Re: BioChemEntity

Hi,

Just catching up with things.

I see that we still have a version number of 0.1 for BioChemEntity on the website, which is probably wrong as Leyla pointed out.

When I was chatting with Dan in October at ISWC he highlighted that the description of BioChemEntity was problematic due to the phrase "and cannot be better represented with any other existing type in schema.org<http://schema.org>.” We will need to come up with a definition that states what BioChemEntity is rather than what it isn’t/

We do not need a profile for BioChemEntity, it is a type that we will use in different way in Protein, Gene, and Samples profiles.

Ken/Riccardo, can you investigate what we need in order to prepare BioChemEntity as a type submission for schema.org<http://schema.org>?

Thanks

Alasdair

On 14 Mar 2018, at 09:36, LJ Garcia Castro <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:


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<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/


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,




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<mailto: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

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