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#+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]]
- [[#testing-the-license-fields][Testing the license fields]]
* Modify Metadata
The public sequence resource uses multiple data formats listed on the
[[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 [[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
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 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
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.
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
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