An ontology-based GIS for genomic data management of rumen
microbes
An application of the concepts and tools of geographic information system combined with ontology
representation to the interpretation and management of microbial genome annotated data. Our
implementation of this application uses the combination of two platforms of ArcGIS and Protégé, and
MySQL as a database management system, that allows biology users to visualize, manage, reuse, share
and query the rumen microbial genome annotated data.
All software requirements are available on the following addresses:
1- ArcGIS is commercial software which is available on http://www.esri.com/software/arcgis/arcgisfor-desktop.
2- Protégé is a free and open-source platform which is available on http://protege.stanford.edu/.
3- Navicat is a powerful solution for MySQL administration which is available on
http://navicat.com/.
Implementation:
1- Download the ArcGIS (free trial), Protégé (free) and Navicat (free trial)
2- Install ArcGIS and then softwares Protégé and Navicat
3- Get a sample excel file containing genome annotated data
http://patricbrc.org/portal/portal/patric/Home.
from
PATRIC:
The application was developed in two steps. In the first step, the genome annotated data ( e.g., Locus tag,
Product name, Ec Number) was extracted from excel file and then prepared and stored in MySQL
database. The second step involved the connection of database to both ArcGIS and Protégé as GIS engine
and ontology platform, respectively.
This work was conducted as part of a PhD thesis at Ferdowsi University of Mashhad and the
National Institute of Genetic Engineering and Biotechnology, Bioinformatics Lab.