OAK disjoints command

This notebook is intended as a supplement to the main OAK CLI docs.

This notebook provides examples for the disjoints command, which can be used to lookup and summarize disjointness axioms

For more on disjointness see The OBook

Help Option

You can get help on any OAK command using --help

[2]:

!runoak disjoints --help

Usage: runoak disjoints [OPTIONS] [TERMS]...

  Show all disjoints for a set of terms, or whole ontology.

  Leave off all arguments for defaults - all terms, YAML OboGraph model
  serialization:

  Example:

      runoak -i sqlite:obo:uberon disjoints

  Note that this will include pairwise disjoints, setwise disjoints, disjoint
  unions, and disjoints involving simple class expressions.

  A tabular format can be easier to browse, and includes labels by default:

  Example:

      runoak -i sqlite:obo:uberon disjoints --autolabel -O csv

  To perform this on a subset:

   Example:

      runoak -i sqlite:obo:cl disjoints --autolabel -O csv  .desc//p=i "immune
      cell"

  Data model:

     https://w3id.org/oak/obograph

Options:
  -p, --predicates TEXT           A comma-separated list of predicates. This
                                  may be a shorthand (i, p) or CURIE
  --autolabel / --no-autolabel    If set, results will automatically have
                                  labels assigned  [default: autolabel]
  -O, --output-type TEXT          Desired output type
  --named-classes-only / --no-namde-classes-only
                                  Only show disjointness axioms between two
                                  named classes.  [default: no-namde-classes-
                                  only]
  -o, --output FILENAME           Output file, e.g. obo file
  --help                          Show this message and exit.

Set up an alias

For convenience we will set up an alias for use in this notebook

[3]:

alias cl runoak -i sqlite:obo:cl

All simple disjointness axioms

Let’s first look at all simple disjointness axioms in the ontology - i.e. those between named classes

[6]:

cl disjoints --named-classes-only > output/cl-disjoints.yaml

[7]:

!head -40 output/cl-disjoints.yaml

classIds:
- BFO:0000002
- BFO:0000003

---
classIds:
- BFO:0000004
- BFO:0000031

---
classIds:
- BFO:0000004
- BFO:0000020

---
classIds:
- BFO:0000016
- BFO:0000023

---
classIds:
- BFO:0000017
- BFO:0000019

---
classIds:
- BFO:0000020
- BFO:0000031

---
classIds:
- BFO:0000040
- BFO:0000141

---
classIds:
- CARO:0000006
- CARO:0000007

---

The YAML here is conformant with OboGraphs. However, it’s not very convenient for viewing, so let’s get a flattened via as both obo format and a TSV

[19]:

cl disjoints --named-classes-only -O obo > output/cl-disjoints.obo

WARNING:root:Skipping DisjointClassExpressionsAxiom with only one class: DisjointClassExpressionsAxiom(meta=None, classIds=['_:riog00151338'], classExpressions=[], unionEquivalentTo=None, unionEquivalentToExpression=None)

[21]:

!head -20 output/cl-disjoints.obo

[Term]
id: BFO:0000002 ! continuant
disjoint_from: BFO:0000003 ! occurrent


[Term]
id: BFO:0000004 ! independent continuant
disjoint_from: BFO:0000031 ! generically dependent continuant


[Term]
id: BFO:0000004 ! independent continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant


[Term]
id: BFO:0000016 ! disposition
disjoint_from: BFO:0000023 ! role

[8]:

cl disjoints --named-classes-only -O csv > output/cl-disjoints.tsv

[9]:

import pandas as pd
df = pd.read_csv("output/cl-disjoints.tsv", sep="\t")
df

[9]:

	classIds	classIds_label	unionEquivalentTo	unionEquivalentToExpression	classExpressionPropertyIds	classExpressionFillerIds
0	BFO:0000002\|BFO:0000003	continuant\|occurrent	NaN	NaN	NaN	NaN
1	BFO:0000004\|BFO:0000031	independent continuant\|generically dependent c...	NaN	NaN	NaN	NaN
2	BFO:0000004\|BFO:0000020	independent continuant\|specifically dependent ...	NaN	NaN	NaN	NaN
3	BFO:0000016\|BFO:0000023	disposition\|role	NaN	NaN	NaN	NaN
4	BFO:0000017\|BFO:0000019	realizable entity\|quality	NaN	NaN	NaN	NaN
...	...	...	...	...	...	...
309	UBERON:0035165\|UBERON:0035523	posterior surface of prostate\|anterior surface...	NaN	NaN	NaN	NaN
310	UBERON:2001156\|UBERON:2001316	posterior lateral line placode\|anterior latera...	NaN	NaN	NaN	NaN
311	UBERON:2001314\|UBERON:2001391	posterior lateral line ganglion\|anterior later...	NaN	NaN	NaN	NaN
312	UBERON:2001468\|UBERON:2001471	anterior lateral line system\|posterior lateral...	NaN	NaN	NaN	NaN
313	_:riog00151338	NaN	NaN	NaN	NaN	NaN

314 rows × 6 columns

Note that many of the columns will never be filled so long as we are querying simple (NC only) disjoints.

This includes lots of ontologies that are merged in.

We can filter this by ID prefix using an i^ (identifier starts with) query

[14]:

cl disjoints --named-classes-only -O csv i^CL: > output/cl-disjoints-cell-types.tsv

[15]:

df = pd.read_csv("output/cl-disjoints-cell-types.tsv", sep="\t")
df

[15]:

	classIds	classIds_label	unionEquivalentTo	unionEquivalentToExpression	classExpressionPropertyIds	classExpressionFillerIds
0	CL:0000000\|GO:0043226	cell\|organelle	NaN	NaN	NaN	NaN
1	CL:0000000\|GO:0032991	cell\|protein-containing complex	NaN	NaN	NaN	NaN
2	CL:0000000\|GO:0031012	cell\|extracellular matrix	NaN	NaN	NaN	NaN
3	CL:0000039\|CL:0002371	germ line cell\|somatic cell	NaN	NaN	NaN	NaN
4	CL:0000049\|CL:0000557	common myeloid progenitor\|granulocyte monocyte...	NaN	NaN	NaN	NaN
5	CL:0000049\|CL:0000051	common myeloid progenitor\|common lymphoid prog...	NaN	NaN	NaN	NaN
6	CL:0000049\|CL:0000050	common myeloid progenitor\|megakaryocyte-erythr...	NaN	NaN	NaN	NaN
7	CL:0000050\|CL:0002009	megakaryocyte-erythroid progenitor cell\|macrop...	NaN	NaN	NaN	NaN
8	CL:0000050\|CL:0000557	megakaryocyte-erythroid progenitor cell\|granul...	NaN	NaN	NaN	NaN
9	CL:0000066\|CL:0000738	epithelial cell\|leukocyte	NaN	NaN	NaN	NaN
10	CL:0000084\|CL:0000945	T cell\|lymphocyte of B lineage	NaN	NaN	NaN	NaN
11	CL:0000225\|CL:0002242	anucleate cell\|nucleate cell	NaN	NaN	NaN	NaN
12	CL:0000255\|CL:0000520	eukaryotic cell\|prokaryotic cell	NaN	NaN	NaN	NaN
13	CL:0000451\|CL:0000542	dendritic cell\|lymphocyte	NaN	NaN	NaN	NaN
14	CL:0000521\|CL:0000548	fungal cell\|animal cell	NaN	NaN	NaN	NaN
15	CL:0000542\|CL:0000766	lymphocyte\|myeloid leukocyte	NaN	NaN	NaN	NaN
16	CL:0000556\|CL:0000764	megakaryocyte\|erythroid lineage cell	NaN	NaN	NaN	NaN
17	CL:0000624\|CL:0000625	CD4-positive, alpha-beta T cell\|CD8-positive, ...	NaN	NaN	NaN	NaN
18	CL:0000737\|CL:0008000	striated muscle cell\|non-striated muscle cell	NaN	NaN	NaN	NaN
19	CL:0000785\|CL:0000818	mature B cell\|transitional stage B cell	NaN	NaN	NaN	NaN
20	CL:0000785\|CL:0000817	mature B cell\|precursor B cell	NaN	NaN	NaN	NaN
21	CL:0000785\|CL:0000816	mature B cell\|immature B cell	NaN	NaN	NaN	NaN
22	CL:0000789\|CL:0000798	alpha-beta T cell\|gamma-delta T cell	NaN	NaN	NaN	NaN
23	CL:0000813\|CL:0000898	memory T cell\|naive T cell	NaN	NaN	NaN	NaN
24	CL:0000817\|CL:0000826	precursor B cell\|pro-B cell	NaN	NaN	NaN	NaN
25	CL:0000823\|CL:0000937	immature natural killer cell\|pre-natural kille...	NaN	NaN	NaN	NaN
26	CL:0000823\|CL:0000824	immature natural killer cell\|mature natural ki...	NaN	NaN	NaN	NaN
27	CL:0000837\|CL:0002032	hematopoietic multipotent progenitor cell\|hema...	NaN	NaN	NaN	NaN
28	CL:0000838\|CL:0000839	lymphoid lineage restricted progenitor cell\|my...	NaN	NaN	NaN	NaN
29	CL:0000851\|CL:0000855	neuromast mantle cell\|sensory hair cell	NaN	NaN	NaN	NaN
30	CL:0000852\|CL:0000855	neuromast supporting cell\|sensory hair cell	NaN	NaN	NaN	NaN
31	CL:0000955\|CL:0000956	pre-B-II cell\|pre-B-I cell	NaN	NaN	NaN	NaN
32	CL:0001008\|CL:0001024	Kit and Sca1-positive hematopoietic stem cell\|...	NaN	NaN	NaN	NaN
33	CL:0001021\|CL:0001025	CD34-positive, CD38-positive common lymphoid p...	NaN	NaN	NaN	NaN
34	CL:0001023\|CL:0001026	Kit-positive, CD34-positive common myeloid pro...	NaN	NaN	NaN	NaN
35	CL:0002031\|CL:0002032	hematopoietic lineage restricted progenitor ce...	NaN	NaN	NaN	NaN
36	CL:0002036\|CL:0002043	Slamf1-positive multipotent progenitor cell\|CD...	NaN	NaN	NaN	NaN
37	CL:0008011\|CL:0008020	skeletal muscle satellite stem cell\|skeletal m...	NaN	NaN	NaN	NaN
38	CL:0008046\|CL:0008047	extrafusal muscle fiber\|intrafusal muscle fiber	NaN	NaN	NaN	NaN
39	_:riog00151338	NaN	NaN	NaN	NaN	NaN

Disjoint Class Expressions

Some ontologies like Uberon make use of more advanced disjointness concepts in order to express things like spatial disjointness. See Uberon wiki.

In OWL terms these are formally known as “General Class Inclusion Axioms”. However, OAK shields you from this and provides these using a simple data model.

To include part-of in lookups, use the --predicates (-p) option (this is a standard OAK option for any command involving relationship types).

Here we will find all spatial disjointness axioms between major organism subdivisions in Uberon:

[16]:

alias uberon runoak -i sqlite:obo:uberon

[18]:

uberon disjoints -p i,p .desc//p=i "subdivision of organism along main body axis"

classExpressions:
- fillerId: UBERON:0000026
  propertyId: BFO:0000050
- fillerId: UBERON:0000915
  propertyId: BFO:0000050

---
classExpressions:
- fillerId: UBERON:0000026
  propertyId: BFO:0000050
- fillerId: UBERON:0002100
  propertyId: BFO:0000050

---
classExpressions:
- fillerId: UBERON:0000033
  propertyId: BFO:0000050
- fillerId: UBERON:0000915
  propertyId: BFO:0000050

---
classExpressions:
- fillerId: UBERON:0000033
  propertyId: BFO:0000050
- fillerId: UBERON:0000948
  propertyId: BFO:0000050

---
classExpressions:
- fillerId: UBERON:0000033
  propertyId: BFO:0000050
- fillerId: UBERON:0002100
  propertyId: BFO:0000050

---
classExpressions:
- fillerId: UBERON:0000033
  propertyId: BFO:0000050
- fillerId: UBERON:0005886
  propertyId: BFO:0000050

---
classExpressions:
- fillerId: UBERON:0000915
  propertyId: BFO:0000050
- fillerId: UBERON:0002417
  propertyId: BFO:0000050

---
classIds:
- _:riog00226101

---
classIds:
- _:riog00226236

---
classIds:
- _:riog00226251

---
classIds:
- _:riog00226988

The OAK OboGraphs data model here allows each axiom to include a list of class expressions, these are tuples of a predicate (property) and a filler.

We can look at the flattened view:

[22]:

uberon disjoints -p i,p .desc//p=i "subdivision of organism along main body axis" -O csv -o output/uberon-part-disjoint-subdivisions.tsv

[23]:

df = pd.read_csv("output/uberon-part-disjoint-subdivisions.tsv", sep="\t")
df

[23]:

	classIds	unionEquivalentTo	unionEquivalentToExpression	classExpressionPropertyIds	classExpressionPropertyIds_label	classExpressionFillerIds	classExpressionFillerIds_label
0	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	UBERON:0000026\|UBERON:0000915	appendage\|thoracic segment of trunk
1	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	UBERON:0000026\|UBERON:0002100	appendage\|trunk
2	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	UBERON:0000033\|UBERON:0000915	head\|thoracic segment of trunk
3	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	UBERON:0000033\|UBERON:0000948	head\|heart
4	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	UBERON:0000033\|UBERON:0002100	head\|trunk
5	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	UBERON:0000033\|UBERON:0005886	head\|post-hyoid pharyngeal arch skeleton
6	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	UBERON:0000915\|UBERON:0002417	thoracic segment of trunk\|abdominal segment of...
7	_:riog00226101	NaN	NaN	NaN	NaN	NaN	NaN
8	_:riog00226236	NaN	NaN	NaN	NaN	NaN	NaN
9	_:riog00226251	NaN	NaN	NaN	NaN	NaN	NaN
10	_:riog00226988	NaN	NaN	NaN	NaN	NaN	NaN

Here the disjointness axiom states that all classIds and all predicate-filler expressions are mutually disjoint.

This is telling us that nothing is part of both an “appendage” and “thoracic segment of trunk”, i.e. there is no spatial overlap.

Generating disjointness axioms

Many ontologies are under-axiomatized. Editors sometimes struggle to add the appropriate disjointness axioms.

OAK provides a heuristic approach to suggesting disjointness axioms.

First we will explore this using the Zebrafish anatomy ontolog as an example. We will find candidate pairwise disjoints under “bone element”:

[34]:

alias zfa runoak -i sqlite:obo:zfa

[37]:

zfa generate-disjoints "bone element" -O csv -o output/zfa-bone-element-gen-disjoint.tsv

[38]:

df = pd.read_csv("output/zfa-bone-element-gen-disjoint.tsv", sep="\t")
df

[38]:

	classIds	classIds_label	unionEquivalentTo	unionEquivalentToExpression	classExpressionPropertyIds	classExpressionFillerIds
0	ZFA:0000170\|ZFA:0000658	basibranchial\|epibranchial bone	NaN	NaN	NaN	NaN
1	ZFA:0000442\|ZFA:0000658	supraneural\|epibranchial bone	NaN	NaN	NaN	NaN
2	ZFA:0000442\|ZFA:0000170	supraneural\|basibranchial	NaN	NaN	NaN	NaN
3	ZFA:0001066\|ZFA:0000658	neural arch\|epibranchial bone	NaN	NaN	NaN	NaN
4	ZFA:0001066\|ZFA:0000170	neural arch\|basibranchial	NaN	NaN	NaN	NaN
...	...	...	...	...	...	...
60	ZFA:0001418\|ZFA:0001551	dorsal fin lepidotrichium\|pectoral fin lepidot...	NaN	NaN	NaN	NaN
61	ZFA:0001421\|ZFA:0001552	anal fin lepidotrichium\|pelvic fin lepidotrichium	NaN	NaN	NaN	NaN
62	ZFA:0001421\|ZFA:0001550	anal fin lepidotrichium\|caudal fin lepidotrichium	NaN	NaN	NaN	NaN
63	ZFA:0001421\|ZFA:0001551	anal fin lepidotrichium\|pectoral fin lepidotri...	NaN	NaN	NaN	NaN
64	ZFA:0001421\|ZFA:0001418	anal fin lepidotrichium\|dorsal fin lepidotrichium	NaN	NaN	NaN	NaN

65 rows × 6 columns

Generating spatial disjointness axioms

Pass in predicates to also generate candidate OWL axioms of the form

(part-of some X) DisjointWith (part-of some Y)

[40]:

zfa generate-disjoints "paired fin skeleton" -p i,p -O csv -o output/zfa-skel-gen-part-disjoint.tsv

[41]:

df = pd.read_csv("output/zfa-skel-gen-part-disjoint.tsv", sep="\t")
df

[41]:

	classIds	unionEquivalentTo	unionEquivalentToExpression	classExpressionPropertyIds	classExpressionPropertyIds_label	classExpressionFillerIds	classExpressionFillerIds_label
0	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0000943\|ZFA:0001387	pectoral fin skeleton\|pelvic fin skeleton
1	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0000257\|ZFA:0001586	pectoral fin cartilage\|pectoral fin radial
2	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001551\|ZFA:0001586	pectoral fin lepidotrichium\|pectoral fin radial
3	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001551\|ZFA:0000257	pectoral fin lepidotrichium\|pectoral fin carti...
4	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0000407\|ZFA:0001586	pectoral girdle\|pectoral fin radial
5	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0000407\|ZFA:0001551	pectoral girdle\|pectoral fin lepidotrichium
6	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001552\|ZFA:0000508	pelvic fin lepidotrichium\|pelvic radial
7	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001459\|ZFA:0000508	pelvic fin cartilage\|pelvic radial
8	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001459\|ZFA:0001552	pelvic fin cartilage\|pelvic fin lepidotrichium

The first row here tells us that the pectoral and pelvic fin skeletons have no parts in common.

Note this is a stronger axiom than simply saying the two structures are class-disjoint.

[ ]:

	classIds	unionEquivalentTo	unionEquivalentToExpression	classExpressionPropertyIds	classExpressionPropertyIds_label	classExpressionFillerIds	classExpressionFillerIds_label
0	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0000943\|ZFA:0001387	pectoral fin skeleton\|pelvic fin skeleton
1	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0000257\|ZFA:0001586	pectoral fin cartilage\|pectoral fin radial
2	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001551\|ZFA:0001586	pectoral fin lepidotrichium\|pectoral fin radial
3	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001551\|ZFA:0000257	pectoral fin lepidotrichium\|pectoral fin carti...
4	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0000407\|ZFA:0001586	pectoral girdle\|pectoral fin radial
5	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0000407\|ZFA:0001551	pectoral girdle\|pectoral fin lepidotrichium
6	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001552\|ZFA:0000508	pelvic fin lepidotrichium\|pelvic radial
7	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001459\|ZFA:0000508	pelvic fin cartilage\|pelvic radial
8	NaN	NaN	NaN	BFO:0000050\|BFO:0000050	part of\|part of	ZFA:0001459\|ZFA:0001552	pelvic fin cartilage\|pelvic fin lepidotrichium