Re: Protein representation with and without BioChemEntity

Regarding the examples, I noticed a large number of casing conventions,
e.g., lowerCamelCase, snake_case and kebab-case in just
"additionalProperty.transcribed_from" and "
http://semanticscience.org/resource/is-transcribed-from". It's unavoidable
if we use third-party terms that have different casing conventions, but
it's something to keep in mind.

This is potentially tangential, but for my use cases, word-sense
disambiguation is the first priority. Theoretically, SKOS, reasoners and
ontology mapping should make it trivial to use overlapping ontologies
(having exact matches). But in practice, overlapping ontologies can end up
adding complexity to word-sense disambiguation, because mappings are not
always available or reliable, so I have to handle handle multiple IRIs in
addition to free text like "is transcribed by", when I really want
schema.org and Bioschemas to reduce complexity.


On Fri, Nov 3, 2017 at 6:43 AM, Melanie Courtot <mcourtot@ebi.ac.uk> wrote:

> +1
> As said below, either existing mappings or some tools - OxO, BioPortal or
> else; I didn't mean to add a constraint there.
>
> For the relations at least users will need to make sure there is a way to
> get to a "known" entity for validation. Do we know how that could look
> like?
> Let's say for example some datasets use "http://semanticscience.org/re
> source/is-transcribed-from"
> <http://semanticscience.org/resource/is-transcribed-from> and some use "
> http://purl.obolibrary.org/obo/RO_0002510" (and I'm sure there are other
> relations than SIO and RO, using those as working examples, not saying
> either SIO or RO should be required), how would that work for the protein
> profile?
>
> Cheers,
> Melanie
>
>
> On 03/11/2017 13:29, Michel Dumontier wrote:
>
> yes of course, i was equally surprised to see SIO there in the first
> place.
>
> m.
>
> On Fri, Nov 3, 2017 at 1:50 PM, Leyla Garcia <ljgarcia@ebi.ac.uk> wrote:
>
>> Hi all,
>>
>> IMHO, if we want to be as inclusive as possible, we should not impose
>> anything outside the scope of type and profile specifications. So, if we
>> are not to impose RO, SIO, PRO, SO or any other, we should not impose
>> either OxO. We might find out that other groups also have their own
>> preferences there (Bioportal mapping, for instance).
>>
>> Regards,
>>
>>
>>
>> On 03/11/2017 11:44, Melanie Courtot wrote:
>>
>> Hi Michel,
>>
>> By "a step further" I was trying to make 2 points (and looking back my
>> email was probably not explicit enough):
>>
>> - Bioschemas should probably steer clear of debating the best choice of
>> ontology. In general, and as I mentioned during the last meeting, we
>> probably don't want to constrain which resources are being used as
>> different communities/users/groups will have their favorite ones, and will
>> probably not want to recode. Leyla mentions exisiting mappings, and we
>> could rely on the OxO tool [1] as well. It'd be interesting to see if we
>> could make this work with validation tools.
>>
>> - I don't think we should declare many Bioschemas specific properties
>> provided there is a mechanism for reusing existing relations. In the
>> current example at https://github.com/BioSchemas/
>> specifications/blob/master/PhysicalEntity/examples/BioChemEn
>> tityAlt-min.jsonld there is a "isContainedin" which I don't think
>> Bioschemas should redefine for example (and I see both SIO and RO have the
>> relation already)
>>
>> Cheers,
>> Melanie
>>
>> [1] https://www.ebi.ac.uk/spot/oxo/index
>>
>> On 03/11/2017 09:52, Michel Dumontier wrote:
>>
>> SIO is a perfectly acceptable choice, if I say so myself :)
>>
>> m.
>>
>> On Thu, Nov 2, 2017 at 11:02 AM, Melanie Courtot <mcourtot@ebi.ac.uk>
>> wrote:
>>
>>> Hi,
>>>
>>> I'm wondering if we could take it a step further, and instead of
>>> defining specific properties we could just reuse terms from RO (or else)?
>>>
>>> For example, "http://semanticscience.org/resource/is-transcribed-from"
>>> <http://semanticscience.org/resource/is-transcribed-from> could be
>>> replaced by http://purl.obolibrary.org/obo/RO_0002510, "transcribed
>>> from", and "isContainedIn" could be  http://purl.obolibrary.org/obo
>>> /RO_0001018, "contained in".
>>>
>>> Cheers,
>>> Melanie
>>>
>>> --
>>> Mélanie Courtot, PhD
>>> GA4GH/BioSamples Project lead
>>> European Bioinformatics Institute (EMBL-EBI)
>>>
>>>
>>>
>>> On 01/11/2017 16:18, Justin Clark-Casey wrote:
>>>
>>> Direct term reuse sounds like a good choice to me, especially as
>>>
>>> a) it's the mechanism that schema.org themselves have to add existing
>>> ontology classes and terms to the structured data
>>> b) will make applications much easier to write as they can use existing
>>> general tooling
>>> c) allows us to do everything we were doing with AdditionalProperty and
>>> d) still allows us to define profiles without having to move everything
>>> through schema.org
>>>
>>> -- Justin
>>>
>>> On Wed, Nov 1, 2017 at 3:56 PM, Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
>>> wrote:
>>>
>>>> Hi All,
>>>>
>>>> Apologies for the delay in sending this email. I have been working with
>>>> Carole on submitting an Implementation Study proposal to the Data Platform
>>>> for more work on Bioschemas.
>>>>
>>>> For representing a specific bioscience type, e.g. a protein, we
>>>> currently have a proposal for using a generic wrapper approach that we then
>>>> specialise, e.g. BioChemEntity specialised with a Protein profile.
>>>>
>>>> Protein profile
>>>> http://bioschemas.org/specifications/Protein/specification/
>>>> BioChemEntity type
>>>> http://bioschemas.org/specifications/BioChemEntity/specification/
>>>>
>>>> To help understand the various advantages and disadvantages of this
>>>> approach, Kenneth and I have drawn up an example of marking up a specific
>>>> protein first using the current proposal and second  if we were to do the
>>>> same with a specific ProteinEntity. Below are the examples and some
>>>> analysis of them.
>>>>
>>>> *BioChemEntity Example*
>>>> Minimum markup using BioChemEntity
>>>> https://github.com/BioSchemas/specifications/blob/master/Phy
>>>> sicalEntity/examples/BioChemEntity-min.jsonld
>>>>
>>>> Minimum + Recommended markup using BioChemEntity
>>>> https://github.com/BioSchemas/specifications/blob/master/Phy
>>>> sicalEntity/examples/BioChemEntity-min%2Brec.jsonld
>>>> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntity-min+rec.jsonld>
>>>>
>>>> One thing to note is that the minimum + recommended markup is not an
>>>> additive extension of the minimum markup. Due to the use of the
>>>> AdditionalProperty relationship, you need to use an JSON array and add the
>>>> properties from the recommended level within the existing array.
>>>>
>>>> An advantage of this approach is that it reuses terms from existing
>>>> ontologies and we can represent types that do not currently exist in
>>>> Schema.org <http://schema.org>, e.g. Genes, Chemicals, etc.
>>>>
>>>> *ProteinEntity example*
>>>> Minimum markup using ProteinEntity
>>>> https://github.com/BioSchemas/specifications/blob/master/Phy
>>>> sicalEntity/examples/ProteinEntity-min.jsonld
>>>>
>>>> Minimum + Recommended markup using ProteinEntity
>>>> https://github.com/BioSchemas/specifications/blob/master/Phy
>>>> sicalEntity/examples/ProteinEntity-min%2Brec.jsonld
>>>> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/ProteinEntity-min+rec.jsonld>
>>>>
>>>> While the markup in these examples using ProteinEntity is easier to
>>>> interpret, the number of items that need to be changed to markup another
>>>> protein is the same as in the BioChemEntity approach. The simplified markup
>>>> should enable easier adoption, although we could help the current proposal
>>>> of using BioChemEntity by using highlighting on the Bioschemas site to show
>>>> which terms need to be changed.
>>>>
>>>> A major downside of this approach is that we would need to add all the
>>>> types to Schema.org <http://schema.org> or host them at Bioschemas.org
>>>> <http://bioschemas.org>. While these could be mapped to existing
>>>> terms, we would be accused of duplicating existing ontology terms.
>>>>
>>>> *Direct term reuse example*
>>>> Last week, I showed the above examples to Dan (we were at ISWC
>>>> together). He pointed out that the additionalProperty relation was added to
>>>> allow the use of property/value pairs where the properties do not exist in
>>>> an ontology. We are in the situation where the properties we are using come
>>>> from ontologies. Dan suggested that we just use them directly. Note that
>>>> the example also exploits the fact that you can define multiple types.
>>>>
>>>> Minimum markup using BioChemEntity and term reuse
>>>> https://github.com/BioSchemas/specifications/blob/master/Phy
>>>> sicalEntity/examples/BioChemEntityAlt-min.jsonld
>>>>
>>>> Minimum + Recommended markup using BioChemEntity and term reuse
>>>> https://github.com/BioSchemas/specifications/blob/master/Phy
>>>> sicalEntity/examples/BioChemEntityAlt-min%2Brec.jsonld
>>>> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min+rec.jsonld>
>>>>
>>>> As you will see, this seems to have the advantages of both the above
>>>> approaches. The markup is more straightforward than the additionalProperty
>>>> approach, but exploits reusing existing domain ontologies. The tooling and
>>>> exploitation will be much more straightforward.
>>>>
>>>> I invite you all to review and comment on these different examples. Do
>>>> we believe that the BioChemEntity with term reuse (the third set of
>>>> examples) is an appropriate path going forward?
>>>>
>>>> Best regards
>>>>
>>>> Alasdair
>>>>
>>>> PS Sorry for the long email
>>>>
>>>> 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
>>>> ORCID: http://orcid.org/0000-0002-5711-4872
>>>> Office: Earl Mountbatten Building 1.39
>>>> Twitter: @gray_alasdair
>>>>
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>>>
>>>
>>
>>
>> --
>> Michel Dumontier
>> Distinguished Professor of Data Science
>> Maastricht University
>> http://dumontierlab.com
>>
>>
>>
>>
>
>
> --
> Michel Dumontier
> Distinguished Professor of Data Science
> Maastricht University
> http://dumontierlab.com
>
>
>