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General

1. Where would information regarding data sources and standard operating procedures be? Which specific domain?

   Data sources should be recorded as described by the input_subdomain in the “io_domain” and the input_list in the “description_domain”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “usability_domain”.

Pipeline Steps

1. Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?

   The standard does not mandate any particular numbering schema, but it’s best practices to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis.. So if, in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).

Inputs and Outputs

1. What is the relationship and difference between input_list in description_domain and input_subdomain ? Does input_subdomain contain all the input files of all the pipeline steps?

   Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for overall view of the pipeline inputs.

2. What is the relationship and difference between output_list in description_domain and output_subdomain? Does output_subdomain contain all the output files of all the pipeline steps?

   The Output Domain is for global outputs. The input_list/output_list is in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for overall view of the pipeline outputs.

3. There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?

   Yes they are, timestamp is used for creation in those cases.

Extensions

1. What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?

   Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard, and is very flexible.

2. How can BCOs be used for knowledgebases?

   Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality-control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.

   BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provides complete transparency to its data submitters (authors, curators, other databases, etc.), collaborators, and users, but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in machine and human-readable formats.

   The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.

Prerequisets

1. What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?

   Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the softwares in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.

Knowledgebases

1. Can BCOs be used for curating databases?

Yes. BCOs have been used in this capacity, such as in the FDA’s ARGOS database of infectious diseases and the GlyGen databse of glycosylation sites. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.

Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality-control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.

BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provides complete transparency to its data submitters (authors, curators, other databases, etc.), collaborators, and users, but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in machine and human-readable formats.

The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.

Saving and Publishing a BCO

1. Why am I unable to save my BCO?

   If you were unable to save your BCO it most likely means that you did not “activate” after you registered for an account. The activation step is what activates the server for saving and publishing, so if you start using your account without that, it will not populate. If you did not respond to the email, you may need to re-register (the link may have expired by now). If so, please re-register and respond to the activation email, and then try to save your BCO as we did in class. If you still need help, please contact me directly.