Venkatesan bosc2010 onto-toolkit

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy Aravind Venkatesan, ONTO-ToolKit: enabling bio-ontology engineering via Galaxy Aravind Venkatesan Systems Biology group, Department of Biology NTNU, Trondheim [email_address]

Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object]

Tool pane – provides various functionality to handle data Data display area History pane –manipulate uploaded data and build workflow Visit Galaxy!! http:// galaxy.psu.edu /

Ontology for Life Sciences ,[object Object],[object Object],[object Object],[object Object]

ONTO-Toolkit ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ONTO-PERL: An API supporting the development and analysis of bio-ontologies . Antezana E, Egana M, De Baets B, Kuiper M, Mironov V. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042

Examples of ONTO-PERL functionalities Scripts Functionality get_ancestor_terms.pl Collects the ancestor terms (list of IDs) from a given term (existing ID) in the given OBO ontology. get_child_terms.pl Collects the child terms (list of term IDs and their names) from a given term (existing ID) in the given OBO ontology. get_descendent_terms.pl Collects the descendent terms (list of IDs) from a given term (existing ID) in the given OBO ontology. get_subontology_from.pl Extracts a subontology (in OBO format) of a given ontology having the given term ID as the root. get_intersection_ontology.pl Provides an intersection of the given ontologies (in OBO format) obo2owl.pl OBO to OWL translator. obo2rdf.pl OBO to RDF translator. obo_trimming.pl This script trims a given branch of an OBO ontology.

ONTO-Toolkit - GALAXY Define arguments

Use Cases ,[object Object],[object Object],[object Object],[object Object],[object Object],Use Case I : Chosen Ontology: Cell Cycle Ontology Chosen Terms: Term 1: id: CCO:F0000004 name: trans-hexaprenyltranstransferase activity Term 2: id: CCO:F0000820 name: homogentisate 1,2-dioxygenase activity Term ID 1 Term ID 2

Use Case I Uploading an obo ontology file – e.g.: cco_S_pombe

Conti… Molecular function Term ID: CCO:F0000004

[object Object],List of ancestor terms for the given Molecular function Term 1 List of ancestor terms for Term 2

Common ancestor terms Gets the overlapping ancestor terms

Use Case II ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Term ID 1 Term ID 2

Use Case II Gets the sub-ontology for the given terms

Generated sub-ontology of Term 1 : CCO:P0000005 Generated sub-ontology of Term 2 : CCO:P0000069

Gets the intersection of the two sub-ontologies

Conclusion ,[object Object],[object Object],[object Object],Future Directions ,[object Object],[object Object]

Acknowledgment ,[object Object],[object Object],[object Object],References ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Venkatesan bosc2010 onto-toolkit

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