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  • Reproducible data management with Maven

    A picture says less than 100 words

    Use case: pharmacological reference data

    Open PHACTS combines pharmacological data in a single Linked Data cache, and provide RESTful APIs to query and examine the data in a uniform interface. Data is loaded from several data providers like EBI and Uniprot - some of it is loaded directly as RDF, other datasets are translated to RDF from more specific data formats. A series of VoID linksets are also loaded to provide identity equivalence across the different RDF graphs. These linksets are derived from existing references in the earlier loaded data sources, but can also be found computationally (e.g. by comparing chemical structures or protein sequences).

    Building Open PHACTS showed a challenge in how to keep all these data sources up to date, particularly when changing our architecture to allow for a Docker-based installation of the Open PHACTS platform and data at customer sites.

    Open PHACTS platform is a service oriented architecture with components like a mySQL database, Virtuoso RDF store, memcache and PHP, Tomcat and ElasticSearch. We found Docker to be a great tool for managing and deploying these components in isolation, and combined with Docker Compose, provide an easy way to link them together to form a uniform and installable platform.

    The mechanism of Dockerfile provides a reproducible way to build docker images, which can be created automatically by the Docker hub, typically based on a GitHub repository. Changes pushed to the GitHub repository causes a new Docker image to be built. Instructions in the Dockerfile consists of commands like ADD and RUN.

    The challenge in setting up the Open PHACTS platform is the data loading. Docker images are stored as a series of differential file system layers, which can be pushed and pull from registries like the Docker Hub and third-party installations of the Docker Registry. This mechanism works well for typical Docker applications, where each layer can have a size in the magnitude of 100 MB, and the full Docker image a size of the magnitude 1 GB. We found that using this mechanism breaks down when used with the Open PHACTS data, which can be in the magnitude of 100 GB as uncompressed RDF.

    Use case: Galaxy and NCBI Blast data

    My open Gigascience review and re-review of Peter Cock's GigaScience article "NCBI BLAST+ integrated into Galaxy": (Cock 2015)

    https://gist.github.com/stain/a107379fc1adbb3e392b

    Open science - with Immediate response and impact:

    https://twitter.com/soilandreyes/status/557144280717074433

    https://twitter.com/soilandreyes/status/557166885763293184

    https://twitter.com/soilandreyes/status/594164533263990784

    https://github.com/peterjc/galaxy_blast/issues/57

    Issues:

    • Docker easy to install Galaxy and BLAST plugin - easy to review paper
    • But not the NCBI Blast reference data (10-100 GB)
    • Could not verify the workflows - not reproducible science
    • Proposed: BLAST Data manager plugin for Galaxy
    • NCBI Blast data changes nightly - which version did you use? No metadata - self-provenance. How to keep it up to date?
    • Suggestion:
      1. Data Docker to be used as an add-on with existing Galaxy plugin.
      2. Automated job for making new, VERSIONED NCBI artifacts.
      3. Inject provenance.
      4. Self-archival and identification of the reference data that was actually used, not just "Come try my Galaxy server, I promise I didn't update anything!"

    Reproducibility in software development

    Apache Maven

    Apache Maven is a build and dependency management system that is widely popular for the Java platform. While newer build systems like