diff options
| -rw-r--r-- | topics/add-metadata-to-trait-page.gmi | 39 |
1 files changed, 39 insertions, 0 deletions
diff --git a/topics/add-metadata-to-trait-page.gmi b/topics/add-metadata-to-trait-page.gmi new file mode 100644 index 0000000..ddef239 --- /dev/null +++ b/topics/add-metadata-to-trait-page.gmi @@ -0,0 +1,39 @@ +# Add Metadata To The Trait Page (RDF) + +Wed 28 Sep 2022 14:49:51 EAT + +## Introduction + +We are migrating the GN2 relational database to a plain text and RDF database. Matrix-like data (E.g. fetching sample data for a given data) will be stored inside GN. + +So far, we are able to convert the sql data to rdf using "dump.scm" defined in: + +=> https://github.com/genenetwork/dump-genenetwork-database + +## What are we trying to solve? + +Data stored in genenetwork resembles a tree. As an example: we have several species; each of these species belong to a group; each group belongs to a "data type"; and each data type belongs to a particular dataset. The first step: capturing - albeit requiring more refinement - this data in RDF has been achieved using the aformentioned scheme script. + +The overall goal is to be ablet to: + +* Incrementally replace MySQL queries with RDF. + +* Annotating existing data with metadata that does not yet exist in GN2. + +## Goals + +* In the Trait Analysis Page, add extrat metadata for "Group", "Tissue", "Gene Symbol". Possibly, a link to a relevant URL with useful information. + +### Non-goals + +* Refactoring base classes/sql to solely use RDF. + +## Actual Design + +* Create endpoints to add extra annotations for Groups, Tissue, Gene Symbol. +* Should this extra data not exist, write a script in Guile to fetch them from wikidata and insert them into RDF as extra nodes. +* Add metadata as links or tooltips to the relevant html section. + +## Resources + +=> https://www.linkedin.com/pulse/six-secret-sparql-ninja-tricks-kurt-cagle/ |