W3C home > Mailing lists > Public > public-bioschemas@w3.org > July 2018

Re: Bioschemas Taxon profile specification

From: ljgarcia <ljgarcia@ebi.ac.uk>
Date: Wed, 04 Jul 2018 21:26:24 +0100
To: Justin Clark-Casey <justinccdev@gmail.com>
Cc: cboettig@gmail.com, Franck Michel <fmichel@i3s.unice.fr>, Melanie Courtot <mcourtot@ebi.ac.uk>, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, public-bioschemas@w3.org
Message-ID: <a00dd58679bcd02b436b8d7f47ce0233@ebi.ac.uk>
+1, the context is not the place for equivalences or so. Using 
DefinedTerm works better in that case but I guess we still have to 
better evaluate how DefinedTerm fits in Bioschemas.

Regards,

On 2018-07-04 18:31, Justin Clark-Casey wrote:
> Yeah, I don't think you would define equivalent terms in the context.
> As Carl says, I think it's actually in an out-of-band document (rdfa
> for schema.org [1], maybe even placeable in the yaml that generates
> the spec pages on Bioschemas.org).  However, at least having this in
> JSON-LD or equivalent will make the relations readable for software,
> even if the format is bespoke to us (hopefully we could be very close
> to the schema.org [1] approach).
> 
> And the 'sparing different communities sensitivity' is actually why I
> propose having Bioschemas define an empty signalling type (e.g.
> http://bioschemas.org/taxon) and the sameas stuff in the out-of-band
> JSON-LD file.  Then many term equivalences can be listed without
> upsetting any particular community.  The empty Bioschemas type is not
> a term, it's just a device for simplifying Bioschemas markup and
> avoiding damaging debates.  It would contain absolutely no term
> definition or description itself and would merely have sameas links to
> other ontologies.
> 
> On Fri, 29 Jun 2018 at 17:32, Carl Boettiger <cboettig@gmail.com>
> wrote:
> 
>> Hi Franck,
>> 
>> I'm not an expert in OWL, but I don't think the context is the
>> correct place to define the OWL relationships.  If you consider the
>> examples of schema.org [1] itself, it does not define any
>> owl:equivalentProperty in the schema.org [1] definitions themselves,
>> but rather includes them in the offical schema.rdfa document where
>> the class definitions are also specified, e.g.
>> 
> https://github.com/schemaorg/schemaorg/blob/master/data/schema.rdfa#L4545
>> defines  that schema:description is the owl:equivalentProperty to
>> dc:description, just as you would expect.
>> 
>> I'm not actually sure if the bioschemas definitions are defined in
>> identical format to the schema.rdfa (personally I find rdfa hard to
>> read and tend to convert that to JSON-LD first for my own use
>> cases), but if so, it seems like that is where we should put the
>> owl:equivalentProperty statements, rather than in the context?
>> 
>> Note that the invalid error you see is not specific to sameAs or
>> owl:equivalentProperty; I believe a context cannot have any
>> 'non-special' terms.  Perhaps you want instead:
>> 
>> {
>> "@context": [
>> "http://schema.org/",
>> {
>> "tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#",
>> "wdt": "http://www.wikidata.org/prop/direct/",
>> "tc:rank": {
>> "@type": "@id",
>> "@id": "https://www.wikidata.org/wiki/Property:P105"
>> }
>> }
>> ],
>> "tc:rank": "http://rs.tdwg.org/ontology/voc/TaxonRank#Species"
>> }
>> 
>> Obviously this is a slightly different statement, since it does not
>> define a property and equivalent property, but literally uses the
>> wikidata URI as the expanded URI definition of "tc:rank".
>> 
>> On Fri, Jun 29, 2018 at 3:26 AM Franck Michel
>> <franck.michel@cnrs.fr> wrote:
>> 
>> First sub-thread:  WHAT DO WE DO WHEN THERE ARE MULTIPLE CANDIDATE
>> TERMS FROM VARIOUS ONTOLOGIES?
>> 
>> I guess there is a consensus here: each specification group proposes
>> a single approved term for each type and each property, that
>> represents the group consensus.
>> The only difficulty may be to reach this consensus while sparing
>> different communities' sensitivity.
>> 
>> It's been suggested that the context may document mappings to
>> equivalent terms in other ontologies. Although the idea is
>> compelling, I'm not sure how this can be achieved technically. I
>> have tried the [invalid] example below. Let us assume the
>> Biodiversity group chooses the TDWG rank property (tc:rank) to
>> denote the taxonomic rank. The context names this property while
>> providing the equivalent Wikidata property (owl:equivalentProperty)
>> and webpage thereof (remember that schema:sameAs gives the "URL of a
>> reference Web page that unambiguously indicates the item's identity
>> (...)".
>> {
>> "@context": [
>> "http://schema.org/" [2],
>> {
>> "tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#"
>> [3],
>> "tc:rank": {
>> "@type": "@id",
>> "owl:equivalentProperty":
>> "http://www.wikidata.org/prop/direct/P105" [4],
>> "sameAs":
>> "https://www.wikidata.org/wiki/Property:P105" [5]
>> }
>> }
>> ],
>> "tc:rank": "http://rs.tdwg.org/ontology/voc/TaxonRank#Species"
>> [6]
>> }
>> 
>> Unfortunately, this example is invalid [7] because a JSON-LD term
>> definition cannot contain a sameAs or owl:equivalent property.
>> Can you think of other ways to express this mapping?
>> 
>> Franck.
>> 
>> Le 28/06/2018 à 19:40, Justin Clark-Casey a écrit :
>> 
>> On Thu, 28 Jun 2018 at 16:42, ljgarcia <ljgarcia@ebi.ac.uk> wrote:
>> Hi,
>> 
>> What Melanie suggests is useful to describe profiles, they would
>> become
>> a DefinedTerm. That would help as well to avoid type/profile
>> confusion.
>> We would talk then about DefinedTerms. If we find a way to also
>> described the properties accepted with their restrictions, that
>> would be
>> even better. That might be a good subject for a different
>> discussion.
>> 
>> This means there will have to be special Bioschemas code that knows
>> to look in a DefinedTerm somewhere for this information.  I still
>> think using a subtype to signify a profile will be simpler.
>> 
>> I also disagree with Alasdair in that I think there should be a
>> http://bioschema.org/Protein type.  This would be an empty type that
>> just signifies we're talking about a Bioschemas defined protein. so
>> it isn't treading on anybodies toes.  This would have information
>> saying it's defined by http://purl.obolibrary.org/obo/PR_000000001
>> and it's same as terms.  Without this, there's not much point having
>> a bioschemas context, and requiring people to use this specific
>> string every time is cumbersome, especially if every group chooses
>> something from a different ontology.  This makes writing and
>> consuming markup harder.
>> 
>> The question remains. How do we choose a term over others to
>> associate
>> it to a profile/DefinedTerm?
>> 
>> I suggest having members of each specification group propose which
>> term they want and then come to consensus via discussion and/or
>> vote.
>> 
>> Regards,
>> 
>> On 2018-06-28 15:45, Melanie Courtot wrote:
>>> Hi,
>>> 
>>> We could consider using the defined terms,
>>> 
>> 
> https://dataliberate.com/2018/06/18/schema-org-introduces-defined-terms/,
>>> to do that.
>>> 
>>> So have a protein be defined as
>>> 
>>> "@type": "DefinedTerm",
>>> "@id": "http://purl.obolibrary.org/obo/PR_000000001",
>>> "name": "Protein",
>>> "inDefinedTermSet": "http://bioschemas.org/terms",
>>> "description": "An amino acid chain that is produced
>> de
>>> novo by ribosome-mediated translation of a genetically-encoded
>> mRNA.",
>>> "sameAs":
>> "http://purl.obolibrary.org/obo/NCIT_C17021",
>>> "sameAs":
>> "http://semanticscience.org/resource/SIO_010043"
>>> 
>>> (Using random examples of sameAs from
>>> https://www.ebi.ac.uk/ols/search?q=protein)
>>> 
>>> Cheers,
>>> Melanie
>>> 
>>> ---
>>> Melanie Courtot, PhD
>>> EMBL-EBI
>>> GA4GH/BioSamples project lead
>>> 
>>>> On 28 Jun 2018, at 15:18, ljgarcia <ljgarcia@ebi.ac.uk> wrote:
>>>> Hi,
>>>> 
>>>> I understood Franck's question in a different way.
>>>> 
>>>> Alasdair says
>>>> 
>>>>> I also agree that a context file should be provided which has
>> the
>>>>> chosen types and terms in it, i.e. the context file would define
>>>>> Protein to be the URI
>> http://purl.obolibrary.org/obo/PR_000000001.
>>>> 
>>>> I think what Franck is asking is how to choose
>>>> http://purl.obolibrary.org/obo/PR_000000001 over other possible
>>>> terms to define a Protein. For the taxon case, same as it happens
>>>> with proteins, there are multiple possibilities. Franck, is this
>>>> your question? If it is, I do not think there is any agreement on
>>>> how to choose, other than going for well-known ontologies broadly
>>>> accepted by the community of interest, even better if the term is
>>>> mapped to other possible ones.
>>>> 
>>>> Regards,
>>>> 
>>>> On 2018-06-28 11:50, Gray, Alasdair J G wrote:
>>>> On 27 Jun 2018, at 19:19, Justin Clark-Casey
>> <justinccdev@gmail.com>
>>>> wrote:
>>>> I think we should have mandatory known @types and properties.  In
>>>> my view, Bioschemas should be as easy as possible to write and
>>>> consume.  Multiple options will increase cognitive load on
>> writers
>>>> (which one do I choose?  Why are these 2 examples using these
>>>> different terms?) and open the door to greater inconsistency.
>>>> Non-mandatory types will also raise the barriers for writing
>>>> Bioschemas software that will have to be aware of equivalent
>>>> mappings.
>>>> I completely agree that we should have a single approved type for
>>>> each profile, and likewise for each property a single chosen
>> term.
>>>> This is the whole point of having the profiles.
>>>> I would go one step further and say that Bioschemas should
>> provide
>>>> an http://bioschemas.org [1] [1]context that will define types
>> such
>>>> as
>>>> Taxon, rather than blessing particular ontology terms.
>>>> I also agree that a context file should be provided which has the
>>>> chosen types and terms in it, i.e. the context file would define
>>>> Protein to be the URI
>> http://purl.obolibrary.org/obo/PR_000000001.
>>>> To
>>>> be completely explicit, we would not be defining a type in the
>>>> bioschemas namespace, e.g. http://bioschemas.org/Protein.
>>>> This context can also document equivalent terms in different
>>>> ontologies.
>>>> I like the idea that this also contains mappings to the
>> equivalent
>>>> terms in other ontologies.
>>>> Alasdair
>>>> Alasdair J G Gray
>>>> Fellow of the Higher Education Academy
>>>> Assistant Professor in Computer Science,
>>>> School of Mathematical and Computer Sciences
>>>> (Athena SWAN Bronze Award)
>>>> Heriot-Watt University, Edinburgh UK.
>>>> Email: A.J.G.Gray@hw.ac.uk
>>>> Web: http://www.macs.hw.ac.uk/~ajg33 [8]
>>>> ORCID: http://orcid.org/0000-0002-5711-4872
>>>> Office: Earl Mountbatten Building 1.39
>>>> Twitter: @gray_alasdair
>>>> Untitled Document
>>>> -------------------------
>>>> _HERIOT-WATT UNIVERSITY IS THE TIMES & THE SUNDAY TIMES
>>>> INTERNATIONAL
>>>> UNIVERSITY OF THE YEAR 2018_
>>>> Founded in 1821, Heriot-Watt is a leader in ideas and solutions.
>>>> With
>>>> campuses and students across the entire globe we span the world,
>>>> delivering innovation and educational excellence in business,
>>>> engineering, design and the physical, social and life sciences.
>>>> This email is generated from the Heriot-Watt University Group,
>> which
>>>> includes:
>>>> * Heriot-Watt University, a Scottish charity registered under
>>>> number
>>>> SC000278
>>>> * Edinburgh Business School a Charity Registered in Scotland,
>>>> SC026900. Edinburgh Business School is a company limited by
>>>> guarantee,
>>>> registered in Scotland with registered number SC173556 and
>>>> registered
>>>> office at Heriot-Watt University Finance Office, Riccarton,
>> Currie,
>>>> Midlothian, EH14 4AS
>>>> * Heriot- Watt Services Limited (Oriam), Scotland's national
>>>> performance centre for sport. Heriot-Watt Services Limited is a
>>>> private limited company registered is Scotland with registered
>>>> number
>>>> SC271030 and registered office at Research & Enterprise Services
>>>> Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS.
>>>> The contents (including any attachments) are confidential. If you
>>>> are
>>>> not the intended recipient of this e-mail, any disclosure,
>> copying,
>>>> distribution or use of its contents is strictly prohibited, and
>> you
>>>> should please notify the sender immediately and then delete it
>>>> (including any attachments) from your system.
>>>> Links:
>>>> ------
>>>> [1] http://bioschemas.org/
>>> 
>>> 
>>> 
>>> Links:
>>> ------
>>> [1] http://bioschemas.org/
> 
> --
> 
> http://carlboettiger.info
> 
> Links:
> ------
> [1] http://schema.org
> [2] http://schema.org/
> [3] http://rs.tdwg.org/ontology/voc/TaxonConcept#
> [4] http://www.wikidata.org/prop/direct/P105
> [5] https://www.wikidata.org/wiki/Property:P105
> [6] http://rs.tdwg.org/ontology/voc/TaxonRank#Species
> [7]
> https://json-ld.org/playground/#startTab=tab-expanded&amp;json-ld=%7B%22%40context%22%3A%5B%22http%3A%2F%2Fschema.org%2F%22%2C%7B%22tc%22%3A%22http%3A%2F%2Frs.tdwg.org%2Fontology%2Fvoc%2FTaxonConcept%23%22%2C%22wdt%22%3A%22http%3A%2F%2Fwww.wikidata.org%2Fprop%2Fdirect%2F%22%2C%22tc%3Arank%22%3A%7B%22%40type%22%3A%22%40id%22%2C%22owl%3AequivalentProperty%22%3A%22wdt%3AP105%22%2C%22sameAs%22%3A%22https%3A%2F%2Fwww.wikidata.org%2Fwiki%2FProperty%3AP105%22%7D%7D%5D%2C%22tc%3Arank%22%3A%22http%3A%2F%2Frs.tdwg.org%2Fontology%2Fvoc%2FTaxonRank%23Species%22%7D
> [8] http://www.macs.hw.ac.uk/%7Eajg33
Received on Wednesday, 4 July 2018 20:26:51 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 4 July 2018 20:26:51 UTC