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Work Completed #Formalization

Wednesday, January 01, 2020

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Major contribution to the rewriting of the ANISEED database schema in the chado formalism (Mungall and Emmert 2007 Bioinformatics, 23, i337-346). In particular to extend the Chado schema in the areas of representating anatomical data (including a 3D digital representation of the developing embryo), and the representating regulatory regions and gene expression analysis.

Wednesday, January 01, 2020

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Definition of an innovative format representating scientific article, where each experiment is identified, categorized and linked to all the evidences described.

Tuesday, January 03, 2023

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Definition of the anatomical ontologies for : Ciona intestinalis, Ciona savignyi, Phallusia mammillata, Boltenia villosa, Halocynthia roretzi. Collaboration initiated on Botryllus schlosseri and Oikopleura dioica.

Thursday, February 23, 2023

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Definition and extension of molecular ontologies: communication with ECO (Evidence Code Ontology), to characterize new types of biological experiments implemented: addition of terms to represent new types of experiments (eg, the term describing an experience blocking the cellular cleavage did not exist and had to be created: ECO: 0000298, cleavage arrested development). Collaboration with PATO (Phenotypic Quality Ontology): identification of terms to be added to describe phenotypes (eg PATO can not describe tissue fate change a tissue).

Sunday, May 28, 2023

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Definition of a cis-regulatory sequence data standard (MISRAA; publication to be submitted), based on the system MISFISHIE (Deutsch et al., 2008, Nature Biotech, 26, 305-312).

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