Re: BioChemEntity

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 (
RSE, Intermine, University of Cambridge
ELIXIR UK node technical co-ordinator

On Thu, Mar 8, 2018 at 1:16 AM, ljgarcia <> wrote:

> Hi all,
> I just realized no one seems to be involved in the BioChemEntity
> specification, see
> oChemEntity/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 Tuesday, 13 March 2018 18:39:21 UTC