OBO flat file import

Converts OBO flat file v1.2 ontology to a topic map and merges converted topic map to Wandora. Import begins with menu option File > Import > OBO import.... Wandora accepts also OBO files to be dropped over Wandora window. If OBO file is dropped to layer stack, new layer is created for the imported file.

OBO flat file format is used mainly in bioinformatics to store and share ontologies related to biosciences. OBO flat file format was initially developed for The Gene Ontology. However, there exists over 60 different and public ontologies in OBO format today. These ontologies can be browsed and downloaded at Open Biological Ontologies Foundry.

As an example of OBO import we have converted the Gene Ontology to a topic map. Below is a screenshot of Wandora with Gene Ontology topic map open. Addition to OBO import, Wandora is also capable to export topic map back to OBO flat file format. Read more at OBO flat file export and OBO round trip.

Conversion details

OBO import creates a root topic for each namespace. Root topic is named obo (namespace) where namespace is a name of the namespace. Namespace specific root topic is associated to a collection of meta-topics:

• category (namespace) collects all subsets specified in the OBO file. Subset is a named category of terms in OBO file. Subset is defined in OBO file header with tag subsetdef. If namespace doesn't contain categories category (namespace) is also missing.
• header (namespace) is a header topic collecting OBO header properties. Each header property is stored as a text occurrences with a type generated using header tag name.
• term (namespace) collects all OBO terms in given namespace. OBO term is an instance of the term (namespace) topic.
• obsolete (namespace) collects all obsolete terms in given namespace. Obsolete OBO term is an instance of the obsolete (namespace) topic. Obsolete term topic is also an instance of term (namespace).
• synonym (namespace) collects all OBO term synonyms in given namespace. OBO term synonym is an instance of the synonym (namespace) topic.
• description (namespace) collects all dbxref description topics.
• typedef collects all relationship topics used in OBO file. Typical relationships used in OBO file are part_of and develops_from. Namespace is not used in relationship names.

OBO terms

OBO term is described with [Term] stanza in OBO file. Each OBO term is converted into a topic. OBO term topic gets a subject identifier constructed using term id. Subject identifier is

http://www.wandora.org/obo/ID

where ID is term's id. For example term GO:0010480 gets subject identifier http://www.wandora.org/obo/GO:0010480.