Detecting inconsistency in biological molecular databases using ontologies

The rapid growth of life science databases demands the fusion of knowledge from heterogeneous databases to answer complex biological questions. The discrepancies in nomenclature, various schemas and incompatible formats of biological databases, however, result in a significant lack of interoperability among databases. Therefore, data preparation is a key prerequisite for biological database mining. Integrating diverse biological molecular databases is an essential action to cope with the heterogeneity of biological databases and guarantee efficient data mining. However, the inconsistency in biological databases is a key issue for data integration. This paper proposes a framework to detect the inconsistency in biological databases using ontologies. A numeric estimate is provided to measure the inconsistency and identify those biological databases that are appropriate for further mining applications. This aids in enhancing the quality of databases and guaranteeing accurate and efficient mining of biological databases.

Baseline comorbidities in a population-bases cohort of rheumatoid arthritis patients receiving biological therapy: data from the Australian Rheumatology Association database

Aims: To describe the baseline characteristics of an Australian population-based cohort of rheumatoid arthritis (RA) patients commencing biological therapy.

Methods: Descriptive analysis from the Australian Rheumatology Association Database (ARAD).

Results: Up to October 2006, there were 681 RA patients taking biologics enrolled in ARAD. Baseline data were available for 624 (72% female, mean (SD) age 57.0 (12.5) years). Of these, 59.5% reported at least one comorbid condition, most commonly hypertension (35.7%) and osteoporosis (30.4%); 61 (9.8%) had a history of malignancy (35 nonmelanoma skin, 5 breast, 4 bowel, 5 cervix, 3 melanoma, 3 prostate and 1 each of lip, lung, myeloma, testis, uterus, vagina). Self-reported infections within the previous 6 months were common (71.5%).

Conclusions: History of comorbidities, including recent infections, is common among Australian RA patients commencing biologics, and 10% have a history of malignancy. This may impact future evaluations of health outcomes among this population, including attribution of adverse events of biologic therapy.

ANNODA: tool for integrating molecular-biological annotation data

Collecting, analyzing, and making Molecularbiological annotation data accessible in different public data sources is still an ongoing project. Integration of such data from these data sources might lead to valuable biological knowledge. There are numerous annotation data and only some of those are structured. The number and contents of related sources are continuously increasing. In addition, the existing data sources have their own storage structure and implementation. As a result, these could lead to a limitation in the combining of annotation. Here, we proposed a tool, called ANNODA, for integrating Molecular-biological annotation data. Unlike the past work on database interoperation in the bioinformatics community, this database design uses web-links which are very useful for interactive navigation and meanwhile it also supports automated large-scale analysis tasks.

Analyzing inconsistency toward enhancing integration of biological molecular databases

The rapid growth of biological databases not only provides biologists with abundant data but also presents a big challenge in relation to the analysis of data. Many data analysis approaches such as data mining, information retrieval and machine learning have been used to extract frequent patterns from diverse biological databases. However, the discrepancies, due to the differences in the structure of databases and their terminologies, result in a significant lack of interoperability. Although ontology-based approaches have been used to integrate biological databases, the inconsistent analysis of biological databases has been greatly disregarded. This paper presents a method by which to measure the degree of inconsistency between biological databases. It not only presents a guideline for correct and efficient database integration, but also exposes high quality data for data mining and knowledge discovery.

A provisional database for the silicon content of foods in the United Kingdom

Si may play an important role in bone formation and connective tissue metabolism. Although biological interest in this element has recently increased, limited literature exists on the Si content of foods. To further our knowledge and understanding of the relationship between dietary Si and human health, a reliable food composition database, relevant for the UK population, is required. A total of 207 foods and beverages, commonly consumed in the UK, were analysed for Si content. Composite samples were analysed using inductively coupled plasma–optical emission spectrometry following microwave-assisted digestion with nitric acid and H2O2. The highest concentrations of Si were found in cereals and cereal products, especially less refined cereals and oat-based products. Fruit and vegetables were highly variable sources of Si with substantial amounts present in Kenyan beans, French beans, runner beans, spinach, dried fruit, bananas and red lentils, but undetectable amounts in tomatoes, oranges and onions. Of the beverages, beer, a macerated whole-grain cereal product, contained the greatest level of Si, whilst drinking water was a variable source with some mineral waters relatively high in Si. The present study provides a provisional database for the Si content of UK foods, which will allow the estimation of dietary intakes of Si in the UK population and investigation into the role of dietary Si in human health.

Stakeholder satisfaction with the Australian Rheumatology Association Database (ARAD)

Background: The Australian Rheumatology Association Database (ARAD) is a voluntary national registry for monitoring the long-term benefits and safety of biological disease-modifying anti-rheumatic drugs (bDMARDs) for inflammatory arthritis. Both rheumatologists and patients contribute data to the ARAD.

Objective: To evaluate the satisfaction of patients and rheumatologists with the ARAD.

Methods: Cross-sectional surveys were distributed to a random sample of 100 community-dwelling ARAD patients in 2007 and to rheumatologists attending the 2007 AustralianRheumatologyAssociation (ARA) annual scientific meeting.

Survey questions included items about the usefulness of the ARAD, workload for participants, frequency of questionnaires, and experience of contact with ARAD staff.

Results: A total of 92.5% of patients perceived the ARAD as very important (scoring 9-10 on a numeric rating scale). Patients reported minimal difficulty in completing questionnaires, and 95.0% indicated that a 6-month interval between questionnaires was reasonable. Of responding rheumatologists, 32.3%, 62.1%, and 53.8% indicated that the ARAD was very important (scoring 8-10) with respect to clinical information, research, and the profession, respectively, while 68% of those participating in the ARAD reported that the workload required to enroll patients was manageable and 30% found it difficult or onerous.

Conclusion: Key stakeholders in the ARAD view it as an important resource and are satisfied with its operations. Efforts will be directed towards assisting those rheumatologists who find the associated workload difficult and to improving the perceived clinical value of information available from the ARAD.

Ankylosing spondylitis patients commencing biologic therapy have high baseline levels of comorbidity: a report from the Australian Rheumatology Association Database

Aims: To compare the baseline characteristics of a population-based cohort of patients with ankylosing spondylitis (AS) commencing biological therapy to the reported characteristics of bDMARD randomised controlled trials (RCTs) participants.
Methods: Descriptive analysis of AS participants in the Australian Rheumatology Association Database (ARAD) who were commencing bDMARD therapy.
Results: Up to December 2008, 389 patients with AS were enrolled in ARAD. 354 (91.0%) had taken bDMARDs at some time, and 198 (55.9%) completed their entry questionnaire prior to or within 6 months of commencing bDMARDs. 131 (66.1%) had at least one comorbid condition, and 24 (6.8%) had a previous malignancy (15 nonmelanoma skin, 4 melanoma, 2 prostate, 1 breast, cervix, and bowel). Compared with RCT participants, ARAD participants were older, had longer disease duration and higher baseline disease activity.
Conclusions: AS patients commencing bDMARDs in routine care are significantly different to RCT participants and have significant baseline comorbidities.