Re: BiologicalEntity - BiologicalType

Hi,

Maybe 5 (outcome, population, sponsor, status, studyLocation) from 7 
properties defined for MedicalStudy 
(http://health-lifesci.schema.org/MedicalStudy) could also work for 
BiologicalStudy.  Maybe 2 (guideline, study) from those inherited from 
MedicalEntity. And those coming from Thing are mainly the usual suspects.

They are both studies but they are not the same. If we decide to specify 
a Biological Study, it would make sense to have a generic Study and then 
both Medical and Biological studies extending from it.

Regards,

On 26/06/2017 11:25, Rodrigo López Serrano wrote:
> Leyla wrote: "... findability, summarization, completeness?"
> Findability, IMHO.
> Do the terms under MedicalStudy apply or help to define what would be 
> under BiologicalStudy? If possible, let's not reinvent the wheel :-)
>
> R:)
>
> -------- Original message --------
> From: Leyla Garcia <ljgarcia@ebi.ac.uk>
> Date: 26/06/2017 11:11 (GMT+00:00)
> To: S-A Sansone <sa.sansone@gmail.com>, "Enckevort, DJ van (medgen)" 
> <david.van.enckevort@umcg.nl>
> Cc: Carlos.Horro@earlham.ac.uk, oxgiraldo@gmail.com, 
> public-bioschemas@w3.org
> Subject: Re: BiologicalEntity - BiologicalType
>
> Hi Olga, Carlos, and David,
>
> There is a MedicalStudy, we could define a BiologicalStudy that can
> aggregates studies. So, if you think an investigation is bigger than a
> study, you just use BiologicalStudy and link it to other 'sub-studies'.
> This could work for experiment (small study) and lab protocols (even
> smaller study). So, there are ways to specify this in a light way which
> is what is needed by now in Bioschemas.
>
> Now, the question is, how useful a BiologicalStudy would be?
> Particularly for the phenotype and lab protocol case (and David's as
> will but I am afraid I do not know which entity he is working on). What
> are the advantages of having a link to the study in your cases? Is it
> findability, summarization, completeness? Or any other use case that you
> have identified?
>
> Cheers,
>
> On 26/06/2017 10:56, S-A Sansone wrote:
> > Dear All,
> >
> > this discussion about Investigation, Study, Project, Experiment,
> > Dataset is a long-standing one, unfortunately. I have witnesses this
> > in the last 15 years working with many standards developing
> > communities, and also during the MIBBI checklists harmonization
> > project (some of you may remember). Unfortunately the unit and
> > sub-units of work are clearly named differently in different
> > community, or worse the same name has different meaning.
> >
> > Can we go back to the original point: what is that we aim to
> > 'discover' in this case?
> >
> > Thanks,
> >
> > Susanna
> >
> >
> > On 26/06/2017 06:24, Enckevort, DJ van (medgen) wrote:
> >> Hi,
> >> In MIABIS we also defined Study, which should also be reflected in
> >> OMIABIS or OBIB. Wouldn’t that be the more appropriate option?
> >>
> >> With kind regards,
> >>
> >> David van Enckevort
> >>
> >>> Op 23 jun. 2017, om 19:03 heeft ljgarcia <ljgarcia@ebi.ac.uk> het
> >>> volgende geschreven:
> >>>
> >>> hi Carlos,
> >>>
> >>> It does not seem to be much about investigations or studies except
> >>> for http://health-lifesci.schema.org/MedicalStudy.
> >>> Olga Giraldo is working on a schema for Lab Protocols which are
> >>> experiments. Experiments can be part of studies, studies can be part
> >>> of investigations. Or you can just see an investigation as an study
> >>> (as I understand was Rodrigo's proposal).
> >>>
> >>> I would suggest you to talk about it with Olga, maybe you can come
> >>> up with something in that regard. Please keep me in the loop, I
> >>> would like to participate in that too if we see that it fits and it
> >>> works for Bioschemas.
> >>>
> >>> @Alasdair, Rafael, Carole. If we decide to model these
> >>> investigations/studies required by phenotypes, we might need an
> >>> extension to deliver the specification as it would be something new.
> >>> Also, Lab Protocols have reagents which are chemicals which, at the
> >>> moment, fit into Biological Entity. I am not sure we are covering
> >>> all the reagent needs from a Lab Protocol perspective so Biological
> >>> Entity is likely to change. I know this is not ideal with the
> >>> deadline on the 30th coming, but we just had a meeting with Olga to
> >>> help her moving her specification to Bioschemas templates.
> >>>
> >>> Regards,
> >>>
> >>> On 2017-06-23 12:03, ljgarcia wrote:
> >>>> Hi all,
> >>>> I would propose the check schema.org to see whether there is 
> something
> >>>> there that can be used for study or investigation.
> >>>> Regards,
> >>>> On 2017-06-22 12:53, Lopez, Rodrigo wrote:
> >>>>> Can I propose the term 'study' to replace 'investigation'? But 
> still,
> >>>>> 'study' is not a biological type but rather a 'collection' or
> >>>>> 'aggregation' of biological types?
> >>>>> Kind regards,
> >>>>> R:)
> >>>>> On 22/06/2017 12:41, ljgarcia wrote:
> >>>>>> Hi,
> >>>>>> I would say "investigation" is not a biological type. You have
> >>>>>> there, for instance, people participating in the investigation,
> >>>>>> starting day, grant, and so on that just does not fit withing
> >>>>>> BiologicalEntity. Is there something more appropriate in 
> schema.org?
> >>>>>> Regards,
> >>>>>> On 2017-06-21 12:00, Carlos Horro (EI) wrote:
> >>>>>>> Hi,
> >>>>>>> We have defined BiologicalEntity - Phenotypes use cases, and we
> >>>>>>> would
> >>>>>>> be interested on one case about searching for an investigation
> >>>>>>> (ie. by
> >>>>>>> its name or description) and obtaining information about it ,
> >>>>>>> organisations and others. For mapping this case to BioSchemas,
> >>>>>>> BiologicalType would have to support something like
> >>>>>>> 'Investigation',
> >>>>>>> which it's not currently supported... would it be OK? do I
> >>>>>>> include it
> >>>>>>> into the biologicalType description?
> >>>>>>> I think the question it would be similar with other use cases we
> >>>>>>> need,
> >>>>>>> as Trials, Cultivars or Traits...
> >>>>>>> Greetings,
> >>>>>>> Carlos
> >>>>> --
> >>>>> ============================================================
> >>>>> Rodrigo Lopez Serrano,
> >>>>> Head of Web Production,
> >>>>> European Bioinformatics Institute (EMBL-EBI),
> >>>>> European Molecular Biology Laboratory,
> >>>>> Wellcome Trust Genome Campus,
> >>>>> South Building,
> >>>>> Hinxton, Cambridge, CB10 1SD
> >>>>> United Kingdom
> >>>>> ------------------------------------------------------------
> >>>>> ORCID: 0000-0003-1256-7306
> >>>>> http://scholar.google.co.uk/citations?user=7fhGnVEAAAAJ&hl=en
> >>>>> ============================================================
> >>>>> Love data? You can now search over 1 billion biological data
> >>>>> records in one go using EBI Search at https://www.ebi.ac.uk
> >>>>> ============================================================
> >
>
>