diff options
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 3 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 3 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part5.org | 29 |
3 files changed, 27 insertions, 8 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index c690e8a..ef55c55 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -1,6 +1,7 @@ $base: http://biohackathon.org/bh20-seq-schema $namespaces: cc: http://creativecommons.org/ns# + dc: http://purl.org/metadata/dublin_core_elements# sch: https://schema.org/ efo: http://www.ebi.ac.uk/efo/ obo: http://purl.obolibrary.org/obo/ @@ -22,7 +23,7 @@ $graph: doc: Attribution title related to data license type: string? jsonldPredicate: - _id: http://semanticscience.org/resource/SIO_001167 + _id: http://purl.org/metadata/dublin_core_elements#Title attribution_name: doc: Attribution NAME related to data license type: string? diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index c48267d..9fab334 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -2,6 +2,7 @@ PREFIX : <https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh2 PREFIX MainSchema: <http://biohackathon.org/bh20-seq-schema#MainSchema/> PREFIX hostSchema: <http://biohackathon.org/bh20-seq-schema#hostSchema/> PREFIX cc: <http://creativecommons.org/ns#> +PREFIX dc: <http://purl.org/metadata/dublin_core_elements#> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX sio: <http://semanticscience.org/resource/> @@ -71,7 +72,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> :licenseShape{ cc:License xsd:string; - sio:SIO_001167 xsd:string ?; + dc:Title xsd:string ?; cc:attributionName xsd:string ?; cc:attributionURL xsd:string ?; cc:attributionSource xsd:string ?; diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org index cb11f43..98c2c31 100644 --- a/doc/blog/using-covid-19-pubseq-part5.org +++ b/doc/blog/using-covid-19-pubseq-part5.org @@ -14,19 +14,20 @@ - [[#how-is-the-website-generated][How is the website generated?]] - [[#modifying-the-schema][Modifying the schema]] - [[#adding-fields-to-the-form][Adding fields to the form]] + - [[#testing-the-license-fields][Testing the license fields]] * Modify Metadata The public sequence resource uses multiple data formats listed on the -[[./download][DOWNLOAD]] page. One of the most exciting features is the full support +[[http://covid19.genenetwork.org/download][download]] page. One of the most exciting features is the full support for RDF and semantic web/linked data ontologies. This technology allows for querying data in unprescribed ways - that is, you can formulate your own queries without dealing with a preset model of that data (so typical of CSV files and SQL tables). Examples of exploring -data are listed [[./blog?id=using-covid-19-pubseq-part1][here]]. +data are listed [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1][here]]. In this BLOG we are going to look at the metadata entered on the -[[./][COVID-19 PubSeq]] website (or command line client). It is important to +COVID-19 PubSeq website (or command line client). It is important to understand that anyone, including you, can change that information! * What is the schema? @@ -42,8 +43,8 @@ All from that one metadata schema. * Modifying the schema One of the first things we want to do is to add a field for the data -license. Initially we only support CC-4.0 as a license by default, but -now we want to give uploaders the option to make it an even more +license. Initially we only supported CC-4.0 as a license, but +we wanted to give uploaders the option to use an even more liberal CC0 license. The first step is to find a good ontology term for the field. Searching for `creative commons cc0 rdf' rendered this useful [[https://creativecommons.org/ns][page]]. We also find an [[https://wiki.creativecommons.org/wiki/CC_License_Rdf_Overview][overview]] where CC0 is represented as URI @@ -127,4 +128,20 @@ loaded in [[https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e With this [[https://github.com/arvados/bh20-seq-resource/commit/b9691c7deae30bd6422fb7b0681572b7b6f78ae3][patch]] the website adds the license input fields on the form. -/Note: work in progress/ +Finally, to make RDF output work we need to add expressions to bh20seq-shex.rdf. This +was done with this [[https://github.com/arvados/bh20-seq-resource/commit/f4ed46dae20abe5147871495ede2d6ac2b0854bc][patch]]. In the end we decided to use the Dublin core title, +http://purl.org/metadata/dublin_core_elements#Title: + +#+BEGIN_SRC js +:licenseShape{ + cc:License xsd:string; + dc:Title xsd:string ?; + cc:attributionName xsd:string ?; + cc:attributionURL xsd:string ?; + cc:attributionSource xsd:string ?; +} +#+END_SRC + +Note that cc:AttributionSource is not really defined in the cc standard. + +* TODO Testing the license fields |