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.

Relationship between the intensity of physical activity, inactivity, cardiorespiratory fitness and body composition in 7-10-year-old Dublin children

OBJECTIVE

To investigate the relationships between the time spent in specific intensities of activity and inactivity, cardiorespiratory fitness and body composition in children.

METHODS

A cross-sectional study was conducted in a random sample of schools. Height, weight and waist circumference were measured in 224 children aged 7-10 years. Cardiorespiratory fitness was estimated by the 20 m multistage running test, and physical activity was measured over 4 days by the RT3 (a triaxial accelerometer). Time each day spent in moderate and vigorous intensities of activity was calculated.

RESULTS

Twelve schools agreed to participate in the study. Body composition and fitness data were obtained for 224 children and activity data for 152 children. Boys were found to take part in about twice as much vigorous and hard activity as girls (mean (95% confidence interval) 64.3 (53.2 to 75.4) min in boys compared with 37 (33.1 to 40.9) min in girls; p<0.001). In boys there was significant difference between those defined as normal, overweight and obese in the time spent in vigorous activity (p<0.05), but no such difference was found in girls. A significant negative correlation between waist circumference and time spent in vigorous activity (r = -0.31, p<0.05) was found in boys but not in girls. Time spent sedentary was positively correlated with waist circumference in boys (r = 0.33, p<0.01) but not in girls. In both boys and girls there were significant negative correlations between fitness and both body mass index (r = -0.274, p<0.001) and waist circumference (boys: r = -0.503, p<0.01; girls: r = -0.286, p<0.01).

CONCLUSION

In boys, body composition was inversely related to fitness and to vigorous activity and was positively related to inactivity. In girls, body composition was related to fitness but not to specific components of physical activity.

Exercise tolerance and physical activity levels in children referred to a weight reduction clinic

The aim of this study was to investigate exercise tolerance and physical activity levels in children with exogenous obesity. Measures included BMI, waist circumference, exercise tolerance and self reported physical activity. Exercise tolerance was measured by the Modified Balke Treadmill Protocol and results were compared to normal values. Physical activity levels were assessed by measuring energy expended in regular activities each week over the past year and number of hours spent watching TV/video using an adaptation of the 'Modifiable Activity Questionnaire for Adolescents'. Details on transport to school were also obtained. Forty five children between September 2002 and June 2004 were assessed. This group comprised of 25 girls and 20 boys with mean ages (standard deviation) of 11.9 +/- 3.0 years and 13.7 +/- 2.5 years respectively. Exercise tolerance as a percentage of normal was below minimal levels in 64% girls and 75% boys. Energy expended in regular activity was less than the minimal recommendation in 80% girls and 65% boys. Seventy six percent of girls and 70% of boys spent 2 hours or more per day watching television and 40% of girls and 70% of boys walked to school. The low levels of activity and exercise tolerance need to be addressed in the managemeni of children with obesity

Development and application of a quality control procedure for short-wave diathermy units

Short-wave diathermy (SWD) is a form of radiofrequency (RF) radiation, operating at 27.12 MHz, that is used therapeutically by physiotherapists. Although this form of therapy is widely available, the management of the equipment is not often addressed by either physiotherapists or by medical physics/clinical engineering. A quality control protocol for SWD units, examining power output and electrical and mechanical condition, was developed and applied to 20 units used in clinical practice. In addition, an environmental assessment of where the units were used was also included. Results showed that the power output was generally stable (coefficient of variation range 0-8.8%) and reproducible (coefficient of variation range 0-6.8%). When the outputs from 12 similar units were compared, it was found that the relationship between the units' intensity settings and power output measurements was non-linear. Two units with mechanical timers were found to have inaccuracies that could contribute, under a 'worst-case' scenario, to a dosage error of up to 45%. Environmental analysis found that all treatment plinths in use contained metal parts, which could constitute a fire hazard, and no department examined was equipped with an RF screened room, a facility that would ensure that other persons in the vicinity were not exposed to excessive stray radiation.

Peripheral muscle strength in young males with cystic fibrosis

BACKGROUND

In children with cystic fibrosis there is a decrease in peak work capacity and oxygen consumption on maximal exercise testing when compared to controls. Previous studies have shown that peripheral muscle force is decreased in children with cystic fibrosis even in those with minimal changes in lung function. However, no studies have examined peripheral muscle strength using isokinetic dynamometry which permits measurement of muscle strength throughout range and is considered the gold standard in orthopaedics and sports medicine.

METHODS

Isokinetic muscle strength was measured in the knee flexors and extensors and shoulder flexors and extensors at two speeds of movement in children with cystic fibrosis and matched controls. Activity levels in both groups were calculated.

RESULTS

Thirteen subjects and 13 age and height matched controls were assessed. Average peak torque was calculated and expressed in terms of body weight. There was a significant difference in peak torque/body weight in children with cystic fibrosis when compared to controls. FEV1 was significantly correlated with knee muscle strength and shoulder flexion at 90 degrees /s in subjects with CF.

CONCLUSION

Children with CF had lower muscle strength than control subjects. Airflow limitation was associated with decreased muscle strength. The relationship between muscle strength and exercise tolerance requires investigation.

Physical activity in Dublin children aged 7-9 years

OBJECTIVES

To investigate the amount of regular activity and time spent in sedentary occupations in children aged 7--9 years. Sex differences in levels of activity and time and facilities for physical education at school were also examined.

METHODS

A 10% sample of Dublin National Schools were selected. Parents of children in second class were surveyed. The questionnaire used was a modification of the Modifiable Activity Questionnaire for Adolescents. Teachers of second class were questioned about the time and facilities for physical education in schools.

RESULTS

Some 39% of children were participating in hard exercise for at least 20 minutes three or more times a week, with fewer girls (28%) than boys (53%) contributing to this result. A further 57% of children were engaging in at least 20 minutes of light exercise three or more times a week, with no sex differences. Estimated energy expenditure in regular activity was higher in boys than girls. Most (78%) of the children were spending one to three hours a day sedentary in front of a screen.

CONCLUSIONS

This study provides comprehensive data on physical activity levels in Dublin schoolchildren aged 7--9 years. The amount of inactivity is of concern. Even at this young age, boys are reported to participate in more physical activity than girls.

Factitious HIV syndrome in young women

Factitious HIV infection has been observed at our center in women presenting with a false history of HIV/AIDS. In a 2-year period, 4 women presented for HIV-related care, indicating they were HIV-seropositive, while repeated serologic testing revealed no evidence of HIV infection. In all cases, the women were either quite angry or appeared surprised when told that they did not have HIV infection. A common denominator in all 4 women was a history of prolonged sexual, physical, or emotional abuse. Three of the 4 had been to other physicians, changing doctors as soon as the absence of HIV infection was established. Appropriate psychiatric support is an important aspect in care of these women, although it may not be accepted. All presentations of HIV infection should be confirmed either by identifying hard-copy data of HIV test results or by retesting all patients before evaluation and treatment of presumed HIV-related illnesses.

A pilot study examining injuries in elite gaelic footballers

OBJECTIVES

To quantify injuries in elite gaelic footballers and to determine the nature, sites, and outcome of injuries and the possible risk factors involved.

METHODS

Information on injuries was collected from six elite gaelic football teams by a questionnaire. The footballers were asked to recall injuries over the preceding six month period.

RESULTS

A total of 88 out of 107 subjects sustained injuries over the study period. Ninety five injuries were recorded, giving an incidence rate of 1.78 injuries per subject per year, of which 35% were recurring. It was found that 35% of injuries were sustained during training sessions. Lower body injuries predominated (77%), the ankle being the most commonly injured anatomic site. Most injuries were soft tissue in nature: muscle, 33%; ligament, 32%; tendon, 16%. The most common situations giving rise to injuries were collision (22%) and twist/turn (19%). Foul play only accounted for about 6% of injuries. Mean time off play as a result of injury was 17.3 days, and hospital admission was necessary for 15% of the injuries.

CONCLUSION

Despite the limitations of a retrospective of this nature, the study provides useful and important information on injuries in gaelic footballers.

National school teachers' knowledge of asthma and its management

Asthma is the most common chronic medical condition that school teachers may encounter among their pupils. However management of asthma in schools and the role school teachers adopt in this condition has only recently been explored. The aim of this study was to determine teachers' knowledge of asthma and its management. A postal questionnaire was circulated to 199 school teachers from 46 schools in Dublin City. A 74 per cent response rate was obtained. The number of children with asthma as identified by teachers was 7.8 per cent which suggests that asthma may be unrecognised in a number of pupils. Knowledge on signs and symptoms of asthma, provoking factors of asthma and the nature of the disease was generally satisfactory. However, knowledge on asthma medications, the purpose of inhalers and teachers' understanding of the treatment and management of asthma was considered poor. Knowledge on exercise-induced asthma was limited. There is a need to provide school teachers with education on asthma and its management. School policies on asthma also need to be developed with particular reference to action necessary in the event of an acute severe attack of asthma.

Retrospective analysis of calcaneal spur removal and complete fascial release for the treatment of chronic heel pain

Doctors Gormley and Kuwada investigate the pathology of chronic heel pain secondary to soft tissue and osseous inflammatory conditions. Pertinent literature review regarding success following fascial release as well as bone spur removal is provided. Ninety-four patients are reported having sustained spur removal with fascia resection according to the authors' technique. They report a 95% success rate postoperatively.

The prevalence of skeletal dysplasias. An estimate of their minimum frequency and the number of patients requiring orthopaedic care

An attempt has been made to estimate the number of living people with skeletal dysplasias (osteochondrodysplasias) in Scotland, England and Wales, ascertained through five orthopaedic centres in different parts of Britain. Index patients and their affected relatives were sought and reassessed. Over the 30-year period between 1950 and 1979 inclusive a minimum prevalence was calculated (excluding stillbirths, perinatal deaths, and patients with chromosome anomalies, metabolic bone disease and short stature per se). The results indicate that there were in the community upwards of 10 000 individuals, at various ages over this period, with these largely genetic disorders. A more accurate estimate is of some 6000 of them requiring substantial orthopaedic care, and who were physically handicapped throughout life, about half of them severely so.

Aetiology and interrelationship of some common skeletal deformities. (Talipes equinovarus and calcaneovalgus, metatarsus varus, congenital dislocation of the hip, and infantile idiopathic scoliosis)

The Edinburgh Register of the Newborn 1964-1968 and the Edinburgh Scoliosis Clinic 1964-1971 have been used to establish the population frequency in the city of the idiopathic forms of talipes equinovarus and calcaneovalgus, metatarsus varus, congenital dislocation of the hip, and infantile scoliosis. A survey of 165 patients now aged 7 to 11 years showed an aetiological relationship, but with differing environmental factors. These factors were established by comparison with the Edinburgh Register control group of 692 normal infants born over the same period, giving a unique opportunity to obtain more accurate antenatal data than has previously been possible. The principal associations were: talipes equinovarus with antepartum haemorrhage and maternal hypertension; metatarsus varus with twin pregnancies; congenital dislocation of the hip with first born children, older than average fathers, breech presentation, a significant lack of menstrual problems in the mother, and maternal upper respiratory infection during pregnancy; infantile idiopathic scoliosis with breech presentation, prematurity, and the onset of the curve in the winter months. No significant association with raised intrauterine pressure (hydramnios or oligohydramnios) was found among these simple idiopathic deformities. It is concluded that the multifactorial genetic background in likely to be similar in all, but that the additional environmental element is variable.

Achondroplasia and hypochondroplasia. Clinical variation and spinal stenosis

Forty-eight patients with achondroplasia and 24 with hypochondroplasia have been reviewed in order to clarify the differences between the two disorders and establish the height, body proportions and other clinical and radiological variations within each group. Some of the "classical" findings in achondroplasia are not always present, and hypochondroplasia at its most severe is indistinguishable from achondroplasia at its least severe. The frequency of spinal stenosis and neurological complications was established in an unselected group of 27 achondroplastic and 12 hypochondroplastic patients aged 10 years and over. Only three of the former were free of symptoms but only three developed serious complications (11 per cent). Measurement of radiographs of the lumbar canal did not in general correlate well with the severity of spinal stenosis symptoms, but it was found that the ratio of interpedicular distances at the first and fourth lumbar vertebrae had some value. Neurological complications were rare in patients with simple narrowing of the spinal canal or with persistence of a thoracolumbar kyphos but when these occurred together there was a high risk of serious neurological involvement.

The aetiology of Perthes' disease. Genetic, epidemiological and growth factors in 310 Edinburgh and Glasgow patients

The aims of this survey were to establish the familial incidence of Perthes' disease, to note any associated developmental anomalies and to collect information on preceding trauma or synovitis, on the pregnancy and birth, and on various sociological factors. Height and weight measurements were obtained for 217 patients, and comparisons made with those of their parents, unaffected sibs and (local) controls. Results showed an extremely low frequency of Perthes' disease among relatives, with no obvious pattern of inheritance. As genetic factors were not apparent, environmental and sociological causes were sought. The disease occurred particularly in children who were third-born or later in the family, and had older than average parents. Many came from low-income families and one in ten had been a breech birth, shown other malposition or had had a version late in pregnancy. Many children were already undersized at the time of developing Perthes' disease and remained short than average throughout life. Neither their parents nor sibs were shorter than normal, indicating that the patients' short stature was not familial. The child who is going to develop Perthes' disease is already constitutionally and socially at a disadvantage, and during the perinatal period and the first few years of life is perhaps more susceptible to trauma than is a normal child.

Observations on the analgesic effects of needle puncture (acupuncture)

The present study was undertaken in order to investigate the analgesic effect of needle puncture in a small self-selected group of patients with chronic or acute pain, and to examine the factors which determine success or failure of this treatment modality. We have found that in chronic painful conditions, needle puncture may be very effective in producing at least transient analgesia. It also can produce permanent relief of acute (self-limited) pains. Needle puncture was not helpful in the management of pain resulting from nerve damage. High score on psychometric indicators of anxiety and depression is a significant predictor os successful needle puncture analgesia in patients with chronic pain. Comparison of our results to studies of counterirritation indicate that the analgesia produced by needle puncture involves a mechanism similar to that of counterirritation-induced analgesia.

Congenital limb anomalies:frequency and aetiological factors. Data from the Edinburgh Register of the Newborn (1964-68)

This paper reports a detailed follow up of 156 patients with structural upper and lower limb anomalies, obtained from the Edinburgh Register of the Newborn (a registration of 52,029 consecutive births between 1964 and 1968). At the time of this survey the patients were between 4 and 9 years of age.

The Register had noted probably 96% of all children born with limb defects in Edinburgh between 1964 and 1968. It was found that the diagnosis was completely accurate in only 26% of cases, and partially so in a further 42%.

The frequency of each anomaly has been noted, subdivided into isolated anomalies; those that occurred with other limb anomalies, and those that formed part of a syndrome. Syndactyly of toes, post-axial polydactyly of the fingers, polysyndactyly, and brachydactyly were found to have a genetic basis. All `absence' defects, pre-axial polydactyly, and multiple limb deformities appeared to be sporadic. Amongst the sporadic group, the main aetiological factors noted were an excess of maternal toxaemia of pregnancy and of illegitimate children, when compared with the Register Control Data.