Semantic Faceted Search: Safe and Expressive Navigation in RDF Graphs

Faceted search and querying are the two main paradigms to search the Semantic Web. Querying languages, such as SPARQL, oer expressive means for searching knowledge bases, but they are dicult to use. Query assistants help users to write well-formed queries, but they do not prevent empty results. Faceted search supports exploratory search, i.e., guided navigation that returns rich feedbacks to users, and prevents them to make navigation steps that lead to empty results (dead-ends). However, faceted search systems do not oer the same expressiveness as query languages. We introduce semantic faceted search, the combination of an expressive query language and faceted search to reconcile the two paradigms. The query language is basically SPARQL, but with a syntax that extends Turtle with disjunction and negation, and that better ts in a faceted search interface: LISQL. We formalize the navigation of faceted search as a navigation graph, where nodes are queries, and navigation links are query transformations. We prove that this navigation graph is safe (no dead-end), and complete (every query that is not a dead-end can be reached by navigation). That formalization itself is a contribution to faceted search. A prototype, Camelis 2, has been implemented, and a usability evaluation with graduate students demonstrated that semantic faceted search retains the ease-of-use of faceted search, and enables most users to build complex queries with little training

An Interactive Guidance Process Supporting Consistent Updates of RDFS Graphs

International audienceWith existing tools, when creating a new object in the Semantic Web, users benefit neither from existing objects and their properties, nor from the already known properties of the new object. We propose UTILIS, an interactive process to help users add new objects. While creating a new object, relaxation rules are applied to its current description to find similar objects, whose properties serve as suggestions to expand the description. A user study conducted on a group of master students shows that students, even the ones disconcerted by the unconventional interface, used UTILIS suggestions. In most cases, they could find the searched element in the first three sets of properties of similar objects. Moreover, with UTILIS users did not create any duplicate whereas with the other tool used in the study more than half of them did

Création et mise à jour guidées d'objets dans une base RDF(S)

National audienceLa mise à jour des bases de connaissances existantes est cruciale pour tenir compte des nouvelles informations, régulièrement découvertes. Toutefois, en pratique, les données actuelles du Web Sémantique sont rarement mises à jour par les utilisateurs. Nous proposons UTILIS, une méthode pour aider les utilisateurs à ajouter de nouveaux objets. Un objet est une ressource de la base. Sa description correspond aux propriétés qu'il possède. Pendant la création d'un nouvel objet o, UTILIS recherche les objets similaires. Les propriétés des objets similaires sont utilisées comme suggestions pour complèter la description de o. Les objets similaires sont trouvés en appliquant des règles de relaxation à la description de o, prise comme une requête. Comparé avec l'état de l'art, la contribution est qu'UTILIS est à la fois incrémental, chaque nouvelle propriété est utilisée pour la recherche, et interactif, l'utilisateur a un rôle actif dans le processus

Aide à la création d'objets dans une base RDF(S) avec des règles de relaxation

National audienceQuand un utilisateur crée un nouvel objet dans le Web sémantique, les outils existants n'exploitent ni les objets existants et leurs propriétés, ni les propriétés déjà connues du nouvel objet. Nous proposons UTILIS, une méthode d'aide à la création de nouveaux objets. UTILIS cherche des objets similaires au nouvel objet en appliquant des règles de relaxation à sa description. Les propriétés des objets similaires servent de suggestions pour compléter la description du nouvel objet. Une étude utilisateur menée avec des étudiants en master montre que les suggestions d'UTILIS ont été utilisées. Les utilisateurs ont trouvé les suggestions pertinentes : dans la plupart des cas, ils pouvaient trouver l'élément recherché dans les trois premiers ensembles de suggestions. De plus, ils les ont appréciées, car la majorité souhaitent les avoir dans un éditeur de données du Web sémantique

Hemophilia treatment in 2021: choosing the”optimal” treatment using an integrative, patient-oriented approach to shared decision-making between patients and clinicians

The mainstay of hemophilia treatment is to prevent bleeding through regular long-term prophylaxis and to control acute breakthrough bleeds. Various treatment options are currently available for prophylaxis, and treatment decision-making is a challenging and multifaceted process of identifying the most appropriate option for each patient. A multidisciplinary expert panel convened to develop a practical, patient-oriented algorithm to facilitate shared treatment decision-making between clinicians and patients. Key variables were identified, and an algorithm proposed based on five variables: bleeding phenotype, musculoskeletal status, treatment adherence, venous access, and lifestyle. A complementary, patient-focused preference tool was also hypothesized, with the aim of exploring individual patients' priorities, preferences, and goals. It is hoped that the proposed algorithm and the hypothesized patient preference tool will assist in selecting a treatment for each patient that is as efficient as possible in preventing bleeds while also accounting for the patient's expectations and prioritiesFunded by a grant from Novo Nordis

Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation (PERSPECTIVE I&I).

Early detection of breast cancer through screening reduces breast cancer mortality. The benefits of screening must also be considered within the context of potential harms (e.g., false positives, overdiagnosis). Furthermore, while breast cancer risk is highly variable within the population, most screening programs use age to determine eligibility. A risk-based approach is expected to improve the benefit-harm ratio of breast cancer screening programs. The PERSPECTIVE I&I (Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation) project seeks to improve personalized risk assessment to allow for a cost-effective, population-based approach to risk-based screening and determine best practices for implementation in Canada. This commentary describes the four inter-related activities that comprise the PERSPECTIVE I&I project. 1: Identification and validation of novel moderate to high-risk susceptibility genes. 2: Improvement, validation, and adaptation of a risk prediction web-tool for the Canadian context. 3: Development and piloting of a socio-ethical framework to support implementation of risk-based breast cancer screening. 4: Economic analysis to optimize the implementation of risk-based screening. Risk-based screening and prevention is expected to benefit all women, empowering them to work with their healthcare provider to make informed decisions about screening and prevention

Genome-Wide Search for Gene-Gene Interactions in Colorectal Cancer

Genome-wide association studies (GWAS) have successfully identified a number of single-nucleotide polymorphisms (SNPs) associated with colorectal cancer (CRC) risk. However, these susceptibility loci known today explain only a small fraction of the genetic risk. Gene-gene interaction (GxG) is considered to be one source of the missing heritability. To address this, we performed a genome-wide search for pair-wise GxG associated with CRC risk using 8,380 cases and 10,558 controls in the discovery phase and 2,527 cases and 2,658 controls in the replication phase. We developed a simple, but powerful method for testing interaction, which we term the Average Risk Due to Interaction (ARDI). With this method, we conducted a genome-wide search to identify SNPs showing evidence for GxG with previously identified CRC susceptibility loci from 14 independent regions. We also conducted a genome-wide search for GxG using the marginal association screening and examining interaction among SNPs that pass the screening threshold (p<$10^{−4}$). For the known locus rs10795668 (10p14), we found an interacting SNP rs367615 (5q21) with replication p = 0.01 and combined p = 4.19×$10^{−8}$. Among the top marginal SNPs after LD pruning (n = 163), we identified an interaction between rs1571218 (20p12.3) and rs10879357 (12q21.1) (nominal combined p = 2.51×$10^{−6}$; Bonferroni adjusted p = 0.03). Our study represents the first comprehensive search for GxG in CRC, and our results may provide new insight into the genetic etiology of CRC

Human TRIM Gene Expression in Response to Interferons

Tripartite motif (TRIM) proteins constitute a family of proteins that share a conserved tripartite architecture. The recent discovery of the anti-HIV activity of TRIM5α in primate cells has stimulated much interest in the potential role of TRIM proteins in antiviral activities and innate immunity.To test if TRIM genes are up-regulated during antiviral immune responses, we performed a systematic analysis of TRIM gene expression in human primary lymphocytes and monocyte-derived macrophages in response to interferons (IFNs, type I and II) or following FcγR-mediated activation of macrophages. We found that 27 of the 72 human TRIM genes are sensitive to IFN. Our analysis identifies 9 additional TRIM genes that are up-regulated by IFNs, among which only 3 have previously been found to display an antiviral activity. Also, we found 2 TRIM proteins, TRIM9 and 54, to be specifically up-regulated in FcγR-activated macrophages.Our results present the first comprehensive TRIM gene expression analysis in primary human immune cells, and suggest the involvement of additional TRIM proteins in regulating host antiviral activities

Telomere structure and maintenance gene variants and risk of five cancer types.

Telomeres cap chromosome ends, protecting them from degradation, double-strand breaks, and end-to-end fusions. Telomeres are maintained by telomerase, a reverse transcriptase encoded by TERT, and an RNA template encoded by TERC. Loci in the TERT and adjoining CLPTM1L region are associated with risk of multiple cancers. We therefore investigated associations between variants in 22 telomere structure and maintenance gene regions and colorectal, breast, prostate, ovarian, and lung cancer risk. We performed subset-based meta-analyses of 204,993 directly-measured and imputed SNPs among 61,851 cancer cases and 74,457 controls of European descent. Independent associations for SNP minor alleles were identified using sequential conditional analysis (with gene-level p value cutoffs ≤3.08 × 10-5 ). Of the thirteen independent SNPs observed to be associated with cancer risk, novel findings were observed for seven loci. Across the DCLRE1B region, rs974494 and rs12144215 were inversely associated with prostate and lung cancers, and colorectal, breast, and prostate cancers, respectively. Across the TERC region, rs75316749 was positively associated with colorectal, breast, ovarian, and lung cancers. Across the DCLRE1B region, rs974404 and rs12144215 were inversely associated with prostate and lung cancers, and colorectal, breast, and prostate cancers, respectively. Near POT1, rs116895242 was inversely associated with colorectal, ovarian, and lung cancers, and RTEL1 rs34978822 was inversely associated with prostate and lung cancers. The complex association patterns in telomere-related genes across cancer types may provide insight into mechanisms through which telomere dysfunction in different tissues influences cancer risk.Funding for the iCOGS infrastructure came from: the European Community’s Seventh Framework Programme under grant agreement n° 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A 10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692, C8197/A16565), the National Institutes of Health (CA128978) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 CA148065 and 1U19 CA148112 – the GAME-ON initiative), the Department of Defense (W81XWH-10-1-0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, Komen Foundation for the Cure, the Breast Cancer Research Foundation, and the Ovarian Cancer Research Fund.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/ijc.3028

Combining Asian and European genome-wide association studies of colorectal cancer improves risk prediction across racial and ethnic populations

Polygenic risk scores (PRS) have great potential to guide precision colorectal cancer (CRC) prevention by identifying those at higher risk to undertake targeted screening. However, current PRS using European ancestry data have sub-optimal performance in non-European ancestry populations, limiting their utility among these populations. Towards addressing this deficiency, we expand PRS development for CRC by incorporating Asian ancestry data (21,731 cases; 47,444 controls) into European ancestry training datasets (78,473 cases; 107,143 controls). The AUC estimates (95% CI) of PRS are 0.63(0.62-0.64), 0.59(0.57-0.61), 0.62(0.60-0.63), and 0.65(0.63-0.66) in independent datasets including 1681-3651 cases and 8696-115,105 controls of Asian, Black/African American, Latinx/Hispanic, and non-Hispanic White, respectively. They are significantly better than the European-centric PRS in all four major US racial and ethnic groups (p-values < 0.05). Further inclusion of non-European ancestry populations, especially Black/African American and Latinx/Hispanic, is needed to improve the risk prediction and enhance equity in applying PRS in clinical practice