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Re: Bioschemas profile specification: multiple candidate terms from various ontologies

From: Justin Clark-Casey <jc955@cam.ac.uk>
Date: Thu, 26 Jul 2018 17:18:28 +0100
To: public-bioschemas@w3.org
Message-ID: <f2809fef-c98e-87fb-f5cc-7a57694ab2ae@cam.ac.uk>
On 04/07/18 21:35, ljgarcia wrote:
> Hi Franck,
> 
> I think we can use the DefinedTerm for mapping but I am not sure we need to go there. At least in the 
> protein case, the Protein Ontology already support mappings to other well-known ontologies. Is it not 
> similar for the taxon case?
> 
> I do not expect (yet?) the Bioschemas tools to support term replacements. I mean, if termA is the 
> official one, I think that is the one that will be recognized by Bioschemas, regarding existing mappings 
> to that term. Maybe Justin or Ricardo can provide more information in this regard.

Yes, this is why I was very keen to have a blessed term, since allowing alternatives gets us into the 
complexity of handling term mappings.  And to avoid a factional fight, have that term just be a neutral 
name in the context and leave mappings to an out-of-band file.

> 
> Regards,
> 
> 
> On 2018-07-02 09:20, Franck Michel wrote:
>> Hi Carl,
>>
>> Thanks for your response, I answer in the other thread with a relevant
>> title.
>>
>> Good point. As you suggest indeed, we would provide in the context the
>> terms selected for each profile, while optional mappings would be
>> provided within companion files like the schema.org shema.rdfa that
>> you mention.
>>
>> Regarding the syntax, I would say we can choose whatever RDF
>> serialization we deem most appropriate (JSON-LD, Turtle...), possibly
>> several. Below, I give an example context and mapping graph in
>> JSON-LD.
>>
>> Context:
>> {  "@context": [
>>         "http://schema.org/" [2],
>>         {  "tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#" [3],
>>             "tc:rank": { "@type": "@id" } }
>>     ],
>>     "tc:rank": "http://rs.tdwg.org/ontology/voc/TaxonRank#Species" [6]
>> }
>>
>> Mappings:
>> {
>>   "@context": {...},
>>   "@graph": [
>>      {  "@id": "tc:rank",
>>         "owl:equivalentProperty":
>> "http://www.wikidata.org/prop/direct/P105" [4],
>>         "sameAs": "https://www.wikidata.org/wiki/Property:P105" [5]
>>      },
>>      ...
>>    ]
>> }
>>
>> Note that the "profile mappings file" inherits the profile context.
>>
>> Does this sound right to you guys?
>>
>> Franck.
>>
>> Le 29/06/2018 à 18:32, Carl Boettiger a écrit :
>>
>>> 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".
>>
>> Le 29/06/2018 à 12:28, Franck Michel a écrit :
>>
>>> (hit the send button too fast: I renamed this one to split the
>>> threads.)
>>>
>>> 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
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>>>>
>>>>
>>>>
>>>> Links:
>>>> ------
>>>> [1] http://bioschemas.org/
>>
>>
>>
>> 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 Thursday, 26 July 2018 16:18:58 UTC

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