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46 results on '"Conte, Nathalie"'

1. The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization

Author

Dudová, Zdenka, Conte, Nathalie, Mason, Jeremy, Stuchlík, Dalibor, Peša, Radim, Halmagyi, Csaba, Perova, Zinaida, Mosaku, Abayomi, Thorne, Ross, Follette, Alex, Pivarč, Ľuboslav, Šašinka, Radim, Usman, Muhammad, Neuhauser, Steven, Begley, Dale A., Krupke, Debra M., Frassà, Massimiliano, Fiori, Alessandro, Corsi, Riccardo, Vezzadini, Luca, Isella, Claudio, Bertotti, Andrea, Bult, Carol, Parkinson, Helen, Medico, Enzo, Meehan, Terrence, and Křenek, Aleš

Published
2022
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2. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models

Author

Meehan, Terrence F, Conte, Nathalie, Goldstein, Theodore, Inghirami, Giorgio, Murakami, Mark A, Brabetz, Sebastian, Gu, Zhiping, Wiser, Jeffrey A, Dunn, Patrick, Begley, Dale A, Krupke, Debra M, Bertotti, Andrea, Bruna, Alejandra, Brush, Matthew H, Byrne, Annette T, Caldas, Carlos, Christie, Amanda L, Clark, Dominic A, Dowst, Heidi, Dry, Jonathan R, Doroshow, James H, Duchamp, Olivier, Evrard, Yvonne A, Ferretti, Stephane, Frese, Kristopher K, Goodwin, Neal C, Greenawalt, Danielle, Haendel, Melissa A, Hermans, Els, Houghton, Peter J, Jonkers, Jos, Kemper, Kristel, Khor, Tin O, Lewis, Michael T, Lloyd, KC Kent, Mason, Jeremy, Medico, Enzo, Neuhauser, Steven B, Olson, James M, Peeper, Daniel S, Rueda, Oscar M, Seong, Je Kyung, Trusolino, Livio, Vinolo, Emilie, Wechsler-Reya, Robert J, Weinstock, David M, Welm, Alana, Weroha, S John, Amant, Frédéric, Pfister, Stefan M, Kool, Marcel, Parkinson, Helen, Butte, Atul J, and Bult, Carol J

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Good Health and Well Being, Animals, Databases as Topic, Disease Models, Animal, Humans, Mice, Neoplasms, Patients, Xenograft Model Antitumor Assays, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study tumor evolution, mechanisms of drug response and resistance, and tailoring chemotherapeutic approaches for individual patients. The lack of robust standards for reporting on PDX models has hampered the ability of researchers to find relevant PDX models and associated data. Here we present the PDX models minimal information standard (PDX-MI) for reporting on the generation, quality assurance, and use of PDX models. PDX-MI defines the minimal information for describing the clinical attributes of a patient's tumor, the processes of implantation and passaging of tumors in a host mouse strain, quality assurance methods, and the use of PDX models in cancer research. Adherence to PDX-MI standards will facilitate accurate search results for oncology models and their associated data across distributed repository databases and promote reproducibility in research studies using these models. Cancer Res; 77(21); e62-66. ©2017 AACR.

Published
2017

3. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.

Author

Meehan, Terrence F, Conte, Nathalie, West, David B, Jacobsen, Julius O, Mason, Jeremy, Warren, Jonathan, Chen, Chao-Kung, Tudose, Ilinca, Relac, Mike, Matthews, Peter, Karp, Natasha, Santos, Luis, Fiegel, Tanja, Ring, Natalie, Westerberg, Henrik, Greenaway, Simon, Sneddon, Duncan, Morgan, Hugh, Codner, Gemma F, Stewart, Michelle E, Brown, James, Horner, Neil, International Mouse Phenotyping Consortium, Haendel, Melissa, Washington, Nicole, Mungall, Christopher J, Reynolds, Corey L, Gallegos, Juan, Gailus-Durner, Valerie, Sorg, Tania, Pavlovic, Guillaume, Bower, Lynette R, Moore, Mark, Morse, Iva, Gao, Xiang, Tocchini-Valentini, Glauco P, Obata, Yuichi, Cho, Soo Young, Seong, Je Kyung, Seavitt, John, Beaudet, Arthur L, Dickinson, Mary E, Herault, Yann, Wurst, Wolfgang, de Angelis, Martin Hrabe, Lloyd, KC Kent, Flenniken, Ann M, Nutter, Lauryl MJ, Newbigging, Susan, McKerlie, Colin, Justice, Monica J, Murray, Stephen A, Svenson, Karen L, Braun, Robert E, White, Jacqueline K, Bradley, Allan, Flicek, Paul, Wells, Sara, Skarnes, William C, Adams, David J, Parkinson, Helen, Mallon, Ann-Marie, Brown, Steve DM, and Smedley, Damian

Subjects
International Mouse Phenotyping Consortium, Animals, Mice, Knockout, Humans, Mice, Genetic Diseases, Inborn, Disease Models, Animal, Genetic Predisposition to Disease, Phenotype, Female, Male, Gene Knockout Techniques, Knockout, Genetic Diseases, Inborn, Disease Models, Animal, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

Although next-generation sequencing has revolutionized the ability to associate variants with human diseases, diagnostic rates and development of new therapies are still limited by a lack of knowledge of the functions and pathobiological mechanisms of most genes. To address this challenge, the International Mouse Phenotyping Consortium is creating a genome- and phenome-wide catalog of gene function by characterizing new knockout-mouse strains across diverse biological systems through a broad set of standardized phenotyping tests. All mice will be readily available to the biomedical community. Analyzing the first 3,328 genes identified models for 360 diseases, including the first models, to our knowledge, for type C Bernard-Soulier, Bardet-Biedl-5 and Gordon Holmes syndromes. 90% of our phenotype annotations were novel, providing functional evidence for 1,092 genes and candidates in genetically uncharacterized diseases including arrhythmogenic right ventricular dysplasia 3. Finally, we describe our role in variant functional validation with The 100,000 Genomes Project and others.

Published
2017

4. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

Author

McMurry, Julie A, Juty, Nick, Blomberg, Niklas, Burdett, Tony, Conlin, Tom, Conte, Nathalie, Courtot, Mélanie, Deck, John, Dumontier, Michel, Fellows, Donal K, Gonzalez-Beltran, Alejandra, Gormanns, Philipp, Grethe, Jeffrey, Hastings, Janna, Hériché, Jean-Karim, Hermjakob, Henning, Ison, Jon C, Jimenez, Rafael C, Jupp, Simon, Kunze, John, Laibe, Camille, Le Novère, Nicolas, Malone, James, Martin, Maria Jesus, McEntyre, Johanna R, Morris, Chris, Muilu, Juha, Müller, Wolfgang, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sariyar, Murat, Snoep, Jacky L, Soiland-Reyes, Stian, Stanford, Natalie J, Swainston, Neil, Washington, Nicole, Williams, Alan R, Wimalaratne, Sarala M, Winfree, Lilly M, Wolstencroft, Katherine, Goble, Carole, Mungall, Christopher J, Haendel, Melissa A, and Parkinson, Helen

Subjects
Humans, Computational Biology, Forecasting, Internet, Software, Software Design, Databases, Factual, Biological Science Disciplines, Data Mining, Databases, Factual, Developmental Biology, Biological Sciences, Medical and Health Sciences, Agricultural and Veterinary Sciences
Abstract

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

Published
2017

7. Data from PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models

Author

Meehan, Terrence F., primary, Conte, Nathalie, primary, Goldstein, Theodore, primary, Inghirami, Giorgio, primary, Murakami, Mark A., primary, Brabetz, Sebastian, primary, Gu, Zhiping, primary, Wiser, Jeffrey A., primary, Dunn, Patrick, primary, Begley, Dale A., primary, Krupke, Debra M., primary, Bertotti, Andrea, primary, Bruna, Alejandra, primary, Brush, Matthew H., primary, Byrne, Annette T., primary, Caldas, Carlos, primary, Christie, Amanda L., primary, Clark, Dominic A., primary, Dowst, Heidi, primary, Dry, Jonathan R., primary, Doroshow, James H., primary, Duchamp, Olivier, primary, Evrard, Yvonne A., primary, Ferretti, Stephane, primary, Frese, Kristopher K., primary, Goodwin, Neal C., primary, Greenawalt, Danielle, primary, Haendel, Melissa A., primary, Hermans, Els, primary, Houghton, Peter J., primary, Jonkers, Jos, primary, Kemper, Kristel, primary, Khor, Tin O., primary, Lewis, Michael T., primary, Lloyd, K.C. Kent, primary, Mason, Jeremy, primary, Medico, Enzo, primary, Neuhauser, Steven B., primary, Olson, James M., primary, Peeper, Daniel S., primary, Rueda, Oscar M., primary, Seong, Je Kyung, primary, Trusolino, Livio, primary, Vinolo, Emilie, primary, Wechsler-Reya, Robert J., primary, Weinstock, David M., primary, Welm, Alana, primary, Weroha, S. John, primary, Amant, Frédéric, primary, Pfister, Stefan M., primary, Kool, Marcel, primary, Parkinson, Helen, primary, Butte, Atul J., primary, and Bult, Carol J., primary

Published
2023
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8. S1 from PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models

Author

Meehan, Terrence F., primary, Conte, Nathalie, primary, Goldstein, Theodore, primary, Inghirami, Giorgio, primary, Murakami, Mark A., primary, Brabetz, Sebastian, primary, Gu, Zhiping, primary, Wiser, Jeffrey A., primary, Dunn, Patrick, primary, Begley, Dale A., primary, Krupke, Debra M., primary, Bertotti, Andrea, primary, Bruna, Alejandra, primary, Brush, Matthew H., primary, Byrne, Annette T., primary, Caldas, Carlos, primary, Christie, Amanda L., primary, Clark, Dominic A., primary, Dowst, Heidi, primary, Dry, Jonathan R., primary, Doroshow, James H., primary, Duchamp, Olivier, primary, Evrard, Yvonne A., primary, Ferretti, Stephane, primary, Frese, Kristopher K., primary, Goodwin, Neal C., primary, Greenawalt, Danielle, primary, Haendel, Melissa A., primary, Hermans, Els, primary, Houghton, Peter J., primary, Jonkers, Jos, primary, Kemper, Kristel, primary, Khor, Tin O., primary, Lewis, Michael T., primary, Lloyd, K.C. Kent, primary, Mason, Jeremy, primary, Medico, Enzo, primary, Neuhauser, Steven B., primary, Olson, James M., primary, Peeper, Daniel S., primary, Rueda, Oscar M., primary, Seong, Je Kyung, primary, Trusolino, Livio, primary, Vinolo, Emilie, primary, Wechsler-Reya, Robert J., primary, Weinstock, David M., primary, Welm, Alana, primary, Weroha, S. John, primary, Amant, Frédéric, primary, Pfister, Stefan M., primary, Kool, Marcel, primary, Parkinson, Helen, primary, Butte, Atul J., primary, and Bult, Carol J., primary

Published
2023
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9. In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution

Author

Fischer, Anja, primary, Lersch, Robert, additional, de Andrade Krätzig, Niklas, additional, Strong, Alexander, additional, Friedrich, Mathias J., additional, Weber, Julia, additional, Engleitner, Thomas, additional, Öllinger, Rupert, additional, Yen, Hsi-Yu, additional, Kohlhofer, Ursula, additional, Gonzalez-Menendez, Irene, additional, Sailer, David, additional, Kogan, Liz, additional, Lahnalampi, Mari, additional, Laukkanen, Saara, additional, Kaltenbacher, Thorsten, additional, Klement, Christine, additional, Rezaei, Majdaddin, additional, Ammon, Tim, additional, Montero, Juan J., additional, Schneider, Günter, additional, Mayerle, Julia, additional, Heikenwälder, Mathias, additional, Schmidt-Supprian, Marc, additional, Quintanilla-Martinez, Leticia, additional, Steiger, Katja, additional, Liu, Pentao, additional, Cadiñanos, Juan, additional, Vassiliou, George S., additional, Saur, Dieter, additional, Lohi, Olli, additional, Heinäniemi, Merja, additional, Conte, Nathalie, additional, Bradley, Allan, additional, Rad, Lena, additional, and Rad, Roland, additional

Published
2023
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10. Integrative ensemble modelling of cetuximab sensitivity in colorectal cancer PDXs

Author

Perron, Umberto, primary, Grassi, Elena, additional, Chatzipli, Aikaterini, additional, Viviani, Marco, additional, Karakoc, Emre, additional, Trastulla, Lucia, additional, Isella, Claudio, additional, Zanella, Eugenia R, additional, Klett, Hagen, additional, Molineris, Ivan, additional, Schueler, Julia, additional, Esteller, Manel, additional, Medico, Enzo, additional, Conte, Nathalie, additional, McDermott, Ultan, additional, Trusolino, Livio, additional, Bertotti, Andrea, additional, and Iorio, Francesco, additional

Published
2023
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12. A mouse informatics platform for phenotypic and translational discovery

Author

Ring, Natalie, Meehan, Terrence F., Blake, Andrew, Brown, James, Chen, Chao-Kung, Conte, Nathalie, Di Fenza, Armida, Fiegel, Tanja, Horner, Neil, Jacobsen, Julius O. B., Karp, Natasha, Lawson, Thomas, Mason, Jeremy C., Matthews, Peter, Morgan, Hugh, Relac, Mike, Santos, Luis, Smedley, Damian, Sneddon, Duncan, Pengelly, Alice, Tudose, Ilinca, Warren, Jonathan W. G., Westerberg, Henrik, Yaikhom, Gagarine, Parkinson, Helen, and Mallon, Ann-Marie

Published
2015
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13. Abstract 3105: PDCM Finder: An open global cancer research platform for patient-derived cancer models

Author

Perova, Zinaida, primary, Halmagyi, Csaba, additional, Follette, Alex, additional, Martinez, Mauricio, additional, Lopez-Gomez, Federico, additional, Mason, Jeremy, additional, Mosaku, Abayomi, additional, Conte, Nathalie, additional, Thorne, Ross, additional, Neuhauser, Steven, additional, Begley, Dale, additional, Krupke, Debra, additional, Meehan, Terrence, additional, Bult, Carol, additional, and Parkinson, Helen, additional

Published
2022
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14. PiggyBac Transposon Mutagenesis: A Tool for Cancer Gene Discovery in Mice

Author

Rad, Roland, Rad, Lena, Wang, Wei, Cadinanos, Juan, Vassiliou, George, Rice, Stephen, Campos, Lia S., Yusa, Kosuke, Banerjee, Ruby, Li, Meng Amy, de la Rosa, Jorge, Strong, Alexander, Lu, Dong, Ellis, Peter, Conte, Nathalie, Yang, Fang Tang, Liu, Pentao, and Bradley, Allan

Published
2010

16. Abstract LB017: PDX Finder: An open and global catalogue of patient-derived xenograft models

Author

Perova, Zinaida, primary, Halmagyi, Csaba, additional, Mosaku, Abayomi, additional, Conte, Nathalie, additional, Mason, Jeremy, additional, Follette, Alex, additional, Thorne, Ross, additional, Martinez, Mauricio, additional, Neuhauser, Steven, additional, Begley, Dale, additional, Krupke, Debra, additional, Parkinson, Helen, additional, Meehan, Terrence, additional, and Bult, Carol, additional

Published
2021
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17. Analysis of Pax6 contiguous gene deletions in the mouse, mus musculus, identifies regions distinct from Pax6 responsible for extreme small-eye and belly-spotting phenotypes

Author

Favor, Jack, Bradley, Alan, Conte, Nathalie, Janik, Dirk, Pretsch, Walter, Reitmeir, Peter, Rosemann, Michael, Schmahl, Wolfgang, Wienberg, Johannes, and Zaus, Irmgard

Subjects
Cell development (Biology) -- Research, Embryonic development -- Research, Eye -- Physiological aspects, Eye -- Genetic aspects, Gene expression -- Research, Biological sciences
Published
2009

23. Identification of genetic elements in metabolism by high-throughput mouse phenotyping

Author

Rozman, Jan, Rathkolb, Birgit, Meehan, Terrence F, Codner, Gemma F, Fiegel, Tanja, Ring, Natalie, Westerberg, Henrik, Greenaway, Simon, Sneddon, Duncan, Morgan, Hugh, Loeffler, Jorik, Stewart, Michelle E, Ramirez-Solis, Ramiro, Mason, Jeremy, Bradley, Allan, Skarnes, William C, Steel, Karen P, Maguire, Simon A, Dench, Joshua, Lafont, David, Vancollie, Valerie E, Pearson, Selina A, Gates, Amy S, Sanderson, Mark, Haselimashhadi, Hamed, Shannon, Carl, Anthony, Lauren F E, Sumowski, Maksymilian T, McLaren, Robbie S B, Doe, Brendan, Wardle-Jones, Hannah, Griffiths, Mark N D, Galli, Antonella, Swiatkowska, Agnieszka, Isherwood, Christopher M, Consortium, IMPC, Speak, Anneliese O, Cambridge, Emma L, Wilson, Heather M, Caetano, Susana S, Maguire, Anna Karin B, Adams, David J, Bottomley, Joanna, Ryder, Ed, Gleeson, Diane, Pouilly, Laurent, Hough, Tertius, Rousseau, Stephane, Auburtin, Aurélie, Reilly, Patrick, Ayadi, Abdel, Selloum, Mohammed, Wood, Joshua A, Clary, Dave, Havel, Peter, Tolentino, Todd, Tolentino, Heather, Mallon, Ann-Marie, Schuchbauer, Mike, Pedroia, Sheryl, Trainor, Amanda, Djan, Esi, Pham, Milton, Huynh, Alison, De Vera, Vincent, Seavitt, John, Gallegos, Juan, Garza, Arturo, Wells, Sara, Mangin, Elise, Senderstrom, Joel, Lazo, Iride, Mowrey, Kate, Bohat, Ritu, Samaco, Rodney, Veeraragavan, Surabi, Beeton, Christine, Kalaga, Sowmya, Kelsey, Lois, Santos, Luis, Vukobradovic, Igor, Berberovic, Zorana, Owen, Celeste, Qu, Dawei, Guo, Ruolin, Newbigging, Susan, Morikawa, Lily, Law, Napoleon, Shang, Xueyuan, Feugas, Patricia, Lelliott, Christopher J, Wang, Yanchun, Eskandarian, Mohammad, Zhu, Yingchun, Penton, Patricia, Laurin, Valerie, Clarke, Shannon, Lan, Qing, Sleep, Gillian, Creighton, Amie, Jacob, Elsa, White, Jacqueline K, Danisment, Ozge, Gertsenstein, Marina, Pereira, Monica, MacMaster, Suzanne, Tondat, Sandra, Carroll, Tracy, Cabezas, Jorge, Hunter, Jane, Clark, Greg, Bubshait, Mohammed, Oestereicher, Manuela A, Sorg, Tania, Miller, David, Sohel, Khondoker, Adissu, Hibret, Ganguly, Milan, Bezginov, Alexandr, Chiani, Francesco, Di Pietro, Chiara, Di Segni, Gianfranco, Ermakova, Olga, Ferrara, Filomena, Champy, Marie-France, Fruscoloni, Paolo, Gambadoro, Aalessia, Gastaldi, Serena, Golini, Elisabetta, La Sala, Gina, Mandillo, Silvia, Marazziti, Daniela, Massimi, Marzia, Matteoni, Rafaele, Orsini, Tiziana, Bower, Lynette R, Pasquini, Miriam, Raspa, Marcello, Rauch, Aline, Rossi, Gianfranco, Rossi, Nicoletta, Putti, Sabrina, Scavizzi, Ferdinando, Tocchini-Valentini, Giuseppe D, Wakana, Shigeharu, Suzuki, Tomohiro, Reynolds, Corey L, Tamura, Masaru, Kaneda, Hideki, Furuse, Tamio, Kobayashi, Kimio, Miura, Ikuo, Yamada, Ikuko, Obata, Yuichi, Yoshiki, Atsushi, Ayabe, Shinya, Chambers, J Nicole, Flenniken, Ann M, Chalupsky, Karel, Seisenberger, Claudia, Bürger, Antje, Beig, Joachim, Kühn, Ralf, Hörlein, Andreas, Schick, Joel, Oritz, Oskar, Giesert, Florian, Graw, Jochen, Murray, Stephen A, Ollert, Markus, Schmidt-Weber, Carsten, Stoeger, Tobias, Önder Yildirim, Ali, Eickelberg, Oliver, Klopstock, Thomas, Busch, Dirk H, Bekeredjian, Raffi, Zimmer, Andreas, Jacobsen, Jules O, Nutter, Lauryl M J, Smedley, Damian, Dickinson, Mary E, Benso, Frank, Morse, Iva, Kim, Hyoung-Chin, Lee, Ho, Cho, Soo Young, Svenson, Karen L, West, David, Tocchini-Valentini, Glauco P, Schütt, Christine, Beaudet, Arthur L, Bosch, Fatima, Braun, Robert B, Dobbie, Michael S, Gao, Xiang, Herault, Yann, Moshiri, Ala, Moore, Bret A, Kent Lloyd, K. C., McKerlie, Colin, Ravindranath, Aakash Chavan, Masuya, Hiroshi, Tanaka, Nobuhiko, Flicek, Paul, Parkinson, Helen E, Sedlacek, Radislav, Seong, Je Kyung, Wang, Chi-Kuang Leo, Moore, Mark, Brown, Steve D, Tschöp, Matthias H, Leuchtenberger, Stefanie, Wurst, Wolfgang, Klingenspor, Martin, Wolf, Eckhard, Beckers, Johannes, Machicao, Fausto, Peter, Andreas, Staiger, Harald, Häring, Hans-Ulrich, Grallert, Harald, Campillos, Monica, Sharma, Sapna, Maier, Holger, Fuchs, Helmut, Gailus-Durner, Valerie, Werner, Thomas, Hrabe de Angelis, Martin, Aguilar-Pimentel, Antonio, Becker, Lore, Treise, Irina, Moreth, Kristin, Garrett, Lillian, Kistler, Martin, Hölter, Sabine M, Zimprich, Annemarie, Marschall, Susan, Amarie, Oana V, Calzada-Wack, Julia, Neff, Frauke, Brachthäuser, Laura, Lengger, Christoph, Stoeger, Claudia, Zapf, Lilly, Willershäuser, Monja, Cho, Yi-Li, da Silva-Buttkus, Patricia, Kraiger, Markus J, Mayer-Kuckuk, Philipp, Gampe, Karen Kristine, Wu, Moya, Conte, Nathalie, Warren, Jonathan, Chen, Chao-Kung, Tudose, Ilinca, Brommage, Robert, Relac, Mike, Matthews, Peter, Cater, Heather L, Natukunda, Helen P, Cleak, James, Teboul, Lydia M, Clementson-Mobbs, Sharon, Szoke-Kovacs, Zsombor, Walling, Alison P, Johnson, Sara J, Rozman, Jan [0000-0002-8035-8904], Kistler, Martin [0000-0003-0116-7761], Mason, Jeremy [0000-0002-2796-5123], Lelliott, Christopher J [0000-0001-8087-4530], Herault, Yann [0000-0001-7049-6900], Kent Lloyd, KC [0000-0002-5318-4144], McKerlie, Colin [0000-0002-2232-0967], Flicek, Paul [0000-0002-3897-7955], Maier, Holger [0000-0003-2514-8290], Fuchs, Helmut [0000-0002-5143-2677], Hrabe de Angelis, Martin [0000-0002-7898-2353], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Blood Glucose, Candidate gene, Cancer Research, Basal Metabolism/genetics, Gene regulatory network, Obesity/genetics, genetics [Metabolic Diseases], General Physics and Astronomy, Genome-wide association study, Genome, Mice, genetics [Obesity], Triglycerides/metabolism, 2.1 Biological and endogenous factors, Gene Regulatory Networks, Aetiology, lcsh:Science, metabolism [Blood Glucose], Mice, Knockout, Multidisciplinary, genetics [Basal Metabolism], Phenotype, Area Under Curve, Diabetes Mellitus, Type 2/genetics, ddc:500, Technology Platforms, Type 2, metabolism [Triglycerides], Knockout, Science, Computational biology, Biology, genetics [Diabetes Mellitus, Type 2], General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Oxygen Consumption, Metabolic Diseases, Body Weight/genetics, Diabetes Mellitus, Genetics, Animals, Humans, Metabolic Diseases/genetics, Obesity, Gene, Gene knockout, Triglycerides, Oxygen Consumption/genetics, Blood Glucose/metabolism, genetics [Body Weight], Human Genome, Body Weight, Promoter, General Chemistry, genetics [Oxygen Consumption], High-Throughput Screening Assays, 030104 developmental biology, Diabetes Mellitus, Type 2, IMPC Consortium, lcsh:Q, Basal Metabolism, Genome-Wide Association Study
Abstract

Metabolic diseases are a worldwide problem but the underlying genetic factors and their relevance to metabolic disease remain incompletely understood. Genome-wide research is needed to characterize so-far unannotated mammalian metabolic genes. Here, we generate and analyze metabolic phenotypic data of 2016 knockout mouse strains under the aegis of the International Mouse Phenotyping Consortium (IMPC) and find 974 gene knockouts with strong metabolic phenotypes. 429 of those had no previous link to metabolism and 51 genes remain functionally completely unannotated. We compared human orthologues of these uncharacterized genes in five GWAS consortia and indeed 23 candidate genes are associated with metabolic disease. We further identify common regulatory elements in promoters of candidate genes. As each regulatory element is composed of several transcription factor binding sites, our data reveal an extensive metabolic phenotype-associated network of co-regulated genes. Our systematic mouse phenotype analysis thus paves the way for full functional annotation of the genome., The genetic basis of metabolic diseases is incompletely understood. Here, by high-throughput phenotyping of 2,016 knockout mouse strains, Rozman and colleagues identify candidate metabolic genes, many of which are associated with unexplored regulatory gene networks and metabolic traits in human GWAS.

Published
2018

25. PDX Finder: A portal for patient-derived tumor xenograft model discovery

Author

Conte, Nathalie, primary, Mason, Jeremy C, additional, Halmagyi, Csaba, additional, Neuhauser, Steven, additional, Mosaku, Abayomi, additional, Yordanova, Galabina, additional, Chatzipli, Aikaterini, additional, Begley, Dale A, additional, Krupke, Debra M, additional, Parkinson, Helen, additional, Meehan, Terrence F, additional, and Bult, Carol C, additional

Published
2018
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26. A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

Author

Bowl, Michael R., Simon, Michelle M., Ingham, Neil J., Greenaway, Simon, Santos, Luis, Cater, Heather, Taylor, Sarah, Mason, Jeremy, Kurbatova, Natalja, Pearson, Selina, Bower, Lynette R., Clary, Dave A., Meziane, Hamid, Reilly, Patrick, Minowa, Osamu, Kelsey, Lois, Allen, Sue, Clementson-Mobbs, Sharon, Codner, Gemma, Fray, Martin, Gardiner, Wendy, Joynson, Russell, Kenyon, Janet, Loeffler, Jorik, Nell, Barbara, Parker, Andrew, Quwailid, Deen, Stewart, Michelle, Walling, Alison, Zaman, Rumana, Chen, Chao Kung, Conte, Nathalie, Matthews, Peter, Relac, Mike, Tudose, Ilinca, Warren, Jonathan, Le Marchand, Elise, El Amri, Amal, El Fertak, Leila, Ennah, Hamid, Ali-Hadji, Dalila, Ayadi, Abdel, Wattenhofer-Donze, Marie, Moulaert, David, Jacquot, Sylvie, André, Philippe, Birling, Marie Christine, Pavlovic, Guillaume, Lalanne, Valérie, Lux, Aline, Riet, Fabrice, Mittelhaeuser, Christophe, Bour, Raphael, Guimond, Alain, Bam'Hamed, Chaouki, Leblanc, Sophie, Vasseur, Laurent, Selloum, Mohammed, Sorg, Tania, Ayabe, Shinya, Furuse, Tamio, Kaneda, Hideki, Kobayashi, Kimio, Masuya, Hiroshi, Miura, Ikuo, Obata, Yuichi, Suzuki, Tomohiro, Tamura, Masaru, Tanaka, Nobuhiko, Yamada, Ikuko, Yoshiki, Atsushi, Berberovic, Zorana, Bubshait, Mohammed, Cabezas, Jorge, Carroll, Tracy, Clark, Greg, Clarke, Shannon, Creighton, Amie, Danisment, Ozge, Eskandarian, Mohammad, Feugas, Patricia, Gertsenstein, Marina, Guo, Ruolin, Hunter, Jane, Jacob, Elsa, Lan, Qing, Laurin, Valerie, Law, Napoleon, MacMaster, Sue, Miller, David, Morikawa, Lily, Newbigging, Susan, Owen, Celeste, Penton, Patricia, Pereira, Monica, Qu, Dawei, Shang, Xueyuan, Sleep, Gillian, Sohel, Khondoker, Tondat, Sandra, Wang, Yanchun, Vukobradovic, Igor, Zhu, Yingchun, Chiani, Francesco, Di Pietro, Chiara, Di Segni, Gianfranco, Ermakova, Olga, Ferrara, Filomena, Fruscoloni, Paolo, Gambadoro, Aalessia, Gastaldi, Serena, Golini, Elisabetta, Sala, Gina La, Mandillo, Silvia, Marazziti, Daniela, Massimi, Marzia, Matteoni, Rafaele, Orsini, Tiziana, Pasquini, Miriam, Raspa, Marcello, Rauch, Aline, Rossi, Gianfranco, Rossi, Nicoletta, Putti, Sabrina, Scavizzi, Ferdinando, Tocchini-Valentini, Giuseppe D., Beig, Joachim, Bürger, Antje, Giesert, Florian, Graw, Jochen, Kühn, Ralf, Oritz, Oskar, Schick, Joel, Seisenberger, Claudia, Amarie, Oana, Garrett, Lillian, Hölter, Sabine M., Zimprich, Annemarie, Aguilar-Pimentel, Antonio, Beckers, Johannes, Brommage, Robert, Calzada-Wack, Julia, Fuchs, Helmut, Gailus-Durner, Valérie, Lengger, Christoph, Leuchtenberger, Stefanie, Maier, Holger, Marschall, Susan, Moreth, Kristin, Neff, Frauke, Östereicher, Manuela A., Rozman, Jan, Steinkamp, Ralph, Stoeger, Claudia, Treise, Irina, Stoeger, Tobias, Yildrim, Ali Önder, Eickelberg, Oliver, Becker, Lore, Klopstock, Thomas, Ollert, Markus, Busch, Dirk H., Schmidt-Weber, Carsten, Bekeredjian, Raffi, Zimmer, Andreas, Rathkolb, Birgit, Wolf, Eckhard, Klingenspor, Martin, Tocchini-Valentini, Glauco P., Gao, Xiang, Bradley, Allan, Skarnes, William C., Moore, Mark, Beaudet, Arthur L., Justice, Monica J., Seavitt, John, Dickinson, Mary E., Wurst, Wolfgang, De Angelis, Martin Hrabe, Herault, Yann, Wakana, Shigeharu, Nutter, Lauryl M.J., Flenniken, Ann M., McKerlie, Colin, Murray, Stephen A., Svenson, Karen L., Braun, Robert E., West, David B., Lloyd, K. C.Kent, Adams, David J., White, Jacqui, Karp, Natasha, Flicek, Paul, Smedley, Damian, Meehan, Terrence F., Parkinson, Helen E., Teboul, Lydia M., Wells, Sara, Steel, Karen P., Mallon, Ann Marie, Brown, Steve D.M., Mason, Jeremy [0000-0002-2796-5123], de Angelis, Martin Hrabe [0000-0002-7898-2353], Herault, Yann [0000-0001-7049-6900], Wakana, Shigeharu [0000-0001-8532-0924], McKerlie, Colin [0000-0002-2232-0967], Lloyd, KC Kent [0000-0002-5318-4144], Flicek, Paul [0000-0002-3897-7955], Smedley, Damian [0000-0002-5836-9850], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Cancer Research, Candidate gene, General Physics and Astronomy, Datasets as Topic, Mice, 2.1 Biological and endogenous factors, Protein Interaction Maps, Aetiology, lcsh:Science, Pediatric, Genetics, Mice, Knockout, Multidisciplinary, medicine.diagnostic_test, Hearing Tests, Ear, Phenotype, medicine.anatomical_structure, Technology Platforms, International Mouse Phenotyping Consortium, medicine.symptom, Biotechnology, Hearing Loss/epidemiology, Hearing loss, Knockout, 1.1 Normal biological development and functioning, Science, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Clinical Research, Underpinning research, medicine, otorhinolaryngologic diseases, Auditory system, Animals, Genetic Testing, IMPC, mouse, auditory dysfunction, Set (psychology), Hearing Loss, Gene, Genetic testing, Auditory dysfunction, Human Genome, General Chemistry, 030104 developmental biology, Protein Interaction Maps/genetics, lcsh:Q
Abstract

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function., The full extent of the genetic basis for hearing impairment is unknown. Here, as part of the International Mouse Phenotyping Consortium, the authors perform a hearing loss screen in 3006 mouse knockout strains and identify 52 new candidate genes for genetic hearing loss.

Published
2017

28. BioMedBridges: Prototype discovery tool for mouse-human phenotype

Author

Parkinson, Helen, Conte, Nathalie, Meehan, Terry, Raess, Michael, Neff, Frauke, Gormanns, Philipp, Smedley, Damian, Lengger, Christoph, Luchinat, Claudio, Maier, Holger, Mueller, Heimo, Reihs, Robert, Tenori, Leonardo, and Tiedemann, Hendrik

Subjects
obesity, diabetes, translational research, phenotypes, human, ontology, data integration, mouse
Abstract

Deliverables 7.1 and 7.2 provided a workshop and an ontology (DIAB) for Type 2 Diabetes (T2D) and evaluated the use of the DIAB ontology annotation and query for TD2 data. Here we evaluate the ontology as an extension of a semantic matching service (PhenoDigm, http://www.sanger.ac.uk/resources/databases/phenodigm/) to test whether the ontology improves recall of mouse models of T2D using three gold standard T2D associated gene lists for the evaluation and comparing DIAB’s T2D associated phenotype list to DIAB subsets, and other available T2D associated phenotype datasets.

Published
2016
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29. 10 Simple rules for design, provision, and reuse of identifiers for web-based life science data

Author

Julie McMurry, Blomberg, Niklas, Burdett, Tony, Conte, Nathalie, Dumontier, Michel, Fellows, Donal K, Gonzalez-Beltran, Alejandra, Gormanns, Philipp, Hastings, Janna, Haendel, Melissa A, Hermjakob, Henning, Hériché, Jean-Karim, Ison, Jon C, Jimenez, Rafael C, Jupp, Simon, Juty, Nick, Laibe, Camille, Le Novère, Nicolas, Malone, James, Martin, Maria J, McEntyre, Johanna R, Morris, Chris, Muilu, Juha, Müller, Wolfgang, Mungall, Christopher J, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sariyar, Murat, Snoep, Jacky L, Stanford, Natalie J, Swainston, Neil, Washington, Nicole, Williams, Alan R, Wolstencroft, Katherine, Goble, Carole, and Parkinson, Helen

Subjects
0303 health sciences, identifiers, databases, identifier design, e-science, interoperability, accessions, 03 medical and health sciences, 0302 clinical medicine, big data, standards, reproducibility, 030217 neurology & neurosurgery, web-based identifiers, synthesis research, 030304 developmental biology
Abstract

Life science data is evolving to be ever larger, more distributed, and more natively web-based. However, our collective handling of identifiers has lagged behind these advances. Diverse identifier issues (for instance “link rot” and “content drift”) have hampered our ability to integrate data and derive new knowledge from it. Optimizing web-based identifiers is harder than it appears and no single scheme is perfect: Identifiers are reused in different ways for different reasons, by different consumers. Moreover, digital entities (e.g., files), physical entities (e.g., biosamples), and descriptive entities (e.g., ‘mitosis’) have different requirements for identifiers. Nevertheless, there is substantial room for improvement throughout the life sciences and several other groups have been converging on identifier standards that are broadly applicable. Building on these efforts and drawing on our experience, we focus on the use case of large-scale data integration: we outline the identifier qualities and best practices that we feel are most important in this context. Specifically, we propose actions that providers of online databases (repositories, registries, and knowledgebases) should take when designing new identifiers or maintaining existing ones (Rules 1-9). In Rule 10, we conclude with guidance to data integrators and redistributors on how best to reference identifiers from these diverse sources. This article may also be useful to data generators and end users as it offers insight into the issues associated with data provision in a web environment. We call upon data providers to take a long-term view of their entities’ scope and lifecycle, and to consider existing identifier platforms and services. Rule 1. Use established identifiers Rule 2. Design identifiers for use by others Rule 3. Help local identifiers travel well: document Prefix and Namespace Rule 4. Opt for simple durable web resolution Rule 5. Avoid embedding meaning Rule 6. Make URIs clear and findable Rule 7. Implement a version management policy Rule 8. Do not re-assign or delete identifiers Rule 9. Document the identifiers you issue and use Rule 10. Reference responsibly

Published
2015
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30. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Author

McMurry, Julie A, primary, Juty, Nick, additional, Blomberg, Niklas, additional, Burdett, Tony, additional, Conlin, Tom, additional, Conte, Nathalie, additional, Courtot, Mélanie, additional, Deck, John, additional, Dumontier, Michel, additional, Fellows, Donal K, additional, Gonzalez-Beltran, Alejandra, additional, Gormanns, Philipp, additional, Grethe, Jeffrey, additional, Hastings, Janna, additional, Hermjakob, Henning, additional, Hériché, Jean-Karim, additional, Ison, Jon C, additional, Jimenez, Rafael C, additional, Jupp, Simon, additional, Kunze, John, additional, Laibe, Camille, additional, Le Novère, Nicolas, additional, Malone, James, additional, Martin, Maria Jesus, additional, McEntyre, Johanna R, additional, Morris, Chris, additional, Muilu, Juha, additional, Müller, Wolfgang, additional, Rocca-Serra, Philippe, additional, Sansone, Susanna-Assunta, additional, Sariyar, Murat, additional, Snoep, Jacky L, additional, Stanford, Natalie J, additional, Soiland-Reyes, Stian, additional, Swainston, Neil, additional, Washington, Nicole, additional, Williams, Alan R, additional, Wimalaratne, Sarala, additional, Winfree, Lilly, additional, Wolstencroft, Katherine, additional, Goble, Carole, additional, Mungall, Christopher J, additional, Haendel, Melissa A, additional, and Parkinson, Helen, additional

Published
2017
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31. 10 Simple rules for design, provision, and reuse of persistent identifiers for life science data

Author

McMurry, Julie, Blomberg, Niklas, Burdett, Tony, Conte, Nathalie, Dumontier, Michel, Fellows, Donal K, Gonzalez-Beltran, Alejandra, Gormanns, Philipp, Hastings, Janna, Haendel, Melissa A, Hermjakob, Henning, Hériché, Jean-Karim, Ison, Jon C, Jimenez, Rafael C, Jupp, Simon, Juty, Nick, Laibe, Camille, Le Novère, Nicolas, Malone, James, Martin, Maria J, McEntyre, Johanna R, Morris, Chris, Muilu, Juha, Müller, Wolfgang, Mungall, Christopher J, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sariyar, Murat, Snoep, Jacky L, Stanford, Natalie J, Swainston, Neil, Washington, Nicole, Williams, Alan R, Wolstencroft, Katherine, Goble, Carole, and Parkinson, Helen

Subjects
0303 health sciences, Standards, Synthesis research, Identifier design, e-Science, Interoperability, Identifiers, Reproducibility, 3. Good health, 03 medical and health sciences, Big data, Databases, 0302 clinical medicine, 030220 oncology & carcinogenesis, Open science, Accessions, 030304 developmental biology
Abstract

In the life sciences, problems with identifiers impede the flow and integrity of information. This is especially challenging within “synthesis research” disciplines such as systems biology, translational medicine, and ecology. Implementation-driven initiatives such as ELIXIR, BD2K, and others have therefore been actively working to understand and address underlying problems with identifiers. Good, global-scale, persistent identifier design is harder than it appears, and is essential for data to be Findable, Accessible, Interoperable, and Reusable (Data FAIRport principles). Here, we build on emerging conventions and existing general recommendations and summarise the identifier characteristics most important to optimising the utility of life-science data. We propose actions to take in the identifier ‘green field’ and offer guidance for using real-world identifiers from diverse sources.

Published
2015
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32. Co-annotated mouse--human datasets

Author

Parkinson, Helen, Conte, Nathalie, McMurry, Julie, Ison, Jon, Burdett, Tony, Vasant, Drashtti, Raess, Michael, Gormanns, Philipp, Neff, Frauke, Bordag, Natalie, Müller, Heimo, Zatloukal, Kurt, Luchinat, Claudio, and Tenori, Leonardo

Subjects
obesity, ComputingMethodologies_PATTERNRECOGNITION, diabetes, translational research, phenotypes, human, ontology, data integration, mouse
Abstract

In order to develop a comprehensive set of terms to describe Type 2 diabetes and obesity phenotypes in mouse and human, Type 2 Diabetes-related phenotypes were mined from the literature for use as new phenotype terms. The mined terms were curated and temporally categorised by expert clinicians/diabetologists. The terms were represented as an ontology in OWL format and the utility of the ontology in the annotation of data resources and partner data sets was evaluated. Using the ontology developed here enabled the annotation of mouse and human datasets with specific terminology representing Type 2 Diabetes progression, which will ultimately support translational research.

Published
2015
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33. Definition of personalised data types within BioMedBridges

Author

Västrik, Imre, Parkinson, Helen, McMurry, Julie, Faulconbridge, Adam, Conte, Nathalie, Merino Martinez, Roxana, Swertz, Morris, and Charbon, Bart

Subjects
data, AML, personalised medicine, acute myeloid leukaemia, 3. Good health
Abstract

The purpose of deliverable 8.2 is to describe the data types pertinent for personalised medicine and the links between them. To do this, we first identified a concrete use case: acute myeloid leukemia and then identified the needs of the key stakeholders: physicians, clinical researchers, biomedical researchers, and patients. Guided by these needs we built a prototype data model for structuring, organising and annotating the patient data accordingly. The data model will form the basis for the prototype implementation of an IT solution for storing, management and querying of the personalised medicine data which will then be used to implement and demonstrate the personalised medicine informatics pipeline (deliverable 8.3). This report starts by briefly explaining the opportunities and challenges related to practising personalised medicine. We then describe a concrete case of applying personalised medicine, analyse the stakeholder needs, enumerate the types of data (both private and public) to actually gain insights into the patient data. The report concludes by specifying a prototype data model for structuring and organising the data in order to meet stakeholder needs.

Published
2015
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34. Report on the development of the BioMedBridges registry of biomedical science data services and tools

Author

Ison, Jon, McMurry, Julie, Parkinson, Helen, Conte, Nathalie, van Denderen, Janneke, Belien, Jeroen, Brunak, Søren, Rapacki, Kristoffer, Gormanns, Philipp, Muilu, Juha, Sariyar, Murat, Bild, Raffael, Morris, Chris, Winn, Martyin, and Sipos, Gergely

Subjects
services, tools, discoverablity, registry, life-science data, software description model
Abstract

The development of a prototype service registry is the objective of BioMedBridges Deliverable 3.3, with contributions from BioMedBridges partners and in collaboration with ELIXIR. The Tools and Data Services Registry is designed to make it easier for researchers to find, compare, and use biomedical software to address a scientific question or research support task. For instance: “What are all of the Gene Ontology tools? Which of these is most highly cited?”. By returning relevant, structured results, the registry aims to complement search engines like Google: The registry user can specify exactly what they need, using various search and filter options, and get a tailored list of suitable resources. From sequencing to structures, imaging to indexing, the registry’s domain scope is very broad; it also encompasses webservices, web GUIs, desktop GUIs, and commandline tools. This broad scope ensures coverage of a substantial portion of the tools and data services of use to Research Infrastructures represented in BioMedBridges. Information about tools includes crucial provenance details, links to relevant publications and grants and key contact information. Consistent with the overall mission of WP3, the service registry implemented and extended existing standards, formats, and ontologies wherever possible. To achieve the objectives, it was necessary to engage with the software community to develop a sustainable, scaleable minimum metadata model and formal schema to describe software; the model was purpose-built to be lightweight and flat in order to facilitate adoption by other software registries that may be looking to provide or aggregate software metadata in the future. The registry data model, software, and content (metadata describing the tools) are fully open access and open source in order to further encourage re-use and community participation. In the following report we summarise technical progress and outcomes of our work to date. Future plans comprise a program of activities lead and coordinated by ELIXIR-DK (tools node) and it is expected that this will ensure long-term sustainability of the registry. The code, schema and data in the prototype tools registry has all been made available to the ELIXIR-DK node and to the wider community via Github. Further contacts have been made with external projects e.g. the NIH funded Gene Ontology and the EC funded RD-Connect project to identify tools that they recommend and to include these in the service registry. This deliverable report provides detailed information on the work performed with BioMedBridges resources.

Published
2015
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35. BioMedBridges: Biomedical sciences research infrastructures Online Dictionary of common molecular identifiers

Author

Ison, Jon, McMurry, Julie, Parkinson, Helen, Conte, Nathalie, Gormanns, Philipp, Sariyar, Murat, Sipos, Gergely, Brunak, Søren, and Rapacki, Kristoffer

Subjects
identifiers, data interoperability, best practice, ontologies, semantic interoperability
Abstract

The provision and use of common and unambiguous identifiers for bio-molecules such as genes, proteins and bioactive compounds is key to supporting the information flow from basic science, model organism biology, bioinformatics and structural biology through to translational research and clinical care. The project partners have determined an interoperable ‘Dictionary’ of identifier types (Appendix 1) used in this project, and within clinical/translational research more broadly. At the request of the scientific advisory board, we have also expanded our WP3.1 activities to include the development of best practices documentation for identifiers (Appendix 2-1) which was based on our identifiers landscape analysis (Appendix 2-2). Part of the expanded work on identifiers includes a shortlist of the most relevant Identifier Resolution and Conversion Tools (Appendix 2-3); these have also been registered with the BioMedBridges Tools and Data Services Registry. Further documentation was developed to guide the selection of ontologies (Appendix 2-4) to support cross-domain data integration. Where no authoritative identifier standard exists, we have worked with the respective community to determine one that would support the activities of WP4 and BioMedBridges use cases. Relevant identifiers include those for samples (Task 2), small molecules, macromolecular assemblies, genes, proteins, drugs, diseases and phenotypes. The report includes a summary of recommendations.

Published
2015
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36. REPORT: BioMedBridges standards workshop

Author

Conte, Nathalie, Hancocks, Tom, and Suhr, Stephanie

Subjects
identifiers, data interoperability, standards
Abstract

This workshop, co-organized by BioMedBridges WP3 and 12, was held on 24-25 June and hosted by BioMedBridges partners at VUMC in Amsterdam. Attendees included BioMedBridges personnel, members from the ESFRI BMS research infrastructures and invited external experts from existing standards organisations. The following aspects of data standardisation were explored: Defining entity identifiers and identifiers best practice Development of a Meta models and Mappings Registry for biomedical standards Data integration occurs when a query proceeds through multiple data sets, thereby relating diverse data extracted from different data sources. Standards and data harmonisation is a prerequisite to data integration, a primary aim of the BioMedBridges project. For the various ESFRI projects to exchange and integrate data in a meaningful way there needs to be agreement on how biomedical data is annotated, formatted and organised. Whilst an ultimate aim would be a single database, with a standardised user interface (UI), this is unlikely and a system of federated databases each specialising in a particular data type is more achievable. Provided that standardisation is implemented across the databases, a common UI could be deployed to allow integrated and simultaneous searching of data. The use of entity identifiers and common standards is essential to achieve the above vision, but many challenges exist. The complex and varied nature of the biomedical sciences, and biology in general, means that each researcher can have their own requirements and reasons for structuring their data in a particular format. To capture the possible extent of these variables, standards would require a high degree of granularity. Therefore organisation is required within the community and compromise needs to be sought.

Published
2014
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38. Assessment of feasible data integration paths in BioMedBridges databases

Author

Parkinson, Helen, Conte, Nathalie, and Jenkinson, Andy

Subjects
data integration, BioMedBridges
Abstract

BioMedBridges deliverable 4.1 described summary scientific use cases for the federated web service strategy for integration by WP4. For the present deliverable, this work was expanded on by: examining the technical status of the WP4 contributors and other partners within BioMedBridges and assessing whether the technical plan is feasible determining which use cases can be delivered with existing technology and which will require de novo development of web services and clarifying external dependencies, such as e.g. authentication software for WP5 or limitations imposed by the RDF technology to be adopted in the latter stages of the project. As there are dependencies between WP3 (standards) and WP4 (technical integration), a joint survey was circulated to all participating research infrastructures to assess the current use of standards, the scientific use cases, the technical approach within each infrastructure, and the current uses of research data. The survey questions, results and a summary are included in Appendix 1, 2 and 3 to this document and are analysed here. In addition, a joint technical workshop was organised by WP3 and 4 that was also attended by WP5 members and members of the use cases. The results from this workshop, a report of which is included in Appendix 4 to this document, have flown into this deliverable and will make a significant contribution towards the further development of the technical integration strategy within the project.

Published
2014
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42. Loss of heterozygosity at microsatellite markers from region p11-21 of chromosome 8 in microdissected breast tumor but not in peritumoral cells

Author

Charafe-Jauffret, Emmanuelle, primary, Moulin, Jean-Francois, additional, Ginestier, Christophe, additional, Bechlian, Didier, additional, Conte, Nathalie, additional, Geneix, Jeannine, additional, Adelaide, Jose, additional, Noguchi, Tetsuro, additional, Hassoun, Jacques, additional, Jacquemier, Jocelyne, additional, and Birnbaum, Daniel, additional

Published
2002
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43. Distinct and Complementary Information Provided by Use of Tissue and DNA Microarrays in the Study of Breast Tumor Markers

Author

Ginestier, Christophe, primary, Charafe-Jauffret, Emmanuelle, additional, Bertucci, François, additional, Eisinger, François, additional, Geneix, Jeannine, additional, Bechlian, Didier, additional, Conte, Nathalie, additional, Adélaïde, José, additional, Toiron, Yves, additional, Nguyen, Catherine, additional, Viens, Patrice, additional, Mozziconacci, Marie-Joelle, additional, Houlgatte, Rémi, additional, Birnbaum, Daniel, additional, and Jacquemier, Jocelyne, additional

Published
2002
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44. Reciprocal translocations in breast tumor cell lines: Cloning of a t(3;20) that targets the FHIT gene

Author

Popovici, Cornel, primary, Basset, Céline, additional, Bertucci, François, additional, Orsetti, Béatrice, additional, Adélaide, José, additional, Mozziconacci, Marie‐Joëlle, additional, Conte, Nathalie, additional, Murati, Anne, additional, Ginestier, Christophe, additional, Charafe‐Jauffret, Emmanuelle, additional, Ethier, Stephen P., additional, Lafage‐Pochitaloff, Marina, additional, Theillet, Charles, additional, Birnbaum, Daniel, additional, and Chaffanet, Max, additional

Published
2002
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45. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium

Author

Meehan, Terrence F, Conte, Nathalie, West, David B, Jacobsen, Julius O, Mason, Jeremy, Warren, Jonathan, Chen, Chao-Kung, Tudose, Ilinca, Relac, Mike, Matthews, Peter, Karp, Natasha, Santos, Luis, Fiegel, Tanja, Ring, Natalie, Westerberg, Henrik, Greenaway, Simon, Sneddon, Duncan, Morgan, Hugh, Codner, Gemma F, Stewart, Michelle E, Brown, James, Horner, Neil, International Mouse Phenotyping Consortium, Haendel, Melissa, Washington, Nicole, Mungall, Christopher J, Reynolds, Corey L, Gallegos, Juan, Gailus-Durner, Valerie, Sorg, Tania, Pavlovic, Guillaume, Bower, Lynette R, Moore, Mark, Morse, Iva, Gao, Xiang, Tocchini-Valentini, Glauco P, Obata, Yuichi, Cho, Soo Young, Seong, Je Kyung, Seavitt, John, Beaudet, Arthur L, Dickinson, Mary E, Herault, Yann, Wurst, Wolfgang, De Angelis, Martin Hrabe, Lloyd, KC Kent, Flenniken, Ann M, Nutter, Lauryl MJ, Newbigging, Susan, McKerlie, Colin, Justice, Monica J, Murray, Stephen A, Svenson, Karen L, Braun, Robert E, White, Jacqueline K, Bradley, Allan, Flicek, Paul, Wells, Sara, Skarnes, William C, Adams, David J, Parkinson, Helen, Mallon, Ann-Marie, Brown, Steve DM, and Smedley, Damian

Subjects
Male, Mice, Knockout, Disease Models, Animal, Gene Knockout Techniques, Mice, Phenotype, Genetic Diseases, Inborn, Animals, Humans, Female, Genetic Predisposition to Disease, 3. Good health
Abstract

Although next-generation sequencing has revolutionized the ability to associate variants with human diseases, diagnostic rates and development of new therapies are still limited by a lack of knowledge of the functions and pathobiological mechanisms of most genes. To address this challenge, the International Mouse Phenotyping Consortium is creating a genome- and phenome-wide catalog of gene function by characterizing new knockout-mouse strains across diverse biological systems through a broad set of standardized phenotyping tests. All mice will be readily available to the biomedical community. Analyzing the first 3,328 genes identified models for 360 diseases, including the first models, to our knowledge, for type C Bernard-Soulier, Bardet-Biedl-5 and Gordon Holmes syndromes. 90% of our phenotype annotations were novel, providing functional evidence for 1,092 genes and candidates in genetically uncharacterized diseases including arrhythmogenic right ventricular dysplasia 3. Finally, we describe our role in variant functional validation with The 100,000 Genomes Project and others.

46. 10 Simple Rules For Design, Provision, And Reuse Of Persistent Identifiers For Life Science Data

Author

McMurry, Julie, Blomberg, Niklas, Burdett, Tony, Conte, Nathalie, Dumontier, Michel, Fellows, Donal K, Gonzalez-Beltran, Alejandra, Gormanns, Philipp, Hastings, Janna, Haendel, Melissa A, Hermjakob, Henning, Hériché, Jean-Karim, Ison, Jon C, Jimenez, Rafael C, Jupp, Simon, Juty, Nick, Laibe, Camille, Le Novère, Nicolas, Malone, James, Martin, Maria J, McEntyre, Johanna R, Morris, Chris, Muilu, Juha, Müller, Wolfgang, Mungall, Christopher J, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sariyar, Murat, Snoep, Jacky L, Stanford, Natalie J, Swainston, Neil, Washington, Nicole, Williams, Alan R, Wolstencroft, Katherine, Goble, Carole, and Parkinson, Helen

Subjects
Big data, Databases, Standards, Synthesis research, Identifier design, e-Science, Open science, Interoperability, Identifiers, Accessions, Reproducibility, 3. Good health
Abstract

In the life sciences, problems with identifiers impede the flow and integrity of information. This is especially challenging within “synthesis research” disciplines such as systems biology, translational medicine, and ecology. Implementation-driven initiatives such as ELIXIR, BD2K, and others have therefore been actively working to understand and address underlying problems with identifiers. Good, global-scale, persistent identifier design is harder than it appears, and is essential for data to be Findable, Accessible, Interoperable, and Reusable (Data FAIRport principles). Here, we build on emerging conventions and existing general recommendations and summarise the identifier characteristics most important to optimising the utility of life-science data. We propose actions to take in the identifier ‘green field’ and offer guidance for using real-world identifiers from diverse sources., ORCIDs corresponding to the authors are: http://orcid.org/0000-0002-9353-5498 http://orcid.org/0000-0003-4155-5910 http://orcid.org/0000-0002-2513-5396 http://orcid.org/0000-0002-1010-3121 http://orcid.org/0000-0003-4727-9435 http://orcid.org/0000-0002-9091-5938 http://orcid.org/0000-0003-3499-8262 http://orcid.org/0000-0001-9823-1621 http://orcid.org/0000-0002-3469-4923 http://orcid.org/0000-0001-9114-8737 http://orcid.org/0000-0001-8479-0262 http://orcid.org/0000-0001-6867-9425 http://orcid.org/0000-0001-6666-1520 http://orcid.org/0000-0001-5404-7670 http://orcid.org/0000-0002-0643-3144 http://orcid.org/0000-0002-2036-8350 http://orcid.org/0000-0002-4625-743X http://orcid.org/0000-0002-6309-7327 http://orcid.org/0000-0002-1615-2899 http://orcid.org/0000-0001-5454-2815 http://orcid.org/0000-0002-1611-6935 http://orcid.org/0000-0002-9533-5684 http://orcid.org/0000-0002-1034-5171 http://orcid.org/0000-0002-4980-3512 http://orcid.org/0000-0002-6601-2165 http://orcid.org/0000-0001-9853-5668 http://orcid.org/0000-0001-5306-5690 http://orcid.org/0000-0002-5595-689X http://orcid.org/0000-0002-0405-8854 http://orcid.org/0000-0003-4958-0184 http://orcid.org/0000-0001-7020-1236 http://orcid.org/0000-0001-8936-9143 http://orcid.org/0000-0003-3156-2105 http://orcid.org/0000-0002-1279-5133 http://orcid.org/0000-0003-1219-2137 http://orcid.org/0000-0003-3035-4195

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