Interaction-based ontology alignment repair with expansion and relaxation

euzenat2017aInternational audienceAgents may use ontology alignments to communicate when they represent knowledge with different ontologies: alignments help reclassifying objects from one ontology to the other. These alignments may not be perfectly correct, yet agents have to proceed. They can take advantage of their experience in order to evolve alignments: upon communication failure, they will adapt the alignments to avoid reproducing the same mistake. Such repair experiments had been performed in the framework of networks of ontologies related by alignments. They revealed that, by playing simple interaction games, agents can effectively repair random networks of ontologies. Here we repeat these experiments and, using new measures, show that previous results were underestimated. We introduce new adaptation operators that improve those previously considered. We also allow agents to go beyond the initial operators in two ways: they can generate new correspondences when they discard incorrect ones, and they can provide less precise answers. The combination of these modalities satisfy the following properties: (1) Agents still converge to a state in which no mistake occurs. (2) They achieve results far closer to the correct alignments than previously found. (3) They reach again 100% precision and coherent alignments

Two Approaches to Ontology Aggregation Based on Axiom Weakening

Axiom weakening is a novel technique that allows for fine-grained repair of inconsistent ontologies. In a multi-agent setting, integrating ontologies corresponding to multiple agents may lead to inconsistencies. Such inconsistencies can be resolved after the integrated ontology has been built, or their generation can be prevented during ontology generation. We implement and compare these two approaches. First, we study how to repair an inconsistent ontology resulting from a voting-based aggregation of views of heterogeneous agents. Second, we prevent the generation of inconsistencies by letting the agents engage in a turn-based rational protocol about the axioms to be added to the integrated ontology. We instantiate the two approaches using real-world ontologies and compare them by measuring the levels of satisfaction of the agents w.r.t. the ontology obtained by the two procedures

Completing and Debugging Ontologies: state of the art and challenges

As semantically-enabled applications require high-quality ontologies, developing and maintaining ontologies that are as correct and complete as possible is an important although difficult task in ontology engineering. A key step is ontology debugging and completion. In general, there are two steps: detecting defects and repairing defects. In this paper we discuss the state of the art regarding the repairing step. We do this by formalizing the repairing step as an abduction problem and situating the state of the art with respect to this framework. We show that there are still many open research problems and show opportunities for further work and advancing the field.Comment: 56 page

Development of an ontology supporting failure analysis of surface safety valves used in Oil & Gas applications

Treball desenvolupat dins el marc del programa 'European Project Semester'.The project describes how to apply Root Cause Analysis (RCA) in the form of a Failure Mode Effect and Criticality Analysis (FMECA) on hydraulically actuated Surface Safety Valves (SSVs) of Xmas trees in oil and gas applications, in order to be able to predict the occurrence of failures and implement preventive measures such as Condition and Performance Monitoring (CPM) to improve the life-span of a valve and decrease maintenance downtime. In the oil and gas industry, valves account for 52% of failures in the system. If these failures happen unexpectedly it can cause a lot of problems. Downtime of the oil well quickly becomes an expensive problem, unscheduled maintenance takes a lot of extra time and the lead-time for replacement parts can be up to 6 months. This is why being able to predict these failures beforehand is something that can bring a lot of benefits to a company. To determine the best course of action to take in order to be able to predict failures, a FMECA report is created. This is an analysis where all possible failures of all components are catalogued and given a Risk Priority Number (RPN), which has three variables: severity, detectability and occurrence. Each of these is given a rating between 0 and 10 and then the variables are multiplied with each other, resulting in the RPN. The components with an RPN above an acceptable risk level are then further investigated to see how to be able to detect them beforehand and how to mitigate the risk that they pose. Applying FMECA to the SSV mean breaking the system down into its components and determining the function, dependency and possible failures. To this end, the SSV is broken up into three sub-systems: the valve, the actuator and the hydraulic system. The hydraulic system is the sub-system of the SSV responsible for containing, transporting and pressurizing of the hydraulic fluid and in turn, the actuator. It also contains all the safety features, such as pressure pilots, and a trip system in case a problem is detected in the oil line. The actuator is, as the name implies, the sub-system which opens and closes the valve. It is made up of a number of parts such as a cylinder, a piston and a spring. These parts are interconnected in a number of ways to allow the actuator to successfully perform its function. The valve is the actual part of the system which interacts with the oil line by opening and closing. Like the actuator, this sub-system is broken down into a number of parts which work together to perform its function. After breaking down and defining each subsystem on a functional level, a model was created using a functional block diagram. Each component also allows for the defining of dependencies and interactions between the different components and a failure diagram for each component. This model integrates the three sub-systems back into one, creating a complete picture of the entire system which can then be used to determine the effects of different failures in components to the rest of the system. With this model completed we created a comprehensive FMECA report and test the different possible CPM solutions to mitigate the largest risks

Epistemic alignment repair

International audienc

Characterization of the Poly (ADP-Ribose) Polymerase Family in the Fusarium oxysporum Species Complex

Fusarium oxysporum is a filamentous fungus that is known to invade over a hundred different hosts and poses a major threat to the economy and food supply world-wide. Poly (Adenosine diphosphate-Ribose) Polymerase (PARP) is a family of regulatory proteins that affect change in the cell through transfer of ADP-Ribose moieties onto target molecules. The most well-studied PARP protein is the human PARP1, a PARylating nuclear protein that serves as our model PARP protein. F. oxysporum was found to contain a large expansion of PARP catalytic-domain-containing proteins compared to other filamentous fungi. We utilized in silico multiple sequence alignments and domain predictions to identify a human PARP1 homolog termed foPARP1 that was conserved within the core chromosomes in all three strains within our comparative system. Our in silico predictions also stated that only one strain, an Arabidopsis pathogen, Fo5176, contained several other predicted catalytically active PARP homologs within the accessory chromosome. To test the effect that foPARP1 knockout would have on DNA damage tolerance, we created a foParp1 knockout and found that only strains Fol4287 and Fo5176 had a significant reduction in tolerance upon being plated with methyl methanesulfonate (MMS), a DNA alkylating agent. To test how global PARylation trends would be affected by foParp1 knockout, we utilized immunodot-blotting with PAR antibodies to assess PARylation in total protein extracts. We found that all strains of the comparative system had the capacity to catalyze the synthesis of long PAR chains, while only Fo47 and Fo5176 had a significant PARylation increase when exposed to MMS, and no samples had a significant increase in PARylation within the foParp1 knockouts. Finally, we utilized RNA-Sequencing to determine the transcriptional impacts that foParp1 knockout would have and found aberrant DNA repair pathways and disruptions in stress responses. Taken together, we conclude that foPARP1 is in fact a functional PARP1 homolog and exhibits similar post-transcriptional modification and transcriptional impacts as its human counterpart. However, we were not able to correlate PARP copy number with DNA stress tolerance, and further research would be needed to assess the full function of the PARP expansion

Tandem amino acid repeats in the green anole (Anolis carolinensis) and other squamates may have a role in increasing genetic variability

Statistics of the other amino acid repeat types in the green anole proteome (supplementary table for Table 2 ). (DOCX 67 kb

The role of positive selection in determining the molecular cause of species differences in disease

Related species, such as humans and chimpanzees, often experience the same disease with varying degrees of pathology, as seen in the cases of Alzheimer's disease, or differing symptomatology as in AIDS. Furthermore, certain diseases such as schizophrenia, epithelial cancers and autoimmune disorders are far more frequent in humans than in other species for reasons not associated with lifestyle. Genes that have undergone positive selection during species evolution are indicative of functional adaptations that drive species differences. Thus we investigate whether biomedical disease differences between species can be attributed to positively selected genes

Chick tendon fibroblast transcriptome and shape depend on whether the cell has made its own collagen matrix

Collagen- and fibrin-based gels are extensively used to study cell behaviour. However, 2D-3D and collagen-fibrin comparisons of gene expression, cell shape and mechanotransduction, with an in vivo reference, have not been reported. Here we compared chick tendon fibroblasts (CTFs) at three stages of embryonic development with CTFs cultured in collagen- or fibrin-based tissue engineered constructs (TECs). CTFs synthesised their own collagen matrix in fibrin-based TECs and better recapitulated the gene expression, collagen fibril alignment and cell shape seen in vivo. In contrast, cells in 3D collagen gels exhibited a 2D-like morphology and expressed fewer of the genes expressed in vivo. Analysis of YAP/TAZ target genes showed that collagen gels desensitise mechanotransduction pathways. In conclusion, gene expression and cell shape are similar on plastic and 3D collagen whereas cells in 3D fibrin have a shape and transcriptome better resembling the in vivo situation. Implications for wound healing are discussed

Identification and Functional Analysis of Healing Regulators in Drosophila

© 2015 Álvarez-Fernández et al. Wound healing is an essential homeostatic mechanism that maintains the epithelial barrier integrity after tissue damage. Although we know the overall steps in wound healing, many of the underlying molecular mechanisms remain unclear. Genetically amenable systems, such as wound healing in Drosophila imaginal discs, do not model all aspects of the repair process. However, they do allow the less understood aspects of the healing response to be explored, e.g., which signal(s) are responsible for initiating tissue remodeling? How is sealing of the epithelia achieved? Or, what inhibitory cues cancel the healing machinery upon completion? Answering these and other questions first requires the identification and functional analysis of wound specific genes. A variety of different microarray analyses of murine and humans have identified characteristic profiles of gene expression at the wound site, however, very few functional studies in healing regulation have been carried out. We developed an experimentally controlled method that is healing-permissive and that allows live imaging and biochemical analysis of cultured imaginal discs. We performed comparative genome-wide profiling between Drosophila imaginal cells actively involved in healing versus their non-engaged siblings. Sets of potential wound-specific genes were subsequently identified. Importantly, besides identifying and categorizing new genes, we functionally tested many of their gene products by genetic interference and overexpression in healing assays. This non-saturated analysis defines a relevant set of genes whose changes in expression level are functionally significant for proper tissue repair. Amongst these we identified the TCP1 chaperonin complex as a key regulator of the actin cytoskeleton essential for the wound healing response. There is promise that our newly identified wound-healing genes will guide future work in the more complex mammalian wound healing response.CAF and FP were supported by the EU FP6 STREP project WOUND and ST held a Spanish FPU PhD studentship. Research in the EMB laboratory is funded by grants of the EU (FP6 STREP project WOUND), the Spanish Ministry of Economy and Competitivity (DGI and CONSOLIDER grants) and the Generalitat de Catalunya (SGR)Peer Reviewe