Re: BiologicalEntity - BiologicalType

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

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Susanna-Assunta Sansone, PhD
skype: susanna-a.sansone
ORCiD: 0000-0001-5306-5690

University of Oxford e-Research Centre
Associate Director and PI
www.oerc.ox.ac.uk/people/susanna-assunta-sansone

Springer Nature
Consultant, Scientific Data
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Received on Monday, 26 June 2017 09:56:52 UTC