God is usually taken to be a necessarily existing being who is unsurpassably powerful, knowledgeable and good. Theism is conceptualized in a single being that is monotheism in some religions and polytheism that is more than one being in some others. Yet some others see theism in everything of human concern that is pantheism. The doctrine of God is strong-minded by means of the religious experiences of men and evident in the conduct of such religious persons. This work intends to (...) show here, the points of similarities and dissimilarities between the concept of theism in Christianity, Islam and Sikhism. This work exposed among others that their major point of way out is that in Christianity, there is a distinctive and central teaching concerning Jesus Christ as unique incarnations, the word of God, pre-eminently manifested in a historic person, on the ground that his moral character perfectly represents the character and purpose of the invisible holy God. While Islam, and Sikhism, have no such doctrine, or theory of incarnation. (shrink)

Several studies have examined the challenges affecting the smooth implementation of inclusive education; focusing on resource inadequacies. However, these studies primarily relied on descriptive statistics: describing resource availability but not assessing their impact on policy implementation. The current study addresses this gap by analysing the extent of critical resource supply for implementing inclusive education and its influence on policy implementation. A descriptive survey design was adopted, targeting 281 principals from public secondary schools across three educational zones in Cross River State. (...) Stratified proportionate sampling was used in selecting 120 principals as the sample. Data collection involved a structured questionnaire with an acceptable validity and a reliability indices. Descriptive statistics were used to answer the research questions, and Simple and multiple linear regression were used to test the hypotheses at the .05 level of significance. The findings of the study revealed low supply levels of physical, human, and financial resources for implementing inclusive education in secondary schools. The extent of inclusive education implementation was also found to be low. The study further indicated that the supply of physical, human, and financial resources collectively affected policy implementation, with physical resources having a greater impact. These results have practical implications for the government and stakeholders; emphasising the need for adequate physical, human, and financial resources to implement inclusive education in secondary schools. Keywords:. (shrink)

Nigeria is constitutionally a secular state but underneath, religion plays a fundamental role in the socio-political governance of the people. The integration of religion and politics in Nigerian political history by her founding fathers is believed to be one major problem behind the current religious violence and political instability bedevilling the country today. The aim of this paper is to understand why the political history of Nigeria is shrouded in religious bigotry by providing the historical overview of the background that (...) has influenced the socio-religious and political activism in Nigeria. The paper also examined the passivism or activism of the two major religions: Christianity and Islam in seeking socio-political justice and control in the political activities of Nigeria and the aftermath of this power play in the affairs of governance. Lastly, the paper critiqued the effect of religious involvement in either promoting or reducing socio-religious and political crisis in contemporary Nigerian society. The paper adopted the historical and descriptive research methods and argues that the present religious violence and political instability, is predicated by the “divide and rule” and the pretentious “amalgamation” policy of the Colonial Administrators that favoured the North against the South. The seed planted by the Colonial Administrators before Independence is what has gradually grown into a monster that is threatening the peaceful co-existence of the Nigerian State. The paper concludes that to restore peaceful co-existence in a heterogeneous State like Nigeria, there is need for a realistic constitutional amendment that will truly reflect the heterogeneous secular nature of Nigeria and consider the wishes of the Federating units and by addressing the political, religious and other social-economic issues that are threatening the peaceful co-existence of Nigeria society and guarantee every religious group equality before the law. (shrink)

There are contradictory results regarding how students' learning outcomes can be predicted by various family and community inputs among previous studies, creating an evidence gap. Furthermore, previous studies have mostly concentrated on the cognitive aspect of students' learning outcomes, ignoring the affective and psychomotor dimensions, creating key knowledge gaps. Bridging these gaps, this predictive correlational study was conducted to understand how cultural capital, parental involvement (family inputs), support for schools, security network and school reforms (community inputs) jointly and partially predict (...) students' overall, cognitive, affective and psychomotor learning outcomes in the context of Calabar Education Zone, Nigeria. A random sample of principals (?? = 78) and students (?? = 915) recruited through a multistage approach, participated in the study. Data were collected through the physical administration of three sets of questionnaires designed by the researchers. The psychometric properties of the questionnaires (such as validity, dimensionality, reliability and goodness of fit) were all analysed and found acceptable based on pilot data. Data analysis was performed using SPSS version 27 and AMOS version 26 software. Results from the main study proved, among others, that family inputs (family social capital and parental involvement) jointly and individually had a significant contribution to students' overall, cognitive, affective and psychomotor learning outcomes. Similarly, community inputs (support for school, security network and school reforms) have significant composite and partial contributions to students' overall, cognitive, affective and psychomotor learning outcomes in public secondary schools. This result implies that parents and host community leaders must strengthen their partnerships with secondary schools and contribute their quota to institutions' curricular and co-curricular activities. (shrink)

The story of Miss Mary Mitchell Slessor is not a story of a clairvoyant legend who existed in an abstract world but a historical reality that worked around the then Old Calabar estuary and died on the 15th of January, 1915 at Ikot Oku Use, near Ikot Obong in the present day Akwa Ibom State and was buried at “Udi Mbakara” (Whiteman’s grave) in Calabar, Cross River State. Mary was one of those early missionaries that went to villages in the (...) then Old Calabar where few missionaries dared to go in order to bring hope and light to the people that were in darkness. Through her evangelistic efforts, schools and hospitals were erected on her initiative, babies and twins saved from death, barbaric rites and customs stopped because of her undaunted love and passion for God and the people. After a centenary of death, one can easily conclude that what immortalizes a person is not what he does for himself but what he does for others. Mary Slessor’s name, work and care for twins can never be forgotten even in another century to come. The tripartite purpose of this paper is to first examine the stepping out of Mary Slessor from her comfort zone to Calabar (her initial struggle), her passion for the people of Old Calabar and her relational method of evangelism that endeared her to the heart of the people. (shrink)

This paper investigated Efik marriage rites from a gender perspective. Marriage in Africa is a union between a man and a woman (monogamy) or mainly between a man and women (polygyny), or between a woman and men (polyandry), though this is very rare. In some cases it may be serial polygyny or polyandry, i.e. the case of marrying more than one wife or husband, but always after divorce. Marriage just like other institutions in Africa has rites of passage in which (...) those who intend to enter into it must pass through. Every culture has a sense of peculiarity as to the way in which it approaches this matter. The Efik people are not an exception to this. The question that may be asked is, how gender-balanced are these rites? The Efik people claim to have gender equality, but is this reflected in her marriage rites? Rites are symbolisms of what the actual institution which those rites represent. It is in the light of this that this paper using gender theory critically looked at the Efik traditional marriage rites from gender perspective. The paper realized that, among the Efik people’s traditional marriage rites, there is gender imbalance. It proffers ways of having gender balance in Efik traditional marriage rites. Apart from adding a voice to the cry for gender equality and equity, it provides scholarship a resource material needed for Efik ethnographic study. (shrink)

Life after retirement is to some people the most dreaded period of their life because of the uncertainty that surrounds it. Even with proper planning by way of contributory pension scheme during one’s active period in service, the uncertainty of both the political and economic policies in the country makes the future of pensioners and the aged very bleak and unpredictable. The delay in payment and the administrative bottle neck creates an atmosphere of fear and insecurity physically, psychologically, economically, socially (...) and emotionally among most employees in Nigeria. Their fear is justified by the incessant corruption scam that has bedeviled the pension scheme in Nigeria over the years. The paper investigated Some Socio-Ethical Implications of Corruption on Retirees, using the management of the Pension Scheme in Nigeria as a case study. The study discovered the multiple negative effect of corruption on retirees to include frustration, depression and poverty that has led to untimely death of many pensioners who gave their all to the nation and were neglected and abandoned after retirement. Many died because their gratuities were not paid; even their monthly pensions that they depended so much on were scarcely paid on time. Some of their adult children who would have taken care of them are unemployed, some are married and taking care of their own families and their responsibility does not allow them take care of their parents as it was in the African traditional setting. The study recommended that the appointment of pension manager should be apolitical and that persons of credible, impeccable and uncompromising track record of honesty and sincerity be appointed as pension manager to reduce the plight of the aged in Nigeria. (shrink)

It is true now that man lives in a world of conflict. Conflict is an ever-present process in human relations. Conflict situations indeed appear frequently in daily, public and private life. Conflict may occur within and among families, groups, communities or nations; and they may be fuelled by ethnic, racial, religious, or economic differences, or may arise from differences in ideologies, values and beliefs. Conflict may be on a small or large scale. Conflict charge the people with tensions, threats, fears, (...) anxieties and uncertainties. What makes a society ideal is the extent to which the conflicting interests and needs in a society are constructively managed so that violence does not threaten its continued existence. Since it is obvious that conflicts in any given society is inevitable, management and resolution of conflict is the very essence of talking about conflict. This is what this work is set to achieve and to offer suggestions on how to manage and resolve conflict thereby reducing its negative and destructive effects. This work showed the church has the potential to contribute to the management and resolution of conflicts in Nigeria. (shrink)

It is the view of most people who claim the authoritative nature of the Bible that, women’s assigned secondary status in relation to men is ordained and supported in the Bible. Many have quoted different texts of the holy writ to support their culturally-biased position on issue of gender equality. Most often views in respect to gender issues are culturally-based and interpreted rather than divinely-based and interpreted. There is therefore the need to look back at Jesus’ words, “But at the (...) beginning of creation God 'made them male and female.” (Matt 19:4; Mark 10:6). The two accounts in the Book of Genesis by the Priestly and Yahwistic strands give a complimentary account of the creation of humankind (both male and female) in the image and likeness of God and their creation from a single stock (<d*aº*) who was not a male gender. At a cursory reading of the creation accounts, one will tend to see <d„`ah*³ as the male gender, but looking at the Hebrew text more closely it will be noticed that the Hebrew words hV*aÍ !and vya !were only introduced after the two genders have been separated. Note carefully that it was not vya! that was asked to tend the garden, who named the animals, was given instruction of what to eat or what not to eat, who fell into a deep sleep or whose ribs was used in the creation of hV*aÍ!, but it was <d„`ah*³ . It was after the creation or ‘separation’ of hVÍ*a ! (woman – the female <d„`ah*³) that the other part was called vya ! (man – the male <d„`ah*³) (see vv 23 & 24). It will therefore not be right to speak of the creation of hV*aÍ ! out of vya!, because as at the time of the creation of the former, the later was not in existence as vya ! To view these creation accounts with the sense of gender superiority (either male over female or vice versa) is to read the texts using lenses which have been obscured and tainted by patriarchal, matriarchal or cultural biases. (shrink)

Purpose: This study evaluates staff Training and Development Programmes (TDPs) in secondary schools based on the views of administrators and teachers. The research was implemented in public secondary schools in Cross River State, Nigeria. Design/Methodology/Approach: The study adopted the survey research design with 5408 participants (administrators = 542; teachers = 4595). Four research questions guided the study. The Staff Training and Development Programmes Questionnaire (STDPQ) was used for data collection. Findings revealed essential areas of staff training and development. Findings: Various (...) methods are employed for staff training and development. The results further showed various constraints that impeded staff TDPs in secondary schools. Conclusion: Based on the findings, it was concluded that staff in secondary schools have different training and development needs adjudged by both the principals and teachers as crucial for job enhancement. Various staff training and development methods can serve as valuable programmes to improve the current methods adopted. Research Limitations and Implications: There are various limitations in this study such as the small scope which may affect the extent to which generalizations can be made. It is suggested that future studies focus on expanding the scope to other regions and nations. Practical Implications: Despite the limitations, the study has made some advances to human capital and self-determination theories by providing findings. The findings of this study may direct the attention of curriculum planners, the government and school management to offer training and development opportunities based on the needs of teachers. Contribution to Literature: The study has contributed to the literature on staff training and development which can constitute a basis for further research in related areas. (shrink)

The study investigated school characteristics and enrolment trend in upper basic schools in Akwa Ibom State Nigeria from 2008-2016. Two research questions were answered while two null hypotheses were also tested. The study adopted a descriptive survey research design. Census technique was adopted in selecting all the 227 public upper basic schools in the area of study. An instrument tagged “School Characteristics and Enrolment in Upper Basic Schools Checklist (SCEUBSC)” was used for data collection. Descriptive statistics (percentages) was used to (...) summarize data relating to the research questions, bar chart was used for illustrations of the enrolment pattern while independent t-test was used to test the two null hypotheses at .05 alpha level. Findings revealed that enrolment in upper basic schools in Akwa Ibom State was high in single-sex schools and boarding schools, while it was low in mixed-sex schools and day schools. Based on the findings, it was concluded that there was an upward trend in enrolment in all the schools from 2008- 2013 and a downward trend from 2015-2016. It was recommended among others that research allocation in terms of personnel and infrastructures should be evenly distributed across the state as these will reduce rural-urban migration. Keywords:. (shrink)

A preponderance of empirical research in higher education exists on the use of electronic resources to promote university education and learning. This suggests that this area of research has attracted significant interest worldwide. However, there seems to be inadequate information on the association between specific electronic infrastructures, how they are utilized for learning, and their effects on students’ learning effectiveness in higher institutions in Nigeria. This research draws on previous studies and seeks to establish how different electronic resources are used (...) in universities and how they impact students’ learning effectiveness. Using a descriptive survey design, this survey examined 1,452 participants (undergraduates and postgraduates) from Nigerian universities. The data were analyzed using mean and standard deviation, while a Polytomous Logistic Regression Model was used in testing the hypothesis formulated. Findings showed that the degree of the use of digital infrastructures in universities is low. The extent of learning effectiveness among students in universities is also low. The usage of e-infrastructures (such as e-learning, e-communication, and e-library tools) significantly predicted students’ levels of learning effectiveness. Based on these results, conclusions and relevant theoretical and practical implications are discussed for policy reforms in education and e-learning. This study faces a limitation arising from the small number of universities studied. However, it is suggested that future related studies extend their focus beyond the context of Nigeria. (shrink)

Recent studies tend to explain the importance of communication in the organisation as well as prescribing the most commonly practised techniques adopted by school managers. Studies on financial management are quite limited with the available ones suggesting that poor financial management is a source of conflict between school leaders and host communities. Little seems to be known on the connection between principals’ communication patterns and funds’ management as predictors of school-community relationship. This study builds on existing studies and appears to (...) be the first to assess the linkages between principals’ communication patterns, fund management practices and school- community relationship based on empirical rather than subjective data. A structural modelling approach was adopted to examine the nexus using quantitative primary data obtained from a random sample of 2108 respondents. A questionnaire which was designed and validated by the researchers served as the data collection device. Collected data were subjected to Exploratory and Confirmatory Factor Analyses, as well as Multiple Regression Analysis. Findings revealed various significant communication, funds management and school-community relationship practices that are available for adoption. However, it was found that the extent to which principals utilised such practices were below expected minimum standards. It was also found that there were no significant partial and composite effects of principals’ communication and funds management practices on school-community relationship (SCR). Based on these results, relevant theoretical, policy and practical implications are discussed. (shrink)

Previous research has assessed school facilities, administrative expenditures and curriculum and their relative contributions to students’ cognitive learning outcomes. This suggested the need to investigate further how these predictors may impact students’ affective and psychomotor outcomes. The current research studied the combined and relative prediction of school facilities, administrative expenses and curriculum on students’ overall cognitive, affective and psychomotor learning outcomes in public secondary schools. A cross-sectional research design was employed in this study, involving 87 school administrators and a randomly (...) selected group of 915 senior secondary class II (SS2) students. For data collection, we utilised the School Inputs Questionnaire (SIQ) and Educational Outcomes Questionnaire (EOQ), both developed by the researchers and validated through expert assessments, including content validity, Exploratory Factor Analysis (EFA) for dimensionality, Confirmatory Factor Analysis (CFA) for goodness of fit, and reliability using Cronbach's alpha. The results of these assessments demonstrated acceptable outcomes aligned with international standards. Hierarchical regression analysis was conducted to analyse the collected data. The findings indicated that enhancing the provision of quality school facilities, administrative expenses, and school curricula improved students' overall cognitive, affective, and psychomotor learning outcomes. Specifically, administrative expenses and school curriculum had significant predictive power for students’ overall cognitive, affective, and psychomotor learning outcomes. However, while school facilities significantly predicted students' overall, affective, and psychomotor dimensions, they did not significantly predict the cognitive dimension. These findings offer valuable insights for policymakers and educators aiming to enhance the educational quality in public secondary schools. (shrink)

This study evaluated the quality of educational resources vis-à-vis effective instructional service delivery in Nigerian universities. Particularly, the study was carried out in university of Calabar, using five hundred and nineteen (519) students selected through the simple random sampling technique from the fifteen faculties of the University of Calabar. To achieve the purpose of the study, two hypotheses were formulated. A questionnaire titled quality of educational resources and effectiveness of instructional service delivery questionnaire (QEREISDQ) was developed by the researchers, this (...) was subjected to face and content validity by three experts in measurement and evaluation and Administration of Higher education all in Faculty of Education University of Calabar. A pilot test was carried out using forty students from University of Uyo in Akwa Ibom state to establish the reliability of the instrument. Using the Cronbach’s alpha reliability method, the instrument had a reliability coefficient of α=.79-.85. The instrument was administered to the respondents and retrieved with Zero attrition rate. The data collected was analyzed through means, standard deviation, Pearson product moment correlation and multiple regression analysis. It was revealed among other things that; the quality of educational resources has a significant relationship with effective of instructional service delivery, with the quality of lecturers being the strongest predictor of effective instructional delivery. However, it was also revealed that the quality of library was significantly low and influenced effective instructional delivery negatively. It was therefore, recommended that government and corporate organizations should provide adequate educational resources and promote viral development programmes for lecturers to enhance effective instructional delivery in Nigerian universities. (shrink)

Background: Previous studies assessing students’ learning outcomes and identifying contributing factors have often dwelt on the cognitive domain. Furthermore, school evaluation decisions are often made using scores from cognitive-based tests to rank students. This practice often skews evaluation results, given that education aims to improve the three learning domains. This study addresses this gap by assessing the contributions of four students’ input to their cognitive, affective and psychomotor skills (CAPs). Methods: A cross-section of senior secondary class II students (n = (...) 870), sampled through the multistage procedure, participated in a physical survey. Students’ Inputs Questionnaire (STIQ) and Learning Outcomes Questionnaire (LOQ) were used for data collection. Based on data obtained from a pilot sample (n = 412), principal axis factoring (PAF) was performed to assess the internal structure of the instruments following an oblique rotation. The KMO value of sampling adequacy were 0.88 and 0.94, while the Bartlett’s test of sphericity were significant χ2 (253) = 5,010; p < 0.001 and χ2 (105) = 3693.38, p < 0.001 for the STIQ and LOQ, respectively. Confirmatory factor analysis was used to assess the models’ acceptability based on the maximum likelihood estimation technique. The main study used hierarchical linear regression for data analysis. Results: Findings indicated that innate ability, health, motivation and social capital relatively and cumulatively predicted students’ overall, cognitive, affective and psychomotor learning outcomes. The proportion of variance explained by the predictors increased at different levels of the models with the addition of new variables. Students’ social capital reduced the effect of students’ innate ability regardless of their motivation and health status. Conclusion/implication: This study has provided evidence that the four students’ inputs are crucial predictors of their learning outcomes in the three domains. This result is helpful for school management to provide services aimed at improving the school climate for students’ motivation and social capital. The result can provide policymakers with a proper understanding of the constituents of learning outcomes and how policies can be aligned to secure quality student inputs for maximum productivity in education. (shrink)

The aim of this study was to investigate the predictive relationship of peer group influence, teacher-student interaction and indiscipline to students' dropout tendency in evening continuing education programmes. The context of this study is the southern senatorial district of Cross River State, Nigeria. The study adopted a predictive correlational research design, and the sample comprised 554 students randomly selected from 11 centres in the district. This represents 20% of the total population of students. The instrument used for data collection was (...) a questionnaire titled: "Social Indicators and Dropout Tendency Scale" (SIDTS). The researchers collected the data that were analysed using Pearson product-moment correlation and multiple linear regression analyses at the .05 level of significance. The results revealed that peer group influence, teacher-student interaction and level of indiscipline collectively and individually predicted dropout tendency among students in evening continuing education programmes. It was recommended, among others, that the teachers discover diverse ways of making their teaching process lively by devising ways of engaging the students in the learning process by forming discussion groups that will promote healthy peer groups, which will increase their eagerness to come to school. (shrink)

This study assessed two motivational strategies and their respective ties to the service delivery in public universities in Cross River State. In achieving the central and specific targets of this research, four research questions and two null hypotheses were answered and tested in the study. The entire population of 440 security personnel in two public universities was studied, based on the census approach and following the ex-post facto research design. Three sets of expert-validated questionnaires, with Cronbach reliability estimates of 0.80, (...) 0.79 and 0.83 respectively, were used for data collection. Collected data were analysed using descriptive statistics and inferential statistics such as Pearson Product Moment Correlation and the One-way ANOVA. The level of incentives provision and security service delivery in universities was moderate. There were notable disparities between promotion, provision of incentives and security service delivery in universities. Security personnel discharged, on average, services beyond the extent of promotion and incentives provided to them. Provision of incentives did not relate significantly to security service delivery; however, staff promotion significantly influences security service delivery in universities. It was concluded that there are loopholes in the motivational practices of universities for security personnel. The service delivery of security personnel at universities in Cross River State is yet to be at an acceptable point that can promote institutional safety and goal attainment in the short- and long run. It was recommended, among other things, that security personnel who are due for promotion should not be denied such an opportunity, as it represents one of the strongest motivational factors in universities. (shrink)

This research studied the interaction influence of demographic characteristics (marital status, job rank, gender and age) and occupational stress level, on the work performance of faculty members in Calabar Metropolis. The descriptive survey design was utilized for this investigation. A sample of 150 respondents was identified using the systematic random sampling procedure from a population of 400 Faculty of Education lecturers from two public universities in Calabar Metropolis. A four-point scale validity and reliability certified questionnaire was used for data collection. (...) Data generated was analyzed using the two-way analysis of variance. Hypotheses were all tested at the 0.05 alpha level. Findings revealed a significant interactive effect of demographic variables (age, gender, job rank and marital status) and stress levels on lecturers' jobs. Results also indicated that the stress level of lecturers affects the degree or quality of job performance, with those having average stress levels reporting better job performance in the universities studied. Recommendations were made that all lecturers, irrespective of age, gender, marital status or rank, should develop or adopt good stress management skills and disengage/reduce extra jobs and other unnecessary stress-inducing activities. ©. (shrink)

Despite the changes in human behaviour and interactions occasioned by the COVID-19 pandemic, many institutions are yet to adapt to the new normal fully. While some educational institutions switched entirely to e-learning to promote teaching and learning, others could not offer education due to physical and social restrictions. Previous studies in Africa have identified reasons for the poor ICT adoption for educational purposes. However, the degree to which these factors affect ICT utilisation is barely analysed. Using a quantitative approach, this (...) study assessed ICT deployment for teaching in the COVID-19 era by focusing on their availability and challenges. A sample of 344 respondents from a population of 2,867 academic staff at two Nigerian public universities participated in the study. After receiving face validity from experts, a structured questionnaire was used for data collection. Cronbach alpha reliability indices of the questionnaire ranged from 0.72 to 0.94. Descriptive statistics (simple percentages, mean, and standard deviation) and inferential statistics (one-way ANOVA) were used for data analysis. Findings generally revealed a moderate extent in the availability of ICT resources in public universities. The cost of data, computer literacy, and electricity supply are challenges that significantly affected ICT deployment in the COVID-19 era. Based on this finding, it was concluded that personal and institutional challenges affect how ICT resources are deployed in public universities. It was recommended, among other things, that the management of each tertiary institution should apportion proceeds from internally generated revenue to procure ICT resources specific to the need of the school. The study provides the ground for further research into students’ use of ICT for educational purposes. (shrink)

This study evaluated the relationship between participative management practices and institutional goal attainment among Nigerian universities, with University of Calabar in focus. To achieve the purpose of the study, two research questions and two null hypotheses where developed to guide the study. The descriptive survey research design was adopted for the study. The population and sample of the study was one hundred and twenty-two (122) deans of faculties and heads of departments using the census approach. An instrument titled Participative Management (...) Practices and Institutional Goal Attainment Questionnaire (PMPIGAQ) was used for data collection. The instrument was validated by three experts in Higher Education Administration and Measurement and Evaluation. The instrument yielded Cronbach’s reliability alpha ranging from α=.75-86. Data were collected and analyzed through mean, Standard deviation, Pearson Product Moment Correlation Analysis. The results of the study showed that there is a significant relationship between participation in decision making, participation in planning and institutional goal attainment. It was recommended that managers of universities should promote participatory management practices to enhance high morale, commitment and enthusiasm among staff in the pursuit and attainment of institutional goals. (shrink)

An assessment of the extent of the use of electronic platforms by African academic staff in universities to disseminate research was done in this study. The study is informed by the growing importance of online repositories and preprint servers in the scientific communication of scholarly output, especially in an era where the use of metrics for research appraisals and funding decisions is commonly practised. The quantitative research method was adopted, based on the descriptive survey research design. The snowball sampling technique (...) was used for data collection. Data were collected from 1,977 respondents, distributed across 24 African countries, through the use of an electronic survey. There was a high rate of willingness among universities’ academic staff in Africa, to adopt various online platforms for research dissemination; ResearchGate is currently utilized the most for research dissemination, but Google Scholar is the platform respondents are more willing to adopt for research dissemination; the rate at which academic staff research output can be found online as a ratio of their total publication is 64.04% and in the ratio of 2.00:3.12; poor access to Internet facilities at home and workplaces are the major challenges academic staff face in the utilization of digital platforms for RD. It was recommended, amongst others that academic staff in universities should endeavour to explore and utilize at least ten of the online platforms mentioned in this study, to enable them disseminate their scholarly works to a wider audience and for increased visibility Keywords:. (shrink)

This study assessed the partial as well as the collaborative impact of age and gender on academic staff preparedness to adopt Internet tools for research sharing in African universities during Covid-19. Although evidence abounds in the literature on gender and age as they affect relatively, scholars’ utilisation of digital tools for research communication, such studies did not examine scholars’ preparedness to adopt from a broad perspective of Africa. This study was conducted based on the argument that the preparedness of scholars (...) may affect their future interest to utilize digital tools for research sharing. A quantitative method, based on the descriptive survey research design, was adopted to provide answers to four prevailing research questions. The examination focused on a populace of 8,591 staff in African universities, nonetheless, information was gathered from 1,977 of them, who deliberately took part from 24 African nations. A validated electronic rating scale, which was mailed/posted to targeted participants, was used as the instrument for data collection. Gender and age significantly affected academic staff preparedness to adopt Internet tools for research sharing partially and interactively in African Universities during Covid-19. Female staff were more prepared than males to adopt internet tools for research sharing during the pandemic. Older lecturers reported a higher rate of preparedness than their younger colleagues to adopt Internet tools for research sharing during Covid-19. In light of these proofs, ramifications and proposals for future exploration are discussed. (shrink)

Previous research has extensively analysed teachers' and students' Facebook use for instructional engagement, writing, research dissemination and e-learning. However, Facebook as a data collection mechanism for research has scarcely been the subject of previous studies. The current study addressed these gaps by analysing students' awareness, willingness, and utilisation of Facebook for research data collection [RDC]. This study aimed to predict students’ Facebook use for research data collection based on their awareness and willingness and to determine age and gender differences in (...) such predictions. A sample of 11,562 students of tertiary institutions participated in an online survey. The researchers designed and validated the online survey. Exploratory Factor Analysis was used for dimensionality. Average Variance Extracted [AVE] was used for convergent validity, whilst the Fornel-Larcker criterion and Heterotrait-Monotrait ratio were used for discriminant validity. Composite reliability indices of .97, .94 and .90 proved the instrument’s three sub-scales usable. One sample t-test and multigroup analysis were conducted using SPSS 27 and Smart PLS 3. The study found high awareness but low usage of Facebook for RDC among Nigerian university students. Younger and male students showed higher willingness and actual use of Facebook for RDC. Awareness directly impacted by awareness, and acted as Facebook usage for RDC, with stronger impacts for males and students aged 19 to 28. Willingness was positively impacted and acted as a negative mediator between awareness and usage for some age groups and genders. These findings provide important insights into using Facebook for RDC among students in Nigerian universities and highlight the need to consider the impact of demographic factors such as age and. (shrink)

This research assessed certain socio-demographic variables and how they affect students’ satisfaction with the study of ICT in secondary schools. The study adopted a survey research design and was guided by six specific objectives. A total of 4,484 senior secondary school students represented the study’s population, while a simple random sampling technique was adopted in selecting a sample of 2,242 respondents. Secondary school Students’ Satisfaction with the Study of ICT Questionnaire (SSSSSICTQ)” was used primarily as the tool for data collection. (...) Although there are differences in students’ satisfaction levels across various groups, age, gender, parents’ income level, students’ education level and school location do not significantly influence students’ satisfaction with the study of ICT in secondary schools respectively. It was concluded that the socio-demographic factors of students do not influence to a notable extent, students’ satisfaction with the study of ICT in secondary schools. Based on this conclusion, the implication imposes additional responsibilities for future studies to attempt to uncover reasons why socio-demographic factors do not affect the satisfaction of students with the study of ICT at the secondary education level. (shrink)

This study examined the degree to which students indulge in six prominent misconducts in Distance Education Institutions (DEIs). The study also quantified how class size, instructional delivery and institutional policies predict students’ indulgence in sharp practices using a general linear modelling approach. A sample of 871 participants was drawn from 1,742 final-year students across two DEIs in Nigeria. A structured questionnaire was used for data collection. The questionnaire had acceptable psychometric estimates of dimensionality, content and construct validity, as well as (...) reliability. Sharp practices such as cheating, plagiarism, falsification, impersonation, and arm-twisting were more prevalent in large classes, whereas only inducement was higher in small classes. Class size influenced students’ indulgence in sharp practices in DEIs. Instructional delivery and institutional policies negatively predicted students’ indulgence in the six sharp practices. Almost all the six sharp practices correlated positively and significantly, except for impersonation and inducement. Therefore, distance education students who cheat, plagiarize, arm-twist, falsify records, induce lecturers, and promote impersonation are more likely to indulge in other forms of sharp practices. It was concluded that large class sizes, poor instructional delivery, and poorly implemented institutional policies promote sharp practices among distance education students. Based on this conclusion, key policy and research implications are discussed. (shrink)

This study analyzed the behavioral characteristics of ICT users among postgraduate students leveraging the Latent Class Analysis (LCA). The study, anchored on the Planned Behavior Theory, followed the exploratory research design. It adopted the cluster random sampling technique in selecting 1,023 respondents from a population of 2,923 postgraduate students in four federal universities in South-South Nigeria. “Behavioural Characteristics and Job Creation Questionnaire (BCJCQ),” developed by the researchers, was used for data collection. Upon data collection and LCA analysis, the five-class solution (...) was accepted as the best-fitting model, based on statistical fit indicators (such as AIC, BIC, entropy, Gsq, and Chsq) and theoretical grounds. Consequently, five classes of behavioral ICT users were identified and named based on their item–response probability, conditional on class. The five classes were named Trendy, Outmoded, Pragmatic, Disciplined, and Social users of ICT, with their unique characteristics discussed. The study tested for job creation differences among the classes using a one-way ANOVA and found a significant difference. On average, pragmatic users of ICT created more jobs than social, disciplined, and outmoded users. Trendy users were, on average, the minor job-creating class of ICT users. The study compared the bivariate differences in job creation among the classes using the Tukey HSD test of multiple pairwise comparisons. Based on the results obtained, discussions were made with implications for further research in the evolving area of LCA. (shrink)

Academic publishing refers to the action taken by individuals or organisations to make scholarly materials publicly available. The research process is not complete and relevant until research results are made available to the public through publication (Owan et al., 2021). The essence of any scholarly venture is to create knowledge or modify existing knowledge. Knowledge cannot be said to have been created if the scholarly output is stored on a personal computer accessible only to the author(s). Through publication, other scholars (...) or the general public become aware of the finished product of a scholarly venture. Scientific publications are the lifeblood of science because they serve as fertilisers for other scientists to think (Clapham, 2005). New hypotheses are generated, rebutted, or verified by publishing new information in the scientific community. In academic settings, the number of publications a person has to their name is commonly used as a proxy for their level of career success. (shrink)

The literature is predominated by studies seeking to clarify the extent of the availability, functionality, accessibility and/or utilisation of library materials in schools at various levels. The extent of principals' management of library resources and their contribution to the lesson preparation activities of teachers seems to have been under-researched. In bridging the gap, the current study was designed to assess the extent and contribution of principals’ management of library resources to teachers’ lesson preparation practices. Six specific objectives were of interest (...) to the researchers. The quantitative research method, following the ex-post facto research design, was adopted. The stratified proportional random sampling technique was used to choose a sample of 743 respondents from a population of 1,857 secondary school teachers in Ikom Education Zone, Cross River State, Nigeria. An instrument named "Management of Library Resources and Teachers' Lesson Preparation Questionnaire" (MLRTLPQ) was used to gather data. The quantitative content validity method was used to assess the degree to which the items in the instrument were clear, relevant, and represented a wide range of the anticipated content based on the views of domain experts. One sample t-test and hierarchical regression analyses were used for data analyses. Four stepwise hierarchical linear models were specified and fitted accordingly. It was found that teachers’ lesson preparation practice is significantly low generally; there is a significantly low extent in principals’ management of textual, auditory, visual and audio-visual library resources; there is a significant composite contribution of principals’ management of library resources on teachers’ lesson preparation practices in public secondary schools in model 3 and model 4. Based on these findings, practical implications are discussed, with recommendations made for a better library management practice in secondary schools for quality lesson preparation practices. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

Since its introduction just over two decades ago, evidence-based medicine (EBM) has come to dominate medical practice, teaching, and policy. There are a growing number of textbooks, journals, and websites dedicated to EBM research, teaching, and evidence dissemination. EBM was most recently defined as a method that integrates best research evidence with clinical expertise and patient values and circumstances in the treatment of patients. There have been debates throughout the early 21st century about what counts as good research evidence between (...) EBM proponents and philosophical critics and even within the EBM community itself. Similar controversy arises about the relative worth of patient values and clinical expertise (and how these can be integrated). EBM has also evolved in ways that have come under scrutiny. Specifically, policymakers have used EBM research methodology to increase the relative importance of clinical guidelines that some clinicians have argued are tyrannical. Philosophers have addressed all of these controversies, and with very few exceptions have been critical of EBM. In addition most philosophical attention has been on the epistemic role of Randomization and evidence hierarchies, with relatively little attention being paid to the role of Diagnosis, expertise, patient values, and Systematic Reviews within EBM. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how (...) an ontology for the obstetric and neonatal domain deals with these general elements documented in health care encounters. Our goal is to promote the interoperability of information among EHRs created in different specialties. To develop our ontology, we used two main approaches: one based on ontological realism, the other based on the principles of the OBO Foundry, including reuse of reference ontologies. (shrink)

The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...) the Foundry’s goal of consistent and non-redundant annotation if appropriate mappings of data annotated with their aid can be achieved. To construct such mappings in reliable fashion, however, it is necessary to analyze terminological resources from an ontologically realistic perspective in such a way as to identify the exact import of the ‘concepts’ and associated terms which they contain. We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...) from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)