OBA tutorial

• author: Harshad Hegde

• created: 2023-01-25

This tutorial walks through OBA.

Create an alias

For convenience we will set a bash alias.

This assumes you have built the sqlite version of oba in the ../../db folder

NOTE an alternative is:

%alias oba runoak -i sqlite:obo:oba

%alias oba runoak -i ../../db/oba.db

Basic lookup queries

Let’s check it’s working:

oba info OBA:1000076

OBA:1000076 ! attribute of cell

Exploring the structure of OBA

oba relationships UBERON:0004535

subject subject_label   predicate       predicate_label object  object_label
UBERON:0004535  cardiovascular system   BFO:0000050     part of UBERON:0001009  circulatory system
UBERON:0004535  cardiovascular system   BFO:0000051     has part        UBERON:0000948  heart
UBERON:0004535  cardiovascular system   BFO:0000051     has part        UBERON:0001981  blood vessel
UBERON:0004535  cardiovascular system   rdfs:subClassOf None    UBERON:0000467  anatomical system
UBERON:0004535  cardiovascular system   owl:equivalentClass     None    _:riog00287837  None

Here we can see linkages to external ontologies using two relations

Querying ancestors

We will try finding all ancestors of OBA:VT0010191 (immune system cell quantity)

IMPORTANT in OAK, all graph commands are parameterized by predicate lists. Consult the OAK docs if you don’t understand what this means!

To find all is-a ancestors (i.e. ancestors following SubClassOf between named classes) we use -p i:

oba ancestors -p i OBA:VT0010191