Re: BioChemEntity

Hi All,

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

Of course, I will prepare the submission to Schema.org for 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

Regarding BioChemEntity I am currently working on improving its version,
examples and documentation, as soon as I have them ready will update the
draft version on website, so we can discuss those changes.

Regards,
Ricardo

On Mon, May 7, 2018 at 11:30 AM Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
wrote:

> 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.” 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?
>
> Thanks
>
> Alasdair
>
> On 14 Mar 2018, at 09:36, LJ Garcia Castro <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)
> 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> 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
> 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
>
> ------------------------------
>
> *Heriot-Watt University is The Times & The Sunday Times International
> University of the Year 2018*
>
> Founded in 1821, Heriot-Watt is a leader in ideas and solutions. With
> campuses and students across the entire globe we span the world, delivering
> innovation and educational excellence in business, engineering, design and
> the physical, social and life sciences.
>
> This email is generated from the Heriot-Watt University Group, which
> includes:
>
>    1. Heriot-Watt University, a Scottish charity registered under number
>    SC000278
>    2. Edinburgh Business School a Charity Registered in Scotland,
>    SC026900. Edinburgh Business School is a company limited by guarantee,
>    registered in Scotland with registered number SC173556 and registered
>    office at Heriot-Watt University Finance Office, Riccarton, Currie,
>    Midlothian, EH14 4AS
>    3. Heriot- Watt Services Limited (Oriam), Scotland's national
>    performance centre for sport. Heriot-Watt Services Limited is a private
>    limited company registered is Scotland with registered number SC271030 and
>    registered office at Research & Enterprise Services Heriot-Watt University,
>    Riccarton, Edinburgh, EH14 4AS.
>
> The contents (including any attachments) are confidential. If you are not
> the intended recipient of this e-mail, any disclosure, copying,
> distribution or use of its contents is strictly prohibited, and you should
> please notify the sender immediately and then delete it (including any
> attachments) from your system.
>