OAK validate-mappings command

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

This notebook provides examples for the validate-mappings command. This forms part of a suite of validate commands.

Help Option

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

[2]:

!runoak validate-mappings --help

Usage: runoak validate-mappings [OPTIONS] [TERMS]...

  Validates mappings in ontology using additional ontologies.

  To run:

      runoak validate-mappings -i db/uberon.db

  For sssom:

      runoak validate-mappings -i db/uberon.db -o bad-mappings.sssom.tsv

  By default this will attempt to download and connect to sqlite versions of
  different ontologies.

  You can customize this:

      runoak validate-mappings -i db/uberon.db --adapter-mapping
      uberon=db/uberon.db             --adapter-mapping zfa=db/zfa.db

  You can use "*" as a wildcard, in the case where you have an application
  ontology with many mapped entities merged in:

      runoak validate-mappings -i db/uberon.db --adapter-mapping
      "*"=db/merged.db"

Options:
  --autolabel / --no-autolabel  If set, results will automatically have labels
                                assigned  [default: autolabel]
  -O, --output-type TEXT        Desired output type
  --adapter-mapping TEXT        Multiple prefix=selector pairs, e.g.
                                --adapter-mapping uberon=db/uberon.db
  -o, --output FILENAME         Output file, e.g. obo file
  --help                        Show this message and exit.

Example: Validate mappings in XAO

XAO is an anatomical ontology for Xenopus. It has mappings to ontologies like UBERON, GO, CL

[3]:

!runoak -i sqlite:obo:xao validate-mappings -O sssom -o output/xao-invalid.sssom.tsv

[5]:

import pandas as pd
df = pd.read_csv("output/xao-invalid.sssom.tsv", sep="\t", comment="#")
df

[5]:

	subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	subject_source	object_source	mapping_cardinality	comment
0	XAO:0000054	trunk region	oio:hasDbXref	UBERON:0002100	trunk	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
1	XAO:0000100	cardiovascular system	oio:hasDbXref	UBERON:0004535	cardiovascular system	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
2	XAO:0000204	peripheral nerve	oio:hasDbXref	UBERON:0002003	obsolete peripheral nerve	semapv:UnspecifiedMatching	XAO	UBERON	1:1	object is obsolete
3	XAO:0000227	eye primordium	oio:hasDbXref	UBERON:0003071	eye primordium	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
4	XAO:0000282	visceral pouch	oio:hasDbXref	UBERON:0004117	pharyngeal pouch	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
5	XAO:0000376	omphalomesenteric vein	oio:hasDbXref	UBERON:0005487	vitelline vein	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
6	XAO:0000427	gasserian ganglion	oio:hasDbXref	UBERON:0001675	trigeminal ganglion	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
7	XAO:0000428	trigeminal ganglion	oio:hasDbXref	UBERON:0001675	trigeminal ganglion	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
8	XAO:0001010	circulatory system	oio:hasDbXref	UBERON:0004535	cardiovascular system	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
9	XAO:0003001	anatomical group	oio:hasDbXref	CARO:0000054	anatomical group	semapv:UnspecifiedMatching	XAO	CARO	1:1	object is obsolete
10	XAO:0003012	cell	oio:hasDbXref	GO:0005623	obsolete cell	semapv:UnspecifiedMatching	XAO	GO	1:1	object is obsolete
11	XAO:0003025	trunk	oio:hasDbXref	UBERON:0002100	trunk	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
12	XAO:0003160	anatomical cluster	oio:hasDbXref	CARO:0000041	anatomical cluster	semapv:UnspecifiedMatching	XAO	CARO	1:1	object is obsolete
13	XAO:0003163	basal lamina	oio:hasDbXref	CARO:0000065	basal lamina	semapv:UnspecifiedMatching	XAO	CARO	1:1	object is obsolete
14	XAO:0003257	myelin accumulating cell	oio:hasDbXref	CL:0000328	obsolete myelin accumulating cell	semapv:UnspecifiedMatching	XAO	CL	1:1	object is obsolete
15	XAO:0004090	optic field	oio:hasDbXref	UBERON:0003071	eye primordium	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
16	XAO:0004147	vitelline vein	oio:hasDbXref	UBERON:0005487	vitelline vein	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
17	XAO:0004165	intersomitic artery	oio:hasDbXref	UBERON:0006001	NaN	semapv:UnspecifiedMatching	XAO	UBERON	1:1	object is obsolete
18	XAO:0004260	pharyngeal pouch	oio:hasDbXref	UBERON:0004117	pharyngeal pouch	semapv:UnspecifiedMatching	XAO	UBERON	1:n	cardinality is 1:n
19	XAO:0004290	cell part	oio:hasDbXref	GO:0044464	obsolete cell part	semapv:UnspecifiedMatching	XAO	GO	1:1	object is obsolete
20	XAO:0004615	basal body	oio:hasDbXref	GO:0005932	NaN	semapv:UnspecifiedMatching	XAO	GO	1:1	object is obsolete
21	XAO:0004621	epidermal cell	oio:hasDbXref	CL:1000396	NaN	semapv:UnspecifiedMatching	XAO	CL	1:1	object is obsolete
22	XAO:0005007	Muller cell	oio:hasDbXref	CL:0011107	obsolete Muller cell	semapv:UnspecifiedMatching	XAO	CL	1:1	object is obsolete
23	XAO:1000007	tailbud stage	oio:hasDbXref	UBERON:0009741	obsolete tailbud stage	semapv:UnspecifiedMatching	XAO	UBERON	1:1	object is obsolete

Here we can see a mixture of cardinality issues and obsoletion issues

Note that behind the scenes this command connected to external ontologies such as GO, CL, and UBERON in order to check obsoletion status etc.

[6]:

df["comment"].unique()

[6]:

array(['cardinality is 1:n', 'object is obsolete'], dtype=object)

[11]:

df.groupby("comment").size().reset_index(name='counts')

[11]:

	comment	counts
0	cardinality is 1:n	12
1	object is obsolete	12

Example: CL

CL has a broader range of mappings, in the ontology as xrefs

[14]:

!runoak --quiet -i sqlite:obo:cl validate-mappings -O sssom -o output/cl-invalid.sssom.tsv >& output/LOG

[15]:

df = pd.read_csv("output/cl-invalid.sssom.tsv", sep="\t", comment="#")
df

[15]:

	subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	subject_source	object_source	mapping_cardinality	comment
0	CARO:0000013	cell	oio:hasDbXref	GO:0005623	obsolete cell	semapv:UnspecifiedMatching	CARO	GO	1:1	object is obsolete
1	CL:0000000	cell	oio:hasDbXref	GO:0005623	obsolete cell	semapv:UnspecifiedMatching	CL	GO	1:1	object is obsolete
2	CL:0000019	sperm	oio:hasDbXref	BTO:0001277	spermatozoon	semapv:UnspecifiedMatching	CL	BTO	n:n	cardinality is n:n
3	CL:0000019	sperm	oio:hasDbXref	BTO:0002046	spermatozoid	semapv:UnspecifiedMatching	CL	BTO	n:1	cardinality is n:1
4	CL:0000019	sperm	oio:hasDbXref	CALOHA:TS-0949	NaN	semapv:UnspecifiedMatching	CL	CALOHA	1:n	cardinality is 1:n
...	...	...	...	...	...	...	...	...	...	...
3824	UBERON:2001316	anterior lateral line placode	oio:hasDbXref	EFO:0003461	obsolete_anterior lateral line placode	semapv:UnspecifiedMatching	UBERON	EFO	1:1	object is obsolete
3825	UBERON:2001389	regeneration epithelium of fin/limb	oio:hasDbXref	EFO:0003682	obsolete_regeneration epithelium	semapv:UnspecifiedMatching	UBERON	EFO	1:1	object is obsolete
3826	UBERON:2001391	anterior lateral line ganglion	oio:hasDbXref	EFO:0003683	obsolete_anterior lateral line ganglion	semapv:UnspecifiedMatching	UBERON	EFO	1:1	object is obsolete
3827	UBERON:2001468	anterior lateral line system	oio:hasDbXref	EFO:0003691	obsolete_anterior lateral line system	semapv:UnspecifiedMatching	UBERON	EFO	1:1	object is obsolete
3828	UBERON:6000004	panarthropod head	oio:hasDbXref	FBbt:00000004	head	semapv:UnspecifiedMatching	UBERON	FBbt	1:n	cardinality is 1:n

3829 rows × 10 columns

[16]:

df.groupby("comment").size().reset_index(name='counts')

[16]:

	comment	counts
0	cardinality is 1:n	608
1	cardinality is n:1	2588
2	cardinality is n:n	155
3	object is obsolete	438
4	object is obsolete \| cardinality is n:1	9
5	subject is obsolete	13
6	subject is obsolete \| cardinality is 1:n	11
7	subject is obsolete \| object is obsolete	2

We can summarize these in groups:

[18]:

df.groupby(["comment", "subject_source", "object_source"]).size().reset_index(name='counts')

[18]:

	comment	subject_source	object_source	counts
0	cardinality is 1:n	CL	BTO	35
1	cardinality is 1:n	CL	CALOHA	25
2	cardinality is 1:n	CL	FAO	3
3	cardinality is 1:n	CL	FMA	20
4	cardinality is 1:n	CL	GOC	4
...	...	...	...	...
121	subject is obsolete \| cardinality is 1:n	CL	FAO	1
122	subject is obsolete \| cardinality is 1:n	CL	FMA	3
123	subject is obsolete \| cardinality is 1:n	CL	ILX	6
124	subject is obsolete \| object is obsolete	CL	FBbt	1
125	subject is obsolete \| object is obsolete	RO	RO	1

126 rows × 4 columns

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