Re: BiologicalEntity - BiologicalType

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
>>>>> ============================================================
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>>>>> ============================================================
>