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Re: BioChemEntity

From: LJ Garcia Castro <ljgarcia@ebi.ac.uk>
Date: Wed, 14 Mar 2018 09:36:58 +0000
To: Justin Clark-Casey <justinccdev@gmail.com>
Cc: public-bioschemas@w3.org
Message-ID: <eaf6aa86-8047-04cb-a62f-590cb98dbe9e@ebi.ac.uk>
Hi Justin,

It was just a glitch (either on the site or my eyes, hard to tell now). 
Contributors are now on a separated tab.

I am not sure though whether examples or ontologies will be attached to 
this type. I know Keneth and Ricardo were working on some examples but 
as this is a wrapper for specialized profiles, well, not sure how to 
proceed. I am happy to provide examples as we point to genes and 
organisms for which there is no specific profile.

I will talk about it with Ricardo, Keneth and Alasdair and will keep the 
list posted on any advance.

Regards,


On 13/03/2018 18:38, Justin Clark-Casey wrote:
> Could Keneth or Ricardo comment on this?  I think that BioChemEntity 
> is a very important schema, as it's the one that allows a description 
> of actual scientific entities, yet afaik there is
> * no clear example of usage
> * no documentation of how other ontologies terms would be used within it
> * or any actual use in the wild, as of yet.
>
> --
> Justin Clark-Casey (http://justincc.org)
> RSE, Intermine, University of Cambridge
> ELIXIR UK node technical co-ordinator
>
> On Thu, Mar 8, 2018 at 1:16 AM, ljgarcia <ljgarcia@ebi.ac.uk 
> <mailto:ljgarcia@ebi.ac.uk>> wrote:
>
>     Hi all,
>
>     I just realized no one seems to be involved in the BioChemEntity
>     specification, see
>     http://bioschemas.org/types/BioChemEntity/specification/
>     <http://bioschemas.org/types/BioChemEntity/specification/>
>
>     BioChemEntity was the agreed named for PhysicalEntity during the
>     last meeting in October. PhysicalEntity and DataRecord were
>     defined during the BioHackathon mainly between Michel Dumontier
>     and myself, with collaboration from Olga Giraldo and Alexander
>     Garcia as well, taking into account previous versions/alternatives
>     of it. Both of them were presented in October when all attendees
>     discussed names, properties ans so on. PhysicalEntity came from
>     BiologicalEntity which I defined as part of the work done for the
>     Protein specification (that later evolved into a profile). The
>     BiologicalEntity was presented during the second meeting and
>     people liked it so it was adopted as a "metatype". It has been an
>     effort where multiple people have participated.
>
>     Giving the history behind BioChemEntity, I am not sure v.0.1 is
>     accurate. For DataRecord v.0.1 seems right.
>
>     And, there is no profile for it. There is probably no mandatory
>     fields but we still have recommendations regarding how to use
>     mainEntityOfPage/mainEntity in order to link to a DataRecord or
>     url in order to link to the official web page for this entity.
>
>     I also think isContainedIn/contains could link to isPartOf/hasPart
>     as defined by the Relation Ontology.
>
>     I know Keneth and Ricardo have been working on some improvements.
>     Just let me know if you need any extra help for BioChemEntity, I
>     am happy to collaborate.
>
>     Regards,
>
>
Received on Wednesday, 14 March 2018 09:37:32 UTC

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