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6. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

Author

Sivade (Dumousseau), M., Alonso-López, D., Ammari, M., Bradley, G., Campbell, N. H., Ceol, A., Cesareni, G., Combe, C., De Las Rivas, J., del-Toro, N., Heimbach, J., Hermjakob, H., Jurisica, I., Koch, M., Licata, L., Lovering, R. C., Lynn, D. J., Meldal, B. H. M., Micklem, G., Panni, S., Porras, P., Ricard-Blum, S., Roechert, B., Salwinski, L., Shrivastava, A., Sullivan, J., Thierry-Mieg, N., Yehudi, Y., Van Roey, K., and Orchard, S.

Published
2018
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7. An open invitation to the Understudied Proteins Initiative

Author

Kustatscher, G., Collins, T., Gingras, A. -C, Guo, T., Hermjakob, H., Ideker, T., Lilley, K. S., Lundberg, Emma, Marcotte, E. M., Ralser, M., Rappsilber, J., Kustatscher, G., Collins, T., Gingras, A. -C, Guo, T., Hermjakob, H., Ideker, T., Lilley, K. S., Lundberg, Emma, Marcotte, E. M., Ralser, M., and Rappsilber, J.

Abstract

QC 20230213

Published
2022
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9. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms (vol 17, e10387, 2021)

Author

Ostaszewski, M, Niarakis, A, Mazein, A, Kuperstein, I, Phair, R, Orta-Resendiz, A, Singh, V, Aghamiri, S, Acencio, M, Glaab, E, Ruepp, A, Fobo, G, Montrone, C, Brauner, B, Frishman, G, Gomez, L, Somers, J, Hoch, M, Gupta, S, Scheel, J, Borlinghaus, H, Czauderna, T, Schreiber, F, Montagud, A, de Leon, M, Funahashi, A, Hiki, Y, Hiroi, N, Yamada, T, Drager, A, Renz, A, Naveez, M, Bocskei, Z, Messina, F, Bornigen, D, Fergusson, L, Conti, M, Rameil, M, Nakonecnij, V, Vanhoefer, J, Schmiester, L, Wang, M, Ackerman, E, Shoemaker, J, Zucker, J, Oxford, K, Teuton, J, Kocakaya, E, Summak, G, Hanspers, K, Kutmon, M, Coort, S, Eijssen, L, Ehrhart, F, Rex, D, Slenter, D, Martens, M, Pham, N, Haw, R, Jassal, B, Matthews, L, Orlic-Milacic, M, Senff-Ribeiro, A, Rothfels, K, Shamovsky, V, Stephan, R, Sevilla, C, Varusai, T, Ravel, J, Fraser, R, Ortseifen, V, Marchesi, S, Gawron, P, Smula, E, Heirendt, L, Satagopam, V, Gm, W, Riutta, A, Golebiewski, M, Owen, S, Goble, C, Xm, H, Overall, R, Maier, D, Bauch, A, Gyori, B, Bachman, J, Vega, C, Groues, V, Vazquez, M, Porras, P, Licata, L, Iannuccelli, M, Sacco, F, Nesterova, A, Yuryev, A, de Waard, A, Turei, D, Luna, A, Babur, O, Soliman, S, Valdeolivas, A, Esteban-Medina, M, Pena-Chilet, M, Rian, K, Helikar, T, Puniya, B, Modos, D, Treveil, A, Olbei, M, De Meulder, B, Ballereau, S, Dugourd, A, Naldi, A, Noel, V, Calzone, L, Sander, C, Demir, E, Korcsmaros, T, Freeman, T, Auge, F, Beckmann, J, Hasenauer, J, Wolkenhauer, O, Willighagen, E, Pico, A, Evelo, C, Gillespie, M, Stein, L, Hermjakob, H, D'Eustachio, P, Saez-Rodriguez, J, Dopazo, J, Valencia, A, Kitano, H, Barillot, E, Auffray, C, Balling, R, and Schneider, R

Subjects
Settore BIO/18, Settore BIO/11
Published
2021

11. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.

Author

Ostaszewski, Marek, Mazein, Alexander, Gillespie, ME, Kuperstein, I, Niarakis, A, Hermjakob, H, Pico, AR, Willinghagen, EL, Evelo, CT, Hasenauer, J, Schreiber, F, Dräger, A, Demir, E, Wolkenhauer, O, Furlong, LI, Barillot, E, Dopazo, J, Orta-Resendiz, A, Messina, F, Valencia, A, Funahashi, A, Kitano, H, Auffray, C, Balling, Rudolf, Schneider, Reinhard, Ostaszewski, Marek, Mazein, Alexander, Gillespie, ME, Kuperstein, I, Niarakis, A, Hermjakob, H, Pico, AR, Willinghagen, EL, Evelo, CT, Hasenauer, J, Schreiber, F, Dräger, A, Demir, E, Wolkenhauer, O, Furlong, LI, Barillot, E, Dopazo, J, Orta-Resendiz, A, Messina, F, Valencia, A, Funahashi, A, Kitano, H, Auffray, C, Balling, Rudolf, and Schneider, Reinhard

Published
2020

12. SBML Level 3: an extensible format for the exchange and reuse of biological models

Author

Keating, S, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C, Bergmann, F, Finney, A, Gillespie, C, Helikar, T, Hoops, S, Malik-Sheriff, R, Moodie, S, Moraru, I, Myers, C, Naldi, A, Olivier, B, Sahle, S, Schaff, J, Smith, L, Swat, M, Thieffry, D, Watanabe, L, Wilkinson, D, Blinov, M, Begley, K, Faeder, J, Gómez, H, Hamm, T, Inagaki, Y, Liebermeister, W, Lister, A, Lucio, D, Mjolsness, E, Proctor, C, Raman, K, Rodriguez, N, Shaffer, C, Shapiro, B, Stelling, J, Swainston, N, Tanimura, N, Wagner, J, Meier-Schellersheim, M, Sauro, H, Palsson, B, Bolouri, H, Kitano, H, Funahashi, A, Hermjakob, H, Doyle, J, Hucka, M, Adams, R, Allen, N, Angermann, B, Antoniotti, M, Bader, G, Červený, J, Courtot, M, Cox, C, Dalle Pezze, P, Demir, E, Denney, W, Dharuri, H, Dorier, J, Drasdo, D, Ebrahim, A, Eichner, J, Elf, J, Endler, L, Evelo, C, Flamm, C, Fleming, R, Fröhlich, M, Glont, M, Gonçalves, E, Golebiewski, M, Grabski, H, Gutteridge, A, Hachmeister, D, Harris, L, Heavner, B, Henkel, R, Hlavacek, W, Hu, B, Hyduke, D, Jong, H, Juty, N, Karp, P, Karr, J, Kell, D, Keller, R, Kiselev, I, Klamt, S, Klipp, E, Knüpfer, C, Kolpakov, F, Krause, F, Kutmon, M, Laibe, C, Lawless, C, Li, L, Loew, L, Machne, R, Matsuoka, Y, Mendes, P, Mi, H, Mittag, F, Monteiro, P, Natarajan, K, Nielsen, P, Nguyen, T, Palmisano, A, Jean-Baptiste, P, Pfau, T, Phair, R, Radivoyevitch, T, Rohwer, J, Ruebenacker, O, Saez-Rodriguez, J, Scharm, M, Schmidt, H, Schreiber, F, Schubert, M, Schulte, R, Sealfon, S, Smallbone, K, Soliman, S, Stefan, M, Sullivan, D, Takahashi, K, Teusink, B, Tolnay, D, Vazirabad, I, Kamp, A, Wittig, U, Wrzodek, C, Wrzodek, F, Xenarios, I, Zhukova, A, Zucker, J, Keating, SM, Bergmann, FT, Gillespie, CS, Malik-Sheriff, RS, Moodie, SL, Moraru, II, Myers, CJ, Olivier, BG, Schaff, JC, Smith, LP, Swat, MJ, Wilkinson, DJ, Blinov, ML, Faeder, JR, Gómez, HF, Hamm, TM, Lister, AL, Proctor, CJ, Shaffer, CA, Shapiro, BE, Sauro, HM, Doyle, JC, Adams, RR, Allen, NA, Angermann, BR, Bader, GD, Cox, CD, Denney, WS, Evelo, CT, Fleming, RM, Harris, LA, Heavner, BD, Hlavacek, WS, Hyduke, DR, Karp, PD, Karr, JR, Kell, DB, Loew, LM, Monteiro, PT, Natarajan, KN, Nielsen, PM, Phair, RD, Rohwer, JM, Ruebenacker, OA, Sealfon, SC, Stefan, MI, Sullivan, DP, Keating, S, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C, Bergmann, F, Finney, A, Gillespie, C, Helikar, T, Hoops, S, Malik-Sheriff, R, Moodie, S, Moraru, I, Myers, C, Naldi, A, Olivier, B, Sahle, S, Schaff, J, Smith, L, Swat, M, Thieffry, D, Watanabe, L, Wilkinson, D, Blinov, M, Begley, K, Faeder, J, Gómez, H, Hamm, T, Inagaki, Y, Liebermeister, W, Lister, A, Lucio, D, Mjolsness, E, Proctor, C, Raman, K, Rodriguez, N, Shaffer, C, Shapiro, B, Stelling, J, Swainston, N, Tanimura, N, Wagner, J, Meier-Schellersheim, M, Sauro, H, Palsson, B, Bolouri, H, Kitano, H, Funahashi, A, Hermjakob, H, Doyle, J, Hucka, M, Adams, R, Allen, N, Angermann, B, Antoniotti, M, Bader, G, Červený, J, Courtot, M, Cox, C, Dalle Pezze, P, Demir, E, Denney, W, Dharuri, H, Dorier, J, Drasdo, D, Ebrahim, A, Eichner, J, Elf, J, Endler, L, Evelo, C, Flamm, C, Fleming, R, Fröhlich, M, Glont, M, Gonçalves, E, Golebiewski, M, Grabski, H, Gutteridge, A, Hachmeister, D, Harris, L, Heavner, B, Henkel, R, Hlavacek, W, Hu, B, Hyduke, D, Jong, H, Juty, N, Karp, P, Karr, J, Kell, D, Keller, R, Kiselev, I, Klamt, S, Klipp, E, Knüpfer, C, Kolpakov, F, Krause, F, Kutmon, M, Laibe, C, Lawless, C, Li, L, Loew, L, Machne, R, Matsuoka, Y, Mendes, P, Mi, H, Mittag, F, Monteiro, P, Natarajan, K, Nielsen, P, Nguyen, T, Palmisano, A, Jean-Baptiste, P, Pfau, T, Phair, R, Radivoyevitch, T, Rohwer, J, Ruebenacker, O, Saez-Rodriguez, J, Scharm, M, Schmidt, H, Schreiber, F, Schubert, M, Schulte, R, Sealfon, S, Smallbone, K, Soliman, S, Stefan, M, Sullivan, D, Takahashi, K, Teusink, B, Tolnay, D, Vazirabad, I, Kamp, A, Wittig, U, Wrzodek, C, Wrzodek, F, Xenarios, I, Zhukova, A, Zucker, J, Keating, SM, Bergmann, FT, Gillespie, CS, Malik-Sheriff, RS, Moodie, SL, Moraru, II, Myers, CJ, Olivier, BG, Schaff, JC, Smith, LP, Swat, MJ, Wilkinson, DJ, Blinov, ML, Faeder, JR, Gómez, HF, Hamm, TM, Lister, AL, Proctor, CJ, Shaffer, CA, Shapiro, BE, Sauro, HM, Doyle, JC, Adams, RR, Allen, NA, Angermann, BR, Bader, GD, Cox, CD, Denney, WS, Evelo, CT, Fleming, RM, Harris, LA, Heavner, BD, Hlavacek, WS, Hyduke, DR, Karp, PD, Karr, JR, Kell, DB, Loew, LM, Monteiro, PT, Natarajan, KN, Nielsen, PM, Phair, RD, Rohwer, JM, Ruebenacker, OA, Sealfon, SC, Stefan, MI, and Sullivan, DP

Abstract

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

Published
2020

14. The IMEx coronavirus interactome: an evolving map ofCoronaviridae–host molecular interactions

Author

Perfetto, L, primary, Pastrello, C, additional, del-Toro, N, additional, Duesbury, M, additional, Iannuccelli, M, additional, Kotlyar, M, additional, Licata, L, additional, Meldal, B, additional, Panneerselvam, K, additional, Panni, S, additional, Rahimzadeh, N, additional, Ricard-Blum, S, additional, Salwinski, L, additional, Shrivastava, A, additional, Cesareni, G, additional, Pellegrini, M, additional, Orchard, S, additional, Jurisica, I, additional, Hermjakob, H, additional, and Porras, P, additional

Published
2020
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16. The IntAct molecular interaction database in 2010

Author

Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A. T., Kerrien, S., Khadake, J., Kerssemakers, J., Leroy, C., Menden, M., Michaut, M., Montecchi-Palazzi, L., Neuhauser, S. N., Orchard, S., Perreau, V., Roechert, B., van Eijk, K., and Hermjakob, H.

Published
2010
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17. Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

Author

del-Toro, N, Duesbury, M, Koch, M, Perfetto, L, Shrivastava, A, Ochoa, D, Wagih, O, Pinero, J, Kotlyar, M, Pastrello, C, Beltrao, P, Furlong, Li, Jurisica, I, Hermjakob, H, Orchard, S, Porras, P, Khadake, J, Meldal, B, Panni, S, Thorneycroft, D, van Roey, K, Abbani, S, Salwinski, L, Pellegrini, M, Iannuccelli, M, Licata, L, Cesareni, G, Roechert, B, Bridge, A, Ammari, Mg, Mccarthy, F, Broackes-Carter, F, Campbell, Nh, Melidoni, An, Rodriguez-Lopez, M, Lovering, Rc, Jagannathan, S, Chen, C, Lynn, Dj, Ricard-Blum, S, Mahadevan, U, Raghunath, A, Institute of Experimental Physics [Graz], Graz University of Technology [Graz] (TU Graz), Institut de Physique Nucléaire d'Orsay (IPNO), Université Paris-Sud - Paris 11 (UP11)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Universidad de Salamanca, and Dpto. Ciencias de los Materiales, Universidad de Cadiz, Spain

Subjects
0301 basic medicine, Nonsynonymous substitution, Computer science, Science, General Physics and Astronomy, 02 engineering and technology, Variation (game tree), Computational biology, Genoma humà, General Biochemistry, Genetics and Molecular Biology, Protein–protein interaction, 03 medical and health sciences, Genetic variation, Animals, Humans, Point Mutation, Disease, Dinàmica molecular, Protein Interaction Maps, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Sequence (medicine), Multidisciplinary, Settore BIO/18, Genetic Variation, Molecular Sequence Annotation, General Chemistry, 021001 nanoscience & nanotechnology, Publisher Correction, Phenotype, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Data set, 030104 developmental biology, Amino Acid Substitution, lcsh:Q, 0210 nano-technology
Abstract

The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release., Nature Communications, 10 (1), ISSN:2041-1723

Published
2019
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18. IntAct—open source resource for molecular interaction data

Author

Kerrien, S., Alam-Faruque, Y., Aranda, B., Bancarz, I., Bridge, A., Derow, C., Dimmer, E., Feuermann, M., Friedrichsen, A., Huntley, R., Kohler, C., Khadake, J., Leroy, C., Liban, A., Lieftink, C., Montecchi-Palazzi, L., Orchard, S., Risse, J., Robbe, K., Roechert, B., Thorneycroft, D., Zhang, Y., Apweiler, R., and Hermjakob, H.

Published
2007

19. CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination

Author

Perfetto, L, primary, Acencio, M L, additional, Bradley, G, additional, Cesareni, G, additional, Del Toro, N, additional, Fazekas, D, additional, Hermjakob, H, additional, Korcsmaros, T, additional, Kuiper, M, additional, Lægreid, A, additional, Lo Surdo, P, additional, Lovering, R C, additional, Orchard, S, additional, Porras, P, additional, Thomas, P D, additional, Touré, V, additional, Zobolas, J, additional, and Licata, L, additional

Published
2019
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20. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

Author

Deutsch, E.W., Orchard, S., Binz, P.A., Bittremieux, W., Eisenacher, M., Hermjakob, H., Kawano, S., Lam, H., Mayer, G., Menschaert, G., Perez-Riverol, Y., Salek, R.M., Tabb, D.L., Tenzer, S., Vizcaíno, J.A., Walzer, M., and Jones, A.R.

Subjects
bioinformatics software, data standard, database, mass spectrometry, metabolomics, molecular interactions, protein identification, protein quantification, proteomics, quality control
Abstract

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.

Published
2017

21. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

Author

Biotechnology and Biological Sciences Research Council (UK), European Commission, Ontario Research Fund, Canada Research Chairs, Fondation pour la Recherche Médicale, British Heart Foundation, European Research Council, Wellcome Trust, National Institutes of Health (US), Sivade (Dumousseau), M., Alonso-López, D., Ammari, M., Bradley, G., Campbell, N. H, Ceol, A., Cesareni, G., Combe, C. W., De Las Rivas, Javier, Toro, N. del, Heimbach, J., Hermjakob, H., Jurisica, I., Koch, M., Licata, L., Lovering, R. C., Lynn, D. J., Meldal, B. H. M., Micklem, G., Panni, S., Porras, P., Ricard-Blum, S., Roechert, B., Salwinski, L., Shrivastava, A., Sullivan, J., Thierry-Mieg, N., Yehudi, Y., Van Roey, K., Orchard, S., Biotechnology and Biological Sciences Research Council (UK), European Commission, Ontario Research Fund, Canada Research Chairs, Fondation pour la Recherche Médicale, British Heart Foundation, European Research Council, Wellcome Trust, National Institutes of Health (US), Sivade (Dumousseau), M., Alonso-López, D., Ammari, M., Bradley, G., Campbell, N. H, Ceol, A., Cesareni, G., Combe, C. W., De Las Rivas, Javier, Toro, N. del, Heimbach, J., Hermjakob, H., Jurisica, I., Koch, M., Licata, L., Lovering, R. C., Lynn, D. J., Meldal, B. H. M., Micklem, G., Panni, S., Porras, P., Ricard-Blum, S., Roechert, B., Salwinski, L., Shrivastava, A., Sullivan, J., Thierry-Mieg, N., Yehudi, Y., Van Roey, K., and Orchard, S.

Abstract

[Background]: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. [Results]: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. [Conclusions]: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and dow

Published
2018

22. Reactome pathway analysis: a high-performance in-memory approach

Author

Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, and Hermjakob H

Subjects
Data structures, Pathway analysis, Over-representation analysis
Abstract

Background: Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway analysis methods have a broad range of applications in physiological and biomedical research; one of the main problems, from the analysis methods performance point of view, is the constantly increasing size of the data samples. Results: Here, we present a new high-performance in-memory implementation of the well-established overrepresentation analysis method. To achieve the target, the over-representation analysis method is divided in four different steps and, for each of them, specific data structures are used to improve performance and minimise the memory footprint. The first step, finding out whether an identifier in the user's sample corresponds to an entity in Reactome, is addressed using a radix tree as a lookup table. The second step, modelling the proteins, chemicals, their orthologous in other species and their composition in complexes and sets, is addressed with a graph. The third and fourth steps, that aggregate the results and calculate the statistics, are solved with a double-linked tree. Conclusion: Through the use of highly optimised, in-memory data structures and algorithms, Reactome has achieved a stable, high performance pathway analysis service, enabling the analysis of genome-wide datasets within seconds, allowing interactive exploration and analysis of high throughput data. The proposed pathway analysis approach is available in the Reactome production web site either via the AnalysisService for programmatic access or the user submission interface integrated into the PathwayBrowser. Reactome is an open data and open source project and all of its source code, including the one described here, is available in the AnalysisTools repository in the Reactome GitHub

Published
2017

24. The IMEx coronavirus interactome: an evolving map of Coronaviridae–host molecular interactions.

Author

Perfetto, L, Pastrello, C, del-Toro, N, Duesbury, M, Iannuccelli, M, Kotlyar, M, Licata, L, Meldal, B, Panneerselvam, K, Panni, S, Rahimzadeh, N, Ricard-Blum, S, Salwinski, L, Shrivastava, A, Cesareni, G, Pellegrini, M, Orchard, S, Jurisica, I, Hermjakob, H, and Porras, P

Subjects
COVID-19, MOLECULAR interactions, CORONAVIRUSES, PANDEMICS, HUMAN biology, SARS-CoV-2
Abstract

The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions can provide fine-grained resolution of the mechanisms behind the virus biology and the human organism response. We present a curated dataset of physical molecular interactions focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family that has been manually extracted by International Molecular Exchange (IMEx) Consortium curators. Currently, the dataset comprises over 4400 binarized interactions extracted from 151 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (https://www.ebi.ac.uk/intact) and will be continuously updated as research on COVID-19 progresses. [ABSTRACT FROM AUTHOR]

Published
2020
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25. CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination

Author

Perfetto, L., primary, Acencio, M.L., additional, Bradley, G., additional, Cesareni, G., additional, Toro, N.Del, additional, Fazekas, D., additional, Hermjakob, H., additional, Korcsmaros, T., additional, Kuiper, M., additional, Lægreid, A., additional, Surdo, P. Lo, additional, Lovering, R.C., additional, Orchard, S., additional, Porras, P., additional, Thomas, PD., additional, Touré, V., additional, Zobolas, J., additional, and Licata, L., additional

Published
2018
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26. Complex Portal - A Unifying Protein Complex Database

Author

Meldal, Birgit, primary, Combe, C., primary, Bye-A-Jee, H., primary, Heimbach, J., primary, Koch, M., primary, Sullivan, J., primary, Yehudi, Y., primary, Micklem, G., primary, Hermjakob, H., primary, Porras Millán, P., primary, and Orchard, S., primary

Published
2017
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27. Proteomics Standards Initiative: Fifteen years of progress and future work.

Author

Deutsch, ew, Orchard, s, Binz, pa, Bittremieux, w, Eisenacher, m, Hermjakob, h, Kawano, s, Lam, Henry Hei Ning, Mayer, g, Menschaert, g, Perez-riverol, y, Salek, rm, Tabb, dl, Tenzer, s, Vizcaino, ja, Walzer, m, Jones, ar, Deutsch, ew, Orchard, s, Binz, pa, Bittremieux, w, Eisenacher, m, Hermjakob, h, Kawano, s, Lam, Henry Hei Ning, Mayer, g, Menschaert, g, Perez-riverol, y, Salek, rm, Tabb, dl, Tenzer, s, Vizcaino, ja, Walzer, m, and Jones, ar

Abstract

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.

Published
2017

28. The InterPro database, an integrated documentation resource for protein families, domains and functional sites

Author

Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M. D. R., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, N. J., Oinn, T. M., Pagni, M., Servant, F., Sigrist, C. J. A., Zdobnov, E.M., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M. D. R., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, N. J., Oinn, T. M., Pagni, M., Servant, F., Sigrist, C. J. A., and Zdobnov, E.M.

Abstract

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1 000 000 hits from 462 500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk

Published
2017

30. Initial sequencing and analysis of the human genome

Author

Lander, ES, Linton, LM, Birren, B, Nusbaum, C, Zody, MC, Baldwin, J, Devon, K, Dewar, K, Doyle, M, FitzHugh, W, Funke, R, Gage, D, Harris, K, Heaford, A, Howland, J, Kann, L, Lehoczky, J, LeVine, R, McEwan, P, McKernan, K, Meldrim, J, Mesirov, JP, Miranda, C, Morris, W, Naylor, J, Raymond, C, Rosetti, M, Santos, R, Sheridan, A, Sougnez, C, Stange-Thomann, N, Stojanovic, N, Subramanian, A, Wyman, D, Rogers, J, Sulston, J, Ainscough, R, Beck, S, Bentley, D, Burton, J, Clee, C, Carter, N, Coulson, A, Deadman, R, Deloukas, P, Dunham, A, Dunham, I, Durbin, R, French, L, Grafham, D, Gregory, S, Hubbard, T, Humphray, S, Hunt, A, Jones, M, Lloyd, C, McMurray, A, Matthews, L, Mercer, S, Milne, S, Mullikin, JC, Mungall, A, Plumb, R, Ross, M, Shownkeen, R, Sims, S, Waterston, RH, Wilson, RK, Hillier, LW, McPherson, JD, Marra, MA, Mardis, ER, Fulton, LA, Chinwalla, AT, Pepin, KH, Gish, WR, Chissoe, SL, Wendl, MC, Delehaunty, KD, Miner, TL, Delehaunty, A, Kramer, JB, Cook, LL, Fulton, RS, Johnson, DL, Minx, PJ, Clifton, SW, Hawkins, T, Branscomb, E, Predki, P, Richardson, P, Wenning, S, Slezak, T, Doggett, N, Cheng, JF, Olsen, A, Lucas, S, Elkin, C, Uberbacher, E, Frazier, M, Gibbs, RA, Muzny, DM, Scherer, SE, Bouck, JB, Sodergren, EJ, Worley, KC, Rives, CM, Gorrell, JH, Metzker, ML, Naylor, SL, Kucherlapati, RS, Nelson, DL, Weinstock, GM, Sakaki, Y, Fujiyama, A, Hattori, M, Yada, T, Toyoda, A, Itoh, T, Kawagoe, C, Watanabe, H, Totoki, Y, Taylor, T, Weissenbach, J, Heilig, R, Saurin, W, Artiguenave, F, Brottier, P, Bruls, T, Pelletier, E, Robert, C, Wincker, P, Smith, DR, Doucette-Stamm, L, Rubenfield, M, Weinstock, K, Lee, HM, Dubois, J, Rosenthal, A, Platzer, M, Nyakatura, G, Taudien, S, Rump, A, Yang, H, Yu, J, Wang, J, Huang, G, Gu, J, Hood, L, Rowen, L, Madan, A, Qin, S, Davis, RW, Federspiel, NA, Abola, AP, Proctor, MJ, Myers, RM, Schmutz, J, Dickson, M, Grimwood, J, Cox, DR, Olson, MV, Kaul, R, Shimizu, N, Kawasaki, K, Minoshima, S, Evans, GA, Athanasiou, M, Schultz, R, Roe, BA, Chen, F, Pan, H, Ramser, J, Lehrach, H, Reinhardt, R, McCombie, WR, de la Bastide, M, Dedhia, N, Blöcker, H, Hornischer, K, Nordsiek, G, Agarwala, R, Aravind, L, Bailey, JA, Bateman, A, Batzoglou, S, Birney, E, Bork, P, Brown, DG, Burge, CB, Cerutti, L, Chen, HC, Church, D, Clamp, M, Copley, RR, Doerks, T, Eddy, SR, Eichler, EE, Furey, TS, Galagan, J, Gilbert, JG, Harmon, C, Hayashizaki, Y, Haussler, D, Hermjakob, H, Hokamp, K, Jang, W, Johnson, LS, Jones, TA, Kasif, S, Kaspryzk, A, Kennedy, S, Kent, WJ, Kitts, P, Koonin, EV, Korf, I, Kulp, D, Lancet, D, Lowe, TM, McLysaght, A, Mikkelsen, T, Moran, JV, Mulder, N, Pollara, VJ, Ponting, CP, Schuler, G, Schultz, J, Slater, G, Smit, AF, Stupka, E, Szustakowski, J, Thierry-Mieg, D, Thierry-Mieg, J, Wagner, L, Wallis, J, Wheeler, R, Williams, A, Wolf, YI, Wolfe, KH, Yang, SP, Yeh, RF, Collins, F, Guyer, MS, Peterson, J, Felsenfeld, A, Wetterstrand, KA, Patrinos, A, Morgan, MJ, de Jong, P, Catanese, JJ, Osoegawa, K, Shizuya, H, Choi, S, Chen, YJ, and Szustakowki, J

Subjects
Genetics, Cancer genome sequencing, Chimpanzee genome project, Multidisciplinary, Cancer Genome Project, Gene density, DNA sequencing theory, Hybrid genome assembly, Computational biology, Biology, Genome, Personal genomics
Abstract

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Published
2016
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32. Towards Coordinated International Support of Core Data Resources for the Life Sciences

Author

Anderson, W., primary, Apweiler, R., additional, Bateman, A., additional, Bauer, G.A., additional, Berman, H., additional, Blake, J.A., additional, Blomberg, N., additional, Burley, S.K., additional, Cochrane, G., additional, Di Francesco, V., additional, Donohue, T., additional, Durinx, C., additional, Game, A., additional, Green, E.D., additional, Gojobori, T., additional, Goodhand, P., additional, Hamosh, A., additional, Hermjakob, H., additional, Kanehisa, M., additional, Kiley, R., additional, McEntyre, J., additional, McKibbin, R., additional, Miyano, S., additional, Pauly, B., additional, Perrimon, N., additional, Ragan, M.A., additional, Richards, G., additional, Teo, Y-Y., additional, Westerfield, M., additional, Westhof, E., additional, and Lasko, P.F., additional

Published
2017
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34. BioModels: Content, Features, Functionality, and Use

Author

Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat M, Wimalaratne S, Hermjakob H, Le Novère N, Camille Laibe, and Chelliah V

Subjects
Tutorial
Abstract

BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales. The resource provides access to over 1,200 models described in literature and over 140,000 models automatically generated from pathway resources. Most model components are cross-linked with external resources to facilitate interoperability. A large proportion of models are manually curated to ensure reproducibility of simulation results. This tutorial presents BioModels' content, features, functionality, and usage.

Published
2015

35. Development of data representation standards by the human proteome organization proteomics standards initiative

Author

Deutsch, E.W., Albar, J.P., Binz, P.A., Eisenacher, M., Jones, A.R., Mayer, G., Omenn, G.S., Orchard, S., Vizcaíno, J.A., and Hermjakob, H.

Abstract

OBJECTIVE: To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI's evolution, and future directions and synergies for the group. MATERIALS AND METHODS: The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release. RESULTS: We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community.Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.info.

Published
2015

36. Testing and Validation of Computational Methods for Mass Spectrometry

Author

University of Cambridge, Gatto, Laurent, Hansen, K.D., Hoopmann, M.R., Hermjakob, H., Kohlbacher, O., Beyer, A., University of Cambridge, Gatto, Laurent, Hansen, K.D., Hoopmann, M.R., Hermjakob, H., Kohlbacher, O., and Beyer, A.

Abstract

High-throughput methods based on mass spectrometry (proteomics, metabolomics, lipidomics, etc.) produce a wealth of data that cannot be analyzed without computational methods. The impact of the choice of method on the overall result of a biological study is often underappreciated, but different methods can result in very different biological findings. It is thus essential to evaluate and compare the correctness and relative performance of computational methods. The volume of the data as well as the complexity of the algorithms render unbiased comparisons challenging. This paper discusses some problems and challenges in testing and validation of computational methods. We discuss the different types of data (simulated and experimental validation data) as well as different metrics to compare methods. We also introduce a new public repository for mass spectrometric reference data sets (http://compms.org/RefData) that contains a collection of publicly available data sets for performance evaluation for a wide range of different methods.

Published
2016

37. Pharmacometrics Markup Language (PharmML) : Opening New Perspectives for Model Exchange in Drug Development

Author

Swat, M. J., Moodie, S., Wimalaratne, S. M., Kristensen, N. R., Lavielle, M., Mari, A., Magni, P., Smith, M. K., Bizzotto, R., Pasotti, L., Mezzalana, E., Comets, E., Sarr, C., Terranova, N., Blaudez, E., Chan, P., Chard, J., Chatel, K., Chenel, M., Edwards, D., Franklin, C., Giorgino, T., Glont, M., Girard, P., Grenon, P., Harling, Kajsa, Hooker, Andrew C., Kaye, R., Keizer, Ron, Kloft, C., Kok, J. N., Kokash, N., Laibe, C., Laveille, C., Lestini, G., Mentré, F., Munafo, A., Nordgren, Rikard, Bjugård Nyberg, Henrik, Parra-Guillen, Z. P., Plan, Elodie, Ribba, B., Smith, G., Trocóniz, I. F., Yvon, F., Milligan, P. A., Harnisch, L., Karlsson, Mats, Hermjakob, H., Le Novère, N., Swat, M. J., Moodie, S., Wimalaratne, S. M., Kristensen, N. R., Lavielle, M., Mari, A., Magni, P., Smith, M. K., Bizzotto, R., Pasotti, L., Mezzalana, E., Comets, E., Sarr, C., Terranova, N., Blaudez, E., Chan, P., Chard, J., Chatel, K., Chenel, M., Edwards, D., Franklin, C., Giorgino, T., Glont, M., Girard, P., Grenon, P., Harling, Kajsa, Hooker, Andrew C., Kaye, R., Keizer, Ron, Kloft, C., Kok, J. N., Kokash, N., Laibe, C., Laveille, C., Lestini, G., Mentré, F., Munafo, A., Nordgren, Rikard, Bjugård Nyberg, Henrik, Parra-Guillen, Z. P., Plan, Elodie, Ribba, B., Smith, G., Trocóniz, I. F., Yvon, F., Milligan, P. A., Harnisch, L., Karlsson, Mats, Hermjakob, H., and Le Novère, N.

Abstract

The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps.

Published
2015
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38. The cardiovascular gene annotation initiative: Impact on data analysis

Author

Lovering, R.C., primary, Rodriguez-Lopez, M., additional, Campbell, N.H., additional, Huntley, R.P., additional, Sawford, T., additional, O’Donovan, C., additional, Orchard, S., additional, Hermjakob, H., additional, Martin, M., additional, Mayr, M., additional, Humphries, S.E., additional, and Talmud, P.J., additional

Published
2015
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39. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development

Author

Swat, MJ, primary, Moodie, S, additional, Wimalaratne, SM, additional, Kristensen, NR, additional, Lavielle, M, additional, Mari, A, additional, Magni, P, additional, Smith, MK, additional, Bizzotto, R, additional, Pasotti, L, additional, Mezzalana, E, additional, Comets, E, additional, Sarr, C, additional, Terranova, N, additional, Blaudez, E, additional, Chan, P, additional, Chard, J, additional, Chatel, K, additional, Chenel, M, additional, Edwards, D, additional, Franklin, C, additional, Giorgino, T, additional, Glont, M, additional, Girard, P, additional, Grenon, P, additional, Harling, K, additional, Hooker, AC, additional, Kaye, R, additional, Keizer, R, additional, Kloft, C, additional, Kok, JN, additional, Kokash, N, additional, Laibe, C, additional, Laveille, C, additional, Lestini, G, additional, Mentré, F, additional, Munafo, A, additional, Nordgren, R, additional, Nyberg, HB, additional, Parra‐Guillen, ZP, additional, Plan, E, additional, Ribba, B, additional, Smith, G, additional, Trocóniz, IF, additional, Yvon, F, additional, Milligan, PA, additional, Harnisch, L, additional, Karlsson, M, additional, Hermjakob, H, additional, and Le Novère, N, additional

Published
2015
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40. Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study

Author

Villaveces, J. M., primary, Jimenez, R. C., additional, Porras, P., additional, del-Toro, N., additional, Duesbury, M., additional, Dumousseau, M., additional, Orchard, S., additional, Choi, H., additional, Ping, P., additional, Zong, N. C., additional, Askenazi, M., additional, Habermann, B. H., additional, and Hermjakob, H., additional

Published
2015
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41. The mzTab data exchange format: Communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

Author

University of Cambridge, Griss, J., Jones, A.R., Sachsenberg, T., Walzer, M., Gatto, Laurent, Hartler, J., Thallinger, G.G., Salek, R.M., Steinbeck, C., Neuhauser, N., Cox, J., Neumann, S., Fan, J., Reisinger, F., Xu, Q.-W., Del Toro, N., Pérez-Riverol, Y., Ghali, F., Bandeira, N., Xenarios, I., Kohlbacher, O., Vizcaíno, J.A., Hermjakob, H., University of Cambridge, Griss, J., Jones, A.R., Sachsenberg, T., Walzer, M., Gatto, Laurent, Hartler, J., Thallinger, G.G., Salek, R.M., Steinbeck, C., Neuhauser, N., Cox, J., Neumann, S., Fan, J., Reisinger, F., Xu, Q.-W., Del Toro, N., Pérez-Riverol, Y., Ghali, F., Bandeira, N., Xenarios, I., Kohlbacher, O., Vizcaíno, J.A., and Hermjakob, H.

Published
2014

42. ProteomeXchange provides globally coordinated proteomics data submission and dissemination

Author

University of Cambridge, Vizcaíno, J.A., Deutsch, E.W., Wang, R., Csordas, A., Reisinger, F., Ríos, D., Dianes, J.A., Sun, Z., Farrah, T., Bandeira, N., Binz, P.-A., Xenarios, I., Eisenacher, M., Mayer, G., Gatto, Laurent, Campos, A., Chalkley, R.J., Kraus, H.-J., Albar, J.P., Martinez-Bartolomé, S., Apweiler, R., Omenn, G.S., Martens, L., Jones, A.R., Hermjakob, H., University of Cambridge, Vizcaíno, J.A., Deutsch, E.W., Wang, R., Csordas, A., Reisinger, F., Ríos, D., Dianes, J.A., Sun, Z., Farrah, T., Bandeira, N., Binz, P.-A., Xenarios, I., Eisenacher, M., Mayer, G., Gatto, Laurent, Campos, A., Chalkley, R.J., Kraus, H.-J., Albar, J.P., Martinez-Bartolomé, S., Apweiler, R., Omenn, G.S., Martens, L., Jones, A.R., and Hermjakob, H.

Published
2014

43. qcML: An exchange format for quality control metrics from mass spectrometry experiments

Author

University of Cambridge, Walzer, M., Pernas, L.E., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., Van Den Toorn, H.W.P., Staes, A., Vandenbussche, J., Mazanek, M., Taus, T., Scheltema, R.A., Kelstrup, C.D., Gatto, Laurent, Van Breukelen, B., Aiche, S., Valkenborg, D., Laukens, K., Lilley, K.S., Olsen, J.V., Heck, A.J.R., Mechtler, K., Aebersold, R., Gevaert, K., Vizcaíno, J.A., Hermjakob, H., Kohlbacher, O., Martens, L., University of Cambridge, Walzer, M., Pernas, L.E., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., Van Den Toorn, H.W.P., Staes, A., Vandenbussche, J., Mazanek, M., Taus, T., Scheltema, R.A., Kelstrup, C.D., Gatto, Laurent, Van Breukelen, B., Aiche, S., Valkenborg, D., Laukens, K., Lilley, K.S., Olsen, J.V., Heck, A.J.R., Mechtler, K., Aebersold, R., Gevaert, K., Vizcaíno, J.A., Hermjakob, H., Kohlbacher, O., and Martens, L.

Abstract

Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities.

Published
2014

44. The cardiovascular gene annotation initiative: current and future aims

Author

Lovering, R.C., primary, Campbell, N.H., additional, Melidoni, A.N., additional, Rodriguez-Lopez, M., additional, Huntley, R.P., additional, Sawford, T., additional, O’Donovan, C., additional, Martin, M., additional, Orchard, S., additional, Hermjakob, H., additional, Mayr, M., additional, Apweiler, R., additional, Humphries, S.E., additional, and Talmud, P.J., additional

Published
2014
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45. ISPIDER Central: an integrated database web-server for proteomics

Author

Siepen, J.A., Belhajjame, K., Selley, J.N., Embury, S.M., Paton, N.W., Goble, C.A., Oliver, S.G., Stevens, R., Zamboulis, Lucas, Martin, Nigel, Poulovassilis, Alexandra, Jones, P., Côté, R., Hermjakob, H., Pentony, M.M., Jones, D.T., Orengo, C.A., and Hubbard, S.J.

Subjects
ComputingMethodologies_PATTERNRECOGNITION, csis
Abstract

Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics.

Published
2008

46. The minimum information about a proteomics experiment (MIAPE)

Author

Taylor, C.F., Paton, N.W., Lilley, K.S., Binz, P-A, Julian, R.K., Jones, A.R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E.W., Dunn, M.J., Heck, A.J.R., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T.A., Patterson, S.D., Ping, P., Seymour, S.L., Souda, P, Tsugita, A., Vandekerckhove, J., Vondriska, T.M., Whitelegge, J.P., Wilkins, M.R., Xenarios, I., Yates, J.R., Hermjakob, H., Biomoleculaire Massaspectrometrie, Massaspectrometrie, Dep Scheikunde, and Dep Farmaceutische wetenschappen

Subjects
Farmacie(FARM)
Published
2007

48. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

Author

Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Brun, C., Jacq, B., Institut de Biologie du Développement de Marseille (IBDM), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.BC]Life Sciences [q-bio]/Cellular Biology
Published
2004

49. The HUPOPSI's Molecular Interaction format - a community standard for the representation of protein interaction data

Author

Hermjakob, H, MONTECCHI-PALAZZI, L, BADER, G, Brun, C., Institut de Biologie du Développement de Marseille (IBDM), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2004

50. Integration of cardiac proteome biology and medicine by a specialized knowledgebase

Author

Zong, N. C., Li, H., Lam, M. P. Y., Jimenez, R. C., Kim, C. S., Deng, N., Kim, A. K., Choi, J. H., Zelaya, I., Liem, D., Meyer, D., Odeberg, Jacob, Fang, C., Lu, H. -J, Xu, T., Weiss, J., Duan, H., Uhlén, Mathias, Yates III, J. R., Apweiler, R., Ge, J., Hermjakob, H., Ping, P., Zong, N. C., Li, H., Lam, M. P. Y., Jimenez, R. C., Kim, C. S., Deng, N., Kim, A. K., Choi, J. H., Zelaya, I., Liem, D., Meyer, D., Odeberg, Jacob, Fang, C., Lu, H. -J, Xu, T., Weiss, J., Duan, H., Uhlén, Mathias, Yates III, J. R., Apweiler, R., Ge, J., Hermjakob, H., and Ping, P.

Abstract

Rationale: Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. Objective: The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. Methods and results: We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10 924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. Conclusions: COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes., QC 20140120

Published
2013
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