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authorMunyoki Kilyungi2022-09-28 16:21:34 +0300
committerMunyoki Kilyungi2022-09-28 16:22:49 +0300
commit4cad0687f837649ecfcab1faaad82241ee6e1d26 (patch)
tree8974405dd86c0f248c166d9ea552ef24c303b4ad
parentfa2f1cdf49e89399eacbc37d33bd24d417a205a2 (diff)
downloadgn-gemtext-4cad0687f837649ecfcab1faaad82241ee6e1d26.tar.gz
Add design doc for annotating the trait page
* topics/add-metadata-to-trait-page.gmi: New topic.
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+# 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/