Fine Grained Software Citations Metadata
CWL's linked data functionality can be used to show how to cite the software being described in a CWL tool description.
Linked data means we aren't making up our own vocabulary to describe things. In the example below we use a single vocabulary: schema.org.
Example. Note that two publications from the main authors are included and a publication for a third-party library.
#!/usr/bin/env cwl-runner
cwlVersion: cwl:draft-3
class: CommandLineTool
$namespaces:
schema: http://schema.org/
$schemas:
- https://schema.org/version/latest/schema.rdf
schema:publication:
- class: schema:ScholarlyArticle
id: http://doi.org/10.12688/f1000research.6924.1
- class: schema:ScholarlyArticle
id: http://arxiv.org/abs/1203.4802
- class: schema:ScholarlyArticle
id: http://doi.org/10.1186/1471-2105-9-11
[rest of command line description]
What if the citation is only appropriate if a particular command line option is used? Easy, move the citation within the tool definition to that command line option.
TODO:
- Simple script to extract citations from CWL tool descriptions
- Bibtex export for the above
- Give example of real-world fine-grained citation
- Give example of tool outputting CWL compatible metadata at run time
Credits:
Initial work on CWL metadata by Andrey Kartashov. Linked data support in the CWL reference implementation by Peter Amstutz. Citation feature inspired by the Galaxy Project, first implemented at 2014 BOSC codefest by John Chilton, Michael Crusoe, Peter Cock, Daniel Blankenberg, Matt Shirley.