RTPrimerDB: the real-time PCR primer and probe database, major update 2006

The RTPrimerDB () project provides a freely accessible data retrieval system and an in silico assay evaluation pipeline for real-time quantitative PCR assays. Over the last year the number of user submitted assays has grown to 3500. Data conveyance from Entrez Gene by establishing an assay-to-gene relationship enables the addition of new primer assays for one of the 1.5 million different genes from 2300 species stored in the system. Easy access to the primer and probe data is possible by using multiple search criteria. Assay reports contain gene information, assay details (such as oligonucleotide sequences, detection chemistry and reaction conditions), publication information, users' experimental evaluation feedback and submitter's contact details. Gene expression assays are extended with a scalable assay viewer that provides detailed information on the alignment of primer and probe sequences on the known transcript variants of a gene, along with Single Nucleotide Polymorphisms (SNP) positions and peptide domain information. Furthermore, an mfold module is implemented to predict the secondary structure of the amplicon sequence, as this has been reported to impact the efficiency of the PCR. RTPrimerDB is also extended with an in silico analysis pipeline to streamline the evaluation of custom designed primer and probe sequences prior to ordering and experimental evaluation. In a secured environment, the pipeline performs automated BLAST specificity searches, mfold secondary structure prediction, SNP or plain sequence error identification, and graphical visualization of the aligned primer and probe sequences on the target gene

An ontology to standardize research output of nutritional epidemiology : from paper-based standards to linked content

Background: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiology. Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Secondly, existing data standards and reporting guidelines for nutritional epidemiology were converted into an ontology. The terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Thirdly, the ontologies of the nutritional epidemiologic standards, reporting guidelines, and the core concepts were gathered in ONE. Three case studies were included to illustrate potential applications: (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts. Results: Ontologies for food and nutrition (n = 37), disease and specific population (n = 100), data description (n = 21), research description (n = 35), and supplementary (meta) data description (n = 44) were reviewed and listed. ONE consists of 339 classes: 79 new classes to describe data and 24 new classes to describe the content of manuscripts. Conclusion: ONE is a resource to automate data integration, searching, and browsing, and can be used to assess reporting completeness in nutritional epidemiology

Diagnositic value of pelvic enthesitis on MRI of the sacroiliac joints in enthesitis related arthritis

Background: To determine the prevalence and diagnostic value of pelvic enthesitis on MRI of the sacroiliac (SI) joints in enthesitis related arthritis (ERA). Methods: We retrospectively studied 143 patients aged 6-18 years old who underwent MRI of the SI joints for clinically suspected sacroiliitis between 2006-2014. Patients were diagnosed with ERA according to the International League of Associations for Rheumatology (ILAR) criteria. All MRI studies were reassessed for the presence of pelvic enthesitis, which was correlated to the presence of sacroiliitis on MRI and to the final clinical diagnosis. The added value for detection of pelvic enthesitis and fulfilment of criteria for the diagnosis of ERA was studied. Results: Pelvic enthesitis was seen in 23 of 143 (16 %) patients. The most commonly affected sites were the entheses around the hip (35 % of affected entheses) and the retroarticular interosseous ligaments (32 % of affected entheses). MRI showed pelvic enthesitis in 21 % of patients with ERA and in 13 % of patients without ERA. Pelvic enthesitis was seen on MRI in 7/51 (14 %) patients with clinically evident enthesitis, and 16/92 (17 %) patients without clinically evident enthesitis. In 7 of 11 ERA-negative patients without clinical enthesitis but with pelvic enthesitis on MRI, the ILAR criteria could have been fulfilled, if pelvic enthesitis on MRI was included in the criteria. There is a high correlation between pelvic enthesitis and sacroiliitis, with sacroiliitis present in 17/23 (74 %) patients with pelvic enthesitis. Conclusions: Pelvic enthesitis may be present in children with or without clinically evident peripheral enthesitis. There is a high correlation between pelvic enthesitis and sacroiliitis on MRI of the sacroiliac joints in children. As pelvic enthesitis indicates active inflammation, it may play a role in assessment of the inflammatory status. Therefore, it should be carefully sought and noted by radiologists examining MRI of the sacroiliac joints in children