sep_018.md

SEP 18 -- Attachment

SEP
Title	Data Attachments
Authors	Bryan Bartley ([email protected]), Chris Myers ([email protected]), Nicholas Roehner ([email protected]), and SBOL Developers (authors, please opt in)
Editor	Nicholas Roehner ([email protected])
Type	Data Model
SBOL Version	2.2
Status	Accepted
Created	13-Sep-2017
Last modified	13-Nov-2017
Issue	#39

Table of Contents

• 1. Rationale
• 2. Specification
  • 2.1 Attachment
    • 2.1.1 Attachment.source
    • 2.1.2 Attachment.format
    • 2.1.3 Attachment.size
    • 2.1.4 Attachment.hash
• 3. Examples
• 4. Backwards Compatibility
• 5. Discussion
• 6. Relation to Other SEPs
• References
• Copyright

Rationale

To specify a general container for a file attachment including metadata that helps tools interpret the file

Specification

2.1 Attachment

The Attachment class is a general container for data files, especially experimental data files. Attachment is a TopLevel object, and any other TopLevel object can refer to a list of attachments. Attachment has the following properties:

2.1.1 Source

The source is a link to the external file and is REQUIRED.

2.1.2 Format

The format is an ontology term indicating the format of the file. It is RECOMMENDED to use the EDAM ontology for file formats, which includes a variety of experimental data formats. The format is an OPTIONAL field

2.1.3 Size

The size is a long integer indicating the file size in bytes. This may be used by client applications accessing files over RESTful APIs. This field is OPTIONAL.

2.1.4 Hash

The hash is a string used to retrieve files from a cache. This field is OPTIONAL.

Figure 1: Diagram of the Attachment class and its associated properties

Examples

3.1 Attachment

Example 1: Attachments wrap an experimental data file and include important meta-data that helps tools interpret the data. This example attaches quality control data in the form of a gel image and sequencing results.

Backwards Compatibility

This proposal does not affect backwards compatibility.

Discussion

This proposal has been discussed extensively at HARMONY 2017 and on the Github issue tracker. There is general consensus that an Attachment is needed.

Relation to Other SEPs

This proposal relates to SEP 019, which deals with how experimental data should be linked to SBOL as part of encoding the provenance for design-build-test-learn cycles in synthetic biology.

References

Copyright

To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP 013. This work is published from: United States.