ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

D6.4 Report on assessment criteria and standardisation of metagenome assembled genomes (MAGs) from Marine samples

The increased depth of sequences and improved algorithms have seen an increase in the number of marine metagenomics datasets that can be assembled. However, no metrics are in place to indicate what constitutes a good assembly. Furthermore, the community is producing more and more MAGs from these assemblies. Papers by Parks et al and Bowers et al have provided a range on different ways of assessing the quality of a MAG, with the former also beginning to outline a set of standards that should be adopted. We will assess these standards against MAGs produced from Marine samples (from both our own and publicly deposited MAGs). We will report on the criteria that we believe should be achieved from inclusion in Marine data resources, such as EBI metagenomics or the MAR databases. (Rob Finn, EBI and Nils Peder Willassen, UiT). EMBL-EBI, NO, FR

D2.3 A report on the features and nature of novel data which are needed within online benchmarking experiments in different subareas

A report on the features and nature of novel data which are needed within online benchmarking experiments in different subareas (Task 2.3, task 2.4).

D9.3 Report on implementation of value-added user applications and cohort integration

Report on implementation of value-added user applications and cohort integration

D6.2 Report on comprehensive metagenomic data standards environment

Report on comprehensive metagenomic data standards environment (Task 6.1)

D10.5 A Node report on regional priorities and channels to use. Available to all relevant partners in the Node network in that country

A Node report on regional priorities and channels to use. Available to all relevant partners in the Node network in that country

D12.4 Updated long- term strategy for the sustainability of data management

Updated long- term strategy for the sustainability of data management

D6.1 Specific marine databases made publicly available

Specific marine databases made publicly available (Task 6.2)

D2.2 A report on the coordination with WP1 on the incorporation of monitoring statistics and benchmarking results in registry releases

A report on the coordination with WP1 on the incorporation of monitoring statistics and benchmarking results in registry releases (Task 2.4).

D11.3 Report on training provided across the ELIXIR community

Report on training provided across the ELIXIR community (Task 11.2).

D1.5 Incorporation of monitoring statistics and benchmarking results in registry releases

Incorporation of monitoring statistics and benchmarking results in registry releases (Task 1.2)

D4.1 ELIXIR Technical Services Roadmap

ELIXIR Technical Services Roadmap: Incorporates the technical requirements coming from the Use Cases, details of the service offerings coming from the ELIXIR Nodes and the public e-Infrastructures, and provides a roadmap detailing when new services will appear within the ELIXIR Technical Services registry and the work being undertaken by the service providers to meet ELIXIR’s requirements (Task 4.1, task 4.2, task 4.3).

D4.4 ELIXIR Technical Services document

ELIXIR Technical Services document: Describes the ELIXIR Technical Services being offered through the cooperating service providers (ELIXIR Nodes and public e-infrastructures) (Task 4.1, task 4.2, task 4.3).

D8.6 Documentation on adequate quality reporting standards for genomics datasets

Documentation on adequate quality reporting standards for genomics datasets

D1.1 Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis

Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis (Task 1.1) - year 1

D8.7 Options for sustainability of RD-Connect within the scope of ELIXIR

Options for sustainability of RD-Connect within the scope of ELIXIR

D8.3 Report on the ELIXIR workshop organized with the rare-disease communities

Report on the ELIXIR workshop organized with the rare-disease communities - year 1 (Task 8.3).

D9.4 Report on implementation of cloud access and secure user and data management

Report on implementation of cloud access and secure user and data management

D9.1 Requirements analysis document

Requirements analysis document

D13.2 Report on ELIXIR’s Communication Strategy

Report on ELIXIR’s Communication Strategy (Task 13.1).

D11.2 Report on the training needs identified across the ELIXIR community

Report on the training needs identified across the ELIXIR community (Task 11.1).

D6.3 Report describing a set of tools, pipelines and search engine for interrogation of marine metagenomic data

Report describing a set of tools, pipelines and search engine for interrogation of marine metagenomic data (Task 6.3 and task 6.4)

D5.1 Interoperability Implementation Regulations

Interoperability Implementation Regulations. A set of standards, rules, controlled vocabularies, authorised unique identifiers and interoperable service APIs for the data repositories and biological knowledge bases agreed and implemented in the field with WP6 to 9, and WP3; resources registered in BioSharing; BioCatalogue and BioRegistry (WP1); ontologies accessible via Ontology Lookup Services (Task 5.1)

D10.3 ELIXIR Advanced workshops on genome annotation

ELIXIR Advanced workshops on genome annotation - Month 4 (Task 10.3).

D3.2 A report describing the semantically enriched Europe PMC that links literature to ELIXIR Core resource data, exemplified by GeneRif annotations

A report describing the semantically enriched Europe PMC that links literature to ELIXIR Core resource data, exemplified by GeneRif annotations (Task 3.3)

D7.3 Implementation of BRAPI (Plant Breeding API) at all participating nodes

Implementation of BRAPI (Plant Breeding API) at all participating nodes

D4.2 Updated ELIXIR Technical Services Roadmap

Updated ELIXIR Technical Services Roadmap: Incorporates the technical requirements coming from the Use Cases, details of the service offerings coming from the ELIXIR Nodes and the public e-Infrastructures, and provides a roadmap detailing when new services will appear within the ELIXIR Technical Services portfolio and the work being undertaken by the service providers to meet ELIXIR’s requirements (Task 4.1, task 4.2, task 4.3).

D1.8 Matchmaking Service: implementation & evaluation of impact

Matchmaking Service: implementation & evaluation of impact

D1.3 Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis

Registry release with comprehensive coverage of ELIXIR Node resources including resource data format curation and analysis Task 11 year 3

D10.4 ELIXIR Advanced workshops on genome annotation

ELIXIR Advanced workshops on genome annotation - Month 22 (Task 10.3).

D13.4 Report on the impact of the Innovation and SME programme on industry users

Report on the impact of the Innovation and SME programme on industry users (Task 13.2).

D5.3 Bring Your Own Data

Bring Your Own Data 8 delivered workshops and established roll-out programme across WP10 Data Node capability network; materials deposited on WP11 TeSS (Task 5.3)

"D10.1 Communities of"" Good Practice"" and Protocols of Transfer"

Communities of Good Practice and Protocols of Transfer Task 101

D2.4 Final report on the impact of ELIXIR infrastructure for hosting scientific benchmarking and technical monitoring results

Final report on the impact of ELIXIR infrastructure for hosting scientific benchmarking and technical monitoring results

D1.6 Workbench integration enabler: implementation & evaluation of impact

Workbench integration enabler: implementation & evaluation of impact (Task 1.3)

D9.2 Report on implementation of submissions interface and API

Report on implementation of submissions interface and API (Task 9.1).

D1.7 Description of the registry user helpdesk & impact on user support via community forums

Description of the registry user helpdesk & impact on user support via community forums

D6.5 Improvement and Application of Eukaryotic Gene

We will release the first set of the reference eukaryotic gene catalog including 292 species of the MMETSP project and 78 species of Roscoff Culture Collection. Thereafter, we will investigate the production of combined assemblies (assemblies built from a unique taxa, but under a range of RNAseq conditions) from MMETSP dataset. We plan to produce 119 new eukaryotic assemblies. Additionally, works we will identify (probable) contamination and/or mixed species populations within eukaryotic assemblies, based on functional annotation (produced by EBI pipeline) and contigs binning. (Rob Finn, EBI and Nils Peder Willassen, UiT). EMBL-EBI, FR

D13.1 Release of a live ELIXIR Communication Strategy, including annual updates thereafter

Release of a live ELIXIR Communication Strategy, including annual updates thereafter - Month 6 (Task 13.1).

D13.3 Report on ELIXIR’s International Strategy

Report on ELIXIR’s International Strategy (Task 13.4).

D3.3 Report describing ELIXIR-wide systems for the computer-assisted collection and delivery of harmonised metrics and quality criteria from multiple ELIXIR resources and collation of these at the ELIXIR Hub

Report describing ELIXIR-wide systems for the computer-assisted collection and delivery of harmonised metrics and quality criteria from multiple ELIXIR resources and collation of these at the ELIXIR Hub (Task 3.2).

D8.1 Portfolio of ELIXIR data resources and tools for the rare diseases communities

Portfolio of ELIXIR data resources and tools for the rare diseases communities (Task 8.1).

D11.1 Deliver the identified evaluation systems and good practice guidelines for training. Deliver a TeSS platform and identify e-learning solutions

Deliver the identified evaluation systems and good practice guidelines for training. Deliver a TeSS platform and identify e-learning solutions (Task 11.1)

D12.2 ELIXIR Handbook of Operations

ELIXIR Handbook of Operations (Task 12.1).

D3.1 List of metrics/quality criteria measuring the scientific impact, service usage, service delivery, and eligibility for “ELIXIR Named Resource” and “ELIXIR Core Resource” labels, to allow construction and extension of the ELIXIR Resource portfolio

List of metrics/quality criteria measuring the scientific impact, service usage, service delivery, and eligibility for “ELIXIR Named Resource” and “ELIXIR Core Resource” labels, to allow construction and extension of the ELIXIR Resource portfolio (Task 3.1).

D7.1 Datasets annotated for at least 1 woody plant, cereal and solanaceous species; genotype, phenotype and sample meta data submitted to appropriate public archives

Datasets annotated for at least 1 woody plant, cereal and solanaceous species; genotype, phenotype and sample meta data submitted to appropriate public archives (Task 7.1, task 7.2 and task 7.3).

D1.2 Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis

Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis (Task 1.1) - year 2

D4.3 ELIXIR Technical Services Roadmap

ELIXIR Technical Services Roadmap: Incorporates the technical requirements coming from the Use Cases, details of the service offerings coming from the ELIXIR Nodes and the public e-Infrastructures, and provides a roadmap detailing when new services will appear within the ELIXIR Technical Services portfolio and the work being undertaken by the service providers to meet ELIXIR’s requirements (Task 4.1, task 4.2, task 4.3).

D10.2 Blueprint on how to set up an ELIXIR data Node

Blueprint on how to set up an ELIXIR data Node (Task 10.2).

D7.2 Phenotypic data exposed through integrating API by all participants

Phenotypic data exposed through integrating API by all participants (Task 7.4).

D8.5 Report on the ELIXIR workshops organised with the rare-disease communities

Report on the ELIXIR workshops organised with the rare-disease communities

D8.2 Documentation of the tools for the data manipulation and standard conversions in the rare-disease field

Documentation of the tools for the data manipulation and standard conversions in the rare-disease field (Task 8.2).

D2.1 Creation of a database warehouse infrastructure for storing and organizing data for online performance assessment experiments

Creation of a database warehouse infrastructure for storing and organizing data for online performance assessment experiments (Tasks 2.2, 2.3, 2.4)

D9.5 Report on implementation of ELSI and policy consideration for controlled access data

Report on implementation of ELSI and policy consideration for controlled access data

D8.4 Report on the ELIXIR workshop organized with the rare-disease communities

Report on the ELIXIR workshop organized with the rare-disease communities - year 2 (Task 8.3).

D1.4 Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis

Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis (Task 1.1) - year 4

Publications

ELIXIR-EXCELERATE: Deliverable 6.2: Report on comprehensive metagenomic data standards environment

Auteurs: Guy Cochrane; Rob Finn; Nils Peder Willassen; Lars Ailo Bongo; Monica Santamaria; Bruno Fosso; Eric Pelletier; Erwan Corre; Alex Mitchell; Simon Potter
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1229221

Plan for collation of metrics and quality data at the ELIXIR Hub

Auteurs: Stockinger, Heinz; Barlow, Mary; Cook, Chuck; Drysdale, Rachel; Gasteiger, Elisabeth; Kim, Jee-Hyub; Lopez, Rodrigo; Redaschi, Nicole; Teixeira, Daniel; Durinx, Christine; McEntyre, Johanna
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1194123

Uniform Resolution of Compact Identifiers for Biomedical Data

Auteurs: Hermjakob, Henning; Mcmurry, Julie; Beard, Niall; Clark, Tim; Janée, Greg; Jimenez, Rafael; Grethe, Jeffrey; Wimalaratne, Sarala; Kunze, John; Juty, Nick
Publié dans: Numéro 1, 2018
Éditeur: BioRxiv
DOI: 10.1101/101279

ELIXIR EXCELERATE Deliverable D7.1

Auteurs: Adam-Blondon, Anne-Françoise; Chaves, Inês; Coppens, Frederik; Finkers, Richard; Horro, Carlos; Kersey, Paul; Michotey, Celia; Miguel, Célia; Papoutsoglu, Evangelia; Pommier, Cyril; Ramsak, Ziva
Publié dans: 2017
Éditeur: Zenodo
DOI: 10.5281/zenodo.1111825

Framework For Quality Assessment Of Whole Genome, Cancer Sequences

Auteurs: Buchhalter, Ivo; Whalley, Justin; Hutter, Barbara; Livitz, Dimitri; Perry, Marc; Rosenberg, Mara; Saksena, Gordon; Trotta, Jean-Rémi; Raine, Keiran; Eils, Roland; Korbel, Jan; Rheinbay, Esther; Network, Pcawg; , Pcawg-Qc; Kleinheinz, Kortine; Gerhard, Daniela; Campbell, Peter; Getz, Gad; Schlesner, Matthias; Werner, Johannes; Beltran, Sergi; Gut, Marta; Huebschmann, Daniel; Gut, Ivo; Stobbe, Mira
Publié dans: 2017
Éditeur: BioRxiv
DOI: 10.1101/140921

Signaling Pathway Activities Improve Prognosis for Breast Cancer

Auteurs: Hidalgo, Marta; Dopazo, Joaquín; Vert, Jean-Philippe; Carbonell-Caballero, Jose; Amadoz, Alicia; Cubuk, Cankut; Jiao, Yunlong
Publié dans: 2017
Éditeur: BioRxiv
DOI: 10.1101/132357

ELIXIR Handbook of Operations

Auteurs: Niklas Blomberg; Martin Cook; Pablo Roman Garcia; Stephanie Suhr; Premysl Velek; Montserrat Gonzalez; Susanna Repo
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1289765

Research Object Community Update

Auteurs: Carole Goble, Stian Soiland-Reyes, Sean Bechhofe
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1313066

Federated Identity Management for Research Collaborations

Auteurs: Christopher John Atherton; Thomas Barton; Jim Basney; Daan Broeder; Alessandro Costa; Mirjam van Daalen; Stephanie Dyke; Willem Elbers; Carl-Fredrik Enell; Enrico Maria Vincenzo Fasanelli; João Fernandes; Licia Florio; Peter Gietz; David L. Groep; Matthias Bernhard Junker; Christos Kanellopoulos; David Kelsey; Philip Kershaw; Cristina Knapic; Thorsten Kollegger
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1307551

REPORT: Portfolio of ELIXIR data resources and tools for the rare diseases communities

Auteurs: Beltran, Sergi; Coward, Eivind; Matalonga, Leslie; Drablos, Finn; Peterson, Hedi; Gut, Ivo; Roos, Marco
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1321650

Datasets annotated for at least 1 woody plant, cereal and solanaceous species; genotype, phenotype and sample metadata submitted to appropriate public archives

Auteurs: Adam-Blondon, Anne-Françoise; Chaves, Inês; Coppens, Friederik; Costa, Bruno; Finkers, Richard; Horro, Carlos; Kersey, Paul; Mihotey, Celia; Miguel, Celia; Papoutsoglu, Evangelia; Pommier, Cyril; Ramsak, Ziva
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1321902

Deliverable 13.2: Report on ELIXIR's Communication Strategy

Auteurs: elek, Premysl; Wiles, Kayla; Smith, Andrew; Garcia Roman, Pablo; Cook, Martin; Cernoskova, Dana
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1321214

ELIXIR Advanced workshops on genome annotation

Auteurs: Lantz, Henrik; Leskosek, Brane
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1321915

REPORT: Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis

Auteurs: Ison, Jon; Brunak, Søren; Tools platform community
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1321740

Release of a live ELIXIR Communication Strategy

Auteurs: Premysl Velek; Andrew Smith
Publié dans: 2017
Éditeur: Zenodo
DOI: 10.5281/zenodo.557084

Report on the ELIXIR workshop organized with the rare-disease communities

Auteurs: Leskosek, Brane; Matalonga, Leslie; Kastrin, Andrej; Dimec, Jure; Femke Francissen; Beltran, Sergi; Coward, Eivind; Peterson, Hedi; Gut, Ivo; Roos, Marco; Varma, Susheel
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1321601

REPORT: Updated ELIXIR Technical Services Roadmap

Auteurs: Nyrönen, Tommi; Matyska, Ludek; Newhouse, Steven; Compute platform community
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1321699

D8.2 Documentation of the tools for the data manipulation and standard conversions in the rare-disease field

Auteurs: Jacobsen, Annika; Thompson, Mark; Hanauer, Marc; Sergi, Beltran; Gray, Alasdair; Juty, Nick; Ehrhart, Friederike; Evelo, Chris
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452468

3.2 A report describing the semantically enriched Europe PMC that links literature to ELIXIR Core resource data, exemplified by GeneRif annotations

Auteurs: McEntyre, Jo; Venkatesan, Aravind; Gobeill Julien; Piovesan, Damiano; Tosatto, Silvio; Ruch, Patrick
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452442

D9.2 Report on implementation of submissions interface and API

Auteurs: de la Torre, Sabela; Moldes, Mauricio; Rambla, Jordi
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452480

D1.5 Incorporation of monitoring statistics and benchmarking results in registry releases

Auteurs: Ison, Jon; Ienasescu, Hans; Kalas, Matus; ELIXIR Tools community
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452910

11.1 Deliver the identified evaluation systems and good practice guidelines for training. Deliver a TeSS platform and identify e-learning solutions

Auteurs: Rustici, Gabriella; Gurwitz, Kim; Louisa, Bellis; ELIXIR Training community
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1453021

D5.1 Interoperability Implementation Regulations.

Auteurs: Goble, Carol; Evelo, Chris; Parkinson, Helen; ELIXIR Interoperability community
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452415

D9.3 Report on implementation of value-added user applications and cohort integration

Auteurs: de la Torre, Sabela; Lloret-Villas, Audald; Rambla, Jordi
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452472

D2.3 A report on the features and nature of novel data which are needed within online benchmarking experiments in different subareas

Auteurs: Capella-Gutierrez, Salvador; Haas, Juergen; Ll. Gelpí, Josep; Mª. Fernández, Jose; Garrayo, Javier
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452425

D2.2 A report on the coordination with WP1 on the incorporation of monitoring statistics and benchmarking results in registry releases

Auteurs: Gelpi Ll., Josep; Mª. Fernández, Jose; Sundesha, Vicky; Repchevsky; Haas, Juergen
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452561

D7.2 Phenotypic data exposed through integrating API by all participants

Auteurs: Miguel, Célia; Pommier, Cyril; Finkers, Richard; Coppens, Frederik; Bolser, Dan
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452452

D9.5 Report on implementation of ELSI and policy consideration for controlled access data

Auteurs: Spalding, Dylan; Rambla, Jordi; Törnroos, Juha; Leinonen, Jaakko; Linden, Mikael; Human data community
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452470

D1.3 Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis

Auteurs: Ison, Jon; Ienasescu, Hans; Chmura, Piotr; Menager, Herve; ELIXIR Tools community
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1456754

D4.3 The ELIXIR Compute Platform: A Technical Services Roadmap for supporting Life Science Research in Europe

Auteurs: Newhouse, Steven; Nyrönen, Tommi; Matyska, Ludek; ELIXIR Compute platform community
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1457169

D1.8 Tools Interoperability and Service Registry

Auteurs: Palmblad, Magnus, Lamprecht, Anna-Lena; Schwämmle, Veit; Ison, Jon
Publié dans: Zenodo, 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1456766

D9.4 Report on implementation of cloud access and secure user and data management

Auteurs: Spalding, Dylan; Parkinson, Helen; Rambla, Jordi; Lappalainen, Ilkka; Tornroos, Juha; Senf, Alexander; Keane, Thomas
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1452474

Strategy for the adoption and use of an AAI within ELIXIR

Auteurs: ELIXIR Compute platform
Publié dans: 2016
Éditeur: ZENODO
DOI: 10.5281/zenodo.148302

ELIXIR-EXCELERATE D8.6: Documentation on adequate quality reporting standards for genomics datasets

Auteurs: Trotta, Jean-Rémi; Laurie, Steve; Matalonga, Leslie; Gut, Marta; Beltran, Sergi; Gut, Ivo G.
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.3209549

FAIR Computational Workflows

Auteurs: Carole Goble; Sarah Cohen-Boulakia; Daniel Schober; Kristian Peters; Stian Soiland-Reyes; Daniel Garijo; Yolanda Gil; Michael R. Crusoe
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.2642530

ELIXIR-EXCELERATE D6.5: Improvement and Application of Eukaryotic Gene catalogue

Auteurs: Pelletier, Eric; Corre, Erwan; Niang, Guita; Meng, Arnaud; Hoebeke, Mark; Finn, Robert
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3234522

ELIXIR-EXCELERATE D5.3: Bring Your Own Data (BYOD)

Auteurs: Hooft, Rob; Goble, Carole; Evelo, Chris; Roos, Marco; Sansone, Susanna; Ehrhart, Friederike; Kuzak, Mateusz; Carta, Claudio; Parkinson, Helen; Jansen, Mascha; Mons, Barend
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3207809

ELIXIR-EXCELERATE D8.5: Report on the ELIXIR workshops organized with the Rare Diseases communities

Auteurs: Leskosek, Brane; Matalonga, Leslie; Beltran, Sergi; Roos, Marco
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3234533

ELIXIR-EXCELERATE D6.3: Report describing a set of tools, pipelines and search engine for interrogation of marine metagenomic data.

Auteurs: Mitchell, Alex; Scheremetjew, Maxim; De Moro, Gianluca; Fosso, Bruno; Santamaria, Monica; Pesole, Graziano; Raj, Shriya; Bongo, Lars Ailo; Willassen, Nils Peder; Finn, Robert D.
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3228302

ELIXIR-EXCELERATE D6.4: Report on assessment criteria and standardisation of metagenome assembled genomes (MAGs) from Marine samples

Auteurs: Finn, Robert; Mitchell, Alex; Cochrane, Guy; Burgin, Josephine; Willassen, Nils Peder
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3234520

ELIXIR-EXCELERATE D8.7: Options for sustainability of RD-Connect within the scope of ELIXIR

Auteurs: Gut, Ivo G.; Beltran, Sergi; Roos, Marco; Blomberg, Niklas; Scollen, Serena; Matalonga, Leslie; Saunders, Gary
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3228294

ELIXIR-EXCELERATE D13.4 The impact of the Innovation and SME Programme on industry users

Auteurs: Lauer, Katharina; Smith, Andrew
Publié dans: Numéro 1, 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3357734

ELIXIR-EXCELERATE D3.3: Report describing ELIXIR-wide systems for the computer-assisted collection and delivery of harmonised metrics and quality criteria from multiple ELIXIR resources and collation of these at the ELIXIR Hub

Auteurs: Durinx, Christine; Drysdale, Rachel; McEntyre, Jo; Stockinger, Heinz; Haas, Juergen; Redaschi, Nicole; Venkatesan, Aravind; Gruhl, Franziska; Cook, Chuck
Publié dans: Numéro 3, 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3362082

"ELIXIR-EXCELERATE D10.1: Communities of ""Good Practice"" and Protocols of Transfer"

Auteurs: Lantz, Henrik; Persson, Bengt; Vondrášek, Jirí; Leskošek, Brane
Publié dans: Numéro 3, 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3354328

ELIXIR-EXCELERATE D2.4: Final report on the impact of ELIXIR infrastructure for hosting scientific benchmarking and technical monitoring results

Auteurs: Capella-Gutierrez, Salvador; Haas, Juergen; Gelpí, Josep Ll.; Fernández, José Maria
Publié dans: Numéro 1, 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3362116

ELIXIR-EXCELERATE D7.3: Implementation of BRAPI (Plant Breeding API) at all participating nodes

Auteurs: Miguel, Célia; Pommier, Cyril; Finkers, Richard; Coppens, Frederik; Bolser, Dan; Ruiz, Manuel; Adam-Blondon, Anne-Françoise; Gruden, Kristina; Ramšak, Živa; Papoutsoglou, Evangelia; Faria, Daniel; Costa, Bruno; Chaves, Inês
Publié dans: Numéro 1, 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3354265

ELIXIR-EXCELERATE D13.3: Fast-track ELIXIR implementation and drive early user exploitation across the life sciences

Auteurs: Martin, Corrine; Smith, Andrew; Blomberg, Niklas; Velek, Premysl; Balzano, Melissa; Berman, Maia; Cook, Martin; Coppens, Frederik; Drysdale, Rachel; Durinx, Christine; Hancock, John; Harrow, Jennifer; Lanfear, Jerry; Lauer, Katharina; Palagi, Patricia; Pommier, Cyril; Repo, Susanna; Sansone, Susanna; Sarntivijai, Sirarat; Saunders, Gary; Tedds, Jonathan; van Gelder, Celia
Publié dans: Numéro 3, 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3384778

ELIXIR-EXCELERATE D4.4: ELIXIR Technical Services document

Auteurs: Blanchet, Christophe; Borg, Mikael; Chien, Jinny; Codo, Laia; Gelpi, Jose Ll.; GonzaLEZ, Montserrat; Laitinen, Jarno; Lappalainen, Ilkka; Linden, Mikael; Matyska, Ludek; Newhouse, Steven; Nyrönen, Tommi; Prochazka, Michael; Ruda, Mirek; Salminen, Harri; Staiger, Christine; Tedds, Jonathan; Törnroos, Juha; Varma, Susheel; Wildish, Tony
Publié dans: Numéro 1, 2019
Éditeur: Zenodo
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ELIXIR-EXCELERATE D10.2: Blueprint on how to set up an ELIXIR data Node

Auteurs: Persson, Bengt; Jareborg, Niclas
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Éditeur: Zenodo
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2017-2018 Activity Report, FRENCH INSTITUTE OF BIOINFORMATICS

Auteurs: DOMINGUEZ DEL ANGEL Victoria; SAND Olivier; MEDIGUE Claudine; VAN HELDEN Jacques
Publié dans: Numéro 2, 2019
Éditeur: Zenodo
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3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures

Auteurs: Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Publié dans: 2017
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The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Auteurs: Pedro G. Ferreira, Manuel Muñoz-Aguirre, Ferran Reverter, Caio P. Sá Godinho, Abel Sousa, Alicia Amadoz, Reza Sodaei, Marta R. Hidalgo, Dmitri Pervouchine, Jose Carbonell-Caballero, Ramil Nurtdinov, Alessandra Breschi, Raziel Amador, Patrícia Oliveira, Cankut Çubuk, João Curado, François Aguet, Carla Oliveira, Joaquin Dopazo, Michael Sammeth, Kristin G. Ardlie, Roderic Guigó
Publié dans: Nature Communications, Numéro 9/1, 2018, ISSN 2041-1723
Éditeur: Nature Publishing Group
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PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

Auteurs: Michiel Van Bel, Tim Diels, Emmelien Vancaester, Lukasz Kreft, Alexander Botzki, Yves Van de Peer, Frederik Coppens, Klaas Vandepoele
Publié dans: Nucleic Acids Research, Numéro 46/D1, 2017, Page(s) D1190-D1196, ISSN 0305-1048
Éditeur: Oxford University Press
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Ten steps to get started in Genome Assembly and Annotation

Auteurs: Victoria Dominguez Del Angel, Erik Hjerde, Lieven Sterck, Salvadors Capella-Gutierrez, Cederic Notredame, Olga Vinnere Pettersson, Joelle Amselem, Laurent Bouri, Stephanie Bocs, Christophe Klopp, Jean-Francois Gibrat, Anna Vlasova, Brane L. Leskosek, Lucile Soler, Mahesh Binzer-Panchal, Henrik Lantz
Publié dans: F1000Research, Numéro 7, 2018, Page(s) 148, ISSN 2046-1402
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mORCA: ubiquitous access to life science web services

Auteurs: Sergio Diaz-del-Pino, Oswaldo Trelles, Juan Falgueras
Publié dans: BMC Genomics, Numéro 19/1, 2018, ISSN 1471-2164
Éditeur: BioMed Central
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A-GAME: improving the assembly of pooled functional metagenomics sequence data

Auteurs: Matteo Chiara, Antonio Placido, Ernesto Picardi, Luigi Ruggiero Ceci, David Stephen Horner, Graziano Pesole
Publié dans: BMC Genomics, Numéro 19/1, 2018, ISSN 1471-2164
Éditeur: BioMed Central
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Identifying temporal patterns in patient disease trajectories using dynamic time warping: A population-based study

Auteurs: Alexia Giannoula, Alba Gutierrez-Sacristán, Álex Bravo, Ferran Sanz, Laura I. Furlong
Publié dans: Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur: Nature Publishing Group
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The MAR databases: development and implementation of databases specific for marine metagenomics

Auteurs: Terje Klemetsen, Inge A Raknes, Juan Fu, Alexander Agafonov, Sudhagar V Balasundaram, Giacomo Tartari, Espen Robertsen, Nils P Willassen
Publié dans: Nucleic Acids Research, Numéro 46/D1, 2017, Page(s) D692-D699, ISSN 0305-1048
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Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes

Auteurs: Joaquin Dopazo, Cesim Erten
Publié dans: BMC Systems Biology, Numéro 11/1, 2017, ISSN 1752-0509
Éditeur: BioMed Central
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Europe PMC in 2017

Auteurs: Maria Levchenko, Yuci Gou, Florian Graef, Audrey Hamelers, Zhan Huang, Michele Ide-Smith, Anusha Iyer, Oliver Kilian, Jyothi Katuri, Jee-Hyub Kim, Nikos Marinos, Rakesh Nambiar, Michael Parkin, Xingjun Pi, Frances Rogers, Francesco Talo, Vid Vartak, Aravind Venkatesan, Johanna McEntyre
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HGVA: the Human Genome Variation Archive

Auteurs: Javier Lopez, Jacobo Coll, Matthias Haimel, Swaathi Kandasamy, Joaquin Tarraga, Pedro Furio-Tari, Wasim Bari, Marta Bleda, Antonio Rueda, Stefan Gräf, Augusto Rendon, Joaquin Dopazo, Ignacio Medina
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Text mining and expert curation to develop a database on psychiatric diseases and their genes

Auteurs: Alba Gutiérrez-Sacristán, Àlex Bravo, Marta Portero-Tresserra, Olga Valverde, Antonio Armario, M.C. Blanco-Gandía, Adriana Farré, Lierni Fernández-Ibarrondo, Francina Fonseca, Jesús Giraldo, Angela Leis, Anna Mané, M.A. Mayer, Sandra Montagud-Romero, Roser Nadal, Jordi Ortiz, Francisco Javier Pavon, Ezequiel Jesús Perez, Marta Rodríguez-Arias, Antonia Serrano, Marta Torrens, Vincent Warn
Publié dans: Database, Numéro 2017/1, 2017, ISSN 1758-0463
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ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR

Auteurs: L. Larcombe, R. Hendricusdottir, T.K. Attwood, F. Bacall, N. Beard, L.J. Bellis, W.B. Dunn, J.M. Hancock, A. Nenadic, C. Orengo, B. Overduin, S-A Sansone, M. Thurston, M.R. Viant, C.L. Winder, C.A. Goble, C.P. Ponting, G. Rustici
Publié dans: F1000Research, Numéro 6, 2017, Page(s) 952, ISSN 2046-1402
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Four simple recommendations to encourage best practices in research software

Auteurs: Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, D
Publié dans: F1000Research, Numéro 6, 2017, Page(s) 876, ISSN 2046-1402
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PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update

Auteurs: Víctor López-Ferrando, Andrea Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Ll Gelpí
Publié dans: Nucleic Acids Research, Numéro 45/W1, 2017, Page(s) W222-W228, ISSN 0305-1048
Éditeur: Oxford University Press
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Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

Auteurs: Kuzmanic, A.; Sutto, L.; Saladino, G.; Nebreda, A. R.; Gervasio, F. L.; Orozco, M.
Publié dans: eLife , 6 , Article e22175. (2017), Numéro 2, 2017, ISSN 2050-084X
Éditeur: eLife Sciences Publications
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The Functional Impact of Alternative Splicing in Cancer

Auteurs: Héctor Climente-González, Eduard Porta-Pardo, Adam Godzik, Eduardo Eyras
Publié dans: Cell Reports, Numéro 20/9, 2017, Page(s) 2215-2226, ISSN 2211-1247
Éditeur: Cell Press
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Enhancing identification of cancer types via lowly-expressed microRNAs

Auteurs: Roni Rasnic, Nathan Linial, Michal Linial
Publié dans: Nucleic Acids Research, Numéro 45/9, 2017, Page(s) 5048-5060, ISSN 0305-1048
Éditeur: Oxford University Press
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Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

Auteurs: Annemarie H. Eckes, Tomasz Gubała, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, John M. Hancock, Graham King, Sarah C. Dyer, Wiktor Jurkowski
Publié dans: F1000Research, Numéro 6, 2017, Page(s) 465, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
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Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

Auteurs: Antonija Kuzmanic, Ludovico Sutto, Giorgio Saladino, Angel R Nebreda, Francesco L Gervasio, Modesto Orozco
Publié dans: eLife, Numéro 6, 2017, ISSN 2050-084X
Éditeur: eLife Sciences Publications
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A community proposal to integrate proteomics activities in ELIXIR

Auteurs: Juan Antonio Vizcaíno, Mathias Walzer, Rafael C. Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J.R. Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane, Kris Laukens, Fredrik Levander, Frederique Lisacek, Petr Novak, Magnus Palmblad, Damiano Piovesan, Alfred Pühler, Veit Schwämmle, Dirk Valkenborg, Merlijn van Rijswijk, Jiri Vondrasek,
Publié dans: F1000Research, Numéro 6, 2017, Page(s) 875, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
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Using bio.tools to generate and annotate workbench tool descriptions

Auteurs: Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager
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psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes

Auteurs: Alba Gutiérrez-Sacristán, Carles Hernández-Ferrer, Juan R González, Laura I Furlong
Publié dans: Bioinformatics, Numéro 33/24, 2017, Page(s) 4004-4006, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx506

The pan-cancer pathological regulatory landscape

Auteurs: Matias M. Falco, Marta Bleda, José Carbonell-Caballero, Joaquín Dopazo
Publié dans: Scientific Reports, Numéro 6/1, 2016, ISSN 2045-2322
Éditeur: Nature Publishing Group
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High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

Auteurs: Marta R. Hidalgo, Cankut Cubuk, Alicia Amadoz, Francisco Salavert, José Carbonell-Caballero, Joaquin Dopazo
Publié dans: Oncotarget, Numéro 8/3, 2017, ISSN 1949-2553
Éditeur: Impact Journals
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European Nucleotide Archive in 2016

Auteurs: Ana Luisa Toribio, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rosello, Nicole Silvester, Dmitriy Smirnov, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
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Éditeur: Oxford University Press
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DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

Auteurs: Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I. Furlong
Publié dans: Nucleic Acids Research, Numéro 45/D1, 2017, Page(s) D833-D839, ISSN 0305-1048
Éditeur: Oxford University Press
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3DBIONOTES: A unified, enriched and interactive view of macromolecular information

Auteurs: D. Tabas-Madrid, J. Segura, R. Sanchez-Garcia, J. Cuenca-Alba, C.O.S. Sorzano, J.M. Carazo
Publié dans: Journal of Structural Biology, Numéro 194/2, 2016, Page(s) 231-234, ISSN 1047-8477
Éditeur: Academic Press
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Reference genome assessment from a population scale perspective: an accurate profile of variability and noise

Auteurs: José Carbonell-Caballero, Alicia Amadoz, Roberto Alonso, Marta R Hidalgo, Cankut Çubuk, David Conesa, Antonio López-Quílez, Joaquín Dopazo
Publié dans: Bioinformatics, Numéro 33/22, 2017, Page(s) 3511-3517, ISSN 1367-4803
Éditeur: Oxford University Press
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BioCIDER: a Contextualisation InDEx for biological Resources discovery

Auteurs: Carlos Horro, Martin Cook, Teresa K Attwood, Michelle D Brazas, John M Hancock, Patricia Palagi, Manuel Corpas, Rafael Jimenez
Publié dans: Bioinformatics, Numéro 33/16, 2017, Page(s) 2607-2608, ISSN 1367-4803
Éditeur: Oxford University Press
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Neuro-symbolic representation learning on biological knowledge graphs

Auteurs: Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf
Publié dans: Bioinformatics, Numéro 33/17, 2017, Page(s) 2723-2730, ISSN 1367-4803
Éditeur: Oxford University Press
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Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology

Auteurs: Joaquim Aguirre-Plans, Janet Piñero, Jörg Menche, Ferran Sanz, Laura Furlong, Harald Schmidt, Baldo Oliva, Emre Guney
Publié dans: Pharmaceuticals, Numéro 11/3, 2018, Page(s) 61, ISSN 1424-8247
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
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Registered access: authorizing data access

Auteurs: Stephanie O. M. Dyke, Mikael Linden, Ilkka Lappalainen, Jordi Rambla De Argila, Knox Carey, David Lloyd, J. Dylan Spalding, Moran N. Cabili, Giselle Kerry, Julia Foreman, Tim Cutts, Mahsa Shabani, Laura L. Rodriguez, Maximilian Haeussler, Brian Walsh, Xiaoqian Jiang, Shuang Wang, Daniel Perrett, Tiffany Boughtwood, Andreas Matern, Anthony J. Brookes, Miro Cupak, Marc Fiume, Ravi Pandya, Ilia Tulch
Publié dans: European Journal of Human Genetics, 2018, ISSN 1018-4813
Éditeur: Natue Publishing Group
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From Wet‐Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing

Auteurs: Chacón, Alejandro; Camps, Jordi; Espinosa, Antonio; Gut, Marta; Laurie, Steve; Marco‐Sola, Santiago; Heath, Simon; Trotta, Jean‐Remi; Beltran, Sergi; Gut, Ivo; Fernandez‐Callejo, Marcos
Publié dans: Human Mutation, Numéro 2, 2016, ISSN 1098-1004
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Integration of EGA secure data access into Galaxy

Auteurs: Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, Dylan Spalding, Sanne Abeln
Publié dans: F1000Research, Numéro 5, 2016, Page(s) 2841, ISSN 2046-1402
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The ELIXIR channel in F1000Research

Auteurs: Niklas Blomberg, Arlindo Oliveira, Barend Mons, Bengt Persson, Inge Jonassen
Publié dans: F1000Research, 2015, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
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SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data

Auteurs: Aravind Venkatesan, Jee-Hyub Kim, Francesco Talo, Michele Ide-Smith, Julien Gobeill, Jacob Carter, Riza Batista-Navarro, Sophia Ananiadou, Patrick Ruch, Johanna McEntyre
Publié dans: Wellcome Open Research, Numéro 1, 2012, Page(s) 25, ISSN 2398-502X
Éditeur: Wellcome Open Research
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Identifying ELIXIR Core Data Resources

Auteurs: Christine Durinx, Jo McEntyre, Ron Appel, Rolf Apweiler, Mary Barlow, Niklas Blomberg, Chuck Cook, Elisabeth Gasteiger, Jee-Hyub Kim, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Alfonso Valencia
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Top 10 metrics for life science software good practices

Auteurs: Haydee Artaza, Neil Chue Hong, Manuel Corpas, Angel Corpuz, Rob Hooft, Rafael C. Jimenez, Brane Leskošek, Brett G. Olivier, Jan Stourac, Radka Svobodová Vařeková, Thomas Van Parys, Daniel Vaughan
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BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

Auteurs: Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codo, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Ramón Goñi, Modesto Orozco, Josep Ll. Gelpí
Publié dans: Nucleic Acids Research, Numéro 44/D1, 2016, Page(s) D272-D278, ISSN 0305-1048
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HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering

Auteurs: Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jan Brezovsky, Jiri Damborsky
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Tools and data services registry: a community effort to document bioinformatics resources

Auteurs: Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gat
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Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models

Auteurs: Francisco Salavert, Marta R. Hidago, Alicia Amadoz, Cankut Çubuk, Ignacio Medina, Daniel Crespo, Jose Carbonell-Caballero, Joaquín Dopazo
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Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text

Auteurs: Àlex Bravo, Tong Shu Li, Andrew I. Su, Benjamin M. Good, Laura I. Furlong
Publié dans: Database, Numéro 2016, 2016, Page(s) baw094, ISSN 1758-0463
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PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.

Auteurs: Jiří Damborský; Jaroslav Zendulka; Miloš Musil; Jan Štourač; Jaroslav Bendl; Jan Brezovský
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Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns

Auteurs: D. Digles, B. Zdrazil, J.-M. Neefs, H. Van Vlijmen, C. Herhaus, A. Caracoti, J. Brea, B. Roibás, M. I. Loza, N. Queralt-Rosinach, L. I. Furlong, A. Gaulton, L. Bartek, S. Senger, C. Chichester, O. Engkvist, C. T. Evelo, N. I. Franklin, D. Marren, G. F. Ecker, E. Jacoby
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A crowdsourcing workflow for extracting chemical-induced disease relations from free text

Auteurs: Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good, Andrew I. Su
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DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases

Auteurs: Núria Queralt-Rosinach, Janet Piñero, Àlex Bravo, Ferran Sanz, Laura I. Furlong
Publié dans: Bioinformatics, Numéro 32/14, 2016, Page(s) 2236-2238, ISSN 1367-4803
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Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing

Auteurs: Janet Piñero, Ariel Berenstein, Abel Gonzalez-Perez, Ariel Chernomoretz, Laura I. Furlong
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MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

Auteurs: Lukáš Pravda, David Sehnal, Dominik Toušek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vařeková, Jaroslav Koča, Michal Otyepka
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A novel duplication of PRMD13 causes North Carolina macular dystrophy: overexpression of PRDM13 orthologue in drosophila eye reproduces the human phenotype

Auteurs: Gaël Manes, Willy Joly, Thomas Guignard, Vasily Smirnov, Sylvie Berthemy, Béatrice Bocquet, Isabelle Audo, Christina Zeitz, José Sahel, Chantal Cazevieille, Audrey Sénéchal, Jean-François Deleuze, Hélène Blanché-Koch, Anne Boland, Patrick Carroll, David Geneviève, Xavier Zanlonghi, Carl Arndt, Christian P Hamel, Sabine Defoort-Dhellemmes, Isabelle Meunier
Publié dans: Human Molecular Genetics, Numéro 26/22, 2017, Page(s) 4367-4374, ISSN 0964-6906
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Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments

Auteurs: Alexandre Almeida, Alex L Mitchell, Aleksandra Tarkowska, Robert D Finn
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Éditeur: GigaScience, Oxford University Press
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mORCA: sailing bioinformatics world with mobile devices

Auteurs: Sergio Díaz-del-Pino, Juan Falgueras, Esteban Perez-Wohlfeil, Oswaldo Trelles
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Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx673

META-pipe Authorization service

Auteurs: Inge Alexander Raknes, Lars Ailo Bongo
Publié dans: F1000Research, Numéro 7, 2018, Page(s) 32, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.13256.2

The Multiple Roles of Waters in Protein Solvation

Auteurs: Adam Hospital, Michela Candotti, Josep Lluís Gelpí, Modesto Orozco
Publié dans: The Journal of Physical Chemistry B, Numéro 121/15, 2017, Page(s) 3636-3643, ISSN 1520-6106
Éditeur: American Chemical Society
DOI: 10.1021/acs.jpcb.6b09676

ReGaTE, Registration of Galaxy Tools in Elixir

Auteurs: Doppelt-Azeroual, O., Mareuil F., Deveaud, E.; Kalaš, M., Soranzo, N.; van den Beek, M., Grüning, B., Ison, J. and Ménager, H.
Publié dans: GigaScience, 2017, ISSN 2047-217X
Éditeur: Oxford University Press
DOI: 10.1093/gigascience/gix022

Validation of ligands in macromolecular structures determined by X-ray crystallography

Auteurs: Oliver S. Smart, Vladimír Horský, Swanand Gore, Radka Svobodová Vařeková, Veronika Bendová, Gerard J. Kleywegt, Sameer Velankar
Publié dans: Acta Crystallographica Section D Structural Biology, Numéro 74/3, 2018, Page(s) 228-236, ISSN 2059-7983
Éditeur: Acta Crystallographica Section D - STRUCTURAL BIOLOGY
DOI: 10.1107/S2059798318002541

neXtA 5 : accelerating annotation of articles via automated approaches in neXtProt

Auteurs: Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, Patrick Ruch
Publié dans: Database, Numéro 2016, 2016, Page(s) baw098, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/baw098

Worldwide Protein Data Bank validation information: usage and trends

Auteurs: Oliver S. Smart, Vladimír Horský, Swanand Gore, Radka Svobodová Vařeková, Veronika Bendová, Gerard J. Kleywegt, Sameer Velankar
Publié dans: Acta Crystallographica Section D Structural Biology, Numéro 74/3, 2018, Page(s) 237-244, ISSN 2059-7983
Éditeur: Acta Crystallographica Section D
DOI: 10.1107/S2059798318003303

Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer‐prone genodermatoses

Auteurs: E. Chacón‐Solano, C. León, F. Díaz, F. García‐García, M. García, M.J. Escámez, S. Guerrero‐Aspizua, C.J. Conti, Á. Mencía, L. Martínez‐Santamaría, S. Llames, M. Pévida, J. Carbonell‐Caballero, J.A. Puig‐Butillé, R. Maseda, S. Puig, R. de Lucas, E. Baselga, F. Larcher, J. Dopazo, M. Río
Publié dans: British Journal of Dermatology, Numéro 181/3, 2019, Page(s) 512-522, ISSN 0007-0963
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/bjd.17698

Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models

Auteurs: Cankut Çubuk, Marta R. Hidalgo, Alicia Amadoz, Kinza Rian, Francisco Salavert, Miguel A. Pujana, Francesca Mateo, Carmen Herranz, Jose Carbonell-Caballero, Joaquín Dopazo
Publié dans: npj Systems Biology and Applications, Numéro 5/1, 2019, ISSN 2056-7189
Éditeur: Europe PMC
DOI: 10.1038/s41540-019-0087-2

ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services

Auteurs: Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen
Publié dans: F1000Research, 2017, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.10443.1

MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data

Auteurs: B. Fosso M. Santamaria M. D’Antonio D. Lovero G. Corrado E. Vizza N. Passaro A.R. Garbuglia M.R. Capobianchi M. Crescenzi G. Valiente G. Pesole
Publié dans: Bioinformatics, 2017, ISSN 1460-2059
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx036

The FAIR Guiding Principles for scientific data management and stewardship

Auteurs: Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J.G. Gray, Paul Groth, Carole Gobl
Publié dans: Sci Data, 2016, ISSN 2052-4463
Éditeur: Springer Nature
DOI: 10.1038/sdata.2016.18

The discovery potential of RNA processing profiles

Auteurs: Amadís Pagès, Ivan Dotu, Joan Pallarès-Albanell, Eulàlia Martí, Roderic Guigó, Eduardo Eyras
Publié dans: Nucleic Acids Research, Numéro 46/3, 2017, Page(s) e15-e15, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkx1115

The European Nucleotide Archive in 2017

Auteurs: Nicole Silvester, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Peter W Harrison, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Manuela Menchi, Kethi Reddy, Nima Pakseresht, Jeena Rajan, Marc Rossello, Dmitriy Smirnov, Ana L Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
Publié dans: Nucleic Acids Research, Numéro 46/D1, 2017, Page(s) D36-D40, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkx1125

ChannelsDB: database of biomacromolecular tunnels and pores

Auteurs: Lukáš Pravda, David Sehnal, Radka Svobodová Vařeková, Veronika Navrátilová, Dominik Toušek, Karel Berka, Michal Otyepka, Jaroslav Koča
Publié dans: Nucleic Acids Research, Numéro 46/D1, 2017, Page(s) D399-D405, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkx868

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

Auteurs: Alex L Mitchell, Maxim Scheremetjew, Hubert Denise, Simon Potter, Aleksandra Tarkowska, Matloob Qureshi, Gustavo A Salazar, Sebastien Pesseat, Miguel A Boland, Fiona M I Hunter, Petra ten Hoopen, Blaise Alako, Clara Amid, Darren J Wilkinson, Thomas P Curtis, Guy Cochrane, Robert D Finn
Publié dans: Nucleic Acids Research, Numéro 46/D1, 2017, Page(s) D726-D735, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkx967

BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets

Auteurs: Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Spiros Skiadopoulos, Theodore Dalamagas
Publié dans: BMC Bioinformatics, Numéro 18/1, 2017, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-017-1812-8

VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy

Auteurs: José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves, Pablo Marín-Garcia, Ignacio Medina, Vicente Arnau, Joaquín Dopazo
Publié dans: BMC Bioinformatics, Numéro 18/1, 2017, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-017-1837-z

The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training

Auteurs: Sarah L Morgan, Patricia M Palagi, Pedro L Fernandes, Eija Koperlainen, Jure Dimec, Diana Marek, Lee Larcombe, Gabriella Rustici, Teresa K Attwood, Allegra Via
Publié dans: F1000Research, Numéro 6, 2017, Page(s) 1557, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.12332.1

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data

Auteurs: Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino Da Silva Santos, Jeroen Belien, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond Fijnema
Publié dans: F1000Research, Numéro 6, 2017, Page(s) 1488, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.12168.1

Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action

Auteurs: Aleksandra Pawlik, Celia W.G. van Gelder, Aleksandra Nenadic, Patricia M. Palagi, Eija Korpelainen, Philip Lijnzaad, Diana Marek, Susanna-Assunta Sansone, John Hancock, Carole Goble
Publié dans: F1000Research, Numéro 6, 2017, Page(s) 1040, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.11718.1

Tackling the challenges of matching biomedical ontologies

Auteurs: Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M. Couto, Isabel F. Cruz
Publié dans: Journal of Biomedical Semantics, Numéro 9/1, 2018, ISSN 2041-1480
Éditeur: Journal of Biomedical Science
DOI: 10.1186/s13326-017-0170-9

The metagenomic data life-cycle: standards and best practices

Auteurs: Petra ten Hoopen, Robert D. Finn, Lars Ailo Bongo, Erwan Corre, Bruno Fosso, Folker Meyer, Alex Mitchell, Eric Pelletier, Graziano Pesole, Monica Santamaria, Nils Peder Willassen, Guy Cochrane
Publié dans: GigaScience, Numéro 6/8, 2017, Page(s) 1-11, ISSN 2047-217X
Éditeur: Oxford Academic
DOI: 10.1093/gigascience/gix047

DATS, the data tag suite to enable discoverability of datasets

Auteurs: Susanna-Assunta Sansone, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, George Alter, Jeffrey S. Grethe, Hua Xu, Ian M. Fore, Jared Lyle, Anupama E. Gururaj, Xiaoling Chen, Hyeon-eui Kim, Nansu Zong, Yueling Li, Ruiling Liu, I. Burak Ozyurt, Lucila Ohno-Machado
Publié dans: Scientific Data, Numéro 4, 2017, Page(s) 170059, ISSN 2052-4463
Éditeur: Nature Research
DOI: 10.1038/sdata.2017.59

The draft genome sequence of cork oak

Auteurs: António Marcos Ramos, Ana Usié, Pedro Barbosa, Pedro M. Barros, Tiago Capote, Inês Chaves, Fernanda Simões, Isabl Abreu, Isabel Carrasquinho, Carlos Faro, Joana B. Guimarães, Diogo Mendonça, Filomena Nóbrega, Leandra Rodrigues, Nelson J. M. Saibo, Maria Carolina Varela, Conceição Egas, José Matos, Célia M. Miguel, M. Margarida Oliveira, Cândido P. Ricardo, Sónia Gonçalves
Publié dans: Scientific Data, Numéro 5, 2018, Page(s) 180069, ISSN 2052-4463
Éditeur: Scientific Data
DOI: 10.1038/sdata.2018.69

Uniform resolution of compact identifiers for biomedical data

Auteurs: Sarala M. Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A. McMurry, Niall Beard, Rafael Jimenez, Jeffrey S. Grethe, Henning Hermjakob, Maryann E. Martone, Tim Clark
Publié dans: Scientific Data, Numéro 5, 2018, Page(s) 180029, ISSN 2052-4463
Éditeur: Scientific Data
DOI: 10.1038/sdata.2018.29

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures

Auteurs: Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Publié dans: Bioinformatics, 2017, ISSN 1460-2059
Éditeur: Oxford Journals
DOI: 10.5281/zenodo.1038019

Report on the training needs identified across the ELIXIR community

Auteurs: Celia van Gelder; Sarah Morgan; Allegra Via; Rita Hendricusdottir; Eija Korpelainen; Chris Ponting; Terri Attwood; Patricia Palagi
Publié dans: Zenodo, 2016, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.61411

Data Quality Assurance Governance

Auteurs: M. Gonzalez; S. Suhr
Publié dans: Zenodo, 2016, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.61417

A Technical Services Roadmap for supporting Life Science Research in Europe

Auteurs: Lars Ailo Bongo; Mikael Borg; Amelie Cornelis; Montserrat Gonzalez; Luis Gracia; Rob Hooft; Jarno Laitinen; Ilkka Lappalainen; Mikael Linden; Ludek Matyska; Steven Newhouse; Tommi Nyrönen; Michal Prochazka; Mirek Ruda; Harri Salminen; Christine Staiger; Tony Wildish
Publié dans: Zenodo, 2016, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.60291

Auteurs: Johanna McEntyre; Christine Durinx; ELIXIR Partners
Publié dans: Zenodo, 2016, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.60706

Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis

Auteurs: All EXCELERATE-funded partners, and many other non- ELIXIR organisations (see https://bio.tools/governance) have contributed to this work
Publié dans: Zenodo, 2016, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.61416

Requirements analysis document

Auteurs: Dylan Spalding; Helen Parkinson; Jordi Rambla; Niclas Jareborg; Abdulrahman Azab; Ilkka Lappalainen; Jeff Almaida-King; Alexander Senf; Saif Ur-Rehman
Publié dans: Zenodo, 2016, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.61414

Creation of a database warehouse infrastructure for storing and organizing data for online performance assessment experiments

Auteurs: Salvador Capella-Gutierrez; Diana de la Iglesia; Jürgen Haas; Josep Lluís Gelpi; José María Fernández
Publié dans: Zenodo, 2017, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.557010

Specific marine databases

Auteurs: Inge Alexander Raknes; Guy Cochrane; Lars Ailo Bongo; Nils Peder Willassen; Rob Finn; Juan Fu; Sudhagar Veerabadran Balasundaram; Espen Robertsen; Terje Klementsen; Giacomo Tartari
Publié dans: Zenodo, 2017, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.557021

ELIXIR Ethics Policy

Auteurs: Stephanie Suhr; Niklas Blomberg
Publié dans: Zenodo, 2016, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.557027

A Node report on regional priorities and channels to use

Auteurs: Jaako Vilo; Ondřej Hradil; Babis Savakis; Brane Leskosek
Publié dans: Zenodo, 2017, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.557029

ELIXIR workshops organized with the Rare Disease community

Auteurs: Ivo Gut; Marco Roos; et al.
Publié dans: Zenodo, 2016, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.557065

ELIXIR Advanced workshops on genome annotation

Auteurs: Henrik Lantz; Bengt Persson
Publié dans: Zenodo, 2016, ISSN 0000-0000
Éditeur: Zenodo
DOI: 10.5281/zenodo.557060

Evaluation of chemical and gene/protein entity recognition systems at BioCreative V.5: the CEMP and GPRO patents tracks

Auteurs: Pérez-Pérez, Martin; Rabal, Obdulia; Pérez-Rodríguez, Gael; Vazquez, Miguel; Fdez-Riverola, Florentino; Oyarzabal, Julen; Valencia, Alfonso; Lourenço, Anália; Krallinger, Martin
Publié dans: 2017
Éditeur: Universidade do Minho

Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem

Auteurs: Palagi, Patricia M.; van Gelder, Celia W. G.; Attwood, Teresa K; Leskosek, Brane L.; Morgan, Sarah; Dimec, Jure; Mulder, Nicola
Publié dans: Numéro 1, 2016
Éditeur: Zenodo
DOI: 10.5281/zenodo.166378

Bioschemas.org

Auteurs: Carole Goble; Rafael Jimenez; Alasdair Gray; Niall Beard; Giuseppe Profiti; Norman Morrison
Publié dans: 2017
Éditeur: f1000Research
DOI: 10.7490/f1000research.1114493.1

EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats

Auteurs: Kalaš, Matúš; Plantard, Laure; Sladoje, Nataša; Lindblad, Joakim; Kirschmann, Moritz,; Jones, Martin; Chessel, Anatole; Scholz, Leandro,; Rössler, Fabienne; Dufour, Alexandre; Bogovic, John; Zhang, Chong; Waithe, Dominic; Sampaio, Paula; Paavolainen, Lassi; Hörl, David; Munck, Sebastien; Golani, Ofra; Moore, Josh; Gaignard, Alban; Levet, Florian; Paul-Gilloteaux, Perrine; Ison, Jon; Miura, K
Publié dans: NEUBIAS, Feb 2019, Luxembourg, Luxembourg, Numéro 1, 2019
Éditeur: HAL

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