# Add Metadata To The Trait Page (RDF)

Fri 30 Sep 2022 11:48:41 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, for example:

=> https://genenetwork.org/show_trait?trait_id=1434280_at&dataset=HC_M2_0606_P

and the corresponding GN1 link:

=> http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db=HC_M2_0606_P&probeset=1434280_at

which on further inspection presents metadata on that specific dataset group here:

=> http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=112

We notice that there's metadata in GN1 - which we have in RDF - that we can add to the GN2 traits page.  As such, this design doc will be limited to using RDF to:

* Append metadata about the tissue
* Append relevant metadata about the dataset group, in particular: about the data values and it's processing; about the array platform; experiment type; and contributors.

Beyond querying metadata, this design doc also proposes the creation of a monadic rdf-fetch similar to what happens in:

=> https://issues.genenetwork.org/topics/maybe-monad

### Non-goals

* Refactoring base classes/sql to solely use RDF.
* Using federated queries - they are slow.
* Writing a script in Guile to fetch and append extra metadata from wikidata and insert them into RDF as extra nodes.  This should be tackled as a separate issue.

## Actual Design

* Rewrite the existing way of fetching RDF using pymonads.
* React to the change-amplification - should any exist - caused by the above change and add tests where feasible.
* Create endpoints to add extra annotations for Tissue, Dataset Group, Dataset Values and Processing; array platform; experiment type; and contributors.
* Add metadata as links, tooltips, or html <summary> tag to the relevant html section(s).

## Resources

=> https://www.linkedin.com/pulse/six-secret-sparql-ninja-tricks-kurt-cagle/