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description Publicationkeyboard_double_arrow_right Article , Other literature type 2021 United Kingdom, France, Germany, France, United Kingdom, Germany, Italy, United Kingdom, Sweden, Netherlands, Germany, Spain, Luxembourg, SpainPublisher:Springer Science and Business Media LLC Funded by:EC | iPLACENTA, EC | PerMedCoE, EC | INFORE +1 projectsEC| iPLACENTA ,EC| PerMedCoE ,EC| INFORE ,NIH| Reactome: An Open Knowledgebase of Human PathwaysMarek Ostaszewski; Anna Niarakis; Alexander Mazein; Inna Kuperstein; Robert Phair; Aurelio Orta-Resendiz; Vidisha Singh; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; Andreas Ruepp; Gisela Fobo; Corinna Montrone; Barbara Brauner; Goar Frishman; Luis Cristobal Monraz Gomez; Julia Somers; Matti Hoch; Shailendra K. Gupta; Julia Scheel; Hanna Borlinghaus; Tobias Czauderna; Falk Schreiber; Arnau Montagud; Miguel Ponce de Leon; Akira Funahashi; Yusuke Hiki; Noriko Hiroi; Takahiro G. Yamada; Andreas Dräger; Alina Renz; Muhammad Naveez; Zsolt Bocskei; Francesco Messina; Daniela Börnigen; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E. Ackerman; Jason E. Shoemaker; Jeremy Zucker; Kristie L. Oxford; Jeremy Teuton; Ebru Kocakaya; Gokce Yagmur Summak; Kristina Hanspers; Martina Kutmon; Susan L. Coort; Lars M. T. Eijssen; Friederike Ehrhart; D A B Rex; Denise Slenter; Marvin Martens; Nhung Pham; Robin Haw; Bijay Jassal; Lisa Matthews; M Orlic-Milacic; Andrea Senff Ribeiro; Karen Rothfels; Veronica Shamovsky; Ralf Stephan; Cristoffer Sevilla; Thawfeek M. Varusai; Jean-Marie Ravel; Rupsha Fraser; Vera Ortseifen; Silvia Marchesi; Piotr Gawron; Ewa Smula; Laurent Heirendt; Venkata P. Satagopam; Guanming Wu; Anders Riutta; Martin Golebiewski; Stuart Owen; Carole Goble; Xiaoming Hu; Rupert W. Overall; Dieter Maier; Angela Bauch; Benjamin M. Gyori; John A. Bachman; Carlos Vega; Valentin Grouès; M. Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Anastasia P. Nesterova; Anton Yuryev; Anita de Waard; Dénes Türei; Augustin Luna; Özgün Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban-Medina; Maria Peña-Chilet; Kinza Rian; Tomáš Helikar; Bhanwar Lal Puniya; Dezso Modos; Agatha Treveil; Marton Olbei; Bertrand De Meulder; Stephane Ballereau; Aurelien Dugourd; Aurélien Naldi; Vincent Noël; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C. Freeman; Franck Augé; Jacques S. Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon L Wilighagen; Alexander R. Pico; Chris T. Evelo; Marc Gillespie; Lincoln Stein; Henning Hermjakob; Peter D'Eustachio; Julio Saez-Rodriguez; Joaquín Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider; Covid Disease Map Community;"Article signat per més de 50 autors/es: Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang,Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya,Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen51,Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco57, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Wilighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider " We would like to thank Andjela Tatarovic, architect, and Gina Crovetto, a researcher in the field of cancer, for their help with the design of the top-level view diagrams. We would like to acknowledge the Responsible and Reproducible Research (R3) team of the Luxembourg Centre for Systems Biomedicine for supporting the project and providing necessary communication and data sharing resources. The work presented in this paper was carried out using the ELIXIR Luxembourg tools and services. This study was supported by the Luxembourg National Research Fund (FNR) COVID-19 Fast-Track grant programme, grant COVID-19/2020-1/14715687/CovScreen (E. Glaab); European Commission, INFORE grant H2020-ICT-825070 (A. Montagud, M. Ponce de Leon, M. Vazques and A. Valencia); European Commission, PerMedCoE grant H2020-ICT-951773 (A. Montagud, M. Ponce de Leon, M. Vazques and A. Valencia) the Federal Ministry of Education and Research (BMBF, Germany) and the Baden-Württemberg Ministry of Science, the Excellence Strategy of the German Federal and State Governments (A. Renz); German Center for Infection Research (DZIF), grant no 8020708703 (A. Dräger); The Netherlands Organisation for Health Research and Development (ZonMw), grant no 10430012010015, (M. Kutmon, S. Coort, F. Ehrhart, N. Pham, E.L. Willighagen, C.T. Evelo); H2020 Marie Skłodowska-Curie Actions, grant number 765274 (J. Scheel); National Institutes of Health, USA (NIH), grant number U41 HG003751 (L.D. Stein). The development of Reactome is supported by grants from the US National Institutes of Health (U41 HG003751) and the European Molecular Biology Laboratory. We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective. Peer Reviewed
Molecular Systems Bi... arrow_drop_down Molecular Systems BiologyArticle . 2021Full-Text: http://europepmc.org/articles/PMC8524328Data sources: PubMed CentralEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8696085Data sources: PubMed CentralMolecular Systems Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; The University of Manchester - Institutional Repository; Archivio della Ricerca - Università di Roma Tor vergataOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYServeur académique lausannoisArticle . 2021License: CC BYData sources: Serveur académique lausannoisUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2022 . 2021Open Repository and Bibliography - LuxembourgArticle . 2021Data sources: Open Repository and Bibliography - LuxembourgArchivio della Ricerca - Università di Roma Tor vergataArticle . 2021Data sources: Archivio della Ricerca - Università di Roma Tor vergataHal-DiderotArticle . 2021Full-Text: https://hal.inria.fr/hal-03385317v2/documentData sources: Hal-Diderotadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 50 citations 50 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 283visibility views 283 download downloads 408 Powered bymore_vert Molecular Systems Bi... arrow_drop_down Molecular Systems BiologyArticle . 2021Full-Text: http://europepmc.org/articles/PMC8524328Data sources: PubMed CentralEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8696085Data sources: PubMed CentralMolecular Systems Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; The University of Manchester - Institutional Repository; Archivio della Ricerca - Università di Roma Tor vergataOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYServeur académique lausannoisArticle . 2021License: CC BYData sources: Serveur académique lausannoisUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2022 . 2021Open Repository and Bibliography - LuxembourgArticle . 2021Data sources: Open Repository and Bibliography - LuxembourgArchivio della Ricerca - Università di Roma Tor vergataArticle . 2021Data sources: Archivio della Ricerca - Università di Roma Tor vergataHal-DiderotArticle . 2021Full-Text: https://hal.inria.fr/hal-03385317v2/documentData sources: Hal-Diderotadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 France, Netherlands, Denmark, Denmark, France, France, France, FrancePublisher:F1000 Research Ltd Funded by:EC | BioExcel-2, EC | EOSC-LifeEC| BioExcel-2 ,EC| EOSC-LifeAnna-Lena Lamprecht; Magnus Palmblad; Jon Ison; Veit Schwämmle; Mohammad Sadnan Al Manir; Ilkay Altintas; Christopher J. O. Baker; A. Amor; Salvador Capella-Gutierrez; Paulos Charonyktakis; Michael R. Crusoe; Yolanda Gil; Carole Goble; Timothy J. Griffin; Paul Groth; Hans Ienasescu; Pratik D. Jagtap; Matúš Kalaš; Vedran Kasalica; Alireza Khanteymoori; Tobias Kuhn; Hailiang Mei; Hervé Ménager; Steffen Möller; Robin A. Richardson; Vincent Robert; Stian Soiland-Reyes; Robert Stevens; Szoke Szaniszlo; Suzan Verberne; Aswin Verhoeven; Katherine Wolstencroft;pmid: 34804501
pmc: PMC8573700
Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future.
NARCIS arrow_drop_down Europe PubMed CentralArticle . 2021 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC8573700Data sources: PubMed CentralLeiden University Scholarly Publications Repository; NARCISOther literature type . Article . 2021License: CC BYUniversity of Southern Denmark Research Output; F1000ResearchOther literature type . Article . 2021Data sources: University of Southern Denmark Research OutputF1000ResearchArticle . 2021Online Research Database In TechnologyArticle . 2021 . Peer-reviewedData sources: Online Research Database In Technologyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 7 citations 7 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert NARCIS arrow_drop_down Europe PubMed CentralArticle . 2021 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC8573700Data sources: PubMed CentralLeiden University Scholarly Publications Repository; NARCISOther literature type . Article . 2021License: CC BYUniversity of Southern Denmark Research Output; F1000ResearchOther literature type . Article . 2021Data sources: University of Southern Denmark Research OutputF1000ResearchArticle . 2021Online Research Database In TechnologyArticle . 2021 . Peer-reviewedData sources: Online Research Database In Technologyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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description Publicationkeyboard_double_arrow_right Article , Other literature type 2021 United Kingdom, France, Germany, France, United Kingdom, Germany, Italy, United Kingdom, Sweden, Netherlands, Germany, Spain, Luxembourg, SpainPublisher:Springer Science and Business Media LLC Funded by:EC | iPLACENTA, EC | PerMedCoE, EC | INFORE +1 projectsEC| iPLACENTA ,EC| PerMedCoE ,EC| INFORE ,NIH| Reactome: An Open Knowledgebase of Human PathwaysMarek Ostaszewski; Anna Niarakis; Alexander Mazein; Inna Kuperstein; Robert Phair; Aurelio Orta-Resendiz; Vidisha Singh; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; Andreas Ruepp; Gisela Fobo; Corinna Montrone; Barbara Brauner; Goar Frishman; Luis Cristobal Monraz Gomez; Julia Somers; Matti Hoch; Shailendra K. Gupta; Julia Scheel; Hanna Borlinghaus; Tobias Czauderna; Falk Schreiber; Arnau Montagud; Miguel Ponce de Leon; Akira Funahashi; Yusuke Hiki; Noriko Hiroi; Takahiro G. Yamada; Andreas Dräger; Alina Renz; Muhammad Naveez; Zsolt Bocskei; Francesco Messina; Daniela Börnigen; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E. Ackerman; Jason E. Shoemaker; Jeremy Zucker; Kristie L. Oxford; Jeremy Teuton; Ebru Kocakaya; Gokce Yagmur Summak; Kristina Hanspers; Martina Kutmon; Susan L. Coort; Lars M. T. Eijssen; Friederike Ehrhart; D A B Rex; Denise Slenter; Marvin Martens; Nhung Pham; Robin Haw; Bijay Jassal; Lisa Matthews; M Orlic-Milacic; Andrea Senff Ribeiro; Karen Rothfels; Veronica Shamovsky; Ralf Stephan; Cristoffer Sevilla; Thawfeek M. Varusai; Jean-Marie Ravel; Rupsha Fraser; Vera Ortseifen; Silvia Marchesi; Piotr Gawron; Ewa Smula; Laurent Heirendt; Venkata P. Satagopam; Guanming Wu; Anders Riutta; Martin Golebiewski; Stuart Owen; Carole Goble; Xiaoming Hu; Rupert W. Overall; Dieter Maier; Angela Bauch; Benjamin M. Gyori; John A. Bachman; Carlos Vega; Valentin Grouès; M. Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Anastasia P. Nesterova; Anton Yuryev; Anita de Waard; Dénes Türei; Augustin Luna; Özgün Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban-Medina; Maria Peña-Chilet; Kinza Rian; Tomáš Helikar; Bhanwar Lal Puniya; Dezso Modos; Agatha Treveil; Marton Olbei; Bertrand De Meulder; Stephane Ballereau; Aurelien Dugourd; Aurélien Naldi; Vincent Noël; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C. Freeman; Franck Augé; Jacques S. Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon L Wilighagen; Alexander R. Pico; Chris T. Evelo; Marc Gillespie; Lincoln Stein; Henning Hermjakob; Peter D'Eustachio; Julio Saez-Rodriguez; Joaquín Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider; Covid Disease Map Community;"Article signat per més de 50 autors/es: Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang,Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya,Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen51,Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco57, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Wilighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider " We would like to thank Andjela Tatarovic, architect, and Gina Crovetto, a researcher in the field of cancer, for their help with the design of the top-level view diagrams. We would like to acknowledge the Responsible and Reproducible Research (R3) team of the Luxembourg Centre for Systems Biomedicine for supporting the project and providing necessary communication and data sharing resources. The work presented in this paper was carried out using the ELIXIR Luxembourg tools and services. This study was supported by the Luxembourg National Research Fund (FNR) COVID-19 Fast-Track grant programme, grant COVID-19/2020-1/14715687/CovScreen (E. Glaab); European Commission, INFORE grant H2020-ICT-825070 (A. Montagud, M. Ponce de Leon, M. Vazques and A. Valencia); European Commission, PerMedCoE grant H2020-ICT-951773 (A. Montagud, M. Ponce de Leon, M. Vazques and A. Valencia) the Federal Ministry of Education and Research (BMBF, Germany) and the Baden-Württemberg Ministry of Science, the Excellence Strategy of the German Federal and State Governments (A. Renz); German Center for Infection Research (DZIF), grant no 8020708703 (A. Dräger); The Netherlands Organisation for Health Research and Development (ZonMw), grant no 10430012010015, (M. Kutmon, S. Coort, F. Ehrhart, N. Pham, E.L. Willighagen, C.T. Evelo); H2020 Marie Skłodowska-Curie Actions, grant number 765274 (J. Scheel); National Institutes of Health, USA (NIH), grant number U41 HG003751 (L.D. Stein). The development of Reactome is supported by grants from the US National Institutes of Health (U41 HG003751) and the European Molecular Biology Laboratory. We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective. Peer Reviewed
Molecular Systems Bi... arrow_drop_down Molecular Systems BiologyArticle . 2021Full-Text: http://europepmc.org/articles/PMC8524328Data sources: PubMed CentralEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8696085Data sources: PubMed CentralMolecular Systems Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; The University of Manchester - Institutional Repository; Archivio della Ricerca - Università di Roma Tor vergataOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYServeur académique lausannoisArticle . 2021License: CC BYData sources: Serveur académique lausannoisUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2022 . 2021Open Repository and Bibliography - LuxembourgArticle . 2021Data sources: Open Repository and Bibliography - LuxembourgArchivio della Ricerca - Università di Roma Tor vergataArticle . 2021Data sources: Archivio della Ricerca - Università di Roma Tor vergataHal-DiderotArticle . 2021Full-Text: https://hal.inria.fr/hal-03385317v2/documentData sources: Hal-Diderotadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 50 citations 50 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 283visibility views 283 download downloads 408 Powered bymore_vert Molecular Systems Bi... arrow_drop_down Molecular Systems BiologyArticle . 2021Full-Text: http://europepmc.org/articles/PMC8524328Data sources: PubMed CentralEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8696085Data sources: PubMed CentralMolecular Systems Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; The University of Manchester - Institutional Repository; Archivio della Ricerca - Università di Roma Tor vergataOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYServeur académique lausannoisArticle . 2021License: CC BYData sources: Serveur académique lausannoisUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2022 . 2021Open Repository and Bibliography - LuxembourgArticle . 2021Data sources: Open Repository and Bibliography - LuxembourgArchivio della Ricerca - Università di Roma Tor vergataArticle . 2021Data sources: Archivio della Ricerca - Università di Roma Tor vergataHal-DiderotArticle . 2021Full-Text: https://hal.inria.fr/hal-03385317v2/documentData sources: Hal-Diderotadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.15252/msb.202110387&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 France, Netherlands, Denmark, Denmark, France, France, France, FrancePublisher:F1000 Research Ltd Funded by:EC | BioExcel-2, EC | EOSC-LifeEC| BioExcel-2 ,EC| EOSC-LifeAnna-Lena Lamprecht; Magnus Palmblad; Jon Ison; Veit Schwämmle; Mohammad Sadnan Al Manir; Ilkay Altintas; Christopher J. O. Baker; A. Amor; Salvador Capella-Gutierrez; Paulos Charonyktakis; Michael R. Crusoe; Yolanda Gil; Carole Goble; Timothy J. Griffin; Paul Groth; Hans Ienasescu; Pratik D. Jagtap; Matúš Kalaš; Vedran Kasalica; Alireza Khanteymoori; Tobias Kuhn; Hailiang Mei; Hervé Ménager; Steffen Möller; Robin A. Richardson; Vincent Robert; Stian Soiland-Reyes; Robert Stevens; Szoke Szaniszlo; Suzan Verberne; Aswin Verhoeven; Katherine Wolstencroft;pmid: 34804501
pmc: PMC8573700
Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future.
NARCIS arrow_drop_down Europe PubMed CentralArticle . 2021 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC8573700Data sources: PubMed CentralLeiden University Scholarly Publications Repository; NARCISOther literature type . Article . 2021License: CC BYUniversity of Southern Denmark Research Output; F1000ResearchOther literature type . Article . 2021Data sources: University of Southern Denmark Research OutputF1000ResearchArticle . 2021Online Research Database In TechnologyArticle . 2021 . Peer-reviewedData sources: Online Research Database In Technologyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.12688/f1000research.54159.1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 7 citations 7 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert NARCIS arrow_drop_down Europe PubMed CentralArticle . 2021 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC8573700Data sources: PubMed CentralLeiden University Scholarly Publications Repository; NARCISOther literature type . Article . 2021License: CC BYUniversity of Southern Denmark Research Output; F1000ResearchOther literature type . Article . 2021Data sources: University of Southern Denmark Research OutputF1000ResearchArticle . 2021Online Research Database In TechnologyArticle . 2021 . Peer-reviewedData sources: Online Research Database In Technologyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.12688/f1000research.54159.1&type=result"></script>'); --> </script>
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