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Re: Biological Entity information in Bioschemas

From: Leyla Garcia <ljgarcia@ebi.ac.uk>
Date: Thu, 15 Jun 2017 10:50:46 +0100
To: public-bioschemas@w3.org
Message-ID: <77db2ba5-b0d3-b0ba-8721-7dd5fb3176a8@ebi.ac.uk>
Hi all,

I have modified biolocation.
It is now named "biocoordinates" with range QuantitativeValue. So far it 
is intended only for maximum 2D coordinates as only use cases for the 
protein group have been identified. If something more is needed, we 
might want to move to a new type.

Regards,

On 13/06/2017 11:40, Rodrigo Lopez wrote:
> In my humble view it would make sense to better differentiate 
> biolocation as it can mean many things. On the other hand, it would be 
> great if some generic term could be use. Biolocation can relates to 
> position of an organelle in a cell or a structure within a tissue. It 
> can also relate, loosely, to the position of a feature within a 
> macromolecule. As Leyla points out, this can be quite confusing. It 
> would be much better to associate locations of different types to what 
> they actually represent, be that biological sequence coordinates (in 
> DNA, RNA and proteins); 3D structure coordinates; geocoordinates; etc.
>
> One can also look at 'biolocation' as a parent term that indicates 
> that children are dealing with specialised biological location 
> determinants.
>
> Just my two cents.
>
> R:)
>
> On 13/06/2017 11:06, ljgarcia wrote:
>> Hi,
>>
>> I can see the name is causing some confusion.
>> bilocation is meant to be used for coordinates, for instance in a
>> sequence. We can change the name to biocoordinates if that works better.
>>
>> For geolocation we use location, an already existing property whose
>> range is a Place, PostalAddress or Text as range.
>>
>> Some people rather having more locations, one for storage place, one for
>> collection place. We could use homeLocation and fromLocation for that,
>> they are subproperties of location.
>>
>> Regards,
>>
>> On 2017-06-12 00:06, Rodrigo Lopez wrote:
>>> 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 [1]
>>>> ORCID: http://orcid.org/0000-0002-5711-4872
>>>> Office: Earl Mountbatten Building 1.39
>>>> Twitter: @gray_alasdair
>>>
>>>
>>>
>>> Links:
>>> ------
>>> [1] http://www.macs.hw.ac.uk/%7Eajg33
>>
>
Received on Thursday, 15 June 2017 09:51:18 UTC

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