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RE: Crfiteria for new type

From: Stian Soiland-Reyes <stain@apache.org>
Date: Thu, 11 Jun 2020 13:54:00 +0100
Message-ID: <20200611135400.GB3087492@biggie>
To: Alan Williams <alan.r.williams@manchester.ac.uk>
Cc: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Talking to Alan I wonder if yes it would make sense to have a new type
Workflow - however it should then in the description be made clear that
it includes also "pipeline scripts".

For instance, new properties schema.org/input and schema.org/output are
meaningless on traditional source code that would be compiled -
associating "FormalParameter"s could arguably be used on a lower-level if
describing software "Function"s or "Metod"s.

Similarly existing scema.org/hasPart on a source code in general would be weird
unless again it pointed to functions and things inside the source code
file, but on a pipeline it is quite sensible that the steps are part of
it (and without needing a formal Step we can just say that the step is

normally SoftwareApplication, SoftwareSourceCode or its subtype Workflow)

But we are not here to make a beautiful formal method description of
any software (many people have spent PhDs on just that), just to
give a quick skeleton features of invokable scripts and workflows.

Many scripts also takes inputs and outputs, or have parts that they call
- but I think as they could be doing weird and wonderful things we
should only consider them "workflows" if they are somewhat pipelines,
that is they pass thing from one tool to another, they are not
primarily calculating things themselves.

Command line tools are kind of the missing piece here - I think
describing those in detail should be left to languages like Common
Workflow Language as you need to describe their files, command line
arguments, environment variables, docker iamges, etc.


On Wed, 10 Jun 2020 19:02:34 +0000, Alan Williams <alan.r.williams@manchester.ac.uk> wrote:
> Thanks Alasdair
> 
> I'll talk with other members of the working group about this.
> 
> Thanks again
> 
> --
> Alan
> 
> The University of Manchester belongs to the European R&D infrastructure IBISBA 1.0
> The project has received funding from the European Union’s Horizon 2020
> Research and Innovation Programme under grant agreement No 730976.
> To find out more visit https://www.ibisba.eu
> 
> ________________________________________
> From: Gray, Alasdair J G [A.J.G.Gray@hw.ac.uk]
> Sent: 10 June 2020 15:09
> To: Alan Williams; public-bioschemas@w3.org
> Subject: Re: Crfiteria for new type
> 
> Hi Alan,
> 
> There is no precise answer to your question.
> 
> In your case, are the new properties ones that would make sense for SoftwareSourceCode? then they can be suggested as extensions to schema.org as new properties for that type.
> 
> For FormalParameter, if there is nothing already in schema.org then we would need to create a new type for that.
> 
> Alasdair
> 
> --
> Alasdair J G Gray
> Associate Professor in Computer Science,
> School of Mathematical and Computer Sciences
> Heriot-Watt University, Edinburgh, UK.
> 
> Email: A.J.G.Gray@hw.ac.uk <mailto:A.J.G.Gray@hw.ac.uk>
> Web: http://www.macs.hw.ac.uk/~ajg33
> ORCID: http://orcid.org/0000-0002-5711-4872
> Office: Earl Mountbatten Building 1.39
> Twitter: @gray_alasdair
> 
> To arrange a meeting: https://doodle.com/mm/alasdairgray/book-a-time
> 
> 
> On 10/06/2020, 15:04, "Alan Williams" <alan.r.williams@manchester.ac.uk> wrote:
> 
>     Hello everyone
> 
>     When is it necessary to create a new Type? At the moment, we have a Workflow profile that says a Workflow is a SoftwareSourceCode, but no distinct Workflow type. However, the Workflow has new properties, including input and output to a new type (FormalParameter). Am I right that we need to create a new type for Workflow?
> 
> 
>     --
>     Alan
> 
>     The University of Manchester belongs to the European R&D infrastructure IBISBA 1.0
>     The project has received funding from the European Union’s Horizon 2020
>     Research and Innovation Programme under grant agreement No 730976.
>     To find out more visit https://www.ibisba.eu
> 
> 
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Received on Thursday, 11 June 2020 12:54:18 UTC

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