June 9, 2019
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Article

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker

Publicated to: GigaScience. 4 (59): 59- - 2015-12-03 4(59), DOI: 10.1186/s13742-015-0092-3

Authors:

Aranguren, ME; Wilkinson, MD
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Affiliations

Eurohelp Consulting - Author
Tech Univ Madrid UPM, Ctr Plant Biotechnol & Genom CBGP, Biol Informat - Author

Abstract

Background: Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. Findings: This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. Conclusions: The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.
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Keywords

dockergalaxyrdfreproducibilitysadisemantic webweb serviceComputational biologyDesignDockerGalaxyImplementationInformation disseminationInformation storage and retrievalLife sciencesRdfReproducibilityReproducibility of resultsSadiSemantic webSoftwareWeb serviceWorkflow

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal GigaScience due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2015, it was in position 6/62, thus managing to position itself as a Q1 (Primer Cuartil), in the category Multidisciplinary Sciences.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-25:

  • WoS: 9
  • Scopus: 7
  • Europe PMC: 6
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-25:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 40.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 40 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 17.
  • The number of mentions on the social network Facebook: 1 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 8 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://oa.upm.es/40479/

As a result of the publication of the work in the institutional repository, statistical usage data has been obtained that reflects its impact. In terms of dissemination, we can state that, as of

  • Views: 341
  • Downloads: 227
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Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: Last Author (WILKINSON, MARK DENIS).

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Awards linked to the item

MEA is funded by the Genomic Resources Group (UPV/EHU). MDW is supported by the Fundacion BBVA, and the Isaac Peral and Marie Curie COFUND Programmes of the Universidad Politecnica de Madrid, Centre for Plant Biotechnology and Genomics UPM-INIA. Jorge Langa, from the Genomic Resources Group (UPV/EHU), provided technical help with the Docker installation and with management of images and containers. John M. Chilton, from the Minnesota Supercomputing Institute at the University of Minnesota, provided help with the setting up of Galaxy server to run the SADI-Docker image.
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