Tissue

lamindb provides access to the following public Tissue 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 Source. 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, 2025-05-28
#terms: 15719

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

df = tissues.df()
df.head()

/tmp/ipykernel_3750/2982313663.py:1: FutureWarning: Use to_dataframe instead of df, df will be removed in the future.
  df = tissues.df()
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... cervical canal of uterus|cervix uteri|uterine ... [UBERON:0001560, UBERON:0005156, UBERON:000099...
UBERON:0000003 naris Orifice Of The Olfactory System. The Naris Is ... None [UBERON:0000161, UBERON:0005725]
UBERON:0000004 nose The Olfactory Organ Of Vertebrates, Consisting... nose|nasal sac|peripheral olfactory organ [UBERON:0002268, UBERON:0004121]
UBERON:0000005 chemosensory organ None chemosensory sensory organ [UBERON:0000020, UBERON:0005726, UBERON:0001016]

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='respiratory alveolus|lung alveolus|pulmonary alveolus|alveolus pulmonis', parents=array(['UBERON:0003215', 'UBERON:0008874', 'UBERON:0002048',
       'UBERON:0010369'], 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='respiratory alveolus|lung alveolus|pulmonary alveolus|alveolus pulmonis', parents=array(['UBERON:0003215', 'UBERON:0008874', 'UBERON:0002048',
       'UBERON:0010369'], 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='lamina propria mucosae of windpipe|windpipe lamina propria mucosa|tracheal lamina propria|lamina propria mucosae of trachea|lamina propria of windpipe|trachea lamina propria|lamina propria mucosa of trachea|windpipe lamina propria|lamina propria mucosa of windpipe|trachea lamina propria mucosa|trachea lamina propria mucosae|windpipe lamina propria mucosae', parents=array(['UBERON:0004779', 'UBERON:0001005', 'UBERON:0001004'], dtype=object))

Search terms

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

tissues.search("lung alveolus").head(3)
name definition synonyms parents
ontology_id
UBERON:0002299 alveolus of lung Spherical Outcropping Of The Respiratory Bronc... respiratory alveolus|lung alveolus|pulmonary a... [UBERON:0003215, UBERON:0008874, UBERON:000204...
UBERON:0002172 alveolar atrium None atrium alveolare|lung alveolus atrium|atrium o... [UBERON:0000064, UBERON:0002299, UBERON:000887...
UBERON:0004861 right lung alveolus An Alveolus That Is Part Of A Right Lung [Auto... alveolus of right lung [UBERON:0002299, UBERON:0002167, UBERON:000652...

By default, search also covers synonyms and all other fileds containing strings:

tissues.search("nasal sac").head(3)
name definition synonyms parents
ontology_id
UBERON:0000004 nose The Olfactory Organ Of Vertebrates, Consisting... nose|nasal sac|peripheral olfactory organ [UBERON:0002268, UBERON:0004121]
UBERON:4300152 accessory nasal sac Accessory Nasal Sacs Are Found In A Variety Of... None [UBERON:0000062]
UBERON:2005085 nasal artery The Nasal Arteries Start At The Internal Carot... NA [UBERON:0001637]

Search specific field (by default, search is done on all fields containing strings):

tissues.search(
    "spherical outcropping of the respiratory",
    field=tissues.definition,
).head()
name definition synonyms parents
ontology_id
UBERON:0002299 alveolus of lung Spherical Outcropping Of The Respiratory Bronc... respiratory alveolus|lung alveolus|pulmonary a... [UBERON:0003215, UBERON:0008874, UBERON:000204...

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 unique 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.Source.filter(entity="bionty.Tissue").df()
Hide code cell output 
/tmp/ipykernel_3750/2870928783.py:1: FutureWarning: Use to_dataframe instead of df, df will be removed in the future.
  bt.Source.filter(entity="bionty.Tissue").df()
uid entity organism name in_db currently_used description url md5 source_website space_id dataframe_artifact_id version run_id created_at created_by_id _aux branch_id
id
17 4U5uYTlc bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... None http://obophenotype.github.io/uberon 1 None 2025-05-28 None 2025-09-08 10:42:04.179000+00:00 1 None 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Tissue", currently_used=True).df()

/tmp/ipykernel_3750/2234030174.py:2: FutureWarning: Use to_dataframe instead of df, df will be removed in the future.
  bt.Source.filter(entity="bionty.Tissue", currently_used=True).df()
uid entity organism name in_db currently_used description url md5 source_website space_id dataframe_artifact_id version run_id created_at created_by_id _aux branch_id
id
17 4U5uYTlc bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... None http://obophenotype.github.io/uberon 1 None 2025-05-28 None 2025-09-08 10:42:04.179000+00:00 1 None 1

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

source = bt.Source.filter(
    name="uberon", organism="all"
).first()
tissues= bt.Tissue.public(source=source)
tissues

PublicOntology
Entity: Tissue
Organism: all
Source: uberon, 2025-05-28
#terms: 15719

The currently used ontologies can be displayed using:

bt.Source.filter(currently_used=True).df()
Hide code cell output 
/tmp/ipykernel_3750/2711573161.py:1: FutureWarning: Use to_dataframe instead of df, df will be removed in the future.
  bt.Source.filter(currently_used=True).df()
uid entity organism name in_db currently_used description url md5 source_website space_id dataframe_artifact_id version run_id created_at created_by_id _aux branch_id
id
1 33TUF039 bionty.Organism vertebrates ensembl False True Ensembl https://ftp.ensembl.org/pub/release-112/specie... None https://www.ensembl.org 1 None release-112 None 2025-09-08 10:42:04.179000+00:00 1 None 1
2 6bbVUTCS bionty.Organism bacteria ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... None https://www.ensembl.org 1 None release-57 None 2025-09-08 10:42:04.179000+00:00 1 None 1
3 6s9nV6xh bionty.Organism fungi ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi... None https://www.ensembl.org 1 None release-57 None 2025-09-08 10:42:04.179000+00:00 1 None 1
4 2PmTrc8x bionty.Organism metazoa ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/metaz... None https://www.ensembl.org 1 None release-57 None 2025-09-08 10:42:04.179000+00:00 1 None 1
5 7GPHh16S bionty.Organism plants ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... None https://www.ensembl.org 1 None release-57 None 2025-09-08 10:42:04.179000+00:00 1 None 1
6 4tsksCMX bionty.Organism all ncbitaxon False True NCBItaxon Ontology http://purl.obolibrary.org/obo/ncbitaxon/2023-... None https://github.com/obophenotype/ncbitaxon 1 None 2023-06-20 None 2025-09-08 10:42:04.179000+00:00 1 None 1
7 4UGNz3fr bionty.Gene human ensembl False True Ensembl s3://bionty-assets/df_human__ensembl__release-... None https://www.ensembl.org 1 None release-112 None 2025-09-08 10:42:04.179000+00:00 1 None 1
8 4r4fvV0S bionty.Gene mouse ensembl False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... None https://www.ensembl.org 1 None release-112 None 2025-09-08 10:42:04.179000+00:00 1 None 1
9 4RPA3Re0 bionty.Gene saccharomyces cerevisiae ensembl False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... None https://www.ensembl.org 1 None release-112 None 2025-09-08 10:42:04.179000+00:00 1 None 1
10 3EYyGRYN bionty.Protein human uniprot False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... None https://www.uniprot.org 1 None 2024-03 None 2025-09-08 10:42:04.179000+00:00 1 None 1
11 01RWXN2V bionty.Protein mouse uniprot False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... None https://www.uniprot.org 1 None 2024-03 None 2025-09-08 10:42:04.179000+00:00 1 None 1
12 3kDh8qAX bionty.CellMarker human cellmarker False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-09-08 10:42:04.179000+00:00 1 None 1
13 7bV5uJo3 bionty.CellMarker mouse cellmarker False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-09-08 10:42:04.179000+00:00 1 None 1
14 6LyRtvz8 bionty.CellLine all clo False True Cell Line Ontology s3://bionty-assets/df_all__clo__2022-03-21__Ce... None https://bioportal.bioontology.org/ontologies/CLO 1 None 2022-03-21 None 2025-09-08 10:42:04.179000+00:00 1 None 1
16 3T9KZcjQ bionty.CellType all cl False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... None https://obophenotype.github.io/cell-ontology 1 None 2025-04-10 None 2025-09-08 10:42:04.179000+00:00 1 None 1
17 4U5uYTlc bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... None http://obophenotype.github.io/uberon 1 None 2025-05-28 None 2025-09-08 10:42:04.179000+00:00 1 None 1
18 IGIkseWQ bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org 1 None 2025-06-03 None 2025-09-08 10:42:04.179000+00:00 1 None 1
19 4kswnHVF bionty.Disease human doid False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... None https://disease-ontology.org 1 None 2024-05-29 None 2025-09-08 10:42:04.179000+00:00 1 None 1
21 2a1HvjdB bionty.ExperimentalFactor all efo False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl None https://bioportal.bioontology.org/ontologies/EFO 1 None 3.70.0 None 2025-09-08 10:42:04.179000+00:00 1 None 1
22 6S4qkDx1 bionty.Phenotype all pato False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... None https://github.com/pato-ontology/pato 1 None 2024-03-28 None 2025-09-08 10:42:04.179000+00:00 1 None 1
23 48fBFLmn bionty.Phenotype human hp False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... None https://hpo.jax.org 1 None 2024-04-26 None 2025-09-08 10:42:04.179000+00:00 1 None 1
25 7Ent3V2y bionty.Pathway all go False True Gene Ontology http://purl.obolibrary.org/obo/go/releases/202... None http://geneontology.org 1 None 2024-06-17 None 2025-09-08 10:42:04.179000+00:00 1 None 1
27 3rm9aOzL BFXPipeline all lamin False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... None https://lamin.ai 1 None 1.0.0 None 2025-09-08 10:42:04.179000+00:00 1 None 1
28 ugaIoIlj Drug all dron False True Drug Ontology http://purl.obolibrary.org/obo/dron/releases/2... None https://bioportal.bioontology.org/ontologies/DRON 1 None 2024-08-05 None 2025-09-08 10:42:04.179000+00:00 1 None 1
30 1GbFkOdz bionty.DevelopmentalStage human hsapdv False True Human Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... 1 None 2024-05-28 None 2025-09-08 10:42:04.179000+00:00 1 None 1
31 10va5JSt bionty.DevelopmentalStage mouse mmusdv False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... 1 None 2024-05-28 None 2025-09-08 10:42:04.179000+00:00 1 None 1
32 MJRqduf9 bionty.Ethnicity human hancestro False True Human Ancestry Ontology http://purl.obolibrary.org/obo/hancestro/relea... None https://github.com/EBISPOT/hancestro 1 None 3.0 None 2025-09-08 10:42:04.179000+00:00 1 None 1
33 5JnVODh4 BioSample all ncbi False True NCBI BioSample attributes s3://bionty-assets/df_all__ncbi__2023-09__BioS... None https://www.ncbi.nlm.nih.gov/biosample/docs/at... 1 None 2023-09 None 2025-09-08 10:42:04.179000+00:00 1 None 1