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Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part5.org')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part5.org | 49 |
1 files changed, 40 insertions, 9 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org index 4b0ea64..78eea66 100644 --- a/doc/blog/using-covid-19-pubseq-part5.org +++ b/doc/blog/using-covid-19-pubseq-part5.org @@ -13,19 +13,21 @@ - [[#what-is-the-schema][What is the schema?]] - [[#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? @@ -41,8 +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 @@ -113,8 +115,37 @@ So, we'll add it simply as a title field. Now the draft schema is _id: https://creativecommons.org/ns#Work #+END_SRC -Now, we are no ontology experts, right? So, next we submit a patch to our source tree and -ask for feedback before wiring it up in the data entry form. The pull request was -submitted here FIXME. +Now, we are no ontology experts, right? So, next we submit a patch to +our source tree and ask for feedback before wiring it up in the data +entry form. The pull request was submitted [[https://github.com/arvados/bh20-seq-resource/pull/97][here]] and reviewed on the +gitter channel and I merged it. -/Note: work in progress/ +* Adding fields to the form + +To add the new fields to the form we have to modify it a little. If we +go to the upload form we need to add the license box. The schema is +loaded in [[https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e8b0efec4abfaf892eb6c45/bh20simplewebuploader/main.py#L229][main.py]] in the 'generate_form' function. + +With this [[https://github.com/arvados/bh20-seq-resource/commit/b9691c7deae30bd6422fb7b0681572b7b6f78ae3][patch]] the website adds the license input fields on the form. + +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. + +When pushing the license info we discovered the workflow broke because +the existing data had no licensing info. So we changed the license +field to be optional - a missing license assumes it is CC-BY-4.0. + +* TODO Testing the license fields |