Re: BioChemEntity

Hi Alasdair, Ricardo, Kenneth, all,

We will submit all types at once, will not? Because it is not just 
BioChemEntity but also LabProtocols and DataRecord. We also need to 
submit changes to current types, like the isBasisFor, a new property for 
CreativeWork. Should we make a list of things to submit? Then 
Ricardo/Kenneth can figure out the submission process.

Regards,


On 08/05/2018 11:23, Ricardo Arcila wrote:
> Hi All,
>
> > Ken/Riccardo, can you investigate what we need in order to prepare 
> BioChemEntity as a type submission for schema.org <http://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 <mailto: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 <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
>     <http://www.macs.hw.ac.uk/%7Eajg33>
>     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.
>