Alignment-based Partitioning of Large-scale Ontologies

Ontology alignment is an important task for information integration systems that can make different resources, described by various and heterogeneous ontologies, interoperate. However very large ontologies have been built in some domains such as medicine or agronomy and the challenge now lays in scaling up alignment techniques that often perform complex tasks. In this paper, we propose two partitioning methods which have been designed to take the alignment objective into account in the partitioning process as soon as possible. These methods transform the two ontologies to be aligned into two sets of blocks of a limited size. Furthermore, the elements of the two ontologies that might be aligned are grouped in a minimal set of blocks and the comparison is then enacted upon these blocks. Results of experiments performed by the two methods on various pairs of ontologies are promising

Nutritional risk factors for postmenopausal osteoporosis

Background: Osteoporosis is a bone disease that combines both a decrease in bone density and its internal architecture changes. Nutrition is one of the major determinants of osteoporosis.Aim: The purpose of our study was to identify nutritional risk factors of osteoporosis of two groups of osteoporotic women and witnesses.Methods: We conducted a comparative cross-sectional study including 60 postmenopausal women and screening for osteoporosis by a bone densitometry, recruited the outpatient service of Rheumatology of the Institute KASSAB.Results: We have identified excessive supply of saturated fatty acids (SFA) in the osteoporotic compared with controls (13.27% vs 10.23%, p= 0.002) and an inadequate intake of monounsaturated fatty acids (MUFA) (12.6% vs 16.16%, p=0.012).A low calcium intake is another factor of risk of osteoporosis (574.27 ± 336.9 mg/day vs 782.45 ± 340.54 mg/day; p= 0.021). This is explained by the low consumption of milk and milk products objectified in the osteoporotic group (p= 0.001). We also found a negative relationship between inadequate intakes of potassium and osteoporosis (2241.55 ±1049.85 mg/day vs 2988.17 ± 1146.52 mg/day; p= 0.011). This may be due to the low consumption in fruit and vegetables, sources of potassium, found in the osteoporotic group (p= 0.003).We found a significant increase in the consumption of the VVPO group in the osteoporotic toward women witness (2.23 ± 0.99 number of times/day vs 1.67 ± 0.76 number of times/day; p= 0.019). A high consumption of coffee appears also as a risk factor since the osteoporotic group consume almost twice than controls (p= 0.002).Conclusion: Nutritional risk factors of osteoporosis are all the most important that they are editable and can take their place in a prevention of public health policy.Keywords: Osteoporosis; Menopause; Risk factors; Nutritio

Uncovering the clinical relevance of unclassified variants in DNA repair genes: a focus on BRCA negative Tunisian cancer families

Introduction: Recent advances in sequencing technologies have significantly increased our capability to acquire large amounts of genetic data. However, the clinical relevance of the generated data continues to be challenging particularly with the identification of Variants of Uncertain Significance (VUSs) whose pathogenicity remains unclear. In the current report, we aim to evaluate the clinical relevance and the pathogenicity of VUSs in DNA repair genes among Tunisian breast cancer families.Methods: A total of 67 unsolved breast cancer cases have been investigated. The pathogenicity of VUSs identified within 26 DNA repair genes was assessed using different in silico prediction tools including SIFT, PolyPhen2, Align-GVGD and VarSEAK. Effects on the 3D structure were evaluated using the stability predictor DynaMut and molecular dynamics simulation with NAMD. Family segregation analysis was also performed.Results: Among a total of 37 VUSs identified, 11 variants are likely deleterious affecting ATM, BLM, CHEK2, ERCC3, FANCC, FANCG, MSH2, PMS2 and RAD50 genes. The BLM variant, c.3254dupT, is novel and seems to be associated with increased risk of breast, endometrial and colon cancer. Moreover, c.6115G>A in ATM and c.592+3A>T in CHEK2 were of keen interest identified in families with multiple breast cancer cases and their familial cosegregation with disease has been also confirmed. In addition, functional in silico analyses revealed that the ATM variant may lead to protein immobilization and rigidification thus decreasing its activity. We have also shown that FANCC and FANCG variants may lead to protein destabilization and alteration of the structure compactness which may affect FANCC and FANCG protein activity.Conclusion: Our findings revealed that VUSs in DNA repair genes might be associated with increased cancer risk and highlight the need for variant reclassification for better disease management. This will help to improve the genetic diagnosis and therapeutic strategies of cancer patients not only in Tunisia but also in neighboring countries

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available

Partitionnement d'ontologies pour le passage à l'échelle des techniques d'alignement

National audienceOntology alignment is an important task for information integration systems that can make different resources described by various and heterogeneous ontologies interoperate. However very large ontologies have been built in some domains like medicine or agronomy and the challenge is now in scaling up alignment techniques that often perform complex tasks. In this paper, we propose two partitioning methods which have been designed to take the alignment objective into account in the partitioning process as soon as possible. These methods transform two ontologies to be aligned into two sets of blocks of a limited size. Furthermore, elements of the two ontologies that might be aligned are grouped in a minimal set of blocks that will be then really compared. Results of experiments performed by the two methods on various pairs of ontologies are convincing

Rôle du facteur gilz (glucocorticoid induced leucine Zipper) dans l'induction de la tolérance immunitaire par les cellules dendritiques

LE KREMLIN-B.- PARIS 11-BU Méd (940432101) / SudocPARIS-BIUP (751062107) / SudocSudocFranceF

TaxoMap in the OAEI 2008 alignment contest

International audienceTaxoMap is an alignment tool which aim is to discover rich correspondences between concepts. It performs an oriented alignment (from a source to a target ontology) and takes into account labels and sub-class descriptions. Our participation in last year edition of the competition have put the emphasis on certain limits. TaxoMap 2 is a new implementation of TaxoMap that reduces significantly runtime and enables parameterization by specifying the ontology language and different thresholds used to extract different mapping relations. The new implementation stresses on terminological techniques, it takes into account synonymy, and multi-label description of concepts. Special effort was made to handle large-scale ontologies by partitioning input ontologies into modules to align. We conclude the paper by pointing out the necessary improvements that need to be made