create and validate dataset descriptions

[micheldumontier]

Need to generate and validate descriptions for

• EBI (Simon Jupp)
• UniProt (Jerven)
• Bio2RDf (Michel)
• NIF (Jeff Grethe)
• Biodbcore (Pascale, Alejandra)
• IntegBio (Asuka)

[micheldumontier]

Status update

• Bio2RDF : code implemented, needs testing.
• NIF: To meet this week to discuss
• BioDBcore : unknown
• IntegBio : michel and asuka discussed outstanding issues. need status update
• identifiers.org: Michel asked for status update
• EBI : Alasdair to contact
• UniProt : Scott to contact.

[nicholsn]

@micheldumontier, is there somewhere other than the spec where I can get the requirements (MUST, SHOULD, etc.) for each dataset description level?

I started curating this in a python script, which was a good start, but perhaps a simple json or turtle file in the github repo would be more reusable.

Happy to send a PR if you think it would be of use.

[micheldumontier]

well! this might be a really good use case for our FAIRport initiative, where we want to specify the metadata standard for describing datasets.

see a prezzie on Mark Wilkinson's demo here: https://github.com/DataFairPort/DataFairPort/blob/master/Documentation/MarksDemo_StrawmanMetaDescriptor.pptx?raw=true

https://github.com/DataFairPort
https://groups.google.com/forum/#!forum/fairport-discuss

Carole Goble also published a paper on metadata elements - http://goo.gl/DZDSwe

what do you think?

[nicholsn]

Very nice! Definitely in the same spirit of my work, which is focused in the neuroimaging community: https://github.com/ni-/ni-dm

I'll need to review in more detail before I can give any concrete feedback, but on first glance it looks reasonable.

[AlasdairGray]

There is also a Shape Expression (ShEx) [1] description of the property table [2] which is forming the basis of the validator implementation. Note that due to some technical limitations of the ShEx javascript parser that I’m currently using that the ‘NEVER’ cases are not currently implemented but commented.

Alasdair

[1] http://www.w3.org/2001/sw/wiki/ShEx
[2] https://github.com/AlasdairGray/HCLSValidator/blob/master/hcls-validator.shex

On 16 Jun 2014, at 17:25, Nolan Nichols <[email protected]mailto:[email protected]> wrote:

Very nice! Definitely in the same spirit of my work, which is focused in the neuroimaging community: https://github.com/ni-/ni-dm

I'll need to review in more detail before I can give any concrete feedback, but on first glance it looks reasonable.

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Reply to this email directly or view it on GitHubhttps://github.com//issues/67#issuecomment-46200745.

Alasdair J G Gray
Lecturer in Computer Science, Heriot-Watt University, UK.
Email: [email protected]:[email protected]
Web: http://www.alasdairjggray.co.ukhttp://www.macs.hw.ac.uk/~ajg33
ORCID: http://orcid.org/0000-0002-5711-4872
Telephone: +44 131 451 3429
Twitter: @gray_alasdair

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[nicholsn]

Thanks, @AlasdairGray. I remember seeing ShEx but wasn't sure if it was in use anywhere - now I know!

I have an example that I worked up that I would like to validate, but it is currently failing. What's the best way to work with you to figure it out?

[AlasdairGray]

On 17 Jun 2014, at 13:53, Nolan Nichols <[email protected]mailto:[email protected]> wrote:

Thanks, @AlasdairGrayhttps://github.com/AlasdairGray. I remember seeing ShEx but wasn't sure if it was in use anywhere - now I know!

I have an examplehttps://github.com/nicholsn/ni-dm/blob/hcls/examples/dataset-descriptors/hcls.ttl that I worked up that I would like to validate, but it is currently failing. What's the best way to work with you to figure it out?

You could send me the description you are trying to validate to
[email protected]:[email protected]

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/67#issuecomment-46302198.

Alasdair J G Gray
Lecturer in Computer Science, Heriot-Watt University, UK.
Email: [email protected]:[email protected]
Web: http://www.alasdairjggray.co.ukhttp://www.macs.hw.ac.uk/~ajg33
ORCID: http://orcid.org/0000-0002-5711-4872
Telephone: +44 131 451 3429
Twitter: @gray_alasdair

---

Sunday Times Scottish University of the Year 2011-2013
Top in the UK for student experience
Fourth university in the UK and top in Scotland (National Student Survey 2012)

We invite research leaders and ambitious early career researchers to
join us in leading and driving research in key inter-disciplinary themes.
Please see www.hw.ac.uk/researchleaders for further information and how
to apply.

Heriot-Watt University is a Scottish charity
registered under charity number SC000278.