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About Delphine DAUGA

Intoduction
Formalization
Management
Communication
Publication
1. Introduction
After obtaining a Masters in Bioinformatics in 2005, I joined the CNRS (France) in 2006 as a research engineer in biological data processing at the Institute of Developmental Biology of Marseille-Luminy (UMR6216). I joined the team of Patrick Lemaire, whose studies the developmental chordate program with an integrative approach tested on ascidian, a model organism family at the transition of vertebrates / invertebrates. When I arrived, the structure of the ANISEED database (ascidian Network for In Situ Expression and Embryological Data) was designed to represent and model the development of the ascidian. My tasks were:

- Data formalization and data management of from ascidian research
- Networking activities to mobilize the scientific community around common tools
- ANISEED development and improvement and system documentation
Since, ANISEED became the reference database for the tunicate community (within 3 years, the site received 20,000 unique visitors mainly from countries with a high concentration ascidian laboratory).
After completing 5 years and 11 months in short term contract in the academic institute, I decided to create Bioself Communication to provide a sustainable manner my experience and engineering skills in biological data processing and scientific communication.

2. Data formalization
  • Definition of the anatomical ontologies for : Ciona intestinalis, Ciona savignyi, Phallusia mammillata, Boltenia villosa, Halocynthia roretzi. Collaboration initiated on Botryllus schlosseri and Oikopleura dioica.
  • Co-definition of the anatomical ontology for the flower meristems of Arabidopsis thaliana.
  • 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).
  • 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).
  • Definition of an innovative format representating scientific article, where each experiment is identified, categorized and linked to all the evidences described.
  • 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.
3. Data management
  • Data extraction from 190 articles from literature
  • Annotation and curation of 230 regulatory sequences from published articles and personal communication
  • Annotation and curation of 1500 expression profiles from published articles and personal communication. These data allowed to reconstruct ciona GRN (Tassy*, Dauga*, Daian*, Sobral* et al., Genome Research, 2010)
  • 3D embryo reconstruction (Robin et al., 2011)
  • Annotation and curation of 100 morphological phenotypes from published article and personal communication
  • Definition of AMIS standard to list the minimal information required to enter data in ANISEED (Article Minimum Information Standard, AMIS ; Tassy*, Dauga*, Daian*, Sobral* et al., Genome Research, 2010).
4. Communication
  • Co-organisation of the first international workshop for the Tunicate Information System (11-13 november 2010, Nice, France) : 50 participants from Japan, USA, Israel, Europe ; thinking on the evolution of information systems for tunicates.
  • Invitated at the GMOD Tools for Evolutionary Biology Hackathon (8-10 novembre 2010, Durham, North Caroline, USA)
  • Invited to give a talk at the 4th international biocurator meeting (11-14 octobre 2010, Tokyo, Japon) : "AMIS, the Article Minimum Information Standard"
  • Oral presentation at the international tunicate meetings 2009 (Okinawa, Japan) and 2011 (Montreal, Canada).
  • ANISEED training for users : visit of 17 laboratoiries (Japon, Italie, France).
  • Writing of reports and tutorials.
  • Organization of video conference between main actors of the Tuncate Information System project (K. Inaba, Shimoda, Japon ; T. Endo, Hokkaido, Japon ; Y. Satou, Kyoto, Japon ; A. Voskoboynik, Stanford, USA ; P. Lemaire, Marseille, France).
  • Implementation of communication tools : web portal, wiki
  • Communication media optimization: internet SEO, website design based on the audience and update.
  • Participation at the scientific activities of the institute: "The days of IBDML" Giens, France, 24-25 September 2009, "Joint meeting of the French Society for Developmental Biology / Developmental Biology of JapaneseSociety?? Giens France, 13-17 September, 2008
5. Publications
*: co-first authors
  • Lucia Manni, Fabio Gasparini, Kohji Hotta, Katherine J Ishizuka, Lorenzo Ricci, Stefano Tiozzo, Ayelet Voskoboynik, Delphine Dauga. (2014) Ontology for the Asexual Development and Anatomy of the Colonial Chordate Botryllus schlosseri. PLoS ONE 01/2014; 9(5):e96434.
  • Robin FB, Dauga D, Tassy O, Sobral D, Daian F, Lemaire P. (2011) Creating 3D digital replicas of ascidian embryos from stacks of confocal images. Cold Spring Harb Protoc. 2011(10):1251-61.
  • Robin FB, Dauga D, Tassy O, Sobral D, Daian F, Lemaire P. (2011) Imaging of fixed ciona embryos for creating 3D digital replicas. Cold Spring Harb Protoc. 2011(10):1247-50.
  • Robin FB, Dauga D, Tassy O, Sobral D, Daian F, Lemaire P. (2011) Time-lapse imaging of live Phallusia embryos for creating 3D digital replicas. Cold Spring Harb Protoc. 2011(10):1244-6
  • Tassy* O, Dauga* D, Daian* F, Sobral* D, Robin F, Khoueiry P, Salgado D, Fox V, Caillol D, Schiappa R, Laporte B, Rios A, Luxardi G, Kusakabe T, Joly JS, Darras S, Christiaen L, Contensin M, Auger H, Lamy C, Hudson C, Rothbächer U, Gilchrist MJ, Makabe KW, Hotta K, Fujiwara S, Satoh N, Satou Y and Lemaire P (2010) The ANISEED database: digital representation, formalisation and elucidation of a chordate developmental program. Genome Research, 20(10):1459-68.
  • Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Christiansen J, Dauga D et al. Minimum Information Specification For In Situ Hybridization and Immunohistochemestry Experiments (MISFISHIE) Nature Biotechnology 2008 March;26(3):305-12.
Colloques :
  • "The 6th International Tunicate Meeting ", Montréal, Canada, 3-7 juillet 2011 ; oral presentation 20 min ; "An update on ANISEED and its future evolution"
  • "The 1st Tunicate Information System Meeting" Nice, France, 11-13 novembre 2010 ; oral presentation 30 min ; "What is Biocuration and why is it important?"
  • "GMOD Tools for Evolutionary Biology Hackathon"; 8-10 novembre 2010
  • "The Fourth International Biocuration Conference" Tokyo, Japan, 11-14 octobre, 2010 ; oral presentation 20 min ; "AMIS, the Article Minimum Information Standard"
  • "The 5th International Tunicate Meeting" Okinawa, Japan, 21-25 juin, 2009 ; oral presentation 15 min ; " The ANISEED project "
Website conception / Community tools :

Delph. Dauga in excellent company
during the tunicate meeting in Montreal in July 2011