Tutorial

Introduction

This tutorial gives a quick introduction to OMeta application about how to setup a project using CLI.

Project Name: MIxS Demo Project
Event Names: ProjectRegistration, ProjectUpdate, SampleRegistration, SampleUpdate, Sequencing Assay

Setup Project and Project Metadata

ProjectSetup.csv file will be used to setup MIxS Demo Project and its metadata.

First column Project describes that section is to create a new project. Second row has project setup attributes and the next row has related data.

Project
ProjectName	ParentProjectName	ProjectLevel	Public
MIxS Demo Project			1

Section starting with ProjectMetaAttributes is to setup project meta attributes. Second row has required attribute names for project metadata setup.

ProjectMetaAttributes
ProjectName	Label	DataType	Required	AttributeName	Desc	Options	Order
MIxS Demo Project		float	F	Submit to INSDC			1

Section starting with EventMetaAttributes is to setup event meta attributes. Second row has required attribute names for event metadata setup.

EventMetaAttributes
ProjectName	EventName	SampleRequired	Label	DataType	Required	AttributeName	Desc	Options	Order
MIxS Demo Project	ProjectRegistration	F		float	F	Submit to INSDC			1

.../ometa/cli/load_multiple.sh ProjectSetup.csv

Setup Sample and Event Metadata

[SampleSequencingAssaySetup.csv(https://github.com/JCVenterInstitute/OMeta-Public/blob/master/build/examples/SampleSequencingAssaySetup.csv) file will be used to setup sample and event metadata for MIxS Demo Project.

Section starting with SampleMetaAttributes is to setup sample meta attributes. Second row has required attribute names for sample metadata setup.

SampleMetaAttributes
ProjectName	Label	DataType	Required	AttributeName	Desc	Options	Order
MIxS Demo Project		string	F	Lat Lon			1

Section starting with EventMetaAttributes is to setup event meta attributes. Second row has required attribute names for event metadata setup.

EventMetaAttributes
ProjectName	EventName	SampleRequired	Label	DataType	Required	AttributeName	Desc	Options	Order
MIxS Demo Project	SampleRegistration	T		string	F	Lat Lon			1
MIxS Demo Project	Sequencing Assay	T		string	F	Seq Meth			1

.../ometa/cli/load_multiple.sh SampleSequencingAssaySetup.csv

Load Project and Event Data

File data template header (first three lines) describes details about data load. First line starts with #DataTemplate: following with EventName. Second line has required attribute names for the related event and third line gives the hint about each attribute.

ProjectUpdate_template.csv file will be used to update MIxS Demo Project data.

#DataTemplate:ProjectUpdate
ProjectName	Submit to INSDC	Investigation Type	project_name	Experimental Factor
#string *Required	#float optional	#string optional[dropdown(eukaryote;bacteria_archaea;plasmid;virus;organelle;metagenome;mimarks-survey;mimarks-specimen)]	#string optional	#string optional
MIxS Demo Project	1111	metagenome	MIxS Human Gut	family history

.../ometa/cli/load_batch.sh ProjectUpdate_template.csv .

SampleRegistration_template.csv file will be used to register sample for MIxS Demo Project.

#DataTemplate:SampleRegistration
ProjectName	SampleName	ParentSample	Public	Lat Lon	Geo Loc Name	Collection Date	Env Biome	Env Feature	Env Material	Env Package	Ref Biomaterial	Isol Growth Condt	Seq Meth	Assembly	Assembly Name	Finishing Strategy	Annot Source
#string *Required	#string *Required	#string optional	#int *Required	#string optional	#string optional	#string optional	#string optional	#string optional	#string optional	#string optional	#string optional	#string optional	#string optional	#string optional	#string optional	#string optional	#string optional
MIxS Demo Project	Test_Sample		1	54 N 8 E	Germany:Sylt:Hausstrand	2008	mud	cliff	soil				Sanger dideoxysequencing		HuRef

.../ometa/cli/load_batch.sh SampleRegistration_template.csv .