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

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

→ connected lamindb: testuser1/test-public-ontologies

PublicOntology
Entity: Tissue
Organism: all
Source: uberon, 2024-08-07
#terms: 15631

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... caudal segment of uterus|canalis cervicis uter... [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... nasal sac|nose|peripheral olfactory organ [UBERON:0004121, UBERON:0000475, UBERON:0002268]
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='pulmonary alveolus|alveolus pulmonis|respiratory alveolus|lung alveolus', parents=array(['UBERON:0003215', 'UBERON:0004119', '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='pulmonary alveolus|alveolus pulmonis|respiratory alveolus|lung alveolus', parents=array(['UBERON:0003215', 'UBERON:0004119', '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='tracheal lamina propria|windpipe lamina propria|lamina propria mucosae of windpipe|lamina propria mucosa of trachea|lamina propria mucosa of windpipe|lamina propria of windpipe|trachea lamina propria|lamina propria mucosae of trachea|windpipe lamina propria mucosae|trachea lamina propria mucosae|trachea lamina propria mucosa|windpipe lamina propria mucosa', 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... pulmonary alveolus|alveolus pulmonis|respirato... [UBERON:0003215, UBERON:0004119, UBERON:000887...
UBERON:0002172 alveolar atrium None atrium of alveolus of lung|atrium of alveolus|... [UBERON:0000064, UBERON:0004119, UBERON:000229...
UBERON:0004861 right lung alveolus An Alveolus That Is Part Of A Right Lung [Auto... alveolus of right lung [UBERON:0002299, UBERON:0006526, UBERON:000216...

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... nasal sac|nose|peripheral olfactory organ [UBERON:0004121, UBERON:0000475, UBERON:0002268]
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... pulmonary alveolus|alveolus pulmonis|respirato... [UBERON:0003215, UBERON:0004119, UBERON:000887...

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
uid entity organism name in_db currently_used description url md5 source_website dataframe_artifact_id version run_id created_at created_by_id
id
40 MUtA bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... http://obophenotype.github.io/uberon None 2024-08-07 None 2024-12-20 15:03:38.346116+00:00 1
41 01Ng bionty.Tissue all uberon False False Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... dc473b764acfe765be31250c853ef23d http://obophenotype.github.io/uberon None 2024-05-13 None 2024-12-20 15:03:38.346141+00:00 1
42 6wOb bionty.Tissue all uberon False False Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... http://obophenotype.github.io/uberon None 2024-03-22 None 2024-12-20 15:03:38.346166+00:00 1
43 Cwzj bionty.Tissue all uberon False False Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... 2048667b5fdf93192384bdf53cafba18 http://obophenotype.github.io/uberon None 2024-02-20 None 2024-12-20 15:03:38.346191+00:00 1
44 2PlK bionty.Tissue all uberon False False Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... 9cff222ef07a1f622a6d12775ada650d http://obophenotype.github.io/uberon None 2024-01-18 None 2024-12-20 15:03:38.346216+00:00 1
45 svSf bionty.Tissue all uberon False False Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... abcee3ede566d1311d758b853ccdf5aa http://obophenotype.github.io/uberon None 2023-09-05 None 2024-12-20 15:03:38.346241+00:00 1
46 1tLk bionty.Tissue all uberon False False Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... 5611dd1375d5a95ac7d7de8e25e6016f http://obophenotype.github.io/uberon None 2023-04-19 None 2024-12-20 15:03:38.346266+00:00 1
47 6VAw bionty.Tissue all uberon False False Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... 3f94e22fae4cdde88a555c5cd59c47da http://obophenotype.github.io/uberon None 2023-02-14 None 2024-12-20 15:03:38.346291+00:00 1
48 7Iby bionty.Tissue all uberon False False Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... c7c958a1ee48fdce146f2c1763eed27e http://obophenotype.github.io/uberon None 2022-08-19 None 2024-12-20 15:03:38.346316+00:00 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Tissue", currently_used=True).df()
uid entity organism name in_db currently_used description url md5 source_website dataframe_artifact_id version run_id created_at created_by_id
id
40 MUtA bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... http://obophenotype.github.io/uberon None 2024-08-07 None 2024-12-20 15:03:38.346116+00:00 1

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

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

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

The currently used ontologies can be displayed using:

bt.Source.filter(currently_used=True).df()
Hide code cell output
uid entity organism name in_db currently_used description url md5 source_website dataframe_artifact_id version run_id created_at created_by_id
id
1 33TU bionty.Organism vertebrates ensembl False True Ensembl https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None release-112 None 2024-12-20 15:03:38.345036+00:00 1
6 6bbV bionty.Organism bacteria ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None release-57 None 2024-12-20 15:03:38.345237+00:00 1
7 6s9n bionty.Organism fungi ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None release-57 None 2024-12-20 15:03:38.345264+00:00 1
8 2PmT bionty.Organism metazoa ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None release-57 None 2024-12-20 15:03:38.345290+00:00 1
9 7GPH bionty.Organism plants ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None release-57 None 2024-12-20 15:03:38.345316+00:00 1
10 4tsk bionty.Organism all ncbitaxon False True NCBItaxon Ontology s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None 2023-06-20 None 2024-12-20 15:03:38.345342+00:00 1
11 4UGN bionty.Gene human ensembl False True Ensembl s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None release-112 None 2024-12-20 15:03:38.345367+00:00 1
15 4r4f bionty.Gene mouse ensembl False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None release-112 None 2024-12-20 15:03:38.345470+00:00 1
19 4RPA bionty.Gene saccharomyces cerevisiae ensembl False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None release-112 None 2024-12-20 15:03:38.345572+00:00 1
22 3EYy bionty.Protein human uniprot False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... b5b9e7645065b4b3187114f07e3f402f https://www.uniprot.org None 2024-03 None 2024-12-20 15:03:38.345647+00:00 1
25 01RW bionty.Protein mouse uniprot False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... b1b6a196eb853088d36198d8e3749ec4 https://www.uniprot.org None 2024-03 None 2024-12-20 15:03:38.345724+00:00 1
28 3kDh bionty.CellMarker human cellmarker False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 2.0 None 2024-12-20 15:03:38.345800+00:00 1
29 7bV5 bionty.CellMarker mouse cellmarker False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 2.0 None 2024-12-20 15:03:38.345825+00:00 1
30 6LyR bionty.CellLine all clo False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO None 2022-03-21 None 2024-12-20 15:03:38.345850+00:00 1
32 1Lhf bionty.CellType all cl False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 8a8638a9e79567935793e5007704c650 https://obophenotype.github.io/cell-ontology None 2024-05-15 None 2024-12-20 15:03:38.345900+00:00 1
40 MUtA bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... http://obophenotype.github.io/uberon None 2024-08-07 None 2024-12-20 15:03:38.346116+00:00 1
49 2L2r bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... c47e8edb894c01f2511dfe0751fbc428 https://mondo.monarchinitiative.org None 2024-06-04 None 2024-12-20 15:03:38.346342+00:00 1
57 4ksw bionty.Disease human doid False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... bbefd72247d638edfcd31ec699947407 https://disease-ontology.org None 2024-05-29 None 2024-12-20 15:03:38.346538+00:00 1
65 2a1H bionty.ExperimentalFactor all efo False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl https://bioportal.bioontology.org/ontologies/EFO None 3.70.0 None 2024-12-20 15:03:38.348787+00:00 1
72 48fB bionty.Phenotype human hp False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... e0f2e534eb2ad44a4d45573ef27b508f https://hpo.jax.org None 2024-04-26 None 2024-12-20 15:03:38.348965+00:00 1
77 4t7Q bionty.Phenotype mammalian mp False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... 795d8378fe48ec13b41d01a86dd1c86c https://github.com/mgijax/mammalian-phenotype-... None 2024-06-18 None 2024-12-20 15:03:38.349111+00:00 1
80 sqPX bionty.Phenotype zebrafish zp False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... 2231ebaa95becf8ff34a33c95a8d4350 https://github.com/obophenotype/zebrafish-phen... None 2024-04-18 None 2024-12-20 15:03:38.349189+00:00 1
84 6S4q bionty.Phenotype all pato False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... 6b1eaacd3d453b34375ce2e31c16328a https://github.com/pato-ontology/pato None 2024-03-28 None 2024-12-20 15:03:38.349288+00:00 1
86 7Ent bionty.Pathway all go False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... 7fa7ade5e3e26eab3959a7e4bc89ad4f http://geneontology.org None 2024-06-17 None 2024-12-20 15:03:38.349338+00:00 1
91 3rm9 BFXPipeline all lamin False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... https://lamin.ai None 1.0.0 None 2024-12-20 15:03:38.349461+00:00 1
92 ugaI Drug all dron False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... https://bioportal.bioontology.org/ontologies/DRON None 2024-08-05 None 2024-12-20 15:03:38.349486+00:00 1
96 1GbF bionty.DevelopmentalStage human hsapdv False True Human Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None 2024-05-28 None 2024-12-20 15:03:38.349585+00:00 1
98 10va bionty.DevelopmentalStage mouse mmusdv False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None 2024-05-28 None 2024-12-20 15:03:38.349634+00:00 1
100 MJRq bionty.Ethnicity human hancestro False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None 3.0 None 2024-12-20 15:03:38.349683+00:00 1
101 5JnV BioSample all ncbi False True NCBI BioSample attributes s3://bionty-assets/df_all__ncbi__2023-09__BioS... 918db9bd1734b97c596c67d9654a4126 https://www.ncbi.nlm.nih.gov/biosample/docs/at... None 2023-09 None 2024-12-20 15:03:38.349708+00:00 1