From 8ec6327b7bf6649671c06901de5cdaa70e74bcb0 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Wed, 12 Oct 2022 18:05:48 +0300 Subject: Close issue on dumping BXD data into RDF * issues/capture-data-on-BXDs-in-RDF.gmi: Close issue after adding extra information on it's resolution. --- issues/capture-data-on-BXDs-in-RDF.gmi | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) (limited to 'issues/capture-data-on-BXDs-in-RDF.gmi') diff --git a/issues/capture-data-on-BXDs-in-RDF.gmi b/issues/capture-data-on-BXDs-in-RDF.gmi index 310c1e3..2d50f6a 100644 --- a/issues/capture-data-on-BXDs-in-RDF.gmi +++ b/issues/capture-data-on-BXDs-in-RDF.gmi @@ -43,10 +43,13 @@ redundant data and complexity increases with time. http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=112 View existing metadata here We should use wikidata because it's based on RDF and is here to stay. For example this mouse gene + => https://www.wikidata.org/wiki/Q18303218 relates to mouse + => https://www.wikidata.org/wiki/Q83310. You can find some models + => https://www.wikidata.org/wiki/Q24082698. To add the BXD we would start by editing wikidata which has the benefit that it gets presented in Wikipedia (wikidata is the backend). @@ -55,6 +58,23 @@ To add the BXD we would start by editing wikidata which has the benefit that it Look at existing ontology. A few are mentioned in: => https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-4-13 The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species +When an ontology exists and it looks sensible we should reuse that. If non-existent, we create our own ontology. Obviously we can't get away from adding free flow textual fields. What we want to lift out is what we want to be able to search on. -When an ontology exists and it looks sensible we should reuse that. If non-existent, we create our own ontology. Obviously we can't get away from adding free flow textual fields. What we want to lift out is what we want to be able to search on. +## Resolution + +Relevant topic: + +=> topics/add-metadata-to-trait-page Add Metadata To The Trait Page (RDF) + +This is currently being worked on in: + +=> issues/add-metadata-to-traits-page Annotate traits page with metadata from RDF + +Work on dumping RDF has already been done in: + +=> https://github.com/genenetwork/dump-genenetwork-database dump-genenetwork-database + +Also, vector/matrix data should be put in lmdb, and this is a separate issue on it's own. + +* closed -- cgit v1.2.3