Command Line

A large subset of ontobio functionality is available via a powerful command line interface that can be used by non-programmers.

You will first need to install, see Installation

After that, set up your PATH:

export PATH $HOME/repos/ontobio/ontobio/bin
ogr -h

For many operations you need to be connected to a network

Note: command line interface may change

Live Demo

You can see the tour on asciinema:

• ontology querying tour
• how remote sparql works

Ontologies

The ogr command handles ontologies

Connecting to ontologies

Specify an ontology with the -r option. this will always be the OBO name, for example go, cl, mp, etc

• -r go connect to GO via default method (currently OntoBee-SPARQL)
• -r obo:go connect to GO via download and cache of ontology from OBO Library PURL
• -r /users/my/my-ontologies/go.json use local download of ontology

See Inputs for possible sources to connect to

In the following we assume default method, but the -r argument can be substituted.

Basic queries

Show all classes named neuron:

ogr -r cl neuron

Multiple arguments can be provided, e.g.:

ogr -r cl neuron hepatocyte erythrocyte

Ancestors queries

List all ancestors:

ogr -r cl neuron

Show ancestors as tree, following only subclass:

ogr -r cl -p subClassOf -t tree neuron

generates:

% GO:0005623 ! cell
 % CL:0000003 ! native cell
  % CL:0000255 ! eukaryotic cell
   % CL:0000548 ! animal cell
    % CL:0002319 ! neural cell
     % CL:0000540 ! neuron *
  % CL:0002371 ! somatic cell
   % CL:0002319 ! neural cell
    % CL:0000540 ! neuron *

Descendants of neuron, parts and subtypes

ogr -r cl -p subClassOf -p BFO:0000050 -t tree -d d neuron

Descendants and ancestors of neuron, parts and subtypes

ogr -r cl -p subClassOf -p BFO:0000050 -t tree -d du neuron

All ancestors of all classes 2 levels down from subclass-roots within CL:

ogr -r cl -P CL -p subClassOf -t tree -d u -L 2

Visualization using obographviz

Requires: https://www.npmjs.com/package/obographviz

Add og2dot.js to path

ogr -p subClassOf BFO:0000050 -r go -t png   a nucleus

This proceeds by:

1. Using the python ontobio library to extract a networkx subgraph around the specified node
2. Write as obographs-json
3. Calls og2dot.js

Output:

img

Search

List exact matches to neuron

ogr -r cl neuron

Terms starting with neuron, SQL style

ogr -r cl neuron%

Terms starting with neuron, regex (equivalent to above)

ogr -r cl -s r ^neuron

Terms ending with neuron

ogr -r cl -s r neuron$

Terms containing the string neuron

ogr -r cl -s r neuron

Note: any of the above can be fed into other renderers, e.g. trees, graphs

E.g. terms containing neuron

ogr -r cl %neuron%

E.g. terms ending neuron, to tree

ogr -r cl %neuron -t tree

Properties

Properties (relations) are treated as nodes in the graph, e.g.

ogr-tree -d ud -r ro 'develops from'

 . RO:0002324 ! developmentally related to
  % RO:0002258 ! developmentally preceded by
   % RO:0002202 ! develops from *
    % RO:0002225 ! develops from part of
    % RO:0002494 ! transformation of
     % RO:0002495 ! immediate transformation of
    % RO:0002207 ! directly develops from
     % RO:0002495 ! immediate transformation of

SPARQL integration

SPARQL where clauses can be inserted using -Q to pipe the results of a query to generate the initial set of IDs, e.g.:

ogr-tree  -r pato -Q "{?x rdfs:subClassOf+ PATO:0000052}"

Associations

The ontobio-assoc command handles ontologies

Subcommands:

subontology         Extract sub-ontology
enrichment          Perform an enrichment test
phenolog            Perform multiple enrichment tests
query               Query based on positive and negative terms
associations        Query for association pairs
intersections       Query intersections
dendrogram          Plot dendrogram from intersections
simmatrix           Plot dendrogram for similarities between subjects

Examples

Enrichment analysis, using all genes associated to a GO term as sample (we expect this GO term to be top results)

ontobio-assoc -v -r go -T NCBITaxon:9606 -C gene function enrichment -q GO:1903010

Plotly:

ontobio-assoc -v -r go -T NCBITaxon:10090 -C gene function dendrogram GO:0003700 GO:0005215 GO:0005634 GO:0005737 GO:0005739 GO:0005694 GO:0005730  GO:0000228 GO:0000262

Show similarity matrix for a set of genes:

ontobio-assoc -v -r go -T NCBITaxon:10090 -C gene function simmatrix MGI:1890081 MGI:97487 MGI:106593 MGI:97250 MGI:2151057 MGI:1347473

Basic queries, using file as input:

ontobio-assoc -C gene function -T pombe -r go -f tests/resources/truncated-pombase.gaf query -q GO:0005622

Parsing assoc files

The ontobio-parse-assocs.py command will parse, validate and convert association files (GAF, GPAD, HPOA etc) of all file types and versions.

Top Level Options

ontobio-parse-assocs.py mostly uses top level options before subcommands to configure parsing.

• -r, --resource is the ontology file, in OBO JSON format
• -f, --file input annotation file
• -F, --format is the format of the input file. GAF will be the default if not provided
• --report-md and --report-json are the paths to output the parsing and validation reports to

Use validate to produce a report validating the input file, -f, --file.

Use convert to convert the input annotation file into a GPAD or GAF of any version. A report will still be produced. * -t, --to is the format to convert to. GAF, GPAD are accepted. * -n, --format-version is the version. For GAF, 2.1 or 2.2 are accepted with 1.2 as default. For GPAD 1.2 or 2.0 are accepted with 1.2 default.

GO Rules

ontobio-parse-assocs.py is capable of running the GO Rules (https://github.com/geneontology/go-site/tree/master/metadata/rules) over each annotation as they are parsed. By default, in this script, annotations are not validated by GO Rules except gorule-0000020, gorule-0000027, and gorule-0000059.

To include a rule in the rule set use the option -l or --rule followed by an integer representing the rule ID.

For example to include gorule-0000006:

ontobio-parse-assocs.py -f my_assoc.gaf --report-md report.md -l 6 validate

Use multiple -l <ID> to build up a list of rules that will be used to validate the input file:

ontobio-parse-assocs.py -f my_assoc.gaf --report-md report.md -l 6 -l 13 validate

To turn on all rules at once, use -l all:

ontobio-parse-assocs.py -f my_assoc.gaf --report-md report.md -l all validate

Under the hood, this is all controlled using a parameter, rule_set attached to the AssocParserConfig class. This accepts a list of integers or the string "all" or None. Setting to None (the default) will include no rules, and using "all" will use all rules.

The parameter passed in is used to create the assocparser.RuleSet dataclass.

GOlr Queries

The qbiogolr.py command is for querying a GOlr instance