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Re: BioSamples type for review

From: Michael Baudis <mbaudis@me.com>
Date: Mon, 13 May 2019 17:36:30 +0200
Message-Id: <2208779C-8D7A-4FA7-B9C5-CC669437FB7F@me.com>
Cc: Matt Styles <Matt.Styles@nottingham.ac.uk>, "Gray, Alasdair J G" <a.j.g.gray@hw.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Melanie Courtot <mcourtot@ebi.ac.uk>
To: Chris Mungall <cjmungall@lbl.gov>
Ah - didn’t know this. Great! 

Michael.

> On 13 May 2019, at 17:27, Chris Mungall <cjmungall@lbl.gov> wrote:
> 
> Prior to this I started on a document that compares different representations of samples across different schemas and domains, here it is if it's useful for the bioschemas effort:
> https://docs.google.com/document/d/1ExjXV5Y42SwH18cV91C9NbWkHooNjPpwL960lbT6eZ4/edit# <https://docs.google.com/document/d/1ExjXV5Y42SwH18cV91C9NbWkHooNjPpwL960lbT6eZ4/edit#>
>> Hi all,
>> 
>> would it make sense to align this between Phenopackets <-> bioschemas <-> schemablocks.org <http://schemablocks.org/> (well, I think it would, to a degree)?
>> 
>> - we are aware that geolocation data has to be provided, but not exactly about the extend (we think more about it in terms of “provenance”, not in a “where the hell is the sample stored”, which is outside of a data model’s scope, IMO)
>> - for material, with a focus on biomedical samples, we started to use new EFO classes w/ a target of “is this a sample representing the individual, or some abnormal part” (not yet in the schema)
>> - etc.
>> 
>> SchemaBlocks aligns (bi-directional) w/ Phenopackets, but tries to represent a larger set of scenarios. So any common parts (e.g. the format of geo data, if not the scoping) could be harmonised.
>> 
>> Michael.
>> 
>> 
>> 
>> 	"provenance" : {
>> 		"material" : {
>> 			"type" : {
>> 				"id" : "EFO:0009656",
>> 				"label" : "neoplastic sample"
>> 			}
>> 		},
>> 		"geo" : {
>> 			"label" : "Antalya, Turkey",
>> 			"precision" : "city",
>> 			"city" : "Antalya",
>> 			"country" : "Turkey",
>> 			"latitude" : 36.91,
>> 			"longitude" : 30.7
>> 		}
>> 	}
Received on Monday, 13 May 2019 15:36:56 UTC

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