Tissue

lamindb provides access to the following public protein ontologies through bionty:

  1. Uberon

Here we show how to access and search Tissue ontologies to standardize new data.

import bionty as bt
import pandas as pd

💡 connected lamindb: testuser1/test-public-ontologies

PublicOntology objects

Let us create a public ontology accessor with .public method, which chooses a default public ontology source from PublicSource. It’s a PublicOntology object, which you can think about as a public registry:

tissues = bt.Tissue.public(organism="all")
tissues

PublicOntology
Entity: Tissue
Organism: all
Source: uberon, 2024-02-20
#terms: 15567

As for registries, you can export the ontology as a DataFrame:

df = tissues.df()
df.head()
name definition synonyms parents
ontology_id
UBERON:0000000 processual entity An Occurrent [Span:Occurrent] That Exists In T... None []
UBERON:0000002 uterine cervix Lower, Narrow Portion Of The Uterus Where It J... uterine cervix|neck of uterus|cervical canal o... [UBERON:0001560, UBERON:0005156]
UBERON:0000003 naris Orifice Of The Olfactory System. The Naris Is ... None [UBERON:0000161]
UBERON:0000004 nose The Olfactory Organ Of Vertebrates, Consisting... nasal sac|peripheral olfactory organ|nose [UBERON:0002268, UBERON:0004121, UBERON:0000475]
UBERON:0000005 chemosensory organ None chemosensory sensory organ [UBERON:0000020]

Unlike registries, you can also export it as a Pronto object via public.ontology.

Look up terms

As for registries, terms can be looked up with auto-complete:

lookup = tissues.lookup()

The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):

lookup.alveolus_of_lung

Tissue(ontology_id='UBERON:0002299', name='alveolus of lung', definition='Spherical Outcropping Of The Respiratory Bronchioles And Primary Site Of Gas Exchange With The Blood. Alveoli Are Particular To Mammalian Lungs. Different Structures Are Involved In Gas Exchange In Other Vertebrates[Wp].', synonyms='alveolus pulmonis|pulmonary alveolus|respiratory alveolus|lung alveolus', parents=array(['UBERON:0004119', 'UBERON:0003215'], dtype=object))

To look up the exact original strings, convert the lookup object to dict and use the [] accessor:

lookup_dict = lookup.dict()
lookup_dict["alveolus of lung"]

Tissue(ontology_id='UBERON:0002299', name='alveolus of lung', definition='Spherical Outcropping Of The Respiratory Bronchioles And Primary Site Of Gas Exchange With The Blood. Alveoli Are Particular To Mammalian Lungs. Different Structures Are Involved In Gas Exchange In Other Vertebrates[Wp].', synonyms='alveolus pulmonis|pulmonary alveolus|respiratory alveolus|lung alveolus', parents=array(['UBERON:0004119', 'UBERON:0003215'], dtype=object))

By default, the name field is used to generate lookup keys. You can specify another field to look up:

lookup = tissues.lookup(tissues.ontology_id)

lookup.uberon_0000031

Tissue(ontology_id='UBERON:0000031', name='lamina propria of trachea', definition='A Lamina Propria That Is Part Of A Respiratory Airway.', synonyms='trachea lamina propria mucosa|trachea lamina propria|tracheal lamina propria|lamina propria mucosae of trachea|lamina propria mucosae of windpipe|trachea lamina propria mucosae|windpipe lamina propria mucosae|windpipe lamina propria|lamina propria mucosa of windpipe|lamina propria of windpipe|windpipe lamina propria mucosa|lamina propria mucosa of trachea', parents=array(['UBERON:0004779'], dtype=object))

Search terms

Search behaves in the same way as it does for registries:

tissues.search("alveolus lung").head(3)
ontology_id definition synonyms parents __ratio__
name
alveolus of lung UBERON:0002299 Spherical Outcropping Of The Respiratory Bronc... alveolus pulmonis|pulmonary alveolus|respirato... [UBERON:0004119, UBERON:0003215] 89.655172
left lung alveolus UBERON:0004862 An Alveolus That Is Part Of A Left Lung [Autom... alveolus of lobe of left lung|alveolus of left... [UBERON:0002299] 76.470588
alveolus UBERON:0003215 Organ Part That Has The Form Of A Hollow Cavit... None [UBERON:0000064] 76.190476

By default, search also covers synonyms:

tissues.search("nasal sac").head(3)
ontology_id definition synonyms parents __ratio__
name
nose UBERON:0000004 The Olfactory Organ Of Vertebrates, Consisting... nasal sac|peripheral olfactory organ|nose [UBERON:0002268, UBERON:0004121, UBERON:0000475] 100.000000
anal sac UBERON:0008978 In Carnivores, Either Of Two Sacs Found Betwee... None [UBERON:0000062, UBERON:0009856] 82.352941
nasal air sac UBERON:0013175 An Air Sac Opening Into The Passage Of The Blo... blowhole air sac [UBERON:0004111] 81.818182

You can turn this off synonym by passing synonyms_field=None:

tissues.search("nasal sac", synonyms_field=None).head(3)
ontology_id definition synonyms parents __ratio__
name
anal sac UBERON:0008978 In Carnivores, Either Of Two Sacs Found Betwee... None [UBERON:0000062, UBERON:0009856] 82.352941
nasal air sac UBERON:0013175 An Air Sac Opening Into The Passage Of The Blo... blowhole air sac [UBERON:0004111] 81.818182
nasal muscle UBERON:0008522 Any Muscle Organ That Is Part Of An Nose. muscle of nose [UBERON:0001577, UBERON:0004121] 76.190476

Search another field (default is .name):

tissues.search(
    "alveolus in the lung",
    field=tissues.definition,
).head()
ontology_id name synonyms parents __ratio__
definition
An Alveolus That Is Part Of A Left Lung [Automatically Generated Definition]. UBERON:0004862 left lung alveolus alveolus of lobe of left lung|alveolus of left... [UBERON:0002299] 78.048780
The Epithelial Layer Of The Alveoli[Mp]. The Layer Of Cells Covering The Lining Of The Tiny Air Sacs At The End Of The Bronchioles[Bto]. UBERON:0004821 pulmonary alveolus epithelium epithelial tissue of alveolus|alveolus epithel... [UBERON:0000487, UBERON:0000115] 76.923077
An Alveolus That Is Part Of A Right Lung [Automatically Generated Definition]. UBERON:0004861 right lung alveolus alveolus of right lung [UBERON:0002299] 76.190476
An Alveolar Duct That Is Part Of A Left Lung [Automatically Generated Definition]. UBERON:0003537 left lung alveolar duct alveolar duct of left lung [UBERON:0002173] 65.217391
An Alveolar Duct That Is Part Of A Right Lung [Automatically Generated Definition]. UBERON:0003536 right lung alveolar duct alveolar duct of right lung [UBERON:0002173] 63.829787

Standardize Tissue identifiers

Let us generate a DataFrame that stores a number of Tissue identifiers, some of which corrupted:

df_orig = pd.DataFrame(
    index=[
        "UBERON:0000000",
        "UBERON:0000005",
        "UBERON:0000001",
        "UBERON:0000002",
        "This tissue does not exist",
    ]
)
df_orig
UBERON:0000000
UBERON:0000005
UBERON:0000001
UBERON:0000002
This tissue does not exist

We can check whether any of our values are validated against the ontology reference:

validated = tissues.validate(df_orig.index, tissues.name)
df_orig.index[~validated]

❗ 5 terms (100.00%) are not validated: UBERON:0000000, UBERON:0000005, UBERON:0000001, UBERON:0000002, This tissue does not exist

Index(['UBERON:0000000', 'UBERON:0000005', 'UBERON:0000001', 'UBERON:0000002',
       'This tissue does not exist'],
      dtype='object')

Ontology source versions

For any given entity, we can choose from a number of versions:

bt.PublicSource.filter(entity="Tissue").df()
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
34 1AyH Tissue all True uberon Uberon multi-species anatomy ontology 2024-02-20 http://purl.obolibrary.org/obo/uberon/releases... 2048667b5fdf93192384bdf53cafba18 http://obophenotype.github.io/uberon None 1 2024-07-01 13:54:37.405910+00:00
35 1PY3 Tissue all False uberon Uberon multi-species anatomy ontology 2023-09-05 http://purl.obolibrary.org/obo/uberon/releases... abcee3ede566d1311d758b853ccdf5aa http://obophenotype.github.io/uberon None 1 2024-07-01 13:54:37.406003+00:00
36 45ES Tissue all False uberon Uberon multi-species anatomy ontology 2023-04-19 http://purl.obolibrary.org/obo/uberon/releases... 5611dd1375d5a95ac7d7de8e25e6016f http://obophenotype.github.io/uberon None 1 2024-07-01 13:54:37.406095+00:00
37 5RC9 Tissue all False uberon Uberon multi-species anatomy ontology 2023-02-14 http://purl.obolibrary.org/obo/uberon/releases... 3f94e22fae4cdde88a555c5cd59c47da http://obophenotype.github.io/uberon None 1 2024-07-01 13:54:37.406187+00:00
38 63JG Tissue all False uberon Uberon multi-species anatomy ontology 2022-08-19 http://purl.obolibrary.org/obo/uberon/releases... c7c958a1ee48fdce146f2c1763eed27e http://obophenotype.github.io/uberon None 1 2024-07-01 13:54:37.406280+00:00

When instantiating a Bionty object, we can choose a source or version:

public_source = bt.PublicSource.filter(
    source="uberon", version="2023-04-19", organism="all"
).one()
tissues= bt.Tissue.public(public_source=public_source)
tissues

❗ loading non-default source inside a LaminDB instance

PublicOntology
Entity: Tissue
Organism: all
Source: uberon, 2023-04-19
#terms: 15499

The currently used ontologies can be displayed using:

bt.PublicSource.filter(currently_used=True).df()
Hide code cell output
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
1 5Dlc Organism vertebrates True ensembl Ensembl release-112 https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None 1 2024-07-01 13:54:37.402741+00:00
6 2Jzh Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None 1 2024-07-01 13:54:37.403243+00:00
7 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None 1 2024-07-01 13:54:37.403338+00:00
8 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None 1 2024-07-01 13:54:37.403434+00:00
9 2XQ6 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None 1 2024-07-01 13:54:37.403530+00:00
10 1Vzs Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None 1 2024-07-01 13:54:37.403626+00:00
11 1hx4 Gene human True ensembl Ensembl release-112 s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None 1 2024-07-01 13:54:37.403722+00:00
15 76FX Gene mouse True ensembl Ensembl release-112 s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None 1 2024-07-01 13:54:37.404100+00:00
19 7LW6 Gene saccharomyces cerevisiae True ensembl Ensembl release-112 s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None 1 2024-07-01 13:54:37.404483+00:00
22 7llW Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org None 1 2024-07-01 13:54:37.404763+00:00
24 5U7J Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org None 1 2024-07-01 13:54:37.404949+00:00
26 5nkB CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-07-01 13:54:37.405133+00:00
27 6AFz CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-07-01 13:54:37.405230+00:00
28 6cbC CellLine all True clo Cell Line Ontology 2022-03-21 https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO None 1 2024-07-01 13:54:37.405323+00:00
29 3DeN CellType all True cl Cell Ontology 2024-02-13 http://purl.obolibrary.org/obo/cl/releases/202... https://obophenotype.github.io/cell-ontology None 1 2024-07-01 13:54:37.405416+00:00
34 1AyH Tissue all True uberon Uberon multi-species anatomy ontology 2024-02-20 http://purl.obolibrary.org/obo/uberon/releases... 2048667b5fdf93192384bdf53cafba18 http://obophenotype.github.io/uberon None 1 2024-07-01 13:54:37.405910+00:00
39 LoCG Disease all True mondo Mondo Disease Ontology 2024-02-06 http://purl.obolibrary.org/obo/mondo/releases/... 78914fa236773c5ea6605f7570df6245 https://mondo.monarchinitiative.org None 1 2024-07-01 13:54:37.406373+00:00
44 2mou Disease human True doid Human Disease Ontology 2024-01-31 http://purl.obolibrary.org/obo/doid/releases/2... b36c15a4610757094f8db64b78ae2693 https://disease-ontology.org None 1 2024-07-01 13:54:37.406834+00:00
51 4usY ExperimentalFactor all True efo The Experimental Factor Ontology 3.63.0 http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl 603e6f6981d53d501c5921aa3940b095 https://bioportal.bioontology.org/ontologies/EFO None 1 2024-07-01 13:54:37.407474+00:00
54 2WLc Phenotype human True hp Human Phenotype Ontology 2024-03-06 https://github.com/obophenotype/human-phenotyp... 36b0d00c24a68edb9131707bc146a4c7 https://hpo.jax.org None 1 2024-07-01 13:54:37.407748+00:00
58 6zE1 Phenotype mammalian True mp Mammalian Phenotype Ontology 2024-02-07 https://github.com/mgijax/mammalian-phenotype-... 31c27ed2c7d5774f8b20a77e4e1fd278 https://github.com/mgijax/mammalian-phenotype-... None 1 2024-07-01 13:54:37.408115+00:00
60 7EnA Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2024-01-22 https://github.com/obophenotype/zebrafish-phen... 01600a5d392419b27fc567362d4cfff8 https://github.com/obophenotype/zebrafish-phen... None 1 2024-07-01 13:54:37.408299+00:00
63 55lY Phenotype all True pato Phenotype And Trait Ontology 2023-05-18 http://purl.obolibrary.org/obo/pato/releases/2... bd472f4971492109493d4ad8a779a8dd https://github.com/pato-ontology/pato None 1 2024-07-01 13:54:37.408575+00:00
64 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org None 1 2024-07-01 13:54:37.408667+00:00
67 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai None 1 2024-07-01 13:54:37.408947+00:00
68 5alK Drug all True dron Drug Ontology 2024-03-02 https://data.bioontology.org/ontologies/DRON/s... 84138459de4f65034e979f4e46783747 https://bioportal.bioontology.org/ontologies/DRON None 1 2024-07-01 13:54:37.409042+00:00
70 7CRn DevelopmentalStage human True hsapdv Human Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/HSAPDV/11... 52181d59df84578ed69214a5cb614036 https://github.com/obophenotype/developmental-... None 1 2024-07-01 13:54:37.409226+00:00
71 16tR DevelopmentalStage mouse True mmusdv Mouse Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/MMUSDV/9/... 5bef72395d853c7f65450e6c2a1fc653 https://github.com/obophenotype/developmental-... None 1 2024-07-01 13:54:37.409318+00:00
72 3Tlc Ethnicity human True hancestro Human Ancestry Ontology 3.0 https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None 1 2024-07-01 13:54:37.411527+00:00
73 5JnV BioSample all True ncbi NCBI BioSample attributes 2023-09 s3://bionty-assets/df_all__ncbi__2023-09__BioS... 918db9bd1734b97c596c67d9654a4126 https://www.ncbi.nlm.nih.gov/biosample/docs/at... None 1 2024-07-01 13:54:37.411638+00:00