compare metadata given for Derby files against FAIR expectations

[egonw]

The current output looks like:

DATASOURCEVERSION    85
DATATYPE    GeneProduct
SERIES    Homo sapiens genes and proteins
DATASOURCENAME    Ensembl
BUILDDATE    20161019
SCHEMAVERSION    3

This may or may not comply with FAIR (quick guess is: no, it does not).

[ariutta]

Good point -- it would be a big improvement to make this FAIR compliant!

The current full result for this query:

DATASOURCEVERSION   2.0
DATATYPE    GeneProduct
SERIES  Homo sapiens genes and proteins
DATASOURCENAME  Ensembl
BUILDDATE   20161018
SCHEMAVERSION   3
DATASOURCEVERSION   1.0.0
DATATYPE    Interaction
SERIES  standard-interaction
DATASOURCENAME  EBI-RHEA
BUILDDATE   20161018
SCHEMAVERSION   3
DATASOURCEVERSION   HMDB3.6-CHEBI144-WIKIDATA2016101120161012
DATATYPE    Metabolite
SERIES  standard_metabolite
DATASOURCENAME  HMDB-CHEBI-WIKIDATA
BUILDDATE   20161012
SCHEMAVERSION   3

The same result in CSV format:

DATASOURCEVERSION,DATATYPE,SERIES,DATASOURCENAME,BUILDDATE,SCHEMAVERSION,
2.0,GeneProduct,Homo sapiens genes and proteins,Ensembl,20161018,3
1.0.0,Interaction,standard-interaction,EBI-RHEA,20161018,3
HMDB3.6-CHEBI144-WIKIDATA2016101120161012,Metabolite,standard_metabolite,HMDB-CHEBI-WIKIDATA,20161012,3

I'm sure we could make it even better, but at least using CSV or TSV would be a good start.

[AlasdairGray]

It would be great to see this follow the hcls community profile.

Alasdair J G Gray Fellow of the Higher Education Academy Assistant Professor in Computer Science Herriot-Watt University, Edinburgh

www.macs.hw.ac.uk/~ajg33http://<br/www.macs.hw.ac.uk/~ajg33>

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From: Anders Riutta [email protected] Sent: Thursday, October 20, 2016 6:21:48 AM To: bridgedb/BridgeDb Subject: Re: [bridgedb/BridgeDb] compare metadata given for Derby files against FAIR expectations (#33)

Good point -- it would be a big improvement to make this FAIRhttp://www.nature.com/articles/sdata201618 compliant!

The current full result for this queryhttp://webservice.bridgedb.org/Human/properties:

DATASOURCEVERSION 2.0 DATATYPE GeneProduct SERIES Homo sapiens genes and proteins DATASOURCENAME Ensembl BUILDDATE 20161018 SCHEMAVERSION 3 DATASOURCEVERSION 1.0.0 DATATYPE Interaction SERIES standard-interaction DATASOURCENAME EBI-RHEA BUILDDATE 20161018 SCHEMAVERSION 3 DATASOURCEVERSION HMDB3.6-CHEBI144-WIKIDATA2016101120161012 DATATYPE Metabolite SERIES standard_metabolite DATASOURCENAME HMDB-CHEBI-WIKIDATA BUILDDATE 20161012 SCHEMAVERSION 3

The same result in CSV format:

DATASOURCEVERSION,DATATYPE,SERIES,DATASOURCENAME,BUILDDATE,SCHEMAVERSION, 2.0,GeneProduct,Homo sapiens genes and proteins,Ensembl,20161018,3 1.0.0,Interaction,standard-interaction,EBI-RHEA,20161018,3 HMDB3.6-CHEBI144-WIKIDATA2016101120161012,Metabolite,standard_metabolite,HMDB-CHEBI-WIKIDATA,20161012,3

I'm sure we could make it even better, but at least using CSV or TSV would be a good start.

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[egonw]

See also http://www.fairmetrics.org/about.html

[egonw]

Last year, in the Google Summer of Code, Ammas worked on a VoID representation. This code is available in master.