Re: Biological Entity information in Bioschemas

Hello,

That is the recommended usage but if more freedom is required any 
PropertyValue could be used. biolocation so far is intended to be used 
to specify sequence coordinates or other kind of "numeric" coordinates.

minValue acts as startValue and maxValue as endValue, we just want to 
avoid creating new properties whenever existing ones also work.

Regards,

On 2017-06-11 23:07, Philippe wrote:
> 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 Tuesday, 13 June 2017 09:59:19 UTC