diff options
| -rw-r--r-- | topics/add-metadata-to-trait-page.gmi | 32 |
1 files changed, 27 insertions, 5 deletions
diff --git a/topics/add-metadata-to-trait-page.gmi b/topics/add-metadata-to-trait-page.gmi index ddef239..8e2d433 100644 --- a/topics/add-metadata-to-trait-page.gmi +++ b/topics/add-metadata-to-trait-page.gmi @@ -1,6 +1,6 @@ # Add Metadata To The Trait Page (RDF) -Wed 28 Sep 2022 14:49:51 EAT +Fri 30 Sep 2022 11:48:41 EAT ## Introduction @@ -22,17 +22,39 @@ The overall goal is to be ablet to: ## Goals -* In the Trait Analysis Page, add extrat metadata for "Group", "Tissue", "Gene Symbol". Possibly, a link to a relevant URL with useful information. +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 -* 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. +* 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 |