences.

METHODS

We analyzed EPR survey data and identified 45 associations between workplace chemical exposures and immune-mediated diseases, as self-reported by study participants (n= 4574), with 20 associations significant at P<.05 after false discovery rate correction. We then used ROBOKOP to (1) validate the associations by determining whether plausible connections exist within the ROBOKOP knowledge graph and (2) propose biological mechanisms that might explain them and serve as hypotheses for subsequent testing. We highlight the following three exemplar associations: carbon monoxide-multiple sclerosis, ammonia-asthma, and isopropanol-allergic disease.

RESULTS

ROBOKOP successfully returned answer sets for three queries that were posed in the context of the driving examples. The answer sets included potential intermediary genes, as well as supporting evidence that might explain the observed associations.

CONCLUSIONS

We demonstrate real-world application of ROBOKOP to generate mechanistic hypotheses for associations between workplace chemical exposures and immune-mediated diseases. We expect that ROBOKOP will find broad application across many biomedical fields and other scientific disciplines due to its generalizability, speed to discovery and generation of mechanistic hypotheses, and open nature.

Urolithiasis in the low birth weight infant: the role and efficacy of extracorporeal shock wave lithotripsy

PURPOSE

Nephrolithiasis in preterm infants rarely requires surgical management. When it persists despite conservative therapy, treatment options are not clearly defined. We report a single institutional experience with extracorporeal shock wave lithotripsy (ESWL)* for the treatment of these small infants.

MATERIALS AND METHODS

We treated 8 infants (mean age 13 months) with a history of prematurity and 9 persistent stones with a Dornier HM3 lithotriptor between 1996 and 1999. Mean weight was 7,700 gm. Of the infants 7 had been treated with furosemide for bronchopulmonary dysplasia and 1 presented with multiple anatomical abnormalities. Gantry modification with a wooden platform and polystyrene foam positioning was used for lung and visceral protection. Ureteral stents were placed in 5 patients before ESWL. Renal ultrasonography was performed before, and 2 and a mean of 8 weeks after ESWL. Stone risk factors in our population were investigated through a multispecialty approach.

RESULTS

Average stone burden was 47.9 mm.2. A total of 9 sessions of ESWL were required for complete fragmentation of the 9 renal stones. A mean total of 2,100 shocks at a mean 16.1 kV. were administered. One patient with bilateral stones was treated in 2 separate sessions after a 4-week interval. No repeat ESWL sessions or other surgical interventions were required in any patient. Renal ultrasonography demonstrated no post-ESWL morphological changes. Practices leading to a higher incidence of neonatal nephrolithiasis at our institution were also identified.

CONCLUSIONS

ESWL is effective treatment for nephrolithiasis in small infants. Short-term safety has been established but continued long-term functional followup is essential. Multifactorial etiologies of nephrolithiasis must be identified and modified promptly in the care of preterm infants.

Mutations in the chloride channel gene, CLCNKB, cause Bartter's syndrome type III

Analysis of patients with inherited hypokalaemic alkalosis resulting from salt-wasting has proved fertile ground for identification of essential elements of renal salt homeostasis and blood-pressure regulation. We now demonstrate linkage of this phenotype to a segment of chromosome 1 containing the gene encoding a renal chloride channel, CLCNKB. Examination of this gene reveals loss-of-function mutations that impair renal chloride reabsorption in the thick ascending limb of Henle's loop. Mutations in seventeen kindreds have been identified, and they include large deletions and nonsense and missense mutations. Some of the deletions are shown to have arisen by unequal crossing over between CLCNKB and the nearby related gene, CLCNKA. Patients who harbour CLCNKB mutations are characterized by hypokalaemic alkalosis with salt-wasting, low blood pressure, normal magnesium and hyper- or normocalciuria; they define a distinct subset of patients with Bartter's syndrome in whom nephrocalcinosis is absent. These findings demonstrate the critical role of CLCNKB in renal salt reabsorption and blood-pressure homeostasis, and demonstrate the potential role of specific CLCNKB antagonists as diuretic antihypertensive agents.

Role of control and support in occupational stress: an integrated model

Drawing from the Demand-Control Model and the conceptual framework of the stress process developed by researchers at the University of Michigan's Institute for Social Research, this paper presents and tests an "integrated model" of occupational stress. The results indicate that control and social support are strongly correlated with negative job feelings. The effect of control on health was found to depend on the type of control and organizational level at which control is exercised. Specifically, the effect of participation on health outcomes was found to differ at the job and organizational levels, and participation without influence was associated with increased negative job feelings. The effect of social support was found to depend on the type of support and from whom the support was provided. Results also indicate that it is important to test for moderating, mediating, and direct effects of control on health, and underscore the complementary nature of qualitative and quantitative data in furthering knowledge and understanding.

The integrated model: implications for worksite health promotion and occupational health and safety practice

Within a single firm it is common to find both occupational safety and health and worksite health promotion interventions operating in isolation from one another, with different intervention targets, methods, and personnel. Overcoming the segmentation of the two fields will require, among other things, the promulgation of an overarching model of work and health. The purpose of this article is to describe an integrated model and to show how it can be applied to improve worksite health interventions for both occupational safety and health and worksite health promotion. Practice examples from both fields are used to illustrate interventions that focus on different areas of the model (individual behavior, psychosocial, organization, and contextual factors). It is argued that occupational safety and health and worksite health promotion practitioners need to develop more comprehensive interventions and rigorously evaluate these programs to determine if they are more effective than programs with a more narrow focus.

Bone density studies: current technology

Osteoporosis is a serious public health problem that causes at least 1.3 million fractures and costs more than $6 billion annually. Bone densitometry studies provide clinicians with a way to detect this silent disease in the early stages, before skeletal fragility has occurred. This article describes the three major techniques of bone densitometry and provides guidelines for screening individuals at risk and for understanding the results in clinical practice. Controversies over techniques and management issues are also discussed.

Appropriateness of antenatal referrals to a regional perinatal center

In an ideal system, all women should receive perinatal care adequate to their needs. For specific high-risk groups, this can only be accomplished by antenatal referral to another source of care. The appropriateness of antenatal referrals for patients at risk for premature delivery (less than or equal to 34 weeks) was studied. Records of 122 women in preterm labor and/or with premature rupture of membranes (PROM) presenting to two level I rural hospitals located 60 miles from the regional perinatal center (RPC) were reviewed. Fifty-three patients were not referred and were delivered of 59 infants within 24 hours of admission. Cervical dilatation greater than or equal to 4 cm (34 patients), vaginal bleeding (6 patients), extreme prematurity (6 patients), and advanced labor (7 patients) precluded referrals. Realistically, two of these patients should have been referred. Twenty-two of the 59 infants weighed less than or equal to 1,500 g at birth, 17 weighed 1,501-2,000 g, and 20 weighed greater than or equal to 2,000 g. Five infants died in the hospital, two during the first month and three later. Twenty-two percent had Apgar scores of less than or equal to 3 at 5 minutes. Thirty-four infants were transported to a level III neonatal intensive care unit (NICU). Fourteen of the 69 antenatal referrals required hospitalization (average 11 days), were returned to their local hospital, and delivered at term. Forty-four patients were delivered within 24 hours and 11 between 1 day and 9 weeks.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparison of an electronic spirometer with a pediatric Wright Peak Flow Meter and their relationship to clinical symptomatology in asthmatic children

To evaluate the correlations between the Wright Peak Flow Meter and an Electronic Spirometer with clinical symptomatology in chronic asthmatic chidlren, objective measurements of Peak Flow (PF) on both electronic (Vanguard Electric Spirometer) and mechanical (Wright Peak Flow Meter) Spirometers, Forced Vital Capacity (FVC), Forced, Expiratory Volune 1/2 second (FEV 0.5), Forced Expiratory Volume 1/2 per cent (FEV 0.5%), AND Maximal Midexpiratory Flow Rate (MMEFR) were obtained. Subjective observations of clinical wheezing were recorded immediately before each flow rate by trained nurses. PF determinations of both the mechanical and electronic spirometers were in close agreement. PF on the electronic spirometer correlated best with clinical wheezing in this study. The MMEFR calculated from the electronically produced graphys had the nex best coefficient of corelation. These were followed by the PF measured mechanically on the WPFM.