oaklib 0.1.4

Ontology Access Kit: Python library for common ontology operations over a variety of backends

Ontology Access Kit

Python lib for common ontology operations over a variety of backends.

This library provides a collection of different interfaces for different kinds of ontology operations, including:

• lookup of basic features of an ontology element, such as it's label, definition, relationships, or aliases
• search an ontology for a term
• validating an ontology
• updating, deleting, or modifying terms
• ontology term matching
• generating and visualizing subgraphs
• provide specialized object models for more advanced operations, such as graph traversal, or OWL axiom processing, or text annotation

These interfaces are separated from any particular backend. This means the same API can be used regardless of whether the ontology:

• is served by a remote API such as OLS or BioPortal
• is present locally on the filesystem in owl, obo, obojson, or sqlite formats
• is to be downloaded from a remote repository such as the OBO library
• is queried from a remote database, including SPARQL endpoints (Ontobee/Ubergraph), A SQL database, a Solr/ES endpoint

Documentation:

• incatools.github.io/ontology-access-kit

Example

resource = OntologyResource(slug='tests/input/go-nucleus.db', local=True)
oi = SqlImplementation(resource)
for curie in oi.basic_search("cell"):
    print(f'{curie} ! {oi.get_label_by_curie(curie)}')
    for rel, fillers in oi.get_outgoing_relationships().items():
        print(f'  RELATION: {rel} ! {oi.get_label_by_curie(rel)}')
        for filler in fillers:
            print(f'     * {filler} ! {oi.get_label_by_curie(filler)}')

For more examples, see

• demo notebook

Command Line

Documentation here is incomplete.

See CLI docs

Search

Use the pronto backend to fetch and parse an ontology from the OBO library, then use the search command

runoak -i obolibrary:pato.obo search osmol 

Returns:

PATO:0001655 ! osmolarity
PATO:0001656 ! decreased osmolarity
PATO:0001657 ! increased osmolarity
PATO:0002027 ! osmolality
PATO:0002028 ! decreased osmolality
PATO:0002029 ! increased osmolality
PATO:0045034 ! normal osmolality
PATO:0045035 ! normal osmolarity

QC and Validation

Perform validation on PR using sqlite/rdftab instance:

runoak validate -i sqlite:../semantic-sql/db/pr.db

List all terms

List all terms obolibrary has for mondo

runoak validate -i obolibrary:mondo.obo terms

Lexical index

Make a lexical index of all terms in Mondo:

runoak lexmatch -i obolibrary:mondo.obo -L mondo.index.yaml

Search

Searching over OBO using ontobee:

runoak  -i ontobee: search tentacle

yields:

http://purl.obolibrary.org/obo/CEPH_0000256 ! tentacle
http://purl.obolibrary.org/obo/CEPH_0000257 ! tentacle absence
http://purl.obolibrary.org/obo/CEPH_0000258 ! tentacle pad
...

Searching over a broader set of ontologies in bioportal (requires API KEY)

runoak set-apikey bioportal YOUR-KEY-HERE
runoak  -i bioportal: search tentacle

yields:

BTO:0001357 ! tentacle
http://purl.jp/bio/4/id/200906071014668510 ! tentacle
CEPH:0000256 ! tentacle
http://www.projecthalo.com/aura#Tentacle ! Tentacle
CEPH:0000256 ! tentacle
...

Searching over more limited set of ontologies in Ubergraph:

runoak -v -i ubergraph: search tentacle

yields

UBERON:0013206 ! nasal tentacle

Annotating Texts

runoak  -i bioportal: annotate neuron from CA4 region of hippocampus of mouse

yields:

object_id: CL:0000540
object_label: neuron
object_source: https://data.bioontology.org/ontologies/NIFDYS
match_type: PREF
subject_start: 1
subject_end: 6
subject_label: NEURON

object_id: http://www.co-ode.org/ontologies/galen#Neuron
object_label: Neuron
object_source: https://data.bioontology.org/ontologies/GALEN
match_type: PREF
subject_start: 1
subject_end: 6
subject_label: NEURON

...

Mapping

Create a SSSOM mapping file for a set of ontologies:

robot merge -I http://purl.obolibrary.org/obo/hp.owl -I http://purl.obolibrary.org/obo/mp.owl convert --check false -o hp-mp.obo
runoak lexmatch -i hp-mp.obo -o hp-mp.sssom.tsv

Visualization of ancestor graphs

Use the sqlite backend to visualize graph up from 'vacuole' using test ontology sqlite:

runoak -i sqlite:tests/input/go-nucleus.db  viz GO:0005773

Same using ubergraph, restricting to is-a and part-of

runoak -i ubergraph:  viz GO:0005773 -p i,BFO:0000050

Same using pronto, fetching ontology from obolibrary

runoak -i obolibrary:go.obo  viz GO:0005773

Documentation

• incatools.github.io/ontology-access-kit

Potential Refactoring

Currently all implementations exist in this repo/module, this results in a lot of dependencies

One possibility is to split out each implementation into its own repo and use a plugin architecture

PyPI release

TODO