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<title>BioCompute Object</title>

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</style><table class="infobox hproduct"><caption class="infobox-title fn">BioCompute Object</caption><tbody><tr><th scope="row" class="infobox-label">Abbreviation</th><td class="infobox-data">BCO</td></tr><tr><th scope="row" class="infobox-label">Status</th><td class="infobox-data"><a rel="nofollow" class="external text" href="https://saaem-stg.ieee.org/project/2791.htm">Active IEEE Working Group</a></td></tr><tr><th scope="row" class="infobox-label">Related standards</th><td class="infobox-data"><a href="Common_Workflow_Language" title="Common Workflow Language">Common Workflow Language</a></td></tr><tr><th scope="row" class="infobox-label">License</th><td class="infobox-data"><a href="BSD_licenses#3-clause_license_("BSD_License_2.0",_"Revised_BSD_License",_"New_BSD_License",_or_"Modified_BSD_License")" title="BSD licenses">BSD-3-clause</a></td></tr><tr><th scope="row" class="infobox-label">Website</th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="https://osf.io/h59uh/">osf<wbr>.io<wbr>/h59uh<wbr>/</a></span></td></tr></tbody></table>

<p>The <b>BioCompute Object</b> (<b>BCO</b>) project is a community-driven initiative to build a framework for standardizing and sharing computations and analyses generated from <a href="High-throughput_sequencing" class="mw-redirect" title="High-throughput sequencing">High-throughput sequencing</a> (HTS—also referred to as <a href="Next-generation_sequencing" class="mw-redirect" title="Next-generation sequencing">next-generation sequencing</a> or <a href="Massively_parallel_sequencing" class="mw-redirect" title="Massively parallel sequencing">massively parallel sequencing</a>). The project has since been <a rel="nofollow" class="external text" href="https://standards.ieee.org/ieee/2791/7337/">standardized</a> as IEEE 2791-2020, and the project files are maintained in an <a rel="nofollow" class="external text" href="https://opensource.ieee.org/2791-object/ieee-2791-schema/">open source repository</a>.<sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> The <a rel="nofollow" class="external text" href="https://www.federalregister.gov/documents/2020/07/22/2020-15771/electronic-submissions-data-standards-support-for-the-international-institute-of-electrical-and">July 22nd, 2020 edition</a> of the Federal Register announced that the <a href="Food_and_Drug_Administration" title="Food and Drug Administration">FDA</a> now supports the use of BioCompute (officially known as IEEE 2791-2020) in regulatory submissions, and the inclusion of the standard in the Data Standards Catalog for the submission of HTS data in <a rel="nofollow" class="external text" href="https://web.archive.org/web/20190612181016/https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications">NDAs, ANDAs, BLAs, and INDs</a> to <a href="Center_for_Biologics_Evaluation_and_Research" title="Center for Biologics Evaluation and Research">CBER</a>, <a href="Center_for_Drug_Evaluation_and_Research" title="Center for Drug Evaluation and Research">CDER</a>, and <a href="Center_for_Food_Safety_and_Applied_Nutrition" title="Center for Food Safety and Applied Nutrition">CFSAN</a>.

</p><p>Originally started as a collaborative contract between the <a href="George_Washington_University" title="George Washington University">George Washington University</a> and the <a href="Food_and_Drug_Administration" title="Food and Drug Administration">Food and Drug Administration</a>, the project has grown to include over 20 universities, biotechnology companies, public-private partnerships and pharmaceutical companies including Seven Bridges and <a href="Harvard_Medical_School" title="Harvard Medical School">Harvard Medical School</a>.<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> The BCO aims to ease the exchange of HTS workflows between various organizations, such as the FDA, pharmaceutical companies, contract research organizations, bioinformatic platform providers, and academic researchers. Due to the sensitive nature of regulatory filings, few direct references to material can be published. However, the project is currently funded to train FDA Reviewers and administrators to read and interpret BCOs, and currently has 4 publications either submitted or nearly submitted.

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<div class="mw-heading mw-heading2"><h2 id="Background">Background</h2></div>

<p>One of the biggest challenges in bioinformatics is documenting and sharing <a href="Scientific_workflow_system#Scientific_workflows" title="Scientific workflow system">scientific workflows</a> in such a way that the computation and its results can be peer-reviewed or reliably reproduced.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> Bioinformatic <a href="Pipeline_(software)" title="Pipeline (software)">pipelines</a> typically use multiple pieces of software, each of which typically has multiple versions available, multiple input parameters, multiple outputs, and possibly platform-specific configurations. As with experimental parameters in a laboratory protocol, small changes in computational parameters may have a large impact on the scientific validity of the results. The BioCompute Framework provides an <a href="Object-oriented_design" class="mw-redirect" title="Object-oriented design">object oriented design</a> from which a BCO that contains details of a pipeline and how it was used can be constructed, <a href="Digitally_signed" class="mw-redirect" title="Digitally signed">digitally signed</a>, and shared. The BioCompute concept was originally developed to satisfy FDA regulatory research and review needs for evaluation, validation, and verification of genomics data. However, the Biocompute Framework follows FAIR Data Principles<sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> and can be used broadly to provide communication and <a href="Interoperability" title="Interoperability">interoperability</a> between different platforms, industries, scientists and regulators<sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup>

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<div class="mw-heading mw-heading2"><h2 id="Utility">Utility</h2></div>

<p>As a standardization for genomic data, BioCompute Objects are mostly useful to three groups of users: 1) academic researchers carrying out new genetic experiments, 2) pharma/biotech companies that wish to submit work to the FDA for regulatory review, and 3) clinical settings (hospitals and labs) that offer genetic tests and <a href="Personalized_medicine" title="Personalized medicine">personalized medicine</a>. The utility to academic researchers is the ability to reproduce experimental data more accurately and with less uncertainty. The utility to entities wishing to submit work to the FDA is a streamlined approach, again with less uncertainty and with the ability to more accurately reproduce work. For clinical settings, it is critical that HTS data and clinical metadata be transmitted in an accurate way, ideally in a standardized way that is readable by any stakeholder, including regulatory partners.

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<div class="mw-heading mw-heading2"><h2 id="Format">Format</h2></div>

<p>The BioCompute Object is in <a href="JSON" title="JSON">json</a> format and, at a minimum, contains all the software versions and parameters necessary to evaluate or verify a computational pipeline. It may also contain input data as files or links, reference genomes, or executable Docker components. A BioCompute Object can be integrated with <a href="FHIR" class="mw-redirect" title="FHIR">HL7 FHIR</a> as a Provenance Resource.<sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> Multiple joint implementations are also under development that leverage BCO's report-centric format, including CWL (one of which is part of an active government funded public contract with a cofounder of CWL to pilot and generate documentation for a joint BCO-CWL, as well as examples) and RO.<sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup>

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<div class="mw-heading mw-heading2"><h2 id="BCO_Consortium">BCO Consortium</h2></div>

<p>The BioCompute Object working group facilitated a means for different stakeholders to provide input on current practices on the BCO. This working group was formed during preparation for the <a rel="nofollow" class="external text" href="https://hive.biochemistry.gwu.edu/htscsrs/workshop_2017">2017 HTS Computational Standards for Regulatory Sciences Workshop</a>, and was initially made up of the workshop participants. The growth and work of the BCO working group, as a direct result of the interaction between a variety of stakeholders from all interested communities, culminated in the official standard, <a rel="nofollow" class="external text" href="https://standards.ieee.org/ieee/2791/7337/">IEEE 2791-2020</a>, which was approved in January 2020. A <a href="Public%E2%80%93private_partnership" title="Public–private partnership">Public-Private partnerships</a> was formed between GWU and CBER and has become an easy point of entry for new individuals or institutions into the BCO project to participate in the discussion of best practices for the objects.

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<div class="mw-heading mw-heading2"><h2 id="Implementations">Implementations</h2></div>

<p>The simple R package biocompute<sup id="cite_ref-biocompute-r_8-0" class="reference"><a href="#cite_note-biocompute-r-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> can create, validate, and export BioCompute Objects. The <a rel="nofollow" class="external text" href="https://github.com/sbg/gcs">Genomics Compliance Suite</a> is a Shiny app that offers similar features to regular expressions found in all modern text editors. There are several internally developed <a href="Open-source_software" title="Open-source software">open source</a> software packages and web applications that implement the BioCompute specification, three of which have been deployed in a publicly accessible <a href="Amazon_Web_Services" title="Amazon Web Services">AWS</a> <a href="Amazon_Elastic_Compute_Cloud" title="Amazon Elastic Compute Cloud">EC2</a> <a href="Cloud_computing" title="Cloud computing">cloud</a>. These include an instance of the <a href="High-performance_Integrated_Virtual_Environment" title="High-performance Integrated Virtual Environment">High-performance Integrated Virtual Environment</a>, the <a rel="nofollow" class="external text" href="https://github.com/biocompute-objects/bco_editor">BioCompute Portal</a><sup id="cite_ref-bco_editor_9-0" class="reference"><a href="#cite_note-bco_editor-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> (a form-based web application that can create and edit BioCompute Objects based on the IEEE-2791-2020 <a href="Open_standard" title="Open standard">standard</a>, and a BioCompute compliant instance of <a rel="nofollow" class="external text" href="https://usegalaxy.org/">Galaxy</a>.

</p><p>Some bioinformatics platforms have built-in support for Biocompute, which let a user automatically create a BCO from a workflow and edit the descriptive content.

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<ul><li>DNAnexus and PrecisionFDA facilitate the generation of BCOs by importing workflows, allowing users to edit descriptive content. The platform supports metadata import and export of WDL and CWL scripts, and offers the BCOnexus tool, which is a high-level, platform-free tool with a graphical user interface that lets a user merge BCOs.</li>

<li>Velsera's Seven Bridges Genomics and Cancer Genomics Cloud also have support for BioCompute by enabling direct pre-population of BCO fields from workflows.</li>

<li>BioCompute has also been integrated into <a rel="nofollow" class="external text" href="https://hivelab.biochemistry.gwu.edu/">HIVE</a> and the main Galaxy instance, both of which similarly enable users to automatically generate BCOs and edit content within these platforms.</li>

<li>BioCompute has also been implemented in the Common Fund Data Elements Playbook Partnership project. This implementation lets a user save a workflow when they're satisfied with the results, which aids in traceability through the network of independently-versioned resources, allowing users to save queries and annotate them for future use, sharing, or repeatability, aligning with its role in advancing bioinformatics practices.</li></ul>

<p>Integration into platforms is meant to improve data handling and collaboration and provide effective ways for users to execute a workflow, and graphical representations of BCOs are often more intuitive ways of browsing or reading BCOs.

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<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

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<li id="cite_note-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-1">^</a></b></span> <span class="reference-text">Simonyan V, Goecks J, Mazumder R. Biocompute Objects—A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA journal of pharmaceutical science and technology. 2017;71(2):136-146. doi:10.5731/pdajpst.2016.006734.</span>

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</style><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://www.europeanpharmaceuticalreview.com/news/67524/biocompute-genomic-data/">"BioCompute Objects specifications to advance genomic data analysis"</a>. <i>www.europeanpharmaceuticalreview.com</i><span class="reference-accessdate">. Retrieved <span class="nowrap">2017-12-21</span></span>.</cite></span>

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<li id="cite_note-4"><span class="mw-cite-backlink"><b><a href="#cite_ref-4">^</a></b></span> <span class="reference-text"><cite id="CITEREFWilkinsonDumontierAalbersbergAppleton2016" class="citation journal cs1">Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan; Appleton, Gabrielle; Axton, Myles; Baak, Arie; Blomberg, Niklas; Boiten, Jan-Willem; Santos, Luiz Bonino da Silva (2016-03-15). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792175">"The FAIR Guiding Principles for scientific data management and stewardship"</a>. <i>Scientific Data</i>. <b>3</b>: 160018. <a href="Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2016NatSD...360018W">2016NatSD...360018W</a>. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1038%2Fsdata.2016.18">10.1038/sdata.2016.18</a>. <a href="PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792175">4792175</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/26978244">26978244</a>.</cite></span>

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<li id="cite_note-5"><span class="mw-cite-backlink"><b><a href="#cite_ref-5">^</a></b></span> <span class="reference-text"><cite id="CITEREFAlterovitzDeanGobleCrusoe2017" class="citation journal cs1">Alterovitz, Gil; Dean, Dennis A.; Goble, Carole; Crusoe, Michael R.; Soiland-Reyes, Stian; Bell, Amanda; Hayes, Anais; King, Charles Hadley H.; Johanson, Elaine; Thompson, Elaine E.; Donaldson, Eric; Tsang, Hsinyi S.; Goecks, Jeremy; Almeida, Jonas S.; Guo, Lydia; Walderhaug, Mark; Walsh, Paul; Kahsay, Robel; Bloom, Toby; Lai, Yuching; Simonyan, Vahan; Mazumder, Raja (21 September 2017). <a rel="nofollow" class="external text" href="https://www.biorxiv.org/content/early/2017/09/21/191783">"Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results"</a>. <i>bioRxiv</i>. <b>16</b> (12): 191783. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1101%2F191783">10.1101/191783</a></span>. <a href="PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338479">6338479</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/30596645">30596645</a> – via www.biorxiv.org.</cite></span>

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<li id="cite_note-6"><span class="mw-cite-backlink"><b><a href="#cite_ref-6">^</a></b></span> <span class="reference-text"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://www.hl7.org/fhir/provenance-example-biocompute-object.html">"Provenance-example-biocompute-object"</a>. <i>HL7 FHIR Release 3 (STU)</i>.</cite></span>

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<li id="cite_note-7"><span class="mw-cite-backlink"><b><a href="#cite_ref-7">^</a></b></span> <span class="reference-text"><cite id="CITEREFSoiland-Reyes2020" class="citation cs2">Soiland-Reyes, Stian (2020-09-01), <a rel="nofollow" class="external text" href="https://biocompute-objects.github.io/bco-ro-crate/"><i>hive-cwl-examples: Packaging BioCompute Objects using RO-Crate</i></a></cite></span>

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<li id="cite_note-biocompute-r-8"><span class="mw-cite-backlink"><b><a href="#cite_ref-biocompute-r_8-0">^</a></b></span> <span class="reference-text"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://cran.r-project.org/package=biocompute">"CRAN - Package biocompute"</a>. cran.r-project.org<span class="reference-accessdate">. Retrieved <span class="nowrap">2019-11-28</span></span>.</cite></span>

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<li id="cite_note-bco_editor-9"><span class="mw-cite-backlink"><b><a href="#cite_ref-bco_editor_9-0">^</a></b></span> <span class="reference-text"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://github.com/biocompute-objects/bco_editor">"BioCompute Portal"</a>. github.com/biocompute-objects<span class="reference-accessdate">. Retrieved <span class="nowrap">2020-06-25</span></span>.</cite></span>

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<div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2></div>

<ul><li><a rel="nofollow" class="external text" href="http://biocomputeobject.org/">Official Website</a></li>

<li><a rel="nofollow" class="external text" href="https://opensource.ieee.org/2791-object/ieee-2791-schema/">IEEE 2791-2020 open source project</a></li></ul></div><div><div class="zim-footer">

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