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diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org index 8d7504e..aa06d5e 100644 --- a/doc/blog/using-covid-19-pubseq-part5.org +++ b/doc/blog/using-covid-19-pubseq-part5.org @@ -1,3 +1,20 @@ +#+TITLE: COVID-19 PubSeq (part 4) +#+AUTHOR: Pjotr Prins +# C-c C-e h h publish +# C-c ! insert date (use . for active agenda, C-u C-c ! for date, C-u C-c . for time) +# C-c C-t task rotate +# RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png + +#+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" /> + + +* Table of Contents :TOC:noexport: + - [[#modify-metadata][Modify Metadata]] + - [[#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]] + * Modify Metadata The public sequence resource uses multiple data formats listed on the @@ -10,8 +27,102 @@ data are listed [[./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 -understand that you and us can change that information. +understand that anyone, including you, can change that information! * What is the schema? +The default metadata schema is listed [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml][here]]. + * How is the website generated? + +Using the schema we use [[https://pypi.org/project/PyShEx/][pyshex]] shex expressions and [[https://github.com/common-workflow-language/schema_salad][schema salad]] to +generate the [[https://github.com/arvados/bh20-seq-resource/blob/edb17e7f7caebfa1e76b21006b1772a33f4f7887/bh20simplewebuploader/templates/form.html#L47][input form]], [[https://github.com/arvados/bh20-seq-resource/blob/edb17e7f7caebfa1e76b21006b1772a33f4f7887/bh20sequploader/qc_metadata.py#L13][validate]] the user input and to build [[https://github.com/arvados/bh20-seq-resource/blob/edb17e7f7caebfa1e76b21006b1772a33f4f7887/workflows/pangenome-generate/merge-metadata.py#L24][RDF]]! +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 +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 +https://creativecommons.org/publicdomain/zero/1.0/. Meanwhile the +attribution license https://creativecommons.org/licenses/by/4.0/. +According to this [[https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf][document]] we should really also add fields for +attributionName and attributionURL. + +A minimal triple should be + +: id xhtml:license <http://creativecommons.org/licenses/by/4.0/> . + +Other suggestions are + +: id dc:title "Description" . +: id cc:attributionName "Your Name" . +: id cc:attributionURL <http://resource.org/id> + +and 'dc:source' which indicates the original source of any modified +work, specified as a URI. +The prefix 'cc:' is an abbreviation for http://creativecommons.org/ns#. + +Going back to the schema, where does it fit? Under host, sample, +virus, technology or submitter block? It could fit under sample, but +actually the license concerns the whole metadata block and sequence, +so I think we can fit under its own license tag. For example + + +id: placeholder + +: license: +: license_type: http://creativecommons.org/licenses/by/4.0/ +: attribution_title: "Sample ID" +: attribution_name: "John doe, Joe Boe, Jonny Oe" +: attribution_url: http://covid19.genenetwork.org/id +: attribution_source: https://www.ncbi.nlm.nih.gov/pubmed/323088888 + +So, let's update the example. Notice the license info is optional - if it is missing +we just assume the default CC-4.0. + +One thing that is interesting is that in the name space https://creativecommons.org/ns there +is no mention of a title. I think it is useful, however, because we have no such field. +So, we'll add it simply as a title field. Now the draft schema is + +#+BEGIN_SRC js +- name: licenseSchema + type: record + fields: + license_type: + doc: License types as refined in https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#License + title: + doc: Attribution title related to license + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + attribution_url: + doc: Attribution URL related to license + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#Work + attribution_source: + doc: Attribution source URL + type: string? + jsonldPredicate: + _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 [[https://github.com/arvados/bh20-seq-resource/pull/97][here]] and reviewed on the +gitter channel and I merged it. + +* 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. + +/Note: work in progress/ |