Welcome to Pheno

Index

• What is Pheno?
• How to setup PHENO locally?
• SparQL
• Instance requirements

What is PHENO?

PHENO has 3 main functions based on international standards:

• Data submission (MIAPPE)
• Data storage (RDF)
• Data sharing (BrAPI)

For more details check out OntoBrAPI's documentation on READ the DOCS

1) Data submission (OntoBrAPI)

OntoBrAPI runs a web server, which provides a Graphical User Interface (GUI) that allows the conversion of the MIAPPE spreadsheet into n-triples format. The GUI allows the user to dynamically map the MIAPPE spreadsheet to the appropriate PPEO ontological properties using a JavaScript Object Notation (JSON). The user can also start from an initial mapping in JSON and adjust any fields deemed necessary. The GUI uses the constraints coded in the ontology to validate the mapping. As an example, the data types allowed for each of the data properties is enforced by the GUI, which are inherited from the rules in the ontology; the same goes for the object properties that can link classes and the data properties that can annotate classes.

2) Data Storage

OntoBrAPI relies on OpenLink Virtuoso to store triples and builds a management system for data curators to validate datasets and select which ones are ready for sharing.

3) Data Sharing

OntoBrAPI provides a BrAPI endpoint which delivers data in the triple store as JSON. This module allows administrators to update the data properties mapped to the respective JSON output in acordance with the BrAPI specification.

How to setup PHENO locally?

Since OntoBrAPI relies on several external components, it's designed as a collection of individual Docker containers. This approach, facilitated by Docker Compose, simplifies the setup process.

Setup your environment (Running on compose)

You can use your computer or an instance on a Virtual Private Cloud (VPC) provider (ex: AWS, Azure, Google Cloud,etc). The dependencies will be installed by running this script on a Ubuntu system.

Dependencies are:

• git
• docker
• compose

wget https://github.com/forestbiotech-lab/PHENO/raw/master/setup.sh -O setup.sh
bash setup.sh 

Setup a development environment

This solution is the best if you want to debug a particular module and deal with the dependencies directly. Most containers are based on node while others are on python. Refer to the dockerfile to check the appropriate setup of each module. To get the files on your setup use git.

Clone repo and init Submodules, replace repository url based on the access to the project. git@github.com...... or https://github.com.......

For collaborators use::

git clone git@github.com:forestbiotech-lab/PHENO.git
cd PHENO
git submodule init
git submodule update
git checkout master

For other users use::

git clone http://github.com/forestbiotech-lab/PHENO.git
cd PHENO
git submodule init

#git submodule set-url [repo] [repo-url]
#Do this for every repo in submodules
git submodule set-url ontobrapi-web  https://github.com/forestbiotech-lab/ontobrapi-web.git
git submodule set-url ontobrapi-admin  https://github.com/forestbiotech-lab/ontobrapi-admin.git
git submodule set-url ontobrapi-brapi  https://github.com/forestbiotech-lab/ontobrapi-brapi.git
git submodule update
cd ontobrapi-web
git checkout master
cd ../ontobrapi-admin
git checkout main
cd ../ontobrapi-brapi
git checkout master
cd ..

Build / Rebuild web module container (First run)

docker-compose up -d --build

or just to spin up the containers

docker-compose up -d

Node modules

For node modules you must have NodeJs installed and use npm to start the web server, check the dockerfile for help on all the dependencies.

#Port should be one that does not colide with the currently active ports on the setup
PORT=3010 npm start

SparQL

This sections describes basic usage of SparQL, but please refer to the Wiki page for more details. The SparQL query editor is accessible on port 8890 (ex: localhost:8890/sparql) and is referenced in docker-compose as DB. Currently, SparQL queries are executed by OpenLink Virtuoso.

Default user and password are: dba

From docker image:

• The Virtuoso password can be set at container start up via the DBA_PASSWORD environment variable. If not set, the default dba password will be used.

SPARQL update permission

The SPARQL_UPDATE permission on the SPARQL endpoint can be granted by setting the SPARQL_UPDATE environment variable to true.

.ini configuration

All properties defined in virtuoso.ini can be configured via the environment variables. The environment variable should be prefixed with VIRT_ and have a format like VIRT_$SECTION_$KEY. $SECTION and $KEY are case sensitive. They should be CamelCased as in virtuoso.ini. E.g. property ErrorLogFile in the Database section should be configured as VIRT_Database_ErrorLogFile=error.log.

Instance requirements

The validation takes some time on small instances because of the

Image	RAM	Disk space
DB	300M	0.27Gb
Mongo	120M	0.70Gb
Admin	42M	1.90Gb
gateway	3M	0.19Gb
validator	25M	1.31Gb
web	25M	1.03Gb
brapi	?M
TOTAL	~520M	~6.00Gb

Runs on t3.micro instance of AWS. (2vcpu, 1GbRAM, 16Gb HDD) But optimum is t3.small instance from AWS (2vCPU, 2GbRAM, 16Gb HDD)