AgroLD

AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. The aim of the Agronomic Linked Data (AgroLD) project is to provide a portal for bioinformatics and domain experts to exploit the homogenized data models towards efficiently generating research hypotheses.

Contact

For bug tracking purpose you can use the GitHub or questions about AgroLG, you can contact the mainteners using the following email addresses:

• nordine.elhassouni_at_cirad.fr
• pierre.larmande_at_ird.fr
• yann.pomie_at_ird.fr

Valorization

• Aravind Venkatesan, Nordine El Hassouni, Florian Phillipe, Cyril Pommier, Hadi Quesneville, Manuel Ruiz, Pierre Larmande. Towards efficient data integration and knowledge management in the Agronomic domain. APIA: Applications Pratiques de l'Intelligence Artificielle , Jul 2015, Rennes, France. 1ère conférence sur les Application Pratiques de l'Intelligence Artificielle (APIA), 2015, http://pfia2015.inria.fr/actes/index.php?procpage=apia. hal-01176903
• Venkatesan, Aravind, Nordine El Hassouni, Florian Phillipe, Cyril Pommier, Hadi Quesneville, Manuel Ruiz, and Pierre Larmande. "Exposing French agronomic resources as linked open data." In IN-OLIVE. 2016. PDF
• Venkatesan, Aravind, Gildas Tagny Ngompe, Nordine El Hassouni, Imene Chentli, Valentin Guignon, Clement Jonquet, Manuel Ruiz, and Pierre Larmande. "Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy." PloS one 13, no. 11 (2018): e0198270. https://doi.org/10.1371/journal.pone.0198270

Contributing

• Intellectual property belongs to IRD, CIRAD, IBC, INRA, IFB, ELIXIR, and SouthGreen development platform.
• Written by Aravind Venkatesan, Pierre Larmande, Gildas Tagny, Imene chentli, Nordine El Hassouni, Manuel Ruiz and Patrick Valduriez.
• Copyright 2014-2019

The Architecture of project

AgroLD project is composed of two component: AgroLD_ETL and AgroLD_webapp

• The first component is a set of Parser and wrapper for translate a dataset. Follow this link for to know what data have been translated in RDF: Documentation

• The second component is the web application who is connected at the triple store for to make queries.

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 AgroLD_ETL moved to another repository 
 agrold_webapp

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AgroLD_ETL

Contains parsers and model used to convert data considered for AgroLD to RDF.

• model: All documents who describe how data are transformed
• rdf_ttl: All output of transformation sort by dataset
• riceKB: Contains scripts used for each data set
• test_files: All test files in input ( heterogeneous format: csv, tabbed files, gff3 )
• riceKBpipeline.py: Script file where we have centralised all execution

The type of each dataset is different, GFF, HapMap, CSV and VCF. In first time we have developed parser for build a dictonary, because is easy to browse a dictionary and create the RDF

AgroLD_webapp

Scripts used for website UI, contains scripts for AgroLD API feature and all SPARQL query. The front office (is any tools that has a direct relation to customers) of AgroLD web application are written in JavaScript and the back office (interne fonctionnalities) is written in JAVA.

Quick search

Quick search is based on keyword search and aids in understanding the underlying knowledge

Explore Relationships

The Explore Relationships tool aids in exploring relationships between existing entities.

Advanced Search

The Advanced Search query form is based on the REST API suite, developed under the AgroLD project. The aim of this effort is to provide non-technical users with a tool to query the knowledge base.

SPARQL Query

The SPARQL Query Editor provides an interactive environment to formulate SPARQL queries.

How to use AgroLD

###agrold_webapp

For execute the projet in your local host:
/agrold_webapp/target/agrold.war
load the war in your tomcat and go in localhost:8080/agrold

###AgroLD_ETL

For example if you want to execute a gff3 parser for to build a dictionary. define a input file

AgroLD/AgroLD_ETL/riceKB/gffParser.py

path = '/os_file_gff3/file.gff3'     # The input

ds = parseGFF3(path)   # The parsing file

The dictionary : The GFF3 Parser is a generic fonction who build a dictionary, it easy to browse this dictionary for build RDF data

{   'attributes': {   'Dbxref': 'InterPro:IPR005333,InterPro:IPR017887',
                          'ID': 'BGIOSGA000770-TA',
                          'Name': 'BGIOSGA000770-TA',
                          'Parent': 'BGIOSGA000770'},
        'end': 35414873,
        'phase': None,
        'score': None,
        'seqid': 'Osi01',
        'source': 'glean',
        'start': 35413950,
        'strand': '-',
        'type': 'mRNA'},
    {   'attributes': {   'Derives_from': 'BGIOSGA000770-TA',
                          'ID': 'BGIOSGA000770-TA_protein',
                          'Name': 'BGIOSGA000770-TA'},
        'end': 35414873,
        'phase': None,
        'score': None,
        'seqid': 'Osi01',
        'source': 'glean',
        'start': 35413950,
        'strand': '-',
        'type': 'polypeptide'},
    {   'attributes': {   'Parent': 'BGIOSGA000770-TA'},
        'end': 35414873,
        'phase': '0',
        'score': None,
        'seqid': 'Osi01',
        'source': 'glean',
        'start': 35413950,
        'strand': '-',
        'type': 'CDS'},
    {   'attributes': {   'Parent': 'BGIOSGA000770-TA'},
        'end': 35414873,
        'phase': None,
        'score': None,
        'seqid': 'Osi01',
        'source': 'glean',
        'start': 35413950,
        'strand': '-',
        'type': 'exon'},

Documentation

• AgroLD includes data on the following species on : Species
• Ontologies in AgroLD : Ontologies
• Data sources in AgroLD : Data
• Species specific break down of the data sources : Link
• Graph Names : Link
• URIs : Link