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Re: BiologicalEntity - BiologicalType

From: Olga Ximena Giraldo <oxgiraldo@gmail.com>
Date: Mon, 26 Jun 2017 13:15:26 +0200
Message-ID: <CA+FAuA2q+pR7qBD7vRJzzkJkijRCMo_kAhFE27j54itzqSLtkA@mail.gmail.com>
To: Leyla Garcia <ljgarcia@ebi.ac.uk>
Cc: S-A Sansone <sa.sansone@gmail.com>, "Enckevort, DJ van (medgen)" <david.van.enckevort@umcg.nl>, "Carlos.Horro@earlham.ac.uk" <Carlos.Horro@earlham.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Hi all.

I would stay away from the discussion investigation/study/assay and
consequently protocol. I agree with Susana, "the unit and sub-units of work
are clearly named differently in different community, or worse the same
name has different meaning."  I would also stay away from the "aggregation"
idea because it implies that you know the boundaries of whatever is being
aggregated.

Extending or adapting a Web-scale vocabulary like schema.org that shall be
applicable for all kinds of research settings  and thousands of
applications is quite a different thing than designing a conceptual data
 model (ontology) in an academic committee-fashion.  We should be aware
that every new element in schema.org adds complexity and cost to the users
of schema.org, in terms of searching the documentation, maintaining
examples and validators, etc. Therefore, bioschemas should be simple and
stay away from pretending to be an ontology.

>From my research, looking into more than 1000 protocols I have seen that
the information they all share is summarized in: sample, instrument,
reagent and objective (SIRO). These elements are common across all
protocols I have seen. For experimental protocols, investigation
information is not so relevant. The elements that I consider important for
protocols are the SIRO elements plus applicability and provenance.

Let me clarify something a protocol is not a study, strictly speaking.
Actually, studies and investigations don't necessarily have a detailed
 description of steps, as in a workflow of operations/actions, whereas
protocols do describe step by step the how to do something.

Best,

Olga


On Mon, Jun 26, 2017 at 12:11 PM, Leyla Garcia <ljgarcia@ebi.ac.uk> wrote:

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


-- 
Olga Ximena Giraldo Pasmin

PhD Student
Ontology Engineering Group
Escuela Técnica Superior de Ingenieros Informáticos
Universidad Politécnica de Madrid
Campus de Montegancedo, sn
Boadilla del Monte, 28660, Spain

Orcid ID: orcid.org/0000-0003-2978-8922

Twiter: @olgaxgiraldo

Skype:olgaximenagiraldo
Website: http://oxgiraldo.wordpress.com
Received on Monday, 26 June 2017 11:18:46 UTC

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