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

Deliverables

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 1.1) - 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 10.1).

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

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Publications

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

Author(s): Guy Cochrane; Rob Finn; Nils Peder Willassen; Lars Ailo Bongo; Monica Santamaria; Bruno Fosso; Eric Pelletier; Erwan Corre; Alex Mitchell; Simon Potter
Published in: 2018
DOI: 10.5281/zenodo.1229221

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

Author(s): Stockinger, Heinz; Barlow, Mary; Cook, Chuck; Drysdale, Rachel; Gasteiger, Elisabeth; Kim, Jee-Hyub; Lopez, Rodrigo; Redaschi, Nicole; Teixeira, Daniel; Durinx, Christine; McEntyre, Johanna
Published in: 2018
DOI: 10.5281/zenodo.1194123

Uniform Resolution of Compact Identifiers for Biomedical Data

Author(s): Hermjakob, Henning; Mcmurry, Julie; Beard, Niall; Clark, Tim; Janée, Greg; Jimenez, Rafael; Grethe, Jeffrey; Wimalaratne, Sarala; Kunze, John; Juty, Nick
Published in: Issue 1, 2018
DOI: 10.1101/101279

ELIXIR EXCELERATE Deliverable D7.1

Author(s): Adam-Blondon, Anne-Françoise; Chaves, Inês; Coppens, Frederik; Finkers, Richard; Horro, Carlos; Kersey, Paul; Michotey, Celia; Miguel, Célia; Papoutsoglu, Evangelia; Pommier, Cyril; Ramsak, Ziva
Published in: 2017
DOI: 10.5281/zenodo.1111825

Framework For Quality Assessment Of Whole Genome, Cancer Sequences

Author(s): 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
Published in: 2017
DOI: 10.1101/140921

Signaling Pathway Activities Improve Prognosis for Breast Cancer

Author(s): Hidalgo, Marta; Dopazo, Joaquín; Vert, Jean-Philippe; Carbonell-Caballero, Jose; Amadoz, Alicia; Cubuk, Cankut; Jiao, Yunlong
Published in: 2017
DOI: 10.1101/132357

ELIXIR Handbook of Operations

Author(s): Niklas Blomberg; Martin Cook; Pablo Roman Garcia; Stephanie Suhr; Premysl Velek; Montserrat Gonzalez; Susanna Repo
Published in: 2018
DOI: 10.5281/zenodo.1289765

Research Object Community Update

Author(s): Carole Goble, Stian Soiland-Reyes, Sean Bechhofe
Published in: 2018
DOI: 10.5281/zenodo.1313066

Federated Identity Management for Research Collaborations

Author(s): 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
Published in: 2018
DOI: 10.5281/zenodo.1307551

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

Author(s): Beltran, Sergi; Coward, Eivind; Matalonga, Leslie; Drablos, Finn; Peterson, Hedi; Gut, Ivo; Roos, Marco
Published in: 2018
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

Author(s): 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
Published in: 2018
DOI: 10.5281/zenodo.1321902

Deliverable 13.2: Report on ELIXIR's Communication Strategy

Author(s): elek, Premysl; Wiles, Kayla; Smith, Andrew; Garcia Roman, Pablo; Cook, Martin; Cernoskova, Dana
Published in: 2018
DOI: 10.5281/zenodo.1321214

ELIXIR Advanced workshops on genome annotation

Author(s): Lantz, Henrik; Leskosek, Brane
Published in: 2018
DOI: 10.5281/zenodo.1321915

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

Author(s): Ison, Jon; Brunak, Søren; Tools platform community
Published in: 2018
DOI: 10.5281/zenodo.1321740

Release of a live ELIXIR Communication Strategy

Author(s): Premysl Velek; Andrew Smith
Published in: 2017
DOI: 10.5281/zenodo.557084

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

Author(s): Leskosek, Brane; Matalonga, Leslie; Kastrin, Andrej; Dimec, Jure; Femke Francissen; Beltran, Sergi; Coward, Eivind; Peterson, Hedi; Gut, Ivo; Roos, Marco; Varma, Susheel
Published in: 2018
DOI: 10.5281/zenodo.1321601

REPORT: Updated ELIXIR Technical Services Roadmap

Author(s): Nyrönen, Tommi; Matyska, Ludek; Newhouse, Steven; Compute platform community
Published in: 2018
DOI: 10.5281/zenodo.1321699

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

Author(s): Jacobsen, Annika; Thompson, Mark; Hanauer, Marc; Sergi, Beltran; Gray, Alasdair; Juty, Nick; Ehrhart, Friederike; Evelo, Chris
Published in: 2018
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

Author(s): McEntyre, Jo; Venkatesan, Aravind; Gobeill Julien; Piovesan, Damiano; Tosatto, Silvio; Ruch, Patrick
Published in: 2018
DOI: 10.5281/zenodo.1452442

D9.2 Report on implementation of submissions interface and API

Author(s): de la Torre, Sabela; Moldes, Mauricio; Rambla, Jordi
Published in: 2018
DOI: 10.5281/zenodo.1452480

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

Author(s): Ison, Jon; Ienasescu, Hans; Kalas, Matus; ELIXIR Tools community
Published in: 2018
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

Author(s): Rustici, Gabriella; Gurwitz, Kim; Louisa, Bellis; ELIXIR Training community
Published in: 2018
DOI: 10.5281/zenodo.1453021

D5.1 Interoperability Implementation Regulations.

Author(s): Goble, Carol; Evelo, Chris; Parkinson, Helen; ELIXIR Interoperability community
Published in: 2018
DOI: 10.5281/zenodo.1452415

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

Author(s): de la Torre, Sabela; Lloret-Villas, Audald; Rambla, Jordi
Published in: 2018
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

Author(s): Capella-Gutierrez, Salvador; Haas, Juergen; Ll. Gelpí, Josep; Mª. Fernández, Jose; Garrayo, Javier
Published in: 2018
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

Author(s): Gelpi Ll., Josep; Mª. Fernández, Jose; Sundesha, Vicky; Repchevsky; Haas, Juergen
Published in: 2018
DOI: 10.5281/zenodo.1452561

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

Author(s): Miguel, Célia; Pommier, Cyril; Finkers, Richard; Coppens, Frederik; Bolser, Dan
Published in: 2018
DOI: 10.5281/zenodo.1452452

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

Author(s): Spalding, Dylan; Rambla, Jordi; Törnroos, Juha; Leinonen, Jaakko; Linden, Mikael; Human data community
Published in: 2018
DOI: 10.5281/zenodo.1452470

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

Author(s): Ison, Jon; Ienasescu, Hans; Chmura, Piotr; Menager, Herve; ELIXIR Tools community
Published in: 2018
DOI: 10.5281/zenodo.1456754

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

Author(s): Newhouse, Steven; Nyrönen, Tommi; Matyska, Ludek; ELIXIR Compute platform community
Published in: 2018
DOI: 10.5281/zenodo.1457169

D1.8 Tools Interoperability and Service Registry

Author(s): Palmblad, Magnus, Lamprecht, Anna-Lena; Schwämmle, Veit; Ison, Jon
Published in: Zenodo, 2018
DOI: 10.5281/zenodo.1456766

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

Author(s): Spalding, Dylan; Parkinson, Helen; Rambla, Jordi; Lappalainen, Ilkka; Tornroos, Juha; Senf, Alexander; Keane, Thomas
Published in: 2018
DOI: 10.5281/zenodo.1452474

Strategy for the adoption and use of an AAI within ELIXIR

Author(s): ELIXIR Compute platform
Published in: 2016
DOI: 10.5281/zenodo.148302

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

Author(s): Trotta, Jean-Rémi; Laurie, Steve; Matalonga, Leslie; Gut, Marta; Beltran, Sergi; Gut, Ivo G.
Published in: 2018
DOI: 10.5281/zenodo.3209549

FAIR Computational Workflows

Author(s): Carole Goble; Sarah Cohen-Boulakia; Daniel Schober; Kristian Peters; Stian Soiland-Reyes; Daniel Garijo; Yolanda Gil; Michael R. Crusoe
Published in: 2019
DOI: 10.5281/zenodo.2642530

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

Author(s): Pelletier, Eric; Corre, Erwan; Niang, Guita; Meng, Arnaud; Hoebeke, Mark; Finn, Robert
Published in: 2019
DOI: 10.5281/zenodo.3234522

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

Author(s): Hooft, Rob; Goble, Carole; Evelo, Chris; Roos, Marco; Sansone, Susanna; Ehrhart, Friederike; Kuzak, Mateusz; Carta, Claudio; Parkinson, Helen; Jansen, Mascha; Mons, Barend
Published in: 2019
DOI: 10.5281/zenodo.3207809

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

Author(s): Leskosek, Brane; Matalonga, Leslie; Beltran, Sergi; Roos, Marco
Published in: 2019
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.

Author(s): Mitchell, Alex; Scheremetjew, Maxim; De Moro, Gianluca; Fosso, Bruno; Santamaria, Monica; Pesole, Graziano; Raj, Shriya; Bongo, Lars Ailo; Willassen, Nils Peder; Finn, Robert D.
Published in: 2019
DOI: 10.5281/zenodo.3228302

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

Author(s): Finn, Robert; Mitchell, Alex; Cochrane, Guy; Burgin, Josephine; Willassen, Nils Peder
Published in: 2019
DOI: 10.5281/zenodo.3234520

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

Author(s): Gut, Ivo G.; Beltran, Sergi; Roos, Marco; Blomberg, Niklas; Scollen, Serena; Matalonga, Leslie; Saunders, Gary
Published in: 2019
DOI: 10.5281/zenodo.3228294

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

Author(s): Lauer, Katharina; Smith, Andrew
Published in: Issue 1, 2019
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

Author(s): Durinx, Christine; Drysdale, Rachel; McEntyre, Jo; Stockinger, Heinz; Haas, Juergen; Redaschi, Nicole; Venkatesan, Aravind; Gruhl, Franziska; Cook, Chuck
Published in: Issue 3, 2019
DOI: 10.5281/zenodo.3362082

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

Author(s): Lantz, Henrik; Persson, Bengt; Vondrášek, Jirí; Leskošek, Brane
Published in: Issue 3, 2019
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

Author(s): Capella-Gutierrez, Salvador; Haas, Juergen; Gelpí, Josep Ll.; Fernández, José Maria
Published in: Issue 1, 2019
DOI: 10.5281/zenodo.3362116

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

Author(s): 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
Published in: Issue 1, 2019
DOI: 10.5281/zenodo.3354265

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

Author(s): 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
Published in: Issue 3, 2019
DOI: 10.5281/zenodo.3384778

ELIXIR-EXCELERATE D4.4: ELIXIR Technical Services document

Author(s): 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
Published in: Issue 1, 2019
DOI: 10.5281/zenodo.3381598

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

Author(s): Persson, Bengt; Jareborg, Niclas
Published in: Issue 3, 2019
DOI: 10.5281/zenodo.3381599

2017-2018 Activity Report, FRENCH INSTITUTE OF BIOINFORMATICS

Author(s): DOMINGUEZ DEL ANGEL Victoria; SAND Olivier; MEDIGUE Claudine; VAN HELDEN Jacques
Published in: Issue 2, 2019
DOI: 10.5281/zenodo.3520131

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

Author(s): Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Published in: 2017
DOI: 10.5281/zenodo.1038018

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Author(s): 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
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-017-02772-x

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

Author(s): Michiel Van Bel, Tim Diels, Emmelien Vancaester, Lukasz Kreft, Alexander Botzki, Yves Van de Peer, Frederik Coppens, Klaas Vandepoele
Published in: Nucleic Acids Research, Issue 46/D1, 2017, Page(s) D1190-D1196, ISSN 0305-1048
DOI: 10.1093/nar/gkx1002

Ten steps to get started in Genome Assembly and Annotation

Author(s): 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
Published in: F1000Research, Issue 7, 2018, Page(s) 148, ISSN 2046-1402
DOI: 10.12688/f1000research.13598.1

mORCA: ubiquitous access to life science web services

Author(s): Sergio Diaz-del-Pino, Oswaldo Trelles, Juan Falgueras
Published in: BMC Genomics, Issue 19/1, 2018, ISSN 1471-2164
DOI: 10.1186/s12864-018-4439-x

A-GAME: improving the assembly of pooled functional metagenomics sequence data

Author(s): Matteo Chiara, Antonio Placido, Ernesto Picardi, Luigi Ruggiero Ceci, David Stephen Horner, Graziano Pesole
Published in: BMC Genomics, Issue 19/1, 2018, ISSN 1471-2164
DOI: 10.1186/s12864-017-4369-z

Identifying temporal patterns in patient disease trajectories using dynamic time warping: A population-based study

Author(s): Alexia Giannoula, Alba Gutierrez-Sacristán, Álex Bravo, Ferran Sanz, Laura I. Furlong
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
DOI: 10.1038/s41598-018-22578-1

The MAR databases: development and implementation of databases specific for marine metagenomics

Author(s): Terje Klemetsen, Inge A Raknes, Juan Fu, Alexander Agafonov, Sudhagar V Balasundaram, Giacomo Tartari, Espen Robertsen, Nils P Willassen
Published in: Nucleic Acids Research, Issue 46/D1, 2017, Page(s) D692-D699, ISSN 0305-1048
DOI: 10.1093/nar/gkx1036

Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes

Author(s): Joaquin Dopazo, Cesim Erten
Published in: BMC Systems Biology, Issue 11/1, 2017, ISSN 1752-0509
DOI: 10.1186/s12918-017-0495-0

Europe PMC in 2017

Author(s): 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
Published in: Nucleic Acids Research, Issue 46/D1, 2017, Page(s) D1254-D1260, ISSN 0305-1048
DOI: 10.1093/nar/gkx1005

HGVA: the Human Genome Variation Archive

Author(s): 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
Published in: Nucleic Acids Research, Issue 45/W1, 2017, Page(s) W189-W194, ISSN 0305-1048
DOI: 10.1093/nar/gkx445

Text mining and expert curation to develop a database on psychiatric diseases and their genes

Author(s): 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
Published in: Database, Issue 2017/1, 2017, ISSN 1758-0463
DOI: 10.1093/database/bax043

ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR

Author(s): 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
Published in: F1000Research, Issue 6, 2017, Page(s) 952, ISSN 2046-1402
DOI: 10.12688/f1000research.11837.1

Four simple recommendations to encourage best practices in research software

Author(s): 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
Published in: F1000Research, Issue 6, 2017, Page(s) 876, ISSN 2046-1402
DOI: 10.12688/f1000research.11407.1

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update

Author(s): Víctor López-Ferrando, Andrea Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Ll Gelpí
Published in: Nucleic Acids Research, Issue 45/W1, 2017, Page(s) W222-W228, ISSN 0305-1048
DOI: 10.1093/nar/gkx313

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

Author(s): Kuzmanic, A.; Sutto, L.; Saladino, G.; Nebreda, A. R.; Gervasio, F. L.; Orozco, M.
Published in: eLife , 6 , Article e22175. (2017), Issue 2, 2017, ISSN 2050-084X
DOI: 10.7554/eLife.22175.001

The Functional Impact of Alternative Splicing in Cancer

Author(s): Héctor Climente-González, Eduard Porta-Pardo, Adam Godzik, Eduardo Eyras
Published in: Cell Reports, Issue 20/9, 2017, Page(s) 2215-2226, ISSN 2211-1247
DOI: 10.1016/j.celrep.2017.08.012

Enhancing identification of cancer types via lowly-expressed microRNAs

Author(s): Roni Rasnic, Nathan Linial, Michal Linial
Published in: Nucleic Acids Research, Issue 45/9, 2017, Page(s) 5048-5060, ISSN 0305-1048
DOI: 10.1093/nar/gkx210

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

Author(s): 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
Published in: F1000Research, Issue 6, 2017, Page(s) 465, ISSN 2046-1402
DOI: 10.12688/f1000research.11301.1

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

Author(s): Antonija Kuzmanic, Ludovico Sutto, Giorgio Saladino, Angel R Nebreda, Francesco L Gervasio, Modesto Orozco
Published in: eLife, Issue 6, 2017, ISSN 2050-084X
DOI: 10.7554/eLife.22175

A community proposal to integrate proteomics activities in ELIXIR

Author(s): 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,
Published in: F1000Research, Issue 6, 2017, Page(s) 875, ISSN 2046-1402
DOI: 10.12688/f1000research.11751.1

Using bio.tools to generate and annotate workbench tool descriptions

Author(s): Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager
Published in: F1000Research, Issue 6, 2017, Page(s) 2074, ISSN 2046-1402
DOI: 10.12688/f1000research.12974.1

psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes

Author(s): Alba Gutiérrez-Sacristán, Carles Hernández-Ferrer, Juan R González, Laura I Furlong
Published in: Bioinformatics, Issue 33/24, 2017, Page(s) 4004-4006, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btx506

The pan-cancer pathological regulatory landscape

Author(s): Matias M. Falco, Marta Bleda, José Carbonell-Caballero, Joaquín Dopazo
Published in: Scientific Reports, Issue 6/1, 2016, ISSN 2045-2322
DOI: 10.1038/srep39709

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

Author(s): Marta R. Hidalgo, Cankut Cubuk, Alicia Amadoz, Francisco Salavert, José Carbonell-Caballero, Joaquin Dopazo
Published in: Oncotarget, Issue 8/3, 2017, ISSN 1949-2553
DOI: 10.18632/oncotarget.14107

European Nucleotide Archive in 2016

Author(s): 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
Published in: Nucleic Acids Research, Issue 45/D1, 2017, Page(s) D32-D36, ISSN 0305-1048
DOI: 10.1093/nar/gkw1106

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

Author(s): Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I. Furlong
Published in: Nucleic Acids Research, Issue 45/D1, 2017, Page(s) D833-D839, ISSN 0305-1048
DOI: 10.1093/nar/gkw943

3DBIONOTES: A unified, enriched and interactive view of macromolecular information

Author(s): D. Tabas-Madrid, J. Segura, R. Sanchez-Garcia, J. Cuenca-Alba, C.O.S. Sorzano, J.M. Carazo
Published in: Journal of Structural Biology, Issue 194/2, 2016, Page(s) 231-234, ISSN 1047-8477
DOI: 10.1016/j.jsb.2016.02.007

Reference genome assessment from a population scale perspective: an accurate profile of variability and noise

Author(s): José Carbonell-Caballero, Alicia Amadoz, Roberto Alonso, Marta R Hidalgo, Cankut Çubuk, David Conesa, Antonio López-Quílez, Joaquín Dopazo
Published in: Bioinformatics, Issue 33/22, 2017, Page(s) 3511-3517, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btx482

BioCIDER: a Contextualisation InDEx for biological Resources discovery

Author(s): Carlos Horro, Martin Cook, Teresa K Attwood, Michelle D Brazas, John M Hancock, Patricia Palagi, Manuel Corpas, Rafael Jimenez
Published in: Bioinformatics, Issue 33/16, 2017, Page(s) 2607-2608, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btx213

Neuro-symbolic representation learning on biological knowledge graphs

Author(s): Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf
Published in: Bioinformatics, Issue 33/17, 2017, Page(s) 2723-2730, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btx275

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology

Author(s): Joaquim Aguirre-Plans, Janet Piñero, Jörg Menche, Ferran Sanz, Laura Furlong, Harald Schmidt, Baldo Oliva, Emre Guney
Published in: Pharmaceuticals, Issue 11/3, 2018, Page(s) 61, ISSN 1424-8247
DOI: 10.3390/ph11030061

Registered access: authorizing data access

Author(s): 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
Published in: European Journal of Human Genetics, 2018, ISSN 1018-4813
DOI: 10.1038/s41431-018-0219-y

From Wet‐Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing

Author(s): 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
Published in: Human Mutation, Issue 2, 2016, ISSN 1098-1004
DOI: 10.1002/humu.23114

Integration of EGA secure data access into Galaxy

Author(s): 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
Published in: F1000Research, Issue 5, 2016, Page(s) 2841, ISSN 2046-1402
DOI: 10.12688/f1000research.10221.1

The ELIXIR channel in F1000Research

Author(s): Niklas Blomberg, Arlindo Oliveira, Barend Mons, Bengt Persson, Inge Jonassen
Published in: F1000Research, 2015, ISSN 2046-1402
DOI: 10.12688/f1000research.7587.1

SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data

Author(s): Aravind Venkatesan, Jee-Hyub Kim, Francesco Talo, Michele Ide-Smith, Julien Gobeill, Jacob Carter, Riza Batista-Navarro, Sophia Ananiadou, Patrick Ruch, Johanna McEntyre
Published in: Wellcome Open Research, Issue 1, 2012, Page(s) 25, ISSN 2398-502X
DOI: 10.12688/wellcomeopenres.10210.1

Identifying ELIXIR Core Data Resources

Author(s): 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
Published in: F1000Research, Issue 5, 2016, Page(s) 2422, ISSN 2046-1402
DOI: 10.12688/f1000research.9656.1

Top 10 metrics for life science software good practices

Author(s): 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
Published in: F1000Research, Issue 5, 2016, Page(s) 2000, ISSN 2046-1402
DOI: 10.12688/f1000research.9206.1

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

Author(s): Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codo, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Ramón Goñi, Modesto Orozco, Josep Ll. Gelpí
Published in: Nucleic Acids Research, Issue 44/D1, 2016, Page(s) D272-D278, ISSN 0305-1048
DOI: 10.1093/nar/gkv1301

HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering

Author(s): Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jan Brezovsky, Jiri Damborsky
Published in: Nucleic Acids Research, Issue 44/W1, 2016, Page(s) W479-W487, ISSN 0305-1048
DOI: 10.1093/nar/gkw416

Tools and data services registry: a community effort to document bioinformatics resources

Author(s): 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
Published in: Nucleic Acids Research, Issue 44/D1, 2016, Page(s) D38-D47, ISSN 0305-1048
DOI: 10.1093/nar/gkv1116

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models

Author(s): Francisco Salavert, Marta R. Hidago, Alicia Amadoz, Cankut Çubuk, Ignacio Medina, Daniel Crespo, Jose Carbonell-Caballero, Joaquín Dopazo
Published in: Nucleic Acids Research, Issue 44/W1, 2016, Page(s) W212-W216, ISSN 0305-1048
DOI: 10.1093/nar/gkw369

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text

Author(s): Àlex Bravo, Tong Shu Li, Andrew I. Su, Benjamin M. Good, Laura I. Furlong
Published in: Database, Issue 2016, 2016, Page(s) baw094, ISSN 1758-0463
DOI: 10.1093/database/baw094

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.

Author(s): Jiří Damborský; Jaroslav Zendulka; Miloš Musil; Jan Štourač; Jaroslav Bendl; Jan Brezovský
Published in: PLoS Computational Biology, Issue 1, 2016, ISSN 1553-734X
DOI: 10.1371/journal.pcbi.1004962

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns

Author(s): 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
Published in: Med. Chem. Commun., Issue 7/6, 2016, Page(s) 1237-1244, ISSN 2040-2503
DOI: 10.1039/C6MD00065G

A crowdsourcing workflow for extracting chemical-induced disease relations from free text

Author(s): Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good, Andrew I. Su
Published in: Database, Issue 2016, 2016, Page(s) baw051, ISSN 1758-0463
DOI: 10.1093/database/baw051

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases

Author(s): Núria Queralt-Rosinach, Janet Piñero, Àlex Bravo, Ferran Sanz, Laura I. Furlong
Published in: Bioinformatics, Issue 32/14, 2016, Page(s) 2236-2238, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btw214

Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing

Author(s): Janet Piñero, Ariel Berenstein, Abel Gonzalez-Perez, Ariel Chernomoretz, Laura I. Furlong
Published in: Scientific Reports, Issue 6, 2016, Page(s) 24570, ISSN 2045-2322
DOI: 10.1038/srep24570

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

Author(s): Lukáš Pravda, David Sehnal, Dominik Toušek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vařeková, Jaroslav Koča, Michal Otyepka
Published in: Nucleic Acids Research, Issue 46/W1, 2018, Page(s) W368-W373, ISSN 0305-1048
DOI: 10.1093/nar/gky309

A novel duplication of PRMD13 causes North Carolina macular dystrophy: overexpression of PRDM13 orthologue in drosophila eye reproduces the human phenotype

Author(s): 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
Published in: Human Molecular Genetics, Issue 26/22, 2017, Page(s) 4367-4374, ISSN 0964-6906
DOI: 10.1093/hmg/ddx322

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments

Author(s): Alexandre Almeida, Alex L Mitchell, Aleksandra Tarkowska, Robert D Finn
Published in: GigaScience, Issue 7/5, 2018, ISSN 2047-217X
DOI: 10.1093/gigascience/giy054

mORCA: sailing bioinformatics world with mobile devices

Author(s): Sergio Díaz-del-Pino, Juan Falgueras, Esteban Perez-Wohlfeil, Oswaldo Trelles
Published in: Bioinformatics, Issue 34/5, 2017, Page(s) 869-870, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btx673

META-pipe Authorization service

Author(s): Inge Alexander Raknes, Lars Ailo Bongo
Published in: F1000Research, Issue 7, 2018, Page(s) 32, ISSN 2046-1402
DOI: 10.12688/f1000research.13256.2

The Multiple Roles of Waters in Protein Solvation

Author(s): Adam Hospital, Michela Candotti, Josep Lluís Gelpí, Modesto Orozco
Published in: The Journal of Physical Chemistry B, Issue 121/15, 2017, Page(s) 3636-3643, ISSN 1520-6106
DOI: 10.1021/acs.jpcb.6b09676

ReGaTE, Registration of Galaxy Tools in Elixir

Author(s): Doppelt-Azeroual, O., Mareuil F., Deveaud, E.; Kalaš, M., Soranzo, N.; van den Beek, M., Grüning, B., Ison, J. and Ménager, H.
Published in: GigaScience, 2017, ISSN 2047-217X
DOI: 10.1093/gigascience/gix022

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

Author(s): Oliver S. Smart, Vladimír Horský, Swanand Gore, Radka Svobodová Vařeková, Veronika Bendová, Gerard J. Kleywegt, Sameer Velankar
Published in: Acta Crystallographica Section D Structural Biology, Issue 74/3, 2018, Page(s) 228-236, ISSN 2059-7983
DOI: 10.1107/S2059798318002541

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

Author(s): Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, Patrick Ruch
Published in: Database, Issue 2016, 2016, Page(s) baw098, ISSN 1758-0463
DOI: 10.1093/database/baw098

Worldwide Protein Data Bank validation information: usage and trends

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

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

Author(s): 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
Published in: British Journal of Dermatology, Issue 181/3, 2019, Page(s) 512-522, ISSN 0007-0963
DOI: 10.1111/bjd.17698

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

Author(s): Cankut Çubuk, Marta R. Hidalgo, Alicia Amadoz, Kinza Rian, Francisco Salavert, Miguel A. Pujana, Francesca Mateo, Carmen Herranz, Jose Carbonell-Caballero, Joaquín Dopazo
Published in: npj Systems Biology and Applications, Issue 5/1, 2019, ISSN 2056-7189
DOI: 10.1038/s41540-019-0087-2

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

Author(s): Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen
Published in: F1000Research, 2017, ISSN 2046-1402
DOI: 10.12688/f1000research.10443.1

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

Author(s): 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
Published in: Bioinformatics, 2017, ISSN 1460-2059
DOI: 10.1093/bioinformatics/btx036

The FAIR Guiding Principles for scientific data management and stewardship

Author(s): 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
Published in: Sci Data, 2016, ISSN 2052-4463
DOI: 10.1038/sdata.2016.18

The discovery potential of RNA processing profiles

Author(s): Amadís Pagès, Ivan Dotu, Joan Pallarès-Albanell, Eulàlia Martí, Roderic Guigó, Eduardo Eyras
Published in: Nucleic Acids Research, Issue 46/3, 2017, Page(s) e15-e15, ISSN 0305-1048
DOI: 10.1093/nar/gkx1115

The European Nucleotide Archive in 2017

Author(s): 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
Published in: Nucleic Acids Research, Issue 46/D1, 2017, Page(s) D36-D40, ISSN 0305-1048
DOI: 10.1093/nar/gkx1125

ChannelsDB: database of biomacromolecular tunnels and pores

Author(s): Lukáš Pravda, David Sehnal, Radka Svobodová Vařeková, Veronika Navrátilová, Dominik Toušek, Karel Berka, Michal Otyepka, Jaroslav Koča
Published in: Nucleic Acids Research, Issue 46/D1, 2017, Page(s) D399-D405, ISSN 0305-1048
DOI: 10.1093/nar/gkx868

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

Author(s): 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
Published in: Nucleic Acids Research, Issue 46/D1, 2017, Page(s) D726-D735, ISSN 0305-1048
DOI: 10.1093/nar/gkx967

BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets

Author(s): Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Spiros Skiadopoulos, Theodore Dalamagas
Published in: BMC Bioinformatics, Issue 18/1, 2017, ISSN 1471-2105
DOI: 10.1186/s12859-017-1812-8

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

Author(s): José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves, Pablo Marín-Garcia, Ignacio Medina, Vicente Arnau, Joaquín Dopazo
Published in: BMC Bioinformatics, Issue 18/1, 2017, ISSN 1471-2105
DOI: 10.1186/s12859-017-1837-z

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

Author(s): Sarah L Morgan, Patricia M Palagi, Pedro L Fernandes, Eija Koperlainen, Jure Dimec, Diana Marek, Lee Larcombe, Gabriella Rustici, Teresa K Attwood, Allegra Via
Published in: F1000Research, Issue 6, 2017, Page(s) 1557, ISSN 2046-1402
DOI: 10.12688/f1000research.12332.1

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

Author(s): 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
Published in: F1000Research, Issue 6, 2017, Page(s) 1488, ISSN 2046-1402
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

Author(s): 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
Published in: F1000Research, Issue 6, 2017, Page(s) 1040, ISSN 2046-1402
DOI: 10.12688/f1000research.11718.1

Tackling the challenges of matching biomedical ontologies

Author(s): Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M. Couto, Isabel F. Cruz
Published in: Journal of Biomedical Semantics, Issue 9/1, 2018, ISSN 2041-1480
DOI: 10.1186/s13326-017-0170-9

The metagenomic data life-cycle: standards and best practices

Author(s): 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
Published in: GigaScience, Issue 6/8, 2017, Page(s) 1-11, ISSN 2047-217X
DOI: 10.1093/gigascience/gix047

DATS, the data tag suite to enable discoverability of datasets

Author(s): 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
Published in: Scientific Data, Issue 4, 2017, Page(s) 170059, ISSN 2052-4463
DOI: 10.1038/sdata.2017.59

The draft genome sequence of cork oak

Author(s): 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
Published in: Scientific Data, Issue 5, 2018, Page(s) 180069, ISSN 2052-4463
DOI: 10.1038/sdata.2018.69

Uniform resolution of compact identifiers for biomedical data

Author(s): 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
Published in: Scientific Data, Issue 5, 2018, Page(s) 180029, ISSN 2052-4463
DOI: 10.1038/sdata.2018.29

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

Author(s): Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Published in: Bioinformatics, 2017, ISSN 1460-2059
DOI: 10.5281/zenodo.1038019

Report on the training needs identified across the ELIXIR community

Author(s): Celia van Gelder; Sarah Morgan; Allegra Via; Rita Hendricusdottir; Eija Korpelainen; Chris Ponting; Terri Attwood; Patricia Palagi
Published in: Zenodo, 2016, ISSN 0000-0000
DOI: 10.5281/zenodo.61411

Data Quality Assurance Governance

Author(s): M. Gonzalez; S. Suhr
Published in: Zenodo, 2016, ISSN 0000-0000
DOI: 10.5281/zenodo.61417

A Technical Services Roadmap for supporting Life Science Research in Europe

Author(s): 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
Published in: Zenodo, 2016, ISSN 0000-0000
DOI: 10.5281/zenodo.60291

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

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

Requirements analysis document

Author(s): Dylan Spalding; Helen Parkinson; Jordi Rambla; Niclas Jareborg; Abdulrahman Azab; Ilkka Lappalainen; Jeff Almaida-King; Alexander Senf; Saif Ur-Rehman
Published in: Zenodo, 2016, ISSN 0000-0000
DOI: 10.5281/zenodo.61414

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

Author(s): Salvador Capella-Gutierrez; Diana de la Iglesia; Jürgen Haas; Josep Lluís Gelpi; José María Fernández
Published in: Zenodo, 2017, ISSN 0000-0000
DOI: 10.5281/zenodo.557010

Specific marine databases

Author(s): Inge Alexander Raknes; Guy Cochrane; Lars Ailo Bongo; Nils Peder Willassen; Rob Finn; Juan Fu; Sudhagar Veerabadran Balasundaram; Espen Robertsen; Terje Klementsen; Giacomo Tartari
Published in: Zenodo, 2017, ISSN 0000-0000
DOI: 10.5281/zenodo.557021

ELIXIR Ethics Policy

Author(s): Stephanie Suhr; Niklas Blomberg
Published in: Zenodo, 2016, ISSN 0000-0000
DOI: 10.5281/zenodo.557027

A Node report on regional priorities and channels to use

Author(s): Jaako Vilo; Ondřej Hradil; Babis Savakis; Brane Leskosek
Published in: Zenodo, 2017, ISSN 0000-0000
DOI: 10.5281/zenodo.557029

ELIXIR workshops organized with the Rare Disease community

Author(s): Ivo Gut; Marco Roos; et al.
Published in: Zenodo, 2016, ISSN 0000-0000
DOI: 10.5281/zenodo.557065

ELIXIR Advanced workshops on genome annotation

Author(s): Henrik Lantz; Bengt Persson
Published in: Zenodo, 2016, ISSN 0000-0000
DOI: 10.5281/zenodo.557060

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

Author(s): Pérez-Pérez, Martin; Rabal, Obdulia; Pérez-Rodríguez, Gael; Vazquez, Miguel; Fdez-Riverola, Florentino; Oyarzabal, Julen; Valencia, Alfonso; Lourenço, Anália; Krallinger, Martin
Published in: 2017

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

Author(s): Palagi, Patricia M.; van Gelder, Celia W. G.; Attwood, Teresa K; Leskosek, Brane L.; Morgan, Sarah; Dimec, Jure; Mulder, Nicola
Published in: Issue 1, 2016
DOI: 10.5281/zenodo.166378

Bioschemas.org

Author(s): Carole Goble; Rafael Jimenez; Alasdair Gray; Niall Beard; Giuseppe Profiti; Norman Morrison
Published in: 2017
DOI: 10.7490/f1000research.1114493.1

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

Author(s): 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
Published in: NEUBIAS, Feb 2019, Luxembourg, Luxembourg, Issue 1, 2019