- From: Leyla Garcia <ljgarcia@ebi.ac.uk>
- Date: Mon, 26 Jun 2017 13:15:05 +0100
- To: "Carlos Horro (EI)" <Carlos.Horro@earlham.ac.uk>, Olga Ximena Giraldo <oxgiraldo@gmail.com>
- Cc: S-A Sansone <sa.sansone@gmail.com>, "Enckevort, DJ van (medgen)" <david.van.enckevort@umcg.nl>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
- Message-ID: <0a29d326-a02e-b90a-7c1f-1700c2e40203@ebi.ac.uk>
Hi Carlos, David, From Olga's email, lab protocols are fine without a 'study' property or type. @Carlos, @David. Do you still need it for your specific cases? If not, then so far there would be no need to take this discussion further. If yes, I would propose Carlos to lead a group to work on it. Regards, On 26/06/2017 13:04, Carlos Horro (EI) wrote: > > Hi all, > > > I would like to mention that I'm collaborating with Elixir WP7 (plants > use case), and, in this use case, we also had to coordinate/map many > different models (7 if I'm not wrong) among them. > > A good compromise solution we reached was to use ISA hierarchy as a > reference for all of us: > > http://isa-tools.org/format/specification/ > > Specifications | ISA tools <http://isa-tools.org/format/specification/> > isa-tools.org > The ISA Abstract Model, originally developed as a tabular format > (ISA-Tab) since 2007, has been developed with several international > collaborators and in synergy with ... > > I think its 4 main entities (Investigation, Study, Assay and Sample) > can fit quite well with most necessities, of course being aware that > in each case there will be unique problems to be solved individually > (ie: distinct-level entities with same name, or same-level entities > with different name, and others). > > > Greetings, > > Carlos > > ------------------------------------------------------------------------ > *From:* Olga Ximena Giraldo <oxgiraldo@gmail.com> > *Sent:* 26 June 2017 12:15:26 > *To:* Leyla Garcia > *Cc:* S-A Sansone; Enckevort, DJ van (medgen); Carlos Horro (EI); > public-bioschemas@w3.org > *Subject:* Re: BiologicalEntity - BiologicalType > 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 > <http://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 <http://schema.org/> adds complexity and cost to the > users of schema.org <http://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 > <mailto: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 <mailto: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 > <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 > <http://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 <http://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 > <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 <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 > <http://orcid.org/0000-0003-2978-8922> > > Twiter: @olgaxgiraldo > > Skype:olgaximenagiraldo > > Website: http://oxgiraldo.wordpress.com >
Received on Monday, 26 June 2017 12:16:17 UTC