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Re: BiologicalEntity - BiologicalType

From: Rodrigo Lopez Serrano <rls@ebi.ac.uk>
Date: Mon, 26 Jun 2017 12:05:45 +0100
To: Leyla Garcia <ljgarcia@ebi.ac.uk>, S-A Sansone <sa.sansone@gmail.com>, "Enckevort, DJ van (medgen)" <david.van.enckevort@umcg.nl>
Cc: "Carlos.Horro@earlham.ac.uk" <Carlos.Horro@earlham.ac.uk>, "oxgiraldo@gmail.com" <oxgiraldo@gmail.com>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <7486fde8-625d-3650-95a0-bc280deeeaae@ebi.ac.uk>
It's good there is an overlap, e.g. in some of the 'demographic' terms. 
We would not need to (re)define them.

Indeed, I agree these studies are different and the effort should not go 
into consolidating them, but into identifying where they overlap and 
exploit that to allow some sort of cross-navigation or bridge to move 
from one and into the other.

Re: "Study": does this not exist in other disciplines in schema.org?

R:)

On 26/06/2017 11:47, Leyla Garcia wrote:
> 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
>> >>>>> ============================================================
>> >
>>
>>
>
Received on Monday, 26 June 2017 11:06:16 UTC

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