Search

Your search keyword '"Navarro, J Daniel"' showing total 13 results
Start Over Author "Navarro, J Daniel"
13 results on '"Navarro, J Daniel"'

3. Human protein reference database as a discovery resource for proteomics

Author

Peri, Suraj, Navarro, J. Daniel, Kristiansen, Troels Z., Amanchy, Ramars, Surendranath, Vineeth, Muthusamy, Babylakshmi, Gandhi, T. K. B., Chandrika, K. N., Deshpande, Nandan, Suresh, Shubha, Rashmi, B. P., Shanker, K., Padma, N., Niranjan, Vidya, Harsha, H. C., Talreja, Naveen, Vrushabendra, B. M., Ramya, M. A., Yatish, A. J., Joy, Mary, Shivashankar, H. N., Kavitha, M. P., Menezes, Minal, Choudhury, Dipanwita Roy, Ghosh, Neelanjana, Saravana, R., Chandran, Sreenath, Mohan, Sujatha, Jonnalagadda, Chandra Kiran, Prasad, C. K., Kumar-Sinha, Chandan, Deshpande, Krishna S., and Pandey, Akhilesh

Published
2004

4. BioBuilder as a database development and functional annotation platform for proteins

Author

Jonnalagadda Chandra, Surendranath Vineeth, Padma N, Rashmi BP, Vrushabendra BM, Peri Suraj, Talreja Naveen, Navarro J Daniel, Kousthub PS, Deshpande Nandan, Shanker K, and Pandey Akhilesh

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. Results BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. Conclusions As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.

Published
2004
Full Text
View/download PDF

5. Development of Human Protein Preference Database as an initial platform for approaching systems biology in humans

Author

Peri, Suraj, Navarro, J. Daniel, Amanchy, Ramars, Kristiansen, Troels Z., Jonnalagadda, Chandra Kiran, Surendranath, Vineeth, Niranjan, Vidya, Muthusamy, Babylakshmi, Gandhi, T. K. B., Gronborg, Mads, Ibarrola, Nieves, Deshpande, Nandan, Shanker, K., Shivashankar, H. N., Rashmi, B. P., Ramya, M. A., Zhao, Zhixing, Chandrika, K. N., Padma, N., Harsha, H. C., Yatish, A. J., Kavitha, M. P., Menezes, Minal, Choudhury, Dipanwita Roy, Suresh, Shubha, Ghosh, Neelanjana, Saravana, R., Chandran, Sreenath, Krishna, Subhalakshmi, Joy, Mary, Anand, Sanjeev K., Madavan, V., Joseph, Ansamma, Wong, Guang W., Schiemann, William P., Constantinescu, Stefan N., Huang, Lily, Khosravi-Far, Roya, Steen, Hanno, Tewari, Muneesh, Ghaffari, Saghi, Blobe, Gerard C., Dang, Chi V., Garcia, Joe G. N., Pevsner, Jonathan, Jensen, Ole N., Roepstorff, Peter, Deshpande, Krishna S., Chinnaiyan, Arul M., Hamosh, Ada, Chakravarti, Aravinda, and Pandey, Alhilesh

Subjects
Methodology -- Analysis, Proteins -- Genetic aspects, Proteins -- Physiological aspects, Genomes -- Research, Genetic research -- Analysis, Health
Abstract

The authors describe the Human Protein Preference Database which integrates information relevant to human protein function in health and disease. They suggest that this database could be used in cataloging proteomic interactions and alterations to be discovered in postgenomic era.

Published
2003

6. BioBuilder as a database development and functional annotation platform for proteins

Author

Navarro, J. Daniel, Talreja, Naveen, Peri, Suraj, Vrushabendra, B. M., Rashmi, B. P., Padma, N., Surendranath, Vineeth, Jonnalagadda, Chandra Kiran, Kousthub, P. S., Deshpande, Nandan, Shanker, K., Pandey, Akhilesh, Universidad Pública de Navarra. Departamento de Automática y Computación, and Nafarroako Unibertsitate Publikoa. Automatika eta Konputazioa Saila

Subjects
Protein databases, BioBuilder
Abstract

UPNa. Departamento de Automática y Computación. Área de Ciencias de la Computación e Inteligencia Artificial. Background: The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. Results: BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. Conclusions: As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL

Published
2004

7. Development of human protein reference database as an initial platform for approaching systems biology in humans.

Author

UCL - SSS/DDUV - Institut de Duve, Peri, Suraj, Navarro, J Daniel, Amanchy, Ramars, Kristiansen, Troels Z, Jonnalagadda, Chandra Kiran, Surendranath, Vineeth, Niranjan, Vidya, Muthusamy, Babylakshmi, Gandhi, T K B, Gronborg, Mads, Ibarrola, Nieves, Deshpande, Nandan, Shanker, K, Shivashankar, H N, Rashmi, B P, Ramya, M A, Zhao, Zhixing, Chandrika, K N, Padma, N, Harsha, H C, Yatish, A J, Kavitha, M P, Menezes, Minal, Choudhury, Dipanwita Roy, Suresh, Shubha, Ghosh, Neelanjana, Saravana, R, Chandran, Sreenath, Krishna, Subhalakshmi, Joy, Mary, Anand, Sanjeev K, Madavan, V, Joseph, Ansamma, Wong, Guang W, Schiemann, William P, Constantinescu, Stefan N., Huang, Lily, Khosravi-Far, Roya, Steen, Hanno, Tewari, Muneesh, Ghaffari, Saghi, Blobe, Gerard C, Dang, Chi V, Garcia, Joe G N, Pevsner, Jonathan, Jensen, Ole N, Roepstorff, Peter, Deshpande, Krishna S, Chinnaiyan, Arul M, Hamosh, Ada, Chakravarti, Aravinda, Pandey, Akhilesh, UCL - SSS/DDUV - Institut de Duve, Peri, Suraj, Navarro, J Daniel, Amanchy, Ramars, Kristiansen, Troels Z, Jonnalagadda, Chandra Kiran, Surendranath, Vineeth, Niranjan, Vidya, Muthusamy, Babylakshmi, Gandhi, T K B, Gronborg, Mads, Ibarrola, Nieves, Deshpande, Nandan, Shanker, K, Shivashankar, H N, Rashmi, B P, Ramya, M A, Zhao, Zhixing, Chandrika, K N, Padma, N, Harsha, H C, Yatish, A J, Kavitha, M P, Menezes, Minal, Choudhury, Dipanwita Roy, Suresh, Shubha, Ghosh, Neelanjana, Saravana, R, Chandran, Sreenath, Krishna, Subhalakshmi, Joy, Mary, Anand, Sanjeev K, Madavan, V, Joseph, Ansamma, Wong, Guang W, Schiemann, William P, Constantinescu, Stefan N., Huang, Lily, Khosravi-Far, Roya, Steen, Hanno, Tewari, Muneesh, Ghaffari, Saghi, Blobe, Gerard C, Dang, Chi V, Garcia, Joe G N, Pevsner, Jonathan, Jensen, Ole N, Roepstorff, Peter, Deshpande, Krishna S, Chinnaiyan, Arul M, Hamosh, Ada, Chakravarti, Aravinda, and Pandey, Akhilesh

Abstract

Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.

Published
2003

8. Human Proteinpedia enables sharing of human protein data

Author

Mathivanan, Suresh, primary, Ahmed, Mukhtar, additional, Ahn, Natalie G, additional, Alexandre, Hainard, additional, Amanchy, Ramars, additional, Andrews, Philip C, additional, Bader, Joel S, additional, Balgley, Brian M, additional, Bantscheff, Marcus, additional, Bennett, Keiryn L, additional, Björling, Erik, additional, Blagoev, Blagoy, additional, Bose, Ron, additional, Brahmachari, Samir K, additional, Burlingame, Alma S, additional, Bustelo, Xosé R, additional, Cagney, Gerard, additional, Cantin, Greg T, additional, Cardasis, Helene L, additional, Celis, Julio E, additional, Chaerkady, Raghothama, additional, Chu, Feixia, additional, Cole, Philip A, additional, Costello, Catherine E, additional, Cotter, Robert J, additional, Crockett, David, additional, DeLany, James P, additional, De Marzo, Angelo M, additional, DeSouza, Leroi V, additional, Deutsch, Eric W, additional, Dransfield, Eric, additional, Drewes, Gerard, additional, Droit, Arnaud, additional, Dunn, Michael J, additional, Elenitoba-Johnson, Kojo, additional, Ewing, Rob M, additional, Eyk, Jennifer Van, additional, Faca, Vitor, additional, Falkner, Jayson, additional, Fang, Xiangming, additional, Fenselau, Catherine, additional, Figeys, Daniel, additional, Gagné, Pierre, additional, Gelfi, Cecilia, additional, Gevaert, Kris, additional, Gimble, Jeffrey M, additional, Gnad, Florian, additional, Goel, Renu, additional, Gromov, Pavel, additional, Hanash, Samir M, additional, Hancock, William S, additional, Harsha, HC, additional, Hart, Gerald, additional, Hays, Faith, additional, He, Fuchu, additional, Hebbar, Prashantha, additional, Helsens, Kenny, additional, Hermeking, Heiko, additional, Hide, Winston, additional, Hjernø, Karin, additional, Hochstrasser, Denis F, additional, Hofmann, Oliver, additional, Horn, David M, additional, Hruban, Ralph H, additional, Ibarrola, Nieves, additional, James, Peter, additional, Jensen, Ole N, additional, Jensen, Pia Hønnerup, additional, Jung, Peter, additional, Kandasamy, Kumaran, additional, Kheterpal, Indu, additional, Kikuno, Reiko F, additional, Korf, Ulrike, additional, Körner, Roman, additional, Kuster, Bernhard, additional, Kwon, Min-Seok, additional, Lee, Hyoung-Joo, additional, Lee, Young-Jin, additional, Lefevre, Michael, additional, Lehvaslaiho, Minna, additional, Lescuyer, Pierre, additional, Levander, Fredrik, additional, Lim, Megan S, additional, Löbke, Christian, additional, Loo, Joseph A, additional, Mann, Matthias, additional, Martens, Lennart, additional, Martinez-Heredia, Juan, additional, McComb, Mark, additional, McRedmond, James, additional, Mehrle, Alexander, additional, Menon, Rajasree, additional, Miller, Christine A, additional, Mischak, Harald, additional, Mohan, S Sujatha, additional, Mohmood, Riaz, additional, Molina, Henrik, additional, Moran, Michael F, additional, Morgan, James D, additional, Moritz, Robert, additional, Morzel, Martine, additional, Muddiman, David C, additional, Nalli, Anuradha, additional, Navarro, J Daniel, additional, Neubert, Thomas A, additional, Ohara, Osamu, additional, Oliva, Rafael, additional, Omenn, Gilbert S, additional, Oyama, Masaaki, additional, Paik, Young-Ki, additional, Pennington, Kyla, additional, Pepperkok, Rainer, additional, Periaswamy, Balamurugan, additional, Petricoin, Emanuel F, additional, Poirier, Guy G, additional, Prasad, T S Keshava, additional, Purvine, Samuel O, additional, Rahiman, B Abdul, additional, Ramachandran, Prasanna, additional, Ramachandra, Y L, additional, Rice, Robert H, additional, Rick, Jens, additional, Ronnholm, Ragna H, additional, Salonen, Johanna, additional, Sanchez, Jean-Charles, additional, Sayd, Thierry, additional, Seshi, Beerelli, additional, Shankari, Kripa, additional, Sheng, Shi Jun, additional, Shetty, Vivekananda, additional, Shivakumar, K, additional, Simpson, Richard J, additional, Sirdeshmukh, Ravi, additional, Michael Siu, K W, additional, Smith, Jeffrey C, additional, Smith, Richard D, additional, States, David J, additional, Sugano, Sumio, additional, Sullivan, Matthew, additional, Superti-Furga, Giulio, additional, Takatalo, Maarit, additional, Thongboonkerd, Visith, additional, Trinidad, Jonathan C, additional, Uhlen, Mathias, additional, Vandekerckhove, Joël, additional, Vasilescu, Julian, additional, Veenstra, Timothy D, additional, Vidal-Taboada, José-Manuel, additional, Vihinen, Mauno, additional, Wait, Robin, additional, Wang, Xiaoyue, additional, Wiemann, Stefan, additional, Wu, Billy, additional, Xu, Tao, additional, Yates, John R, additional, Zhong, Jun, additional, Zhou, Ming, additional, Zhu, Yunping, additional, Zurbig, Petra, additional, and Pandey, Akhilesh, additional

Published
2008
Full Text
View/download PDF

10. Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans

Author

Peri, Suraj, primary, Navarro, J. Daniel, additional, Amanchy, Ramars, additional, Kristiansen, Troels Z., additional, Jonnalagadda, Chandra Kiran, additional, Surendranath, Vineeth, additional, Niranjan, Vidya, additional, Muthusamy, Babylakshmi, additional, Gandhi, T.K.B., additional, Gronborg, Mads, additional, Ibarrola, Nieves, additional, Deshpande, Nandan, additional, Shanker, K., additional, Shivashankar, H.N., additional, Rashmi, B.P., additional, Ramya, M.A., additional, Zhao, Zhixing, additional, Chandrika, K.N., additional, Padma, N., additional, Harsha, H.C., additional, Yatish, A.J., additional, Kavitha, M.P., additional, Menezes, Minal, additional, Choudhury, Dipanwita Roy, additional, Suresh, Shubha, additional, Ghosh, Neelanjana, additional, Saravana, R., additional, Chandran, Sreenath, additional, Krishna, Subhalakshmi, additional, Joy, Mary, additional, Anand, Sanjeev K., additional, Madavan, V., additional, Joseph, Ansamma, additional, Wong, Guang W., additional, Schiemann, William P., additional, Constantinescu, Stefan N., additional, Huang, Lily, additional, Khosravi-Far, Roya, additional, Steen, Hanno, additional, Tewari, Muneesh, additional, Ghaffari, Saghi, additional, Blobe, Gerard C., additional, Dang, Chi V., additional, Garcia, Joe G.N., additional, Pevsner, Jonathan, additional, Jensen, Ole N., additional, Roepstorff, Peter, additional, Deshpande, Krishna S., additional, Chinnaiyan, Arul M., additional, Hamosh, Ada, additional, Chakravarti, Aravinda, additional, and Pandey, Akhilesh, additional

Published
2003
Full Text
View/download PDF

11. Human Proteinpedia enables sharing of human protein data

Author

Mathivanan, Suresh, Ahmed, Mukhtar, Ahn, Natalie G, Alexandre, Hainard, Amanchy, Ramars, Andrews, Philip C, Bader, Joel S, Balgley, Brian M, Bantscheff, Marcus, Bennett, Keiryn L, Björling, Erik, Blagoev, Blagoy, Bose, Ron, Brahmachari, Samir K, Burlingame, Alma S, Bustelo, Xosé R, Cagney, Gerard, Cantin, Greg T, Cardasis, Helene L, Celis, Julio E, Chaerkady, Raghothama, Chu, Feixia, Cole, Philip A, Costello, Catherine E, Cotter, Robert J, Crockett, David, DeLany, James P, De Marzo, Angelo M, DeSouza, Leroi V, Deutsch, Eric W, Dransfield, Eric, Drewes, Gerard, Droit, Arnaud, Dunn, Michael J, Elenitoba-Johnson, Kojo, Ewing, Rob M, Eyk, Jennifer Van, Faca, Vitor, Falkner, Jayson, Fang, Xiangming, Fenselau, Catherine, Figeys, Daniel, Gagné, Pierre, Gelfi, Cecilia, Gevaert, Kris, Gimble, Jeffrey M, Gnad, Florian, Goel, Renu, Gromov, Pavel, Hanash, Samir M, Hancock, William S, Harsha, HC, Hart, Gerald, Hays, Faith, He, Fuchu, Hebbar, Prashantha, Helsens, Kenny, Hermeking, Heiko, Hide, Winston, Hjernø, Karin, Hochstrasser, Denis F, Hofmann, Oliver, Horn, David M, Hruban, Ralph H, Ibarrola, Nieves, James, Peter, Jensen, Ole N, Jensen, Pia Hønnerup, Jung, Peter, Kandasamy, Kumaran, Kheterpal, Indu, Kikuno, Reiko F, Korf, Ulrike, Körner, Roman, Kuster, Bernhard, Kwon, Min-Seok, Lee, Hyoung-Joo, Lee, Young-Jin, Lefevre, Michael, Lehvaslaiho, Minna, Lescuyer, Pierre, Levander, Fredrik, Lim, Megan S, Löbke, Christian, Loo, Joseph A, Mann, Matthias, Martens, Lennart, Martinez-Heredia, Juan, McComb, Mark, McRedmond, James, Mehrle, Alexander, Menon, Rajasree, Miller, Christine A, Mischak, Harald, Mohan, S Sujatha, Mohmood, Riaz, Molina, Henrik, Moran, Michael F, Morgan, James D, Moritz, Robert, Morzel, Martine, Muddiman, David C, Nalli, Anuradha, Navarro, J Daniel, Neubert, Thomas A, Ohara, Osamu, Oliva, Rafael, Omenn, Gilbert S, Oyama, Masaaki, Paik, Young-Ki, Pennington, Kyla, Pepperkok, Rainer, Periaswamy, Balamurugan, Petricoin, Emanuel F, Poirier, Guy G, Prasad, T S Keshava, Purvine, Samuel O, Rahiman, B Abdul, Ramachandran, Prasanna, Ramachandra, Y L, Rice, Robert H, Rick, Jens, Ronnholm, Ragna H, Salonen, Johanna, Sanchez, Jean-Charles, Sayd, Thierry, Seshi, Beerelli, Shankari, Kripa, Sheng, Shi Jun, Shetty, Vivekananda, Shivakumar, K, Simpson, Richard J, Sirdeshmukh, Ravi, Michael Siu, K W, Smith, Jeffrey C, Smith, Richard D, States, David J, Sugano, Sumio, Sullivan, Matthew, Superti-Furga, Giulio, Takatalo, Maarit, Thongboonkerd, Visith, Trinidad, Jonathan C, Uhlen, Mathias, Vandekerckhove, Joël, Vasilescu, Julian, Veenstra, Timothy D, Vidal-Taboada, José-Manuel, Vihinen, Mauno, Wait, Robin, Wang, Xiaoyue, Wiemann, Stefan, Wu, Billy, Xu, Tao, Yates, John R, Zhong, Jun, Zhou, Ming, Zhu, Yunping, Zurbig, Petra, Pandey, Akhilesh, Mathivanan, Suresh, Ahmed, Mukhtar, Ahn, Natalie G, Alexandre, Hainard, Amanchy, Ramars, Andrews, Philip C, Bader, Joel S, Balgley, Brian M, Bantscheff, Marcus, Bennett, Keiryn L, Björling, Erik, Blagoev, Blagoy, Bose, Ron, Brahmachari, Samir K, Burlingame, Alma S, Bustelo, Xosé R, Cagney, Gerard, Cantin, Greg T, Cardasis, Helene L, Celis, Julio E, Chaerkady, Raghothama, Chu, Feixia, Cole, Philip A, Costello, Catherine E, Cotter, Robert J, Crockett, David, DeLany, James P, De Marzo, Angelo M, DeSouza, Leroi V, Deutsch, Eric W, Dransfield, Eric, Drewes, Gerard, Droit, Arnaud, Dunn, Michael J, Elenitoba-Johnson, Kojo, Ewing, Rob M, Eyk, Jennifer Van, Faca, Vitor, Falkner, Jayson, Fang, Xiangming, Fenselau, Catherine, Figeys, Daniel, Gagné, Pierre, Gelfi, Cecilia, Gevaert, Kris, Gimble, Jeffrey M, Gnad, Florian, Goel, Renu, Gromov, Pavel, Hanash, Samir M, Hancock, William S, Harsha, HC, Hart, Gerald, Hays, Faith, He, Fuchu, Hebbar, Prashantha, Helsens, Kenny, Hermeking, Heiko, Hide, Winston, Hjernø, Karin, Hochstrasser, Denis F, Hofmann, Oliver, Horn, David M, Hruban, Ralph H, Ibarrola, Nieves, James, Peter, Jensen, Ole N, Jensen, Pia Hønnerup, Jung, Peter, Kandasamy, Kumaran, Kheterpal, Indu, Kikuno, Reiko F, Korf, Ulrike, Körner, Roman, Kuster, Bernhard, Kwon, Min-Seok, Lee, Hyoung-Joo, Lee, Young-Jin, Lefevre, Michael, Lehvaslaiho, Minna, Lescuyer, Pierre, Levander, Fredrik, Lim, Megan S, Löbke, Christian, Loo, Joseph A, Mann, Matthias, Martens, Lennart, Martinez-Heredia, Juan, McComb, Mark, McRedmond, James, Mehrle, Alexander, Menon, Rajasree, Miller, Christine A, Mischak, Harald, Mohan, S Sujatha, Mohmood, Riaz, Molina, Henrik, Moran, Michael F, Morgan, James D, Moritz, Robert, Morzel, Martine, Muddiman, David C, Nalli, Anuradha, Navarro, J Daniel, Neubert, Thomas A, Ohara, Osamu, Oliva, Rafael, Omenn, Gilbert S, Oyama, Masaaki, Paik, Young-Ki, Pennington, Kyla, Pepperkok, Rainer, Periaswamy, Balamurugan, Petricoin, Emanuel F, Poirier, Guy G, Prasad, T S Keshava, Purvine, Samuel O, Rahiman, B Abdul, Ramachandran, Prasanna, Ramachandra, Y L, Rice, Robert H, Rick, Jens, Ronnholm, Ragna H, Salonen, Johanna, Sanchez, Jean-Charles, Sayd, Thierry, Seshi, Beerelli, Shankari, Kripa, Sheng, Shi Jun, Shetty, Vivekananda, Shivakumar, K, Simpson, Richard J, Sirdeshmukh, Ravi, Michael Siu, K W, Smith, Jeffrey C, Smith, Richard D, States, David J, Sugano, Sumio, Sullivan, Matthew, Superti-Furga, Giulio, Takatalo, Maarit, Thongboonkerd, Visith, Trinidad, Jonathan C, Uhlen, Mathias, Vandekerckhove, Joël, Vasilescu, Julian, Veenstra, Timothy D, Vidal-Taboada, José-Manuel, Vihinen, Mauno, Wait, Robin, Wang, Xiaoyue, Wiemann, Stefan, Wu, Billy, Xu, Tao, Yates, John R, Zhong, Jun, Zhou, Ming, Zhu, Yunping, Zurbig, Petra, and Pandey, Akhilesh

Abstract

Proteomic technologies, such as yeast two-hybrid, mass spectrometry (MS), protein/peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories.

12. NetPath: a public resource of curated signal transduction pathways

Author

Kandasamy, Kumaran, Mohan, S Sujatha, Raju, Rajesh, Keerthikumar, Shivakumar, Kumar, Ghantasala, Venugopal, Abhilash, Telikicherla, Deepthi, Navarro, J Daniel, Mathivanan, Suresh, Pecquet, Christian, Gollapudi, Sashi, Tattikota, Sudhir, Mohan, Shyam, Padhukasahasram, Hariprasad, Subbannayya, Yashwanth, Goel, Renu, Jacob, Harrys, Zhong, Jun, Sekhar, Raja, Nanjappa, Vishalakshi, Balakrishnan, Lavanya, Subbaiah, Roopashree, Ramachandra, YL, Rahiman, B Abdul, Prasad, TS Keshava, Lin, Jian-Xin, Houtman, Jon, Desiderio, Stephen, Renauld, Jean-Christophe, Constantinescu, Stefan, Ohara, Osamu, Hirano, Toshio, Kubo, Masato, Singh, Sujay, Khatri, Purvesh, Draghici, Sorin, Bader, Gary, Sander, Chris, Leonard, Warren, and Pandey, Akhilesh

Abstract

We have developed NetPath as a resource of curated human signaling pathways. As an initial step, NetPath provides detailed maps of a number of immune signaling pathways, which include approximately 1,600 reactions annotated from the literature and more than 2,800 instances of transcriptionally regulated genes - all linked to over 5,500 published articles. We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches.

Published
2010
Full Text
View/download PDF

13. From biological databases to platforms for biomedical discovery.

Author

Navarro JD, Niranjan V, Peri S, Jonnalagadda CK, and Pandey A

Subjects
Biomedical Engineering methods, Computational Biology methods, Databases, Nucleic Acid, Databases, Protein, Internet, Algorithms, Database Management Systems, Databases, Factual, Documentation, Information Storage and Retrieval methods
Abstract

The use of high-throughput DNA sequencing and proteomic methods has led to an unprecedented increase in the amount of genomic and proteomic data. Application of computing technologies and development of computational tools to analyze and present these data has not kept pace with the accumulation of information. Here, we discuss the use of different database systems to store biological information and mention some of the key emerging computing technologies that are likely to have a key role in the future of bioinformatics.

Published
2003
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results