Donor's support tool: Enabling informed secondary use of patient's biomaterial and personal data.

Formal data is supported by means of specific languages from which the syntax and semantics have to be mastered, which represents an obstacle for collective intelligence. In contrast, informal knowledge relies on weak/ambiguous contributions e.g., I like. Reconciling the two forms of knowledge is a big challenge. We propose a brain-inspired knowledge representation approach called ViewpointS where formal data and informal contributions are merged into an adaptive knowledge graph which is then topologically, rather than logically, explored and assessed. We firstly illustrate within a mock-up simulation, where the hypothesis of knowledge emerging from preference dissemination is positively tested. Then we use a real-life web dataset (MovieLens) that mixes formal data about movies with user ratings. Our results show that ViewpointS is a relevant, generic and powerful innovative approach to capture and reconcile formal and informal knowledge and enable collective intelligence.

/pdf/viewpoints-capturing-formal-data-and-informal-contributions-3mekvsz7n4.pdf

ViewpointS: Capturing formal data and informal contributions into an adaptive knowledge graph

Cet article porte sur une langue de specialite relativement peu etudiee en anglais : celle de la chimie organique. Le discours de specialite chimique est analyse a travers la mise en evidence de deux phenomenes linguistiques egalement meconnus : l’indetermination terminologique et la multidimensionnalite dans les sciences exactes. En effet, malgre la presence d’une nomenclature en chimie, une exploration textuelle outillee d’un double corpus, associee a une analyse componentielle revisitee des enonces definitoires de certains termes cles a permis d’etablir clairement que ces derniers etaient non seulement imprecis, mais qu’ils ne se pretaient pas a une approche conceptuelle et logique des unites linguistiques. L’auteur montre egalement que cette indetermination est partiellement compensee par une tres forte creativite lexicale, une structuration conceptuelle extremement dense et une construction semantique des termes par incrementation. Neanmoins, ce fonctionnement par stratification est egalement a l’origine de la multidimensionnalite latente du domaine et donc des nombreuses difficultes de classification et de representation notionnelles de la discipline.

/pdf/l-anglais-de-specialite-en-chimie-organique-entre-9tknr9ax78.pdf

L’anglais de spécialité en chimie organique : entre indétermination terminologique et multidimensionnalité

Fundamental chemical entities are identified in the context of organic reactivity and classified as appropriate concept classes namely ElectronEntity, AtomEntity, AtomGroupEntity, FunctionalGroupEntity and MolecularEntity. The entity classes and their subclasses are organized into a chemical ontology named “ChemEnt” for the purpose of assertion, restriction and modification of properties through entity relations. Individual instances of entity classes are defined and encoded as a library of chemical entities in XML. The instances of entity classes are distinguished with a unique notation and identification values in order to map them with the ontology definitions. A model GUI named Entity Table is created to view graphical representations of all the entity instances. The detection of chemical entities in chemical structures is achieved through suitable algorithms. The possibility of asserting properties to the entities at different levels and the mechanism of property flow within the hierarchical entity levels is outlined.

Encoding of Fundamental Chemical Entities of Organic Reactivity Interest using chemical ontology and XML

In 1984, more than 30 years ago, a short review highlighting our work on organoselenium chemistry appeared in the “Janssen Chimica Acta” topromote someofour reagents the JanssenChimica Company was selling. Shortly after we received a request from the late M. Albrecht Holzer (Figure1) a pharmacist from Saarbrucken, whoalsoownedURSAPHARM,oneof the leadingcompanies inthe field of ophthalmology (Figure 2) to provide him with 20 g of (d,l)-selenomethionine, which he was expecting to possess antioxidant properties and to have beneficial effects on cataract. Although I was reluctant to enter the field of amino acids, I was attracted by the opportunity to provide seed money to initiate the PhD thesis of M. MahmoudTrabelsi (Figure 3), a chemical engineer who just came to our lab on recommendation of my colleague and friend Prof. Leon Ghosez from the neighbor Université Catholique de Louvain (UCL). We agreed to provide M. Holzer, within 6 months, the requested amount with no liability in case of failure and twice the financial support in case of earlier release. This was effectively achieved one month later as the result of testing several published syntheses! The topic became the PhD subject of Mahmoud since at around this time it was published that selenomethionine is a natural compound that is converted in vivo to selenocysteine, the 21th natural amino acid, which is present in mammals in the active site of (a) glutathione peroxidase, a powerful natural antioxidant that plays a crucial role to destroy peroxides and (b) iodothyrosine deiodinase, which transforms the thyroid pro-hormone T4 produced in the thyroid gland to the thyroid hormone T3 that increases, inter alias, the basal metabolic rate and affects protein synthesis. Selenomethionine, which possesses a heavy atom, is also used to aid structure elucidation of

Adventures in Chemistry and in Information Technology: Using Chemistry Skill to Finance Partnership with Computers.

We are building an encyclopaedia of organic chemistry (EnCOrE) in English and making it freely available on the internet. We expect the tools to be used by novice as well as advanced researchers from university and industry. They will allow cross-searches based on chemical structures and equations, and on explanatory texts and an elaborated dictionary. EnCOrE will be created under a strong editorial organisation but also collaboratively between chemists. This will ensure that it is kept up to date and will favour a consensual approach. We will disclose our effort to develop, in this way, the EnCOrE dictionary and the protocols to favour collaboration.

Building the EnCOrE dictionary collaboratively: strategy and practice

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Building the EnCOrE dictionary collaboratively: strategy and practice