GEN2PHEN Dissemination Activities
| Title | Description | Date | Citation | Status | External link | DOI |
|---|---|---|---|---|---|---|
| Major European project to create new knowledgebase of gene-disease relationships | Jan 2008 | Completed | ||||
| Major European project to create new knowledgebase of gene-disease relationships. |
Published at PHENO website |
Jan 2008 | Major European project to create new knowledgebase of gene-disease relationships.[Online]. 2008. Available from: URL:http://www.phenosystems.com/ | Published | Link | |
| La Fundació IMIM gestionará el Proyecto GEN2PHEN, financiado con 12 millones de euros. |
Communication tool. Published at Diari de Girona, Diario Médico, acceso.com, IMAS Intranet, prbb.net; El.lipse |
Jan 2008 | Completed | |||
| Major European Project To Create New Knowledge Base Of Gene-Disease Relationships. |
Published in Medical News Today |
Jan 2008 | Major European Project To Create New Knowledge Base Of Gene-Disease Relationships. [Online]. 2008. Available from: URL: http://www.medicalnewstoday.com | Published | Link | |
| EU Consortium aims to coordinate rising number of genotype/phenotype databases. |
Published in Bio1nform - Genome Web News |
Feb 2008 | EU Consortium aims to coordinate rising number of genotype/phenotype databases. 2008. Available from: URL: http://www.genomeweb.com | Published | Link | |
| Internet pour cataloguer et étudier les variations génétiques. |
Article published in Biofutur |
Mar 2008 | Andujar G. Internet pour cataloguer et étudier les variations génétiques. Biofutur 2008; 27(287):5-10. | Published | Link | |
| 22nd Immunogenetics and histocompatibility conference - Eurovillage special session |
Poster presented as part of 22nd Immunogenetics and histocompatibility conference - Eurovillage special session (2-5 April) |
Apr 2008 | Proceedings of the 22nd Immunogenetics and histocompatibility conference - Eurovillage special session; 2008 Apr 2-5; Toulouse, France. | Completed | Link | |
| Annual Meeting of the German Society of Human Genetics |
Dissemination materials display and distribution at the Annual Meeting of the German Society of Human Genetics (8-10 April). Booth decoration; poster; press release; flyers. |
Apr 2008 | Completed | |||
| ELIXIR meeting |
Participation in ELIXIR Meeting (European Life Sciences Infrastructure for Biological Information) |
Apr 2008 | Completed | Link | ||
| GEN2PHEN: An international effort towards the universal databasing of gene-disease relationships. |
Poster (ULEIC) and brochure distribution (BCP) |
May 2008 | European Human Genetics Conference. GEN2PHEN: An international effort towards the universal databasing of gene-disease relationships. 2008 May 31. European Human Genetics Conference. | Completed | Link | |
| GEN2PHEN Project - Harnessing the Web for Genomics. |
Article published in eHealthNews.eu |
Mar 2008 | GEN2PHEN Project - Harnessing the Web for Genomics [Online]. 2008 Feb 25. Available from: URL: http://www.ehealthnews.eu/content/view/1003/27/ | Published | Link | |
| Bioinformatics and Systems Biology: Collaborative Research and Resources. |
Book by Fred Marcus |
Jun 2008 | Marcus FB. Bioinformatics and Systems Biology: Collaborative Research and Resources. Brussels (Belgium). Springer; 2008. | Completed | Link | |
| Major European project to create new knowledgebase of gene-disease relationships. |
News article published at the Wallonie NCP website |
Feb 2008 | Major European project to create new knowledgebase of gene-disease relationships. Laboratory Talk [Online]. 2008 Feb 26. http://www.ncpwallonie.be/ | Published | Link | |
| From genotype to phenotype. |
News article published at Laboratorytalk |
Mar 2008 | From genotype to phenotype. Laboratory Talk [Online]. 2008 Mar 11. http://www.laboratorytalk.com/news/phy/phy101.html | Published | Link | |
| Genotype–phenotype databases: challenges and solutions for the post-genomic era. |
Review on G2P DBs at Nature Reviews Genetics. Structure agreed for review on G2P DBs. Synopsis accepted in Nature Reviews Genetics |
Mar 2008 | Gudmundur T, Muilu J & Brookes AJ. Genotype–phenotype databases: challenges and solutions for the post-genomic era. Nature Rev. Gen. 2009:10, 9-18. | Published | Link | 10.1038/nrg2483 |
| Tracing biological collections: between books and clinical trials. |
Journal of the American Medical Association (JAMA). Authors: Francine Kauffmann; Anne Cambon-Thomsen |
Apr 2008 | Kauffmann F; Cambon-Thomsen A. Tracing biological collections: between books and clinical trials. JAMA. 2008; 299(19):2316-2318. | Published | Link | 10.1001/jama.299.19.2316 |
| HGVbaseG2P: a Central Genetic Association Database. |
HGVbaseG2P: a Central Genetic Association Database. |
Jan 2009 | Thorisson GA, Lancaster O, R.C.Free, R.K.Hastings, P.Sarmah, D.Dash,S.Brahmachari and A.J.Brookes. HGVbaseG2P: a Central Genetic Association Database. Nucleic Acids Res. 37:D797-802. | Published | Link | 10.1093/nar/gkn7 |
| The Phenotype and Genotype Experiment Object Model (PaGE-OM): A robust data structure for information related to DNA variation. |
The Phenotype and Genotype Experiment Object Model (PaGE-OM): A robust data structure for information related to DNA variation. |
Jan 2009 | Brookes AJ, Lehvaslaiho H, Muilu J, Shigemoto Y, Oroguchi T, Tomiki T, Mukaiyama A, Konagaya A, Kojima T, Inoue I, Kuroda M, Mizushima H, Thorisson GA, D.Dash, Rajeevan H, Darlison MW, M.Woon, Fredman D, Smith AV, Senger M, Naito K and Sugawara H. The Phenotype and Genotype Experiment Object Model (PaGE-OM): A robust data structure for information related to DNA variation. Hum Mutat. 2009 Mar 18. 30(6): 968-977. | Published | 10.1002/humu.20973 | |
| Ethical issues and subsequent governance in the GEN2PHEN project. |
Abstract. European Society of Human Genetics - ESHG Conference 2009. Selected to be presented at the ESHG Workshop 4 (WS4) “Genetic Education”. |
Feb 2009 | Cambon-Thomsen A, Pigeon A, Rial-Sebbag E, Gourraud PA, Thomsen M, & GEN2PHEN consortium. Ethical issues and subsequent governance in the GEN2PHEN project. European Journal of Human Genetics. 2009 May. 17(2):45. | Completed | Link | |
| Specific Brochure |
Brochure under development to promote the LSDB software developed within WP4 amongst LSDB curators. |
Feb 2009 | Completed | |||
| Planning the Human Variome Project: The Spain Report. | Dec 2008 | Kaput J, Cotton RGH, Hardman L, Al Aqeel AI, Al-Aama JY,Al-Mulla F, et al. Planning the Human Variome Project: The Spain Report. Hum Mutat. 30 (4): 496–510. | Published | Link | 10.1002/humu.20972 | |
| ARABELLA - A Directed Web Crawler. |
Paper accepted in KDIR 2009 |
Oct 2009 | Lopes P, Davide C, Oliveira J L. ARABELLA - A Directed Web Crawler. KDIR International Conference on Knowledge Discovery and Information Retieval. 2009 Apr 28; Madeira, Portugal. | Completed | Link | |
| Building a knowledge base for systems pathology. |
Paper published in Briefings in Bioinformatics |
Dec 2008 | Michael H, Hogan J, Kel A, Kel-Margoulis O, Schacherer F, Voss N and Wingender E. Building a knowledge base for systems pathology. Brief Bioinform. 2008 Nov; 9(6):518-31. Epub 2008 Dec 10. | Published | Link | 10.1093/bib/bbn038 |
| Collecting gene sequence variants and their phenotypic consequences in web-based LSDBs for Mendelian disorders. |
Abstract. HUGO Mutation Detection Course 2009. |
Apr 2009 | Fokkema IFAC, Taschner PEM, van Ommen GJB, den Dunnen JT. Collecting gene sequence variants and their phenotypic consequences in web-based LSDBs for Mendelian disorders. HUGO Mutation Detection Course. 2009 May 28-31; Cyprus. | Published | ||
| Human Splicing Finder: an online bioinformatics tool to predict splicing signals. |
Article describing a new annotation tool for mutations disrupting splicing signals. |
Apr 2009 | Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009;37(9):e67. Epub 2009 Apr 1. | Published | Link | |
| Genotype-phenotype analysis in 2,405 patients with a dystrophinopathy using the UMD-DMD database: a model of nationwide knowledgebase. |
Article describing a new LSDB. |
Jan 2009 | Tuffery-Giraud S, Béroud C, Leturcq F, Yaou RB, Hamroun D, Michel-Calemard L, Moizard MP, Bernard R, Cossée M, Boisseau P, Blayau M, Creveaux I, Guiochon-Mantel A, de Martinville B, Philippe C, Monnier N, Bieth E, Van Kien PK, Desmet FO, Humbertclaude V, Kaplan JC, Chelly J, Claustres M. Genotype-phenotype analysis in 2,405 patients with a dystrophinopathy using the UMD-DMD database: a model of nationwide knowledgebase. Hum Mutat. 2009 Jun;30(6):934-45. | Published | Link | 10.1002/humu.20976 |
| Set-up of international collaborations to build LSDBs for genes involved in Congenital Muscular Dystrophies |
CMD workshop. 02-03/04/2009 |
Apr 2009 | Completed | Link | ||
| Grid-enabling G2P association studies: a knowledge discovery scenario. |
Publication. Theme 1. Biomedical Signal Processing; Track 1.9 Algorithms for Data Mining and Data Processing. Engineering in Medicine and Biology Society (EMBC'09). 2009 Sep 2-6; Minesota, USA. |
Sep 2009 | Potamias G. Grid-enabling G2P association studies: a knowledge discovery scenario. Engineering in Medicine and Biology Society (EMBC'09). 2009 Sep 2-6; Minesota, USA. | Published | Link | |
| LSDB INTEGRATOR - A Link-based Information Integration Architecture |
Paper accepted in KDIR 2009. Lopes P, Arrais J , Oliveira J L. LSDB INTEGRATOR - A Link-based Information Integration Architecture. KDIR 2009 |
Apr 2009 | Lopes P, Arrais J , Oliveira J L. LSDB INTEGRATOR - A Link-based Information Integration Architecture. KDIR International Conference on Knowledge Discovery and Information Retieval. 2009 Oct 6 - 8; Madeira, Portugal. | Completed | ||
| GEN2PHEN: Unifying human and model organism genetic variation databases. |
Gen2Phen poster exhibit and 50 brochures distributed. 29 a 30th of May. Workshop Internacional - Genomic Disorders, Disease-Associated Chromosome Rearrangements and Position Effect. Instituto Nacional de Saúde Dr Ricardo Jorge de Lisboa. |
May 2009 | Oliveira JL , Brookes AJ , and the GEN2PHEN Consortium. GEN2PHEN: Unifying human and model organism genetic variation databases. Workshop Internacional - Genomic Disorders, Disease-Associated Chromosome Rearrangements and Position Effect. 2009 May 29; Lisboa, Portugal. | Completed | ||
| The First GEN2PHEN Pilot Project: Documenting the bioinformatics requirements of clinical scientists. |
Abstract submitted to the British Society for Human Genetics (BSHG) |
May 2009 | Cornell M. The First GEN2PHEN Pilot Project: Documenting the bioinformatics requirements of clinical scientists. British Society for Human Genetics (BSHG). 2009 Aug 31- Sept 2; Warwick, United Kingdom. | Completed | ||
| Mission d’information sur la révision des lois bioéthiques |
Contribution to the French national consultation on the revision of the bioethics law on genetic testing following a series of 6 workshops on ethical aspects of genetic testing. Ms Cambon-Thomsen, Geneticist, reserch director at CNRS, l'INSERM, member of "groupe européen d'éthique des sciences et des nouvelles technologie (GEE)". |
Jul 2009 | Cambon-Thomsen A. Mission d’information sur la révision des lois bioéthiques. National Parliament. 2009 Jul 08; France. Available at: URL: http://www.assemblee-nationale.fr/13/commissions/bioethique/bioethique-20090708-4.asp. | Completed | Link | |
| Describing complex sequence variants by extending HGVS. |
Abstract. European Society of Human Genetics - ESHG Conference 2009. |
May 2009 | Taschner PEM, den Dunnen J T. Describing complex sequence variants by extending HGVS | Published | ||
| Developing an application ontology for annotation of experimental variables – Experimental Factor Ontology. |
Poster at the International Conference on Biomedical Ontology |
Jul 2009 | Malone J, Adamusiak T, Holloway E, Parkinson H. Developing an application ontology for annotation of experimental variables – Experimental Factor Ontology. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3806.1> (2009) | Completed | Link | 10.1038/npre.2009.3806.1 |
| CMGS Trainee meeting |
Presentation during Trainee Scientist meeting organised by the Clinical Molecular Genetics Society (CMGS) |
Oct 2009 | Completed | |||
| Describing complex sequence variants by extending HGVS |
Taschner P E M, den Dunnen J T. Describing complex sequence variants by extending HGVS sequence variation nomenclature. Abstract. ISMB Conference 2009. June 27 - July 2 |
Jun 2009 | Taschner PEM, den Dunnen JT. Describing complex sequence variants by extending HGVS sequence variation nomenclature. ISMB Conference. 2009 Jun 27 - Jul 2; Stockholm, Sweden. | Completed | Link | |
| Genes, mutations and disease |
den Dunnen JT. DNA, genes, mutations and disease; gene variant databases. Lecture including LSDB promotion. University of Applied Sciences. |
Sep 2009 | Completed | |||
| Describing complex sequence variants by extending HGVS sequence variation nomenclature. |
Taschner P E M, den Dunnen J T. Describing complex sequence variants by extending HGVS sequence variation nomenclature. Abstract. Genome Informatics Conference 2009. October 27-30. |
Nov 2009 | Completed | |||
| PaGE-OM meeting |
Organized meeting for preparation of PaGE-OM OMG submission. 2009 Jun 22-26 . |
Jun 2009 | Completed | |||
| 2nd GEN2PHEN Domain Modelling Workshop |
Organized workshop on domain modelling 2009 Jan 19-22. |
Jan 2009 | Completed | |||
| Synthesis of 6 Toulouse workshops | Published a synthesis of 6 Toulouse workshops on: 'Ethical aspects of genetic tests: from exception to routinisation' (2008) ftp://ftp.cordis.europa.eu/pub/fp7/docs/agenda-eu-funded-biobanking-proj... and 'Are human genetic data special?' (2009) http://societal.genotoul.fr/fileadmin/template/pf_Societal/download/Atel... | Dec 2009 | Cambon-Thomsen, A. Synthesis of 6 Toulouse workshops. L’information genetique humaine est-elle particuliere? 2009 | Completed | Link | |
| From medical biobanks to research tools: re-use of samples, governance and human rights in New Challenges for Biobanks. |
Published a book chapter referring to GEN2PHEN. |
Dec 2009 | RIAL-SEBBAG E, DUGUET AM, CAMBON-THOMSEN A. From medical biobanks to research tools: re-use of samples, governance and human rights in New Challenges for Biobanks. Ethics, Law and Governance, Kris Dierickx and Pascal Borry Eds, Intersentia, 87-98, 2009 | Completed | ||
| Practical guidelines addressing ethical issues pertaining to the curation of human locus specific variation databases (LSDBs) | Paper submitted to Human Mutation. | Dec 2009 | Povey S, Al Aqueel AI, Cambon-Thomsen A, Dalgleish R, Den Dunnen JT, Firth HV, Greenblatt M, Isaacson Barash C, Parker M, Patrinos GP, Savige J, Sobrido MJ, Winship I, Cotton RGH. Practical guidelines addressing ethical issues pertaining to the curation of human locus specific variation databases (LSDBs). Hum Mutat. 1098-1004. | Published | Link | 10.1002/humu.21339 |
| Construction of an ethics policy for a bioinformatics European project GEN2PHEN. | Abstract submited to ESHG about the GEN2PHEN ethics policy. | Jun 2010 | Cambon-Thomsen A, Pigeon A, Rial-Sebbag E and the GEN2PHEN consortium. Construction of an ethics policy for a bioinformatics European project GEN2PHEN. Eur J Hum Genet. 2010;18 Suppl 1:47. | Published | Link | https://www.eshg.org/eshg2010.0.html |
| Gen2Phen Knowledge Center cited in a blog article | The blog post tries to summarize some of the problems that have to be solved to develop a unique identifier for scientists. Martin Fenner's blog on scientific publishing in the internet age. | Jan 2010 | Fenner M. ORCID or how to build a unique identifier for scientists in 10 easy steps. 2010 Jan 3. [Online] Available from http://network.nature.com/people/mfenner/blog/2010/01/03/orcid-or-how-to-build-a-unique-identifier-for-scientists-in-10-easy-steps. | Completed | Link | |
| 12th European Workshop on Cytogenetics and Molecular Genetics of Solid Tumors, distribution of brochures | We will be exhibiting at the above mentioned workshop in Nijmegen, NL and distibuting project brochures. | Jun 2010 | Completed | |||
| Improving cross mapping in biomedical databases | Paper accepted in the 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010), Guimarães, Portugal, 2010. Published on Advances in Intelligent and Soft Computing (Springer). | Jun 2010 | Arrais J, Pereira J, Lopes P, Matos S, Oliveira JL. Improving cross mapping in biomedical databases. 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010). 2010 June, 16-18; Guimarães, Portugal. Springer. | Completed | Link | 10.1007/978-3-642-13214-8 |
| Modeling Sample Variables with an Experimental Factor Ontology | Ontology paper in BMC Bioinformatics | Mar 2010 | Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A and Parkinson H. Modeling sample variables with an Experimental Factor Ontology. Bioinformatics 2010 26(8):1112-1118. | Published | Link | 10.1093/bioinformatics/btq099 |
| XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments |
Article published in Genome Biology. |
Mar 2010 | Swertz MA, van der Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE, members of the Coordination of Mouse Informatics Resources (CASIMIR), Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC. XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biology. 2010 11:R27. | Published | Link | 10.1186/gb-2010-11-3-r27 |
| Locus Reference Genomic sequences: an improved basis for describing human DNA variants. |
ISSN 1756-994X Article type Correspondence Publication date 15 April 2010 |
Apr 2010 | Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Beroud C, Dobson G, Lehvaslaiho H, Taschner PEM, den Dunnen JT, Devereau A, Birney E, Brookes AJ and Maglott DR. Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Medicine 2010, 2:24. | Published | Link | 10.1186/gm145 |