Usability-domain

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Usability Domain (usability_domain)

This section defines the usability_domain part of the BCO structure. The associated IEEE schema that contains the definition can be found here.

The usability domain of a BCO is an array of free text values, or plain language description, of what was done in the workflow and conveys the purpose of the BCO. It provides a specific scientific use case and a description of the function of the BCO.

Condensed example:

   "usability_domain": [
   ],

Required Components of the Usability Domain

Field	Required
description (free text)	REQUIRED

The usability domain should align with the actual steps described elsewhere in the BCO and should be consistent with the terminology used in the name, external references (xref), and keywords sections. This domain, along with keywords, can help determine when and how the BCO can be used. It is recommended that a novel use of a specific BCO would result in the creation of a new BCO with a new usability domain.

A usability domain should read like an abstract and conceptually can be broken down into the following sections.

1. Need
2. Method
3. Results
4. How the results can be used/interpreted

Usability Domain Examples

    "usability_domain": [
        "Identify baseline single nucleotide polymorphisms (SNPs)[SO:0000694], (insertions)[SO:0000667], and (deletions)[SO:0000045] that correlate with reduced (ledipasvir)[pubchem.compound:67505836] antiviral drug efficacy in (Hepatitis C virus subtype 1)[taxonomy:31646]", 
        "Identify treatment-emergent amino acid (substitutions)[SO:1000002] that correlate with antiviral drug treatment failure", 
        "Determine whether the treatment-emergent amino acid (substitutions)[SO:1000002] identified to correlate with treatment failure involving other drugs against the same virus", 
        "GitHub CWL example: https://github.com/mr-c/hive-cwl-examples/blob/master/workflow/hive-viral-mutation-detection.cwl#L20"]
]

    "usability_domain": [
      "Olduvai protein domains (formerly \"DUF1220\") are the most duplicated protein coding sequence in the human genome (https://doi.org/10.1371/journal.pbio.0020207). They are expressed in many tissues, including strongly in the brain (https://doi.org/10.1126/science.1127980). The copy number of Olduvai domains has been linked to increased brain size (https://doi.org/10.1007/s00429-014-0814-9), and performance on IQ tests (https://doi.org/10.1007/s00439-014-1489-2), as well as neurodiverse states like autism (https://doi.org/10.1371/journal.pgen.1004241).",
      "Precise evaluation of copy number in humans has been difficult to achieve, as ratiometric approaches fail to identify small changes when the total number is in the ~300 range, as in humans.  Read depth approaches using short read WGS data are promising, but most existing pipelines mask repeats altogether (potentially including these sequences), and those that do measure copy number do it relative to the gene. However, Olduvai domains are known to exist in different number and kind within a family of genes, rendering this approach inoperative. The pipeline described here is used to identify the copy number of genetic sequences independent of the genes in which they occur, and with higher fidelity than existing methods, designed specifically with Olduvai copy number in mind.",
      "Approximately 25 individuals were randomly chosen from each of the American (Utah -- Northern and Western European ancestry; CEU), Nigerian (Yoruba; YRI), Han Chinese (Beijing; CHB), Japanese (Tokyo; JPT), Mexican-American (Los Angeles; MXL), Colombian (Medellin; CLM), Puerto Rican (Puerto Rico; PUR), African-American (Southwest US; ASW), Luhya (Webuye, Kenya; LWK), Han Chinese (South China; CHS), Tuscan (Toscana, Italia; TSI), Spanish (Iberian populations; IBS), Finnish (Finland; FIN), and BGR populations for a total of 324 individuals. Where domains were more than 1 kb apart, the boundaries of the domains were extended up to 250 bp to allow the possibility of capturing unique sequence directly adjacent to the domain. No intermediate files were generated because the commands were run executed as a pipe at the command line, so uuids were used for the file IOs in the Description Domain. Relative file paths refer to the local machine on which this pipeline was run. This pipeline was created based on the work of Astling et al. doi: 10.1186/s12864-017-3976-z"
    ]