how to stay ontop of your data databases ontologies and more

Ontop is an Ontology Based Data Access system allowing users to access a relational database through a conceptual layer provided by an ontology. In this demo, we use the recently developed NPD benchmark +4 billion triples to demonstrate the features of Ontop. First we use Ontop as a SPARQL end-point to load the ontology and mappings, and answer SPARQL queries. Then, we will show how to use Ontop to check inconsistencies and exploit SWRL ontologies

The Ontop framework for ontology based data access

Ontology Based Data Access Ontology Based Data Access (OBDA) Formally, an OBDA system is a triple O = T , S, M , where: -T is the intensional level of an ontology. We consider ontologies formalized in description logics (DLs), hence T is a DL TBox. -S is a relational database representing the sources. -M is a set of mapping assertions, each one of the form • Φ(x) is a query over S, returning tuples of values for x • Ψ (x) is a query over T whose free variables are from x. The main functionality of OBDA systems is query answering. A schematic description of the query transformation process (usually SPARQL to SQL) performed by a typical OBDA system is provided i

Transferrin receptor 2 controls bone mass and pathological bone formation via BMP and Wnt signalling

Transferrin receptor 2 (Tfr2) is mainly expressed in the liver and controls iron homeostasis. Here, we identify Tfr2 as a regulator of bone homeostasis that inhibits bone formation. Mice lacking Tfr2 display increased bone mass and mineralization independent of iron homeostasis and hepatic Tfr2. Bone marrow transplantation experiments and studies of cell-specific Tfr2 knockout mice demonstrate that Tfr2 impairs BMP-p38MAPK signaling and decreases expression of the Wnt inhibitor sclerostin specifically in osteoblasts. Reactivation of MAPK or overexpression of sclerostin rescues skeletal abnormalities in Tfr2 knockout mice. We further show that the extracellular domain of Tfr2 binds BMPs and inhibits BMP-2-induced heterotopic ossification by acting as a decoy receptor. These data indicate that Tfr2 limits bone formation by modulating BMP signaling, possibly through direct interaction with BMP either as a receptor or as a co-receptor in a complex with other BMP receptors. Finally, the Tfr2 extracellular domain may be effective in the treatment of conditions associated with pathological bone formation

Accelerating functional gene discovery in osteoarthritis.

Osteoarthritis causes debilitating pain and disability, resulting in a considerable socioeconomic burden, yet no drugs are available that prevent disease onset or progression. Here, we develop, validate and use rapid-throughput imaging techniques to identify abnormal joint phenotypes in randomly selected mutant mice generated by the International Knockout Mouse Consortium. We identify 14 genes with functional involvement in osteoarthritis pathogenesis, including the homeobox gene Pitx1, and functionally characterize 6 candidate human osteoarthritis genes in mouse models. We demonstrate sensitivity of the methods by identifying age-related degenerative joint damage in wild-type mice. Finally, we phenotype previously generated mutant mice with an osteoarthritis-associated polymorphism in the Dio2 gene by CRISPR/Cas9 genome editing and demonstrate a protective role in disease onset with public health implications. We hope this expanding resource of mutant mice will accelerate functional gene discovery in osteoarthritis and offer drug discovery opportunities for this common, incapacitating chronic disease

Accelerating functional gene discovery in osteoarthritis.

Osteoarthritis causes debilitating pain and disability, resulting in a considerable socioeconomic burden, yet no drugs are available that prevent disease onset or progression. Here, we develop, validate and use rapid-throughput imaging techniques to identify abnormal joint phenotypes in randomly selected mutant mice generated by the International Knockout Mouse Consortium. We identify 14 genes with functional involvement in osteoarthritis pathogenesis, including the homeobox gene Pitx1, and functionally characterize 6 candidate human osteoarthritis genes in mouse models. We demonstrate sensitivity of the methods by identifying age-related degenerative joint damage in wild-type mice. Finally, we phenotype previously generated mutant mice with an osteoarthritis-associated polymorphism in the Dio2 gene by CRISPR/Cas9 genome editing and demonstrate a protective role in disease onset with public health implications. We hope this expanding resource of mutant mice will accelerate functional gene discovery in osteoarthritis and offer drug discovery opportunities for this common, incapacitating chronic disease

Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease.

Osteocytes are master regulators of the skeleton. We mapped the transcriptome of osteocytes from different skeletal sites, across age and sexes in mice to reveal genes and molecular programs that control this complex cellular-network. We define an osteocyte transcriptome signature of 1239 genes that distinguishes osteocytes from other cells. 77% have no previously known role in the skeleton and are enriched for genes regulating neuronal network formation, suggesting this programme is important in osteocyte communication. We evaluated 19 skeletal parameters in 733 knockout mouse lines and reveal 26 osteocyte transcriptome signature genes that control bone structure and function. We showed osteocyte transcriptome signature genes are enriched for human orthologs that cause monogenic skeletal disorders (P = 2.4 × 10-22) and are associated with the polygenic diseases osteoporosis (P = 1.8 × 10-13) and osteoarthritis (P = 1.6 × 10-7). Thus, we reveal the molecular landscape that regulates osteocyte network formation and function and establish the importance of osteocytes in human skeletal disease

Nouvelles approches thérapeutiques pour l’achondroplasie

Missense mutations in the tyrosine kinase receptor FGFR3 (Fibroblast Growth Factor Receptor 3) lead to its overactivation causing biological dysfunctions in several diseases. Achondroplasia, the most common Fgfr3-related chondrodysplasia, is a rare genetic disorder, affecting 1 in 20000 live births, characterized by particular clinical features: rhizomelic dwarfism, short limbs, macrocephaly, midface hypoplasia, cervicomedullary compression. The abnormal activity of the receptor induces endochondral ossification defects that are responsible for the pathological phenotype. For a long time the only treatment for this disease was the limb lengthening surgery, however in recent years several researchers have developed potential therapeutic strategies based on molecular studies. The objective of my thesis was to evaluate a novel therapeutic approach for achondroplasia. A promising therapeutic strategy involved the use of small chemical inhibitors, known as tyrosine kinase inhibitors, that are able to arrest the FGFR3 activity. I have assessed the effects of one of these compounds, NVP-BGJ398, in a mouse model mimicking the acondroplastic dwarfism (Fgfr3Y367C/+). The experiments performed showed an improvement of all pathological hallmarks in NVP-BGJ398 treated mice. We have also inspected the impact of the activating FGFR3 mutation on the mandibular development. The study established a defect in mandibular growth in both affected patients and mice. Furthermore we could investigate the mandibular bone growth and correct the pathological defect with NVP-BGJ398. Finally I have participated in molecular analyses to describe how three FGFR3 mutations at the same position could lead to three different dwarfisms with increasing severity. The results provided a better understanding of FGFR3 pathological molecular mechanisms and could lead to new targets for therapeutic approaches.Des mutations faux-sens au niveau du récepteur à activité tyrosine kinase FGFR3 (Fibroblast Growth Factor Receptor 3) entrainent sa suractivation qui apporte des dysfonctions biologiques dans plusieurs maladies. L’achondroplasie, la forme la plus commune de chondrodysplasie liée à Fgfr3, est une maladie génétique rare, touchant 1 nouveau-né sur 20 000, caractérisée par des signes cliniques spécifiques : nanisme rhizomélique, membres courts, macrocéphalie, hypoplasie de l’étage moyen de la face, compression cervico-médullaire. L’activité anormale du récepteur induit des défauts de l’ossification endochondrale responsables du phénotype pathologique. Pendant longtemps le seul traitement pour cette maladie a été l’allongement chirurgical des membres, cependant au cours des dernières années de nombreux chercheurs ont développé des potentielles stratégies thérapeutiques basées sur des études moléculaires. L’objectif de ma thèse était d’évaluer une nouvelle approche thérapeutique pour l’achondroplasie. Une stratégie thérapeutique prometteuse prévoit l’utilisation de petits inhibiteurs chimiques, connus sous le nom d’inhibiteurs de tyrosine kinases, qui sont capables d’arrêter l’activité de FGFR3. J’ai estimé les effets d’un de ces composés, NVP-BGJ398, dans un modèle murin mimant le nanisme achondroplase (Fgfr3Y367C/+). Des expérimentations effectuées ont montré une amélioration des caractéristiques pathologiques dans les souris traitées avec NVP-BGJ398. Nous avons également examiné l’impact de la mutation activatrice de FGFR3 sur le développement mandibulaire. L’étude a reconnu un défaut dans la croissance mandibulaire chez l’homme et la souris atteints. En outre nous avons pu investiguer la croissance osseuse de la mandibule et corriger le défaut pathologique avec NVP-BGJ398. Enfin j’ai participé à des analyses moléculaires pour décrire comment trois mutations de FGFR3 localisées à la même position (Lys650) peuvent induire trois différents nanismes avec sévérité croissante. Les résultats ont fourni une meilleure compréhension des mécanismes moléculaires pathologiques et pourront mener à des nouvelles cibles pour des approches thérapeutiques

New therapeutic approaches for achondroplasia

Des mutations faux-sens au niveau du récepteur à activité tyrosine kinase FGFR3 (Fibroblast Growth Factor Receptor 3) entrainent sa suractivation qui apporte des dysfonctions biologiques dans plusieurs maladies. L’achondroplasie, la forme la plus commune de chondrodysplasie liée à Fgfr3, est une maladie génétique rare, touchant 1 nouveau-né sur 20 000, caractérisée par des signes cliniques spécifiques : nanisme rhizomélique, membres courts, macrocéphalie, hypoplasie de l’étage moyen de la face, compression cervico-médullaire. L’activité anormale du récepteur induit des défauts de l’ossification endochondrale responsables du phénotype pathologique. Pendant longtemps le seul traitement pour cette maladie a été l’allongement chirurgical des membres, cependant au cours des dernières années de nombreux chercheurs ont développé des potentielles stratégies thérapeutiques basées sur des études moléculaires. L’objectif de ma thèse était d’évaluer une nouvelle approche thérapeutique pour l’achondroplasie. Une stratégie thérapeutique prometteuse prévoit l’utilisation de petits inhibiteurs chimiques, connus sous le nom d’inhibiteurs de tyrosine kinases, qui sont capables d’arrêter l’activité de FGFR3. J’ai estimé les effets d’un de ces composés, NVP-BGJ398, dans un modèle murin mimant le nanisme achondroplase (Fgfr3Y367C/+). Des expérimentations effectuées ont montré une amélioration des caractéristiques pathologiques dans les souris traitées avec NVP-BGJ398. Nous avons également examiné l’impact de la mutation activatrice de FGFR3 sur le développement mandibulaire. L’étude a reconnu un défaut dans la croissance mandibulaire chez l’homme et la souris atteints. En outre nous avons pu investiguer la croissance osseuse de la mandibule et corriger le défaut pathologique avec NVP-BGJ398. Enfin j’ai participé à des analyses moléculaires pour décrire comment trois mutations de FGFR3 localisées à la même position (Lys650) peuvent induire trois différents nanismes avec sévérité croissante. Les résultats ont fourni une meilleure compréhension des mécanismes moléculaires pathologiques et pourront mener à des nouvelles cibles pour des approches thérapeutiques.Missense mutations in the tyrosine kinase receptor FGFR3 (Fibroblast Growth Factor Receptor 3) lead to its overactivation causing biological dysfunctions in several diseases. Achondroplasia, the most common Fgfr3-related chondrodysplasia, is a rare genetic disorder, affecting 1 in 20000 live births, characterized by particular clinical features: rhizomelic dwarfism, short limbs, macrocephaly, midface hypoplasia, cervicomedullary compression. The abnormal activity of the receptor induces endochondral ossification defects that are responsible for the pathological phenotype. For a long time the only treatment for this disease was the limb lengthening surgery, however in recent years several researchers have developed potential therapeutic strategies based on molecular studies. The objective of my thesis was to evaluate a novel therapeutic approach for achondroplasia. A promising therapeutic strategy involved the use of small chemical inhibitors, known as tyrosine kinase inhibitors, that are able to arrest the FGFR3 activity. I have assessed the effects of one of these compounds, NVP-BGJ398, in a mouse model mimicking the acondroplastic dwarfism (Fgfr3Y367C/+). The experiments performed showed an improvement of all pathological hallmarks in NVP-BGJ398 treated mice. We have also inspected the impact of the activating FGFR3 mutation on the mandibular development. The study established a defect in mandibular growth in both affected patients and mice. Furthermore we could investigate the mandibular bone growth and correct the pathological defect with NVP-BGJ398. Finally I have participated in molecular analyses to describe how three FGFR3 mutations at the same position could lead to three different dwarfisms with increasing severity. The results provided a better understanding of FGFR3 pathological molecular mechanisms and could lead to new targets for therapeutic approaches

The virtual knowledge graph system ontop

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