RE: Biological Entity information in Bioschemas

Can I kindly draw your attention to the following document in relation to location as used by the INSDC feature table. It’s a rather long document so I’m pointing at the section that contains the geolocation features, FYI. 

http://www.insdc.org/files/feature_table.html#7.3.1

The following geographical qualifiers are of potential interest here:

/country
and
/lat_lon

In terms of biolocation, qualifiers such as:

/isolation_source
and
/culture_collection

May be pertinent.

Kind regards,

R😊


From: Philippe
Sent: 11 June 2017 23:08
To: Leyla Garcia; Gray, Alasdair J G; Carlos Horro (EI)
Cc: Philippe; Rafael C. Jimenez; public-bioschemas@w3.org
Subject: Re: Biological Entity information in Bioschemas

Hello Leyla, all

Thank you for circulating the information and documents.

I am fine with declaring distinct property type for refering to various types of sites.

    i. collectionlocation -> Place,geographicalPlace,
    ii.   biolocation 

What I am now missing is why use only min value/max value  as filler for 'biolocation'.
I was wondering if we should extend and create a new type: 'Site', which could be inspired by http://schema.org/Place but could have properties such as 'startAt' and 'endsAt' where the filler would be 'biocoordinate' against a reference genome or other bioreference point.

We may also want to revisit what Scientific Entity and if Biological Entity can be further categorized into  MaterialEntities or Processes.

Best wishes

Philippe

On 02/06/2017 10:57, Leyla Garcia wrote:
Hello, 

All documents corresponding to BiologicalEntity are in the Google Drive provided for it, please see https://drive.google.com/drive/folders/0B7X2x2IPBve7R3Uza1d6MGpuYVE

There you will find:
* mapping template. @Philippe please take a look to the sample location. Alasdair wants to use location only for the storage place and add another property for the collection location. I think the same can be used for both with some additional information in the PropertyValue. "location" is used for samples, not for proteins so please take a look and make a decision. All sample people should have access to this document so feel free to share the discussion with them.
* specification. Still empty, waiting for Guillermo to create an easy way to move things from the mapping to the specification.
* diagram corresponding to the model
* frozen initial document used during the meeting.

In the mapping template, same as it has been done with Datasets, all participating groups/entities should add their use cases and examples. A bit of that will be repeat in the specification and full examples should be provided in the sub-folder https://drive.google.com/drive/folders/0B2htA1DHhWokQzZ4NE16RUR0S00. I will communicate with the protein people. I guess Philippe will coordinate samples and Carlos phenotypes.

A similar structure (mapping, specification and graph) should be replicate for each biological type. I already created the folders for proteins, protein structure and protein annotations. There we will put the usage of the BiologicalEntity for each type so Bioschemas can validate that on the tools. BiologicalEntity so far is the only type that will be proposed to schema.org.

One question, should not we use the w3c mailing list for all of this?

Regards,


On 01/06/2017 16:58, Gray, Alasdair J G wrote:
Hi Carlos, 

Thank you for sending through these links. I have added the group to the website with the links that you have provided (I also removed the commons group). I took the liberty of writing an abstract and objectives for the group.
http://bioschemas.org/groups/biologicalentity/

Do you have a link to a document describing the use cases that the Biological Entity is to support?

Best regards,

Alasdair

On 26 May 2017, at 11:43, Carlos Horro (EI) <Carlos.Horro@earlham.ac.uk> wrote:

Hi Alasdair,

I send you the information about new Biological Entity specification (which is supposed to replace previous Sample specification)

Biological Entity shared folder:
https://drive.google.com/open?id=0B7X2x2IPBve7R3Uza1d6MGpuYVE

Document with current specification:
https://docs.google.com/document/d/1fn-of4cxGJLYiw1G3-KepZsIE0Ptq4GSx-h3jPmvdvc/edit?usp=sharing
Official mapping file (with future mapped use cases):
https://docs.google.com/spreadsheets/d/1h0-fgqnRe25-tVCmu2yWNQjthLzgkW4a1TVNMpCABlc/edit#gid=1261485211

As leaders of Biological Entity, can be:
Carlos Horro (from phenotypes)
Leyla García (proteins)
Philipe Rocca-Serra (samples)

Greetings,
Carlos

Alasdair J G Gray
Fellow of the Higher Education Academy
Assistant Professor in Computer Science, 
School of Mathematical and Computer Sciences 
(Athena SWAN Bronze Award)
Heriot-Watt University, Edinburgh UK.

Email: 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