From dacd49e0265fc8fe86fd6d8fc0bcbaa40d05f86a Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Tue, 12 Sep 2023 12:18:45 -0700 Subject: [PATCH 1/4] update description for CMDR data model --- README.md | 30 ++++++++++++++++++++++++------ 1 file changed, 24 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 1ce57ff..0c93242 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,31 @@ -# cmdr +# CMDR -Core Model for Data Research (Tentative) +CMDR (pronunciation: “com-mo-dore” or sometimes “com-man-der”), the Core Model for Data Research, is a LinkML schema/data model for the collection of biological sample data, and its analysis. -_Currently most influenced by the Include schema, https://github.com/include-dcc/include_linkml_ +The purpose of this schema is to act as a *base* schema for other LinkML schemas/data models to bootstrap for their specific use case. -recommended: +# Project Setup -- `make test` -- `make test_transform` +1. Clone *cmdr* project repository + +``` +$ git clone https://github.com/linkml/cmdr.git +``` + +2. Create virtual environment and install project dependencies +``` +$ make install +``` + +3. Create downstream schema artifacts, run unit tests, and also validate examples/instance data against schema +``` +make test +``` + +4. LinkML transformer mapping between source and target schemas on a class +``` +make test_transform +``` ## Website From c7734ef47b3abbc79039f22855e21534354091ae Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Tue, 12 Sep 2023 12:20:33 -0700 Subject: [PATCH 2/4] sync header sizes --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0c93242..3c49c25 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ CMDR (pronunciation: “com-mo-dore” or sometimes “com-man-der”), the Core The purpose of this schema is to act as a *base* schema for other LinkML schemas/data models to bootstrap for their specific use case. -# Project Setup +## Project Setup 1. Clone *cmdr* project repository From 441665f15be6e6e6599a18118e7127c61981c3fe Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Tue, 12 Sep 2023 12:21:27 -0700 Subject: [PATCH 3/4] formatting fixes --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 3c49c25..8a5d90c 100644 --- a/README.md +++ b/README.md @@ -19,12 +19,12 @@ $ make install 3. Create downstream schema artifacts, run unit tests, and also validate examples/instance data against schema ``` -make test +$ make test ``` 4. LinkML transformer mapping between source and target schemas on a class ``` -make test_transform +$ make test_transform ``` ## Website From 5f7c12c070dc008b093b9fa561b305fde3bd9ebc Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Thu, 21 Sep 2023 13:57:27 -0700 Subject: [PATCH 4/4] add INLCUDE context for CMDR model --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 8a5d90c..7e6337c 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,8 @@ CMDR (pronunciation: “com-mo-dore” or sometimes “com-man-der”), the Core The purpose of this schema is to act as a *base* schema for other LinkML schemas/data models to bootstrap for their specific use case. +The CMDR data model was inspired by the LinkML [data model](https://github.com/include-dcc/include_linkml) for the INCLUDE project. + ## Project Setup 1. Clone *cmdr* project repository