14,592 research outputs found
PPIDomainMiner (PPIDM)
No full textThis archive contains all the data associated with the following publication
PPIDomainMiner : Inferring domain-domain interactions from multiple sources of protein-protein interactions
Seyed Ziaeddine Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W Ritchie and Marie-Dominique Devignes.
doi: https://doi.org/10.1101/2021.03.03.433732
to be published in PLOS Computational Biology in 2021.
The archive is organized as follows
A. Directory "Input Data" : all the files required to compute the PPIDM dataset
B. Directory "Output Data" : all result files
C. Directory "Evaluation Data" : all datasets used to evaluate the PPIDM datasetThis work was funded by Agence Nationale de la Recherche (grant numbers: ANR-11-MONU-006-02 and ANR-15-RHUS-0004), Inria Nancy Grand Est, and FEDER-Region Lorraine (CPER IT2MP). SZA was recipient of an Inria CORDI-S PhD fellowhip and AAN was recipient of a post-doctoral fellowship funded by the Region Lorraine and the Faculty Hospital of Nancy
Construction and use of a pharmacogenomic knowledge base for data integration and knowledge discovery
No full textCette thèse porte sur l’utilisation d’ontologies et de bases de connaissances pour guider différentes étapes du processus d’extraction de connaissances à partir de bases de données (ECBD) et une application dans le domaine de la pharmacogénomique. Les données relatives à ce domaine sont hétérogènes, complexes, et distribuées dans diverses bases de données, ce qui rend cruciale l’étape préliminaire de préparation et d’intégration des données à fouiller. Je propose pour guider cette étape une approche originale d’intégration de données qui s’appuie sur une représentation des connaissances du domaine sous forme de deux ontologies en logiques de description : SNP-Ontology et SO-Pharm. Cette approche a été implémentée grâce aux technologies du Web sémantique et conduit au peuplement d’une base de connaissances pharmacogénomique. Le fait que les données à fouiller soient alors disponibles dans une base de connaissances entraîne de nouvelles potentialités pour le processus d’extraction de connaissances. Je me suis d’abord intéressé au problème de la sélection des données les plus pertinentes à fouiller en montrant comment la base de connaissances peut être exploitée dans ce but. Ensuite j’ai décrit et appliqué à la pharmacogénomique, une méthode qui permet l’extraction de connaissances directement à partir d’une base de connaissances. Cette méthode appelée Analyse des Assertions de Rôles (ou AAR) permet d’utiliser des algorithmes de fouille de données sur un ensemble d’assertions de la base de connaissances pharmacogénomique et d’expliciter des connaissances nouvelles et pertinentes qui y étaient enfouies.This thesis studies the use of ontology and knowledge base for guiding various steps of the Knowledge Discovery in Databases (KDD) process in the domain of pharmacogenomics. Data related to this domain are heterogeneous, complex, and disseminated through several data sources. Consequently, the preliminary step that consists in the preparation and the integration of data is crucial. For guiding this step, an original approach is proposed, based on a knowledge representation of the domain within two ontologies in description logics : SNP-Ontology and SO-Pharm. This approach has been implemented using semantic Web technologies and leads finally to populating a pharmacogenomic knowledge base. As a result, data to analyze are represented in the knowledge base, which is a benefit for guiding following steps of the knowledge discovery process. Firstly, I study this benefit for feature selection by illustrating how the knowledge base can be used for this purpose. Secondly, I describe and apply to pharmacogenomics a new method named Role Assertion Analysis (or RAA) that enables knowledge discovery directly from knowledge bases. This method uses data mining algorithms over assertions of our pharmacogenomic knowledge base and results in the discovery of new and relevant knowledge
Using domain knowledge in the Transcriptomic analysis : Semantic similarity, functional classification and fuzzy profiles. Application to colorectal cancer
No full textL'analyse bioinformatique des données de transcriptomique a pour but d'identifier les gènes qui présentent des variations d'expression entre différentes situations, par exemple entre des échantillons de tissu sain et de tissu malade et de caractériser ces gènes à partir de leurs annotations fonctionnelles. Dans ce travail de thèse, je propose quatre contributions pour la prise en compte des connaissances du domaine dans ces méthodes. Tout d'abord je définis une nouvelle mesure de similarité sémantique et fonctionnelle (IntelliGO) entre les gènes, qui exploite au mieux les annotations fonctionnelles issues de l'ontologie GO ('Gene Ontology'). Je montre ensuite, grâce à une méthodologie d'évaluation rigoureuse, que la mesure IntelliGO est performante pour la classification fonctionnelle des gènes. En troisième contribution je propose une approche différentielle avec affectation floue pour la construction de profils d'expression différentielle (PED). Je définis alors un algorithme d'analyse de recouvrement entre classes fonctionnelles et ensemble des références, ici les PEDs, pour mettre en évidence des gènes ayant à la fois les mêmes variations d'expression et des annotations fonctionnelles similaires. Cette méthode est appliquée à des données expérimentales produites à partir d'échantillons de tissus sains, de tumeur colo-rectale et de lignée cellulaire cancéreuse. Finalement, la mesure de similarité IntelliGO est généralisée à d'autres vocabulaires structurés en graphe acyclique dirigé et enraciné (rDAG) comme l'est l'ontologie GO, avec un exemple d'application concernant la réduction sémantique d'attributs avant la fouille.Bioinformatic analyses of transcriptomic data aims to identify genes with variations in their expression level in different tissue samples, for example tissues from healthy versus seek patients, and to characterize these genes on the basis of their functional annotation. In this thesis, I present four contributions for taking into account domain knowledge in these methods. Firstly, I define a new semantic and functional similarity measure which optimally exploits functional annotations from Gene Ontology (GO). Then, I show, thanks to a rigorous evaluation method, that this measure is efficient for the functional classification of genes. In the third contribution, I propose a differential approach with fuzzy assignment for building differential expression profiles (DEPs). I define an algorithm for analyzing overlaps between functional clusters and reference sets such as DEPs here, in order to point out genes that have both similar functional annotation and similar variations in expression. This method is applied to experimental data produced from samples of healthy tissue, colorectal tumor and cancerous cultured cell line. Finally the similarity measure IntelliGO is generalized to another structured vocabulary organized as GO as a rooted directed acyclic graph, with an application concerning the semantic reduction of attributes before mining
Supporting information for the RNAct Data Science Wizard (DSW) knowledge model for early-stage researchers.
No full text<p>The two attached Excel sheets contain information about the datasets collected by the Early Stage Researchers (ESRs) in the RNAct MSCA-ITN project (RNAct_datasets.xlsx) and on the questionnaire that was put to the ESRs in relation to the Data Science Wizard (DSW) knowledge model that was developed as part of RNAct. </p>
<p>The zip file contains data in relation to the Data Science Wizard template development:</p>
<p>- DMP_1stRound_introductory_presentation.pdf: Presentation for the ESRs to prepare them for filling in the first version of the DMP</p>
<p>- DMPs_1stRound, DMPs_2ndRound: The filled in DMPs by the ESRs in the first and second round</p>
<p>- RNAct-ESRtraining-KM_1.0.3.km: The first version of the knowledge model to create the DMP</p>
<p>- RNAct-ESRtraining-KM_1.0.14.km: The second and final version of the knowledge model to create the DMP</p>
<p>- TemplateDMP_RNAct-ESRtraining-KM_1.0.14.pdf: A PDF overview of the second and final version of the knowledge model</p>
‘A Dayspring to the Dimness of Us: The Symbolic Reality of Edith Stein, Gerard Manley Hopkins and Marie-Dominique Chenu’
No full textThis article explores ‘the symbolic reality’ of two twentieth century theologians inspired by the works of Dionysius the Areopagite: Edith Stein/Teresia Benedicta a Cruce O.C.D. (1891 – 1942) and Marie-Dominique Chenu O.P. (1895 – 1990). To illustrate their arguments about the role of the symbolic in Christian life, the author takes as his text the great narrative poem of the English Jesuit Gerard Manley Hopkins (1844 – 1889), The Wreck of the Deutschland. The article argues that the symbolic theology provides resilience to those undergoing psychological and physical trauma as they enter into what Stein called ‘the Science of the Cross’
Alternative usage of 5' exons in the chicken nerve growth factor gene: refined characterization of a weakly expressed gene
No full textArticle dans revue scientifique avec comité de lecture. internationale.International audienceNerve growth factor (NGF) is the prototype member of the neurotrophin family. Identification of transcript structures and promoter regions is described here in view of clarifying the molecular basis of chicken NGF gene regulation. Chicken NGF complementary DNA (cDNA) was amplified from heart and brain mRNA using the single-strand ligation to cDNA (SLIC) procedure. Several cloning and sequencing rounds were necessary to elucidate the diversity of NGF transcripts. The chicken NGF gene was shown to possess, in addition to its unique 3′ coding exon, five 5′ exons grouped into two clusters that have been entirely sequenced. The first cluster encompasses three leader exons (1a, 1b and 1c) and is separated from the second cluster by a ~15 kilobases (kb) intronic sequence. "Exon walking" based on reverse transcription–polymerase chain reaction (RT–PCR) allowed to ascertain the length of the three leader exons. The second cluster contains exons 2 and 3, separated from each other by a ~2.4 kb intron, and lies ~0.5 kb upstream from coding exon 4. Combination of several mechanisms, such as differential usage of leader and internal exons, alternative transcription start inside exon 1b, second donor and acceptor sites in exon 1c and 4, respectively, leads to the production of at least 21 different transcripts. This remarkable diversity may represent a common feature largely underestimated for other weakly expressed genes. Preliminary RT–PCR expression study in a panel of chicken tissues shows that transcripts containing exon 1b are present in most tissues tested. Transcripts containing exon 1a are represented mainly in heart and reproductive organs, whereas transcripts containing exon 1c are mostly represented in peripheral organs other than heart. Complementary data are published as a Web supplement available at http://www.loria.fr/~devignes/NGF/index.html
Alternative usage of 5' exons in the chicken nerve growth factor gene: refined characterization of a weakly expressed gene
No full textArticle dans revue scientifique avec comité de lecture. internationale.International audienceNerve growth factor (NGF) is the prototype member of the neurotrophin family. Identification of transcript structures and promoter regions is described here in view of clarifying the molecular basis of chicken NGF gene regulation. Chicken NGF complementary DNA (cDNA) was amplified from heart and brain mRNA using the single-strand ligation to cDNA (SLIC) procedure. Several cloning and sequencing rounds were necessary to elucidate the diversity of NGF transcripts. The chicken NGF gene was shown to possess, in addition to its unique 3′ coding exon, five 5′ exons grouped into two clusters that have been entirely sequenced. The first cluster encompasses three leader exons (1a, 1b and 1c) and is separated from the second cluster by a ~15 kilobases (kb) intronic sequence. "Exon walking" based on reverse transcription–polymerase chain reaction (RT–PCR) allowed to ascertain the length of the three leader exons. The second cluster contains exons 2 and 3, separated from each other by a ~2.4 kb intron, and lies ~0.5 kb upstream from coding exon 4. Combination of several mechanisms, such as differential usage of leader and internal exons, alternative transcription start inside exon 1b, second donor and acceptor sites in exon 1c and 4, respectively, leads to the production of at least 21 different transcripts. This remarkable diversity may represent a common feature largely underestimated for other weakly expressed genes. Preliminary RT–PCR expression study in a panel of chicken tissues shows that transcripts containing exon 1b are present in most tissues tested. Transcripts containing exon 1a are represented mainly in heart and reproductive organs, whereas transcripts containing exon 1c are mostly represented in peripheral organs other than heart. Complementary data are published as a Web supplement available at http://www.loria.fr/~devignes/NGF/index.html
On Pina Bausch’s Legacy: an interview with Dominique Mercy
No full textPerhaps no other author has better characterized the work of Pina’s
dancers – and, therefore, the artist’s herself – than José Sasportes – a
remarkable Portuguese dance critic and historian. This brief observation of
Sasportes, made in a text entitled Acção para bailarinos [Action for dancers],
and regarding an event held in Lisbon in honor to Pina Bausch, allows to perceive in quite clearly the meaning of the experience and legacy of a remarkable artist, that are summarized in the figure of one of her greatest collaborators, Dominique Mercy.
Certainly, there is no need to introduce Dominique. It is worthy,
though, to recover some moments that preceded his fortuitous encounter with Pina in the early 1970’s in Saratoga, United States. Born in 1950 in the city of Mauzac, France, Dominique’s first professional steps in the dance world from the mid-1960’s on were in the Bordeaux Grand Théâtre,
later followed by the Amiens Ballet du Art Contemporain. In 1973, two
years after his first encounter with Pina in the Summer Festival of Saratoga,
in 1971, Dominique goes to Germany, to Wuppertal, to be part of the
recently founded Tanztheater.
His close relationship with Pina allowed, in fact, that her legacy could
be kept alive following her sudden death in 2009. Dominique took over the
artistic direction of the Company with Robert Sturm for some of the
following years, having later transferred the position to his co-worker and
dancer Lutz Forster. It was beside Pina and so many others from the
Wuppertal ensemble that Dominique ended up writing one of the major
pages in the annals of dance history in the 20th century.
The experience of – or rather, with – Pina that each one of us
apparently has with her when meeting her work for the first time, allowing
to understand in a certain extent the fascination that she exerts until
nowadays on the audience, passes as well and indispensably through those
who worked with her and by her means. My first time with Pina was, for
sure, beside Dominique Mercy, or rather, in front of him. Dominique was
half-naked, wearing only a tutu and carrying a watering can. It was 2006,
for the presentation of Fur die kinder von gestern, heunte und morgen, in
Porto Alegre. Pina was also there.
The unusual encounter – even though separated by the proscenium
arch – would happen again years later in Paris. However, this time, in
2011, without Pina and with no line dividing us. I was introduced to
Dominique following one of the presentations of Como el musguito em la
piedra..., by the also Tanztheater Wuppertal dancer Daphnis Kokkinos. On
that occasion, Dominique had an extremely light and welcoming attitude.
Over the years, I noticed that it was not a protocol way of introduction, but
Dominique Mercy; Marcelo de Andrade Pereira – On Pina
Bausch’s Legacy: an interview with Dominique Mercy
the very donation of part of what he was, how he was, not in a way, but in
his way, with or without tutu. In January 2018, when recollecting that
encounter with Dominique in his house in Barmen, Wuppertal, he did not
remember it. And he certainly could not, as I, absorbed in my amazement,
had articulated little – or nothing – at that moment. However, even in my
involuntary contemplation, something had been given to me, a long-lasting
presence.
It was according to Dominique’s generous, honest and delicate way
that this interview actually happened. I thank him for the attention and for
the coffee. I also thank my dear friend Eddie Martinez, who made this and
so many other happy encounters possible to me
Contribution of domain ontologies for knowledge discovery in biomedical data
No full textLe Web sémantique propose un ensemble de standards et d'outils pour la formalisation et l'interopérabilité de connaissances partagées sur le Web, sous la forme d'ontologies. Les ontologies biomédicales et les données associées constituent de nos jours un ensemble de connaissances complexes, hétérogènes et interconnectées, dont l'analyse est porteuse de grands enjeux en santé, par exemple dans le cadre de la pharmacovigilance. On proposera dans cette thèse des méthodes permettant d'utiliser ces ontologies biomédicales pour étendre les possibilités d'un processus de fouille de données, en particulier, permettant de faire cohabiter et d'exploiter les connaissances de plusieurs ontologies biomédicales. Les travaux de cette thèse concernent dans un premier temps une méthode fondée sur les structures de patrons, une extension de l'analyse formelle de concepts pour la découverte de co-occurences de événements indésirables médicamenteux dans des données patients. Cette méthode utilise une ontologie de phénotypes et une ontologie de médicaments pour permettre la comparaison de ces événements complexes, et la découverte d'associations à différents niveaux de généralisation, par exemple, au niveau de médicaments ou de classes de médicaments. Dans un second temps, on utilisera une méthode numérique fondée sur des mesures de similarité sémantique pour la classification de déficiences intellectuelles génétiques. On étudiera deux mesures de similarité utilisant des méthodes de calcul différentes, que l'on utilisera avec différentes combinaisons d'ontologies phénotypiques et géniques. En particulier, on quantifiera l'influence que les différentes connaissances de domaine ont sur la capacité de classification de ces mesures, et comment ces connaissances peuvent coopérer au sein de telles méthodes numériques. Une troisième étude utilise les données ouvertes liées ou LOD du Web sémantique et les ontologies associées dans le but de caractériser des gènes responsables de déficiences intellectuelles. On utilise ici la programmation logique inductive, qui s'avère adaptée pour fouiller des données relationnelles comme les LOD, en prenant en compte leurs relations avec les ontologies, et en extraire un modèle prédictif et descriptif des gènes responsables de déficiences intellectuelles. L'ensemble des contributions de cette thèse montre qu'il est possible de faire coopérer avantageusement une ou plusieurs ontologies dans divers processus de fouille de donnéesThe semantic Web proposes standards and tools to formalize and share knowledge on the Web, in the form of ontologies. Biomedical ontologies and associated data represents a vast collection of complex, heterogeneous and linked knowledge. The analysis of such knowledge presents great opportunities in healthcare, for instance in pharmacovigilance. This thesis explores several ways to make use of this biomedical knowledge in the data mining step of a knowledge discovery process. In particular, we propose three methods in which several ontologies cooperate to improve data mining results. A first contribution of this thesis describes a method based on pattern structures, an extension of formal concept analysis, to extract associations between adverse drug events from patient data. In this context, a phenotype ontology and a drug ontology cooperate to allow a semantic comparison of these complex adverse events, and leading to the discovery of associations between such events at varying degrees of generalization, for instance, at the drug or drug class level. A second contribution uses a numeric method based on semantic similarity measures to classify different types of genetic intellectual disabilities, characterized by both their phenotypes and the functions of their linked genes. We study two different similarity measures, applied with different combinations of phenotypic and gene function ontologies. In particular, we investigate the influence of each domain of knowledge represented in each ontology on the classification process, and how they can cooperate to improve that process. Finally, a third contribution uses the data component of the semantic Web, the Linked Open Data (LOD), together with linked ontologies, to characterize genes responsible for intellectual deficiencies. We use Inductive Logic Programming, a suitable method to mine relational data such as LOD while exploiting domain knowledge from ontologies by using reasoning mechanisms. Here, ILP allows to extract from LOD and ontologies a descriptive and predictive model of genes responsible for intellectual disabilities. These contributions illustrates the possibility of having several ontologies cooperate to improve various data mining processe
Les passions vertueuses. L'anthropologie de saint Thomas
No full textIn 1277, the two great Universities at that time, Paris and Oxford, placed under interdict several of Thomas Aquinas' philosophical propositions. The main thesis under attack in these decrees concerned the consubstantiality of the soul and of the body in man. The author examines this thesis from the particular point of view of an analysis of the morality of the passions. Contrary to the Augustinian line of thought, St Thomas maintains, chiefly in the De virtutibus, that the passions are properly the subjects of the virtues and criticizes the dualism of the ratio inferior and superior. The passions are virtuous due to the intimate penetration of the mind and the sensibilities.En 1277, les deux grandes Universités de l'époque, Paris et Oxford, frappaient d'interdit plusieurs propositions philosophiques de Thomas d'Aquin. La thèse centrale visée par ces décrets concernait la consubstantialité de l'âme et du corps dans l'homme. L'A. examine cette thèse sous l'angle particulier d'une analyse de la moralité des passions. A l'encontre du courant de pensée augustinien, Saint Thomas soutient, principalement dans le De virtutibus, que les passions sont proprement les sujets des vertus et critique le dualisme de la ratio inferior et superior. Les passions sont vertueuses par la pénétration intime de l'esprit et des sensibilités.Chenu Marie-Dominique. Les passions vertueuses. L'anthropologie de saint Thomas. In: Revue Philosophique de Louvain. Quatrième série, tome 72, n°13, 1974. pp. 11-18
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