Re: {Disarmed} Re: DataRecord and Dataset Search

Hi All,

I just wanted to note that

<script type="application/ld+json">
{ "@context" : "http://schema.org",
"@type" : "Dataset",
"name" : "Superset" ,
"dataset" : { "@type" : "DataSet",
"name" : "Subset" }}
} }
</script>

Is currently not accepted by the google structured data testing tool.

Regards,
Jerven

On 2018-09-24 15:44, Gray, Alasdair J G wrote:
> It would seem that there is no real argument for having DataRecord as
> a separate type from Dataset. All the properties that we need for a
> DataRecord are already in the schema.org/Dataset [8] type. In fact, in
> the specification we even say that a record is a dataset
> 
>> A Record acts itself as a dataset although it refers to what could
>> be seen as the minimum compact, complete and auto-descriptive unit
>> in a dataset, i.e., a record. Bioschemas usage In Life Sciences,
>> records will represent a BioChemEntity
> 
> Are there any objections to us changing the DataRecord profile to use
> the schema.org/Dataset [8] type and removing the suggestion of a
> DataRecord type?
> 
> Alasdair
> 
>> On 10 Sep 2018, at 16:31, Shimoyama, Mary <shimoyama@mcw.edu> wrote:
>> 
>> 
>> Absolutely agree with (b) – the elements on a web page change
>> regularly – for most of the MODs, these can change daily, weekly,
>> monthly. He is right that the elements displayed on a webpage are
>> integrated from queries and present views of data from multiple
>> datasets within the overall structure of the resource. As for (c) on
>> a gene page there are elements that each have unique identifiers
>> 
>> FROM: Clark, Timothy W. [mailto:TWCLARK@mgh.harvard.edu]
>> SENT: Monday, September 10, 2018 10:06 AM
>> TO: Rafael Jimenez <rafael.jimenez@elixir-europe.org>
>> CC: Shimoyama, Mary <shimoyama@mcw.edu>; Leyla Garcia
>> <ljgarcia@ebi.ac.uk>; Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>; Dan
>> Brickley <danbri@google.com>; public-bioschemas@w3.org; Natasha Noy
>> <noy@google.com>; Vicki Tardif Holland <vtardif@google.com>
>> SUBJECT: Re: DataRecord and Dataset Search
>> 
>> ATTENTION: This email originated from a sender outside of MCW. Use
>> caution when clicking on links or opening attachments.
>> 
>> -------------------------
>> 
>> (a) Pointing out that since a set may have cardinality = 1, a data
>> record is certainly a data set.
>> 
>> (b) I wonder if using the concept “record” to mean the contents
>> of a web page could be problematic when pages are constructed by
>> queries and views on underlying data resources and assembled not
>> based on normalization rules but for best UX purposes and contain a
>> melange of many elements some of which are repeating.
>> 
>> (c)  For example, supposing we assign FOO:0010 to identify a web
>> page containing some information, all of which is not in 1st normal
>> form, i.e. it contains some unique attributes and some repeating
>> groups? And those group elements have their own identifiers
>> assigned, e.g FOO:0001, FOO:0002, etc?  What are we looking at ?
>> Does FOO:0010 identify a dataset or a data record?
>> 
>> (d) But if you stick with dataset “all the way down” you may be
>> better off, FOO:0010, FOO:0001, and FOO:0002 are all datasets.
>> 
>> Something to consider.
>> 
>> Tim
>> 
>> On Sep 10, 2018, at 10:40 AM, Rafael C. Jimenez
>> <rafael.jimenez@elixir-europe.org> wrote:
>> 
>> EXTERNAL EMAIL - USE CAUTION
>> 
>> To me, a data record could belong to one or more datasets. It
>> depends on the structure and organisation of the data resource. Data
>> records could be organised in datasets in many different ways. For
>> instance, by the species they belong to, the disease they have been
>> classified to (ie. cardiomegaly) or the experiment they were
>> identified in.
>> 
>> To give some examples of data records, below some links pointing to
>> different types of data records:
>> 
>> - Protein record in UniProt: MAILSCANNER HAS DETECTED A POSSIBLE
>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE
>> http://identifiers.org/uniprot:P69905 [1]
>> 
>> - Protein record in PDB: MAILSCANNER HAS DETECTED A POSSIBLE
>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE
>> http://identifiers.org/pdb:4n7n [2]
>> 
>> - Chemical record in ChEBI: MAILSCANNER HAS DETECTED A POSSIBLE
>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE
>> http://identifiers.org/CHEBI:27732 [3]
>> 
>> - Gene record in ENSEMBL: MAILSCANNER HAS DETECTED A POSSIBLE
>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE
>> http://identifiers.org/ensembl:ENSG00000244734 [4]
>> 
>> I like in Bioschmeas we are trying to annotate all our data
>> resources using few types and relationships: DataCatalog -> DataSet
>> -> DataRecord[BioChemEntity]. Some of our data resources like EGA or
>> OmicsDI will have a high number of datasets, but I think the
>> majority of our resources (UniProt, PDB, ChEBI or ENSEMBL mentioned
>> above) will have a high number of data records and few datasets.
>> Sometimes some of our data resources might even have just one
>> dataset for all their data records.
>> 
>> The alternative Alasdair is talking about is to use the DataSet
>> type for the concept of DataRecord. It would be to change to
>> DataCatalog -> DataSet -> DataSet[BioChemEntity]. Though for some
>> people it might not be semantically that correct I think this
>> approach has some advantages: 1. We do not need to propose a new
>> type DataRecord type to MAILSCANNER HAS DETECTED A POSSIBLE FRAUD
>> ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE schema.org
>> [5], 2.- The properties we wanted to use for DataRecord are already
>> in the DataSet type, 3.- Our data records will also be displayed in
>> the Google dataset search, 4.- It does not really change much the
>> way we have been working in Bioschemas.
>> 
>> Bringing back the question from Alisdair, which I think it is
>> important. Should we push for a new DataRecord type in MAILSCANNER
>> HAS DETECTED A POSSIBLE FRAUD ATTEMPT FROM
>> "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE Schema.org [6] or should
>> we re-use the DataSet type instead?
>> 
>> Regards,
>> 
>> Rafa
>> 
>> On Mon, 10 Sep 2018 at 15:19, Shimoyama, Mary <shimoyama@mcw.edu>
>> wrote:
>> Is there some thought to the idea of a data record belonging to
>> multiple datasets? For example, there is an annotation for the rat
>> A2m gene indicating it is associated with cardiomegaly. Does this
>> A2m-cardiomegaly record belong to the dataset of the A2m gene and
>> all of the data related to A2m, does it belong to the dataset of
>> Cardiomegaly and all of the genes associated with cardiomegaly, does
>> it belong to the dataset of  all the annotations and data taken from
>> PMID:12494268/RGDID:1549856, does it belong to the dataset of all
>> rat genes and their disease annotations or does it belong to the
>> dataset of the entire RGD corpus of data?
>> 
>> -----Original Message-----
>> From: Clark, Timothy W. [mailto:TWCLARK@mgh.harvard.edu]
>> Sent: Monday, September 10, 2018 8:04 AM
>> To: ljgarcia <ljgarcia@ebi.ac.uk>
>> Cc: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>; Dan Brickley
>> <danbri@google.com>; public-bioschemas@w3.org; Natasha Noy
>> <noy@google.com>; Vicki Tardif Holland <vtardif@google.com>;
>> Shimoyama, Mary <shimoyama@mcw.edu>
>> Subject: Re: DataRecord and Dataset Search
>> 
>> ATTENTION: This email originated from a sender outside of MCW. Use
>> caution when clicking on links or opening attachments.
>> ________________________________
>> 
>> Just adding in Mary Shimoyama PI of RGB to this discussion.
>> 
>>> On Sep 10, 2018, at 8:35 AM, ljgarcia <ljgarcia@ebi.ac.uk> wrote:
>>> 
>>> External Email - Use Caution
>>> Hi Alasdair,
>>> 
>>> I sounds to me you have covered it all. Maybe just some more
>> information about how we link sdo:Dataset, bs:DataRecord and
>> bs:BioChemEntity. sdo:Dataset sdo:hasPart bs:DataRecord (DataRecord
>> actually extends from Dataset) and then sdo:DataRecord sdo:isPartOf
>> sdo:Dataset. A sdo:DataRecord has sdo:maiEntity bs:BioChemEntity and
>> then a bs:BioChemEntity is sdo:mainEntityOfPage of a sdo:DataRecord.
>>> 
>>> DataRecord include two additional properties:
>>> * sdo:additionalProperty because we want everybody to be able to
>> add
>>> no-named properties as needed
>>> * bs:seeAlso so ther can be links to related data records in other
>> datasets, this one is very important in Life Sciences.
>>> 
>>> Note: I am using sdo for MAILSCANNER HAS DETECTED A POSSIBLE FRAUD
>> ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE schema.org
>> [5] and bs for bioschemas, although bioschemas types along with
>> their properties should go to MAILSCANNER HAS DETECTED A POSSIBLE
>> FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE
>> schema.org [5] at some point (hopefully soon).
>>> 
>>> Regards,
>>> 
>>> On 2018-09-09 19:03, Gray, Alasdair J G wrote:
>>>> Hi Dan
>>>> In the life sciences datasets, the individual records tend to get
>> 
>>>> their own web page, i.e. each concept in the database would have
>> its
>>>> own page. The idea for the DataRecord is to be able declare that
>> the
>>>> page about a concept is part of a Dataset.
>>>> I believe the approach is agnostic to the underlying storage,
>> i.e.
>>>> the page could be generated from a relational database which
>> pulls
>>>> data about the concept from multiple tables, a triplestore, or
>> some
>>>> other form of database. It is more about the granularity of this
>>>> being about a single concept, e.g. row in a relational database
>> with
>>>> its foreign keys.
>>>> Leyla, Rafa, Susanna, what do you think? Have I characterised
>> this
>>>> correctly or are there things in Dan’s email that I am missing.
>>>> Alasdair
>>>>> On 7 Sep 2018, at 18:12, Dan Brickley <danbri@google.com> wrote:
>>>>> (+Natasha Noy, +Vicki Tardif Holland) On Fri, 7 Sep 2018 at
>> 15:54,
>>>>> Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk> wrote:
>>>>>> Hi Dan,
>>>>>> Great to see the announcement this week about the Google
>> Dataset
>>>>>> search. Here is a link to a blog post for anyone who has not
>> seen
>>>>>> it yet
>>>> 
>> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.blog.google_
>>>> 
>> 
> products_search_making-2Dit-2Deasier-2Ddiscover-2Ddatasets_&d=DwIGaQ&
>>>> 
>> 
> c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5Tsee
>>>> 
>> 
> hzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQKLroB0DANNTw2d0tisoNx7KJQZ1xegXqyg&
>>>> s=X7OaasRJiIqJhU4v5NnlNJGHFRGBPnsqrNJMduz-DKQ&e=
>>>>>> Within Bioschemas, we have been building up a profile usage of
>>>>>> DataCatalog containing Dataset(s) which themselves contain
>>>>>> DataRecords. A DataRecord is something that we would be
>> proposing
>>>>>> as an addition to MAILSCANNER HAS DETECTED A POSSIBLE FRAUD
>> ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE schema.org
>> [5] [1]. The idea is that a DataRecord is
>>>>>> contained within a Dataset and would specify the types of
>> entity
>>>>>> that the record is about, e.g. Protein.
>>>>>> 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioschemas.org_
>>>>>> 
>> types_DataRecord_specification_&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iq
>>>>>> 
>> Fn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m
>>>>>> 
>> =9Do_KY8oQKLroB0DANNTw2d0tisoNx7KJQZ1xegXqyg&s=VQXoaBLgxbCy_Qxi4h8R
>>>>>> bqij_biYI-o3xrRcqvYMSPg&e= We would like to understand whether
>>>>>> DataRecord is an idea to which the MAILSCANNER HAS DETECTED A
>> POSSIBLE FRAUD ATTEMPT FROM "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO
>> BE schema.org [5] [1] community would
>>>>>> be receptive. An alternative approach would be to use Dataset
>> for
>>>>>> both records within a Dataset and the Dataset itself.
>>>>> It is certainly a direction worth exploring and discussing.
>>>>> One issue to think through (and I think I raised this at a
>>>>> bioschemas f2f last year) is that "Dataset" is a very broad
>> notion.
>>>>> Some but not all datasets are tabular for example. And tabular
>> (e.g.
>>>>> csv, sql) structures have non-trivial mappings to
>> "entity"-oriented
>>>>> and "record"-oriented representations. Other formats will have
>>>>> different (and possibly simpler) ideas about "records". Thinking
>> 
>>>>> about tabular first, there are complex mapping languages like
>> D2RQ
>>>>> or
>>>>> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.w3.org_TR_r
>>>>> 
>> 
> 2rml_&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQKLroB0DANNTw2d0tisoNx7KJQZ1xegXqyg&s=MYcr4sn8940aywRFbBWENNFVPxseMcirke2j3PEHUcM&e=
>> and the RDF graph it generates versus a rows-as-records view, how
>> would your draft design deal with multi-table datasets?
>>>>> Nearby in this world are specs like W3C CSVW, Data Cube, ...
>> lots of
>>>>> overlaps. It would be great to work through some examples in
>>>>> detail...
>>>>> Dan
>>>>>> Thanks
>>>>>> Alasdair
>>>>>> --
>>>>>> Alasdair J G Gray
>>>>>> Associate Professor in Computer Science, School of Mathematical
>> and
>>>>>> Computer Sciences Heriot-Watt University, Edinburgh, UK.
>>>>>> Email: A.J.G.Gray@hw.ac.uk
>>>>>> Web:
>>>>>> 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.macs.hw.ac.
>>>>>> 
>> uk_-7Eajg33&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&
>>>>>> 
>> r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQKLroB0DANN
>>>>>> 
>> Tw2d0tisoNx7KJQZ1xegXqyg&s=g-Y7L58vpqNcKEE1Av3OwMNwrCN0DZuOoxkll837
>>>>>> 5ZY&e=
>>>>>> ORCID:
>>>>>> 
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>>>>>> 
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>>>>>> 
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>>>>>> qMu07RxqWC8o&e=
>>>>>> Office: Earl Mountbatten Building 1.39
>>>>>> Twitter: @gray_alasdair
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>>>> Alasdair J G Gray
>>>> Associate Professor in Computer Science, School of Mathematical
>> and
>>>> Computer Sciences Heriot-Watt University, Edinburgh, UK.
>>>> Email: A.J.G.Gray@hw.ac.uk
>>>> Web:
>>>> 
>> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.macs.hw.ac.uk
>>>> 
>> 
> _-7Eajg33&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9L
>>>> 
>> 
> vaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQKLroB0DANNTw2d0t
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>> isoNx7KJQZ1xegXqyg&s=g-Y7L58vpqNcKEE1Av3OwMNwrCN0DZuOoxkll8375ZY&e=
>>>> ORCID:
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>> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__orcid.org_0000-2D
>>>> 
>> 
> 0002-2D5711-2D4872&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgs
>>>> 
>> 
> pw4Y&r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQKLroB0D
>>>> 
>> 
> ANNTw2d0tisoNx7KJQZ1xegXqyg&s=m2htr8bZ5GnacvnHur2nmU2ZA_whdHaqMu07Rxq
>>>> WC8o&e=
>>>> Office: Earl Mountbatten Building 1.39
>>>> Twitter: @gray_alasdair
>>>> Links:
>>>> ------
>>>> [1]
>>>> 
>> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__schema.org_&d=DwI
>>>> 
>> 
> GaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=9LvaCUW2sYxo387m5
>>>> 
>> 
> TseehzDcIGIVxSis9TsUt73Qqg&m=9Do_KY8oQKLroB0DANNTw2d0tisoNx7KJQZ1xegX
>>>> qyg&s=nbyl2sZnvQQv_BYn3lmWOze4_KC9X71SP_xPlR7OBlQ&e=
>>> 
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>> RAFAEL C JIMENEZ
>> 
>> ELIXIR Chief Data Architect
>> MAILSCANNER HAS DETECTED A POSSIBLE FRAUD ATTEMPT FROM
>> "URLDEFENSE.PROOFPOINT.COM" CLAIMING TO BE www.elixir-europe.org [7]
>> 
>> 
>> ELIXIR Hub, South Building
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> 
>  --
>  Alasdair J G Gray
>  Associate Professor in Computer Science,
> School of Mathematical and Computer Sciences
> 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
> 
> 
> 
> Links:
> ------
> [1]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__identifiers.org_uniprot-3AP69905&amp;d=DwMGaQ&amp;c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&amp;r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&amp;m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&amp;s=fcvRDFkHxKmxBT5NqR3zy23AhHgrcqxJhBrr1YQIxbc&amp;e=
> [2]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__identifiers.org_pdb-3A4n7n&amp;d=DwMGaQ&amp;c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&amp;r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&amp;m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&amp;s=6bhzIha2rtBDN1b-UapJW6wNsUDYmlpTTc7RkVIwJGk&amp;e=
> [3]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__identifiers.org_CHEBI-3A27732&amp;d=DwMGaQ&amp;c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&amp;r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&amp;m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&amp;s=3euSTTFX7v7hVnJZ_pNaJt_UyX-pFPSl_lvgBzDh91M&amp;e=
> [4]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__identifiers.org_ensembl-3AENSG00000244734&amp;d=DwMGaQ&amp;c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&amp;r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&amp;m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&amp;s=LOx1vWRdWE3jr5V1dFSg55lp6iGm8dl6NKwu5e0xsnI&amp;e=
> [5]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__schema.org_&amp;d=DwMGaQ&amp;c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&amp;r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&amp;m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&amp;s=pWdXlfBCWDRHFvEWI4bEWwBlqRlBzfaiJY2FFHH0yaM&amp;e=
> [6]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__Schema.org&amp;d=DwMGaQ&amp;c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&amp;r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&amp;m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&amp;s=0dpHewweLhkTKo1BgBEW71rBPWIKeH7QrO3-TDdQ7yI&amp;e=
> [7]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.elixir-2Deurope.org_&amp;d=DwMGaQ&amp;c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&amp;r=9LvaCUW2sYxo387m5TseehzDcIGIVxSis9TsUt73Qqg&amp;m=4c6VLbGuyLBfnCbZjSqnsP4IcONzzE5HnaQt8gEBM0A&amp;s=KR4sA_rKQ8wSkfEz0yrQ7flS0WlBByOWK55z8EEX-UQ&amp;e=
> [8] http://schema.org/Dataset

-- 
Jerven Tjalling Bolleman
SIB | Swiss Institute of Bioinformatics
CMU - 1, rue Michel Servet - 1211 Geneva 4
t: +41 22 379 58 85 - f: +41 22 379 58 58
Jerven.Bolleman@sib.swiss - http://www.sib.swiss

Received on Tuesday, 25 September 2018 20:15:30 UTC