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, 2023-09-05
#terms: 15539

📖 .df(): ontology reference table
🔎 .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
✅ .validate(): strictly validate values
🧐 .inspect(): full inspection of values
👽 .standardize(): convert to standardized names
🪜 .diff(): difference between two versions
🔗 .to_pronto(): Pronto.Ontology object

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... neck of uterus|canalis cervicis uteri|cervical... [UBERON:0005156, UBERON:0001560]
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:0000475, UBERON:0004121, UBERON:001031...
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='lung alveolus|pulmonary alveolus|alveolus pulmonis|respiratory alveolus', parents=array(['UBERON:0003215', 'UBERON:0004119'], 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='lung alveolus|pulmonary alveolus|alveolus pulmonis|respiratory alveolus', parents=array(['UBERON:0003215', 'UBERON:0004119'], 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 trachea|trachea lamina propria mucosae|lamina propria of windpipe|windpipe lamina propria mucosa|lamina propria mucosa of trachea|tracheal lamina propria|trachea lamina propria mucosa|windpipe lamina propria|lamina propria mucosa of windpipe|trachea lamina propria|windpipe lamina propria mucosae|lamina propria mucosae of windpipe', 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... lung alveolus|pulmonary alveolus|alveolus pulm... [UBERON:0003215, UBERON:0004119] 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:0000475, UBERON:0004121, UBERON:001031... 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 epithelium of pulmonary alveolus|epithelial ti... [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:0000000UBERON:0000005UBERON:0000001UBERON:0000002This 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]

❗ 1 term (100.00%) is not validated: UBERON:0000000UBERON:0000005UBERON:0000001UBERON:0000002This tissue does not exist

Index(['UBERON:0000000UBERON:0000005UBERON:0000001UBERON:0000002This 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 created_at updated_at created_by_id
id
25 1PY3 Tissue all True uberon Uberon multi-species anatomy ontology 2023-09-05 http://purl.obolibrary.org/obo/uberon/releases... abcee3ede566d1311d758b853ccdf5aa http://obophenotype.github.io/uberon 2024-05-01 18:49:19.737762+00:00 2024-05-01 18:49:19.737771+00:00 1
26 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 2024-05-01 18:49:19.737849+00:00 2024-05-01 18:49:19.737858+00:00 1
27 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 2024-05-01 18:49:19.737936+00:00 2024-05-01 18:49:19.737945+00:00 1
28 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 2024-05-01 18:49:19.738026+00:00 2024-05-01 18:49:19.738035+00:00 1

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

📖 .df(): ontology reference table
🔎 .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
✅ .validate(): strictly validate values
🧐 .inspect(): full inspection of values
👽 .standardize(): convert to standardized names
🪜 .diff(): difference between two versions
🔗 .to_pronto(): Pronto.Ontology object

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 created_at updated_at created_by_id
id
1 6IUo Organism vertebrates True ensembl Ensembl release-110 https://ftp.ensembl.org/pub/release-110/specie... f3faf95648d3a2b50fd3625456739706 https://www.ensembl.org 2024-05-01 18:49:19.735543+00:00 2024-05-01 18:49:19.735579+00:00 1
4 2Jzh Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org 2024-05-01 18:49:19.735884+00:00 2024-05-01 18:49:19.735894+00:00 1
5 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org 2024-05-01 18:49:19.735975+00:00 2024-05-01 18:49:19.735985+00:00 1
6 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org 2024-05-01 18:49:19.736067+00:00 2024-05-01 18:49:19.736077+00:00 1
7 2XQ6 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org 2024-05-01 18:49:19.736161+00:00 2024-05-01 18:49:19.736171+00:00 1
8 1Vzs Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon 2024-05-01 18:49:19.736251+00:00 2024-05-01 18:49:19.736260+00:00 1
9 4yVc Gene human True ensembl Ensembl release-110 s3://bionty-assets/df_human__ensembl__release-... 832f3947e83664588d419608a469b528 https://www.ensembl.org 2024-05-01 18:49:19.736341+00:00 2024-05-01 18:49:19.736350+00:00 1
11 2akp Gene mouse True ensembl Ensembl release-110 s3://bionty-assets/df_mouse__ensembl__release-... fa4ce130f2929aefd7ac3bc8eaf0c4de https://www.ensembl.org 2024-05-01 18:49:19.736525+00:00 2024-05-01 18:49:19.736534+00:00 1
13 2UvD Gene saccharomyces cerevisiae True ensembl Ensembl release-110 s3://bionty-assets/df_saccharomyces cerevisiae... 2e59495a3e87ea6575e408697dd73459 https://www.ensembl.org 2024-05-01 18:49:19.736703+00:00 2024-05-01 18:49:19.736712+00:00 1
14 7llW Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org 2024-05-01 18:49:19.736792+00:00 2024-05-01 18:49:19.736801+00:00 1
16 5U7J Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org 2024-05-01 18:49:19.736970+00:00 2024-05-01 18:49:19.736979+00:00 1
18 5nkB CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker 2024-05-01 18:49:19.737147+00:00 2024-05-01 18:49:19.737156+00:00 1
19 6AFz CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker 2024-05-01 18:49:19.737234+00:00 2024-05-01 18:49:19.737243+00:00 1
20 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 2024-05-01 18:49:19.737322+00:00 2024-05-01 18:49:19.737331+00:00 1
21 6tvq CellType all True cl Cell Ontology 2023-08-24 http://purl.obolibrary.org/obo/cl/releases/202... 46e7dd89421f1255cf0191eca1548f73 https://obophenotype.github.io/cell-ontology 2024-05-01 18:49:19.737410+00:00 2024-05-01 18:49:19.737419+00:00 1
25 1PY3 Tissue all True uberon Uberon multi-species anatomy ontology 2023-09-05 http://purl.obolibrary.org/obo/uberon/releases... abcee3ede566d1311d758b853ccdf5aa http://obophenotype.github.io/uberon 2024-05-01 18:49:19.737762+00:00 2024-05-01 18:49:19.737771+00:00 1
29 6EOm Disease all True mondo Mondo Disease Ontology 2023-08-02 http://purl.obolibrary.org/obo/mondo/releases/... 7f33767422042eec29f08b501fc851db https://mondo.monarchinitiative.org 2024-05-01 18:49:19.738114+00:00 2024-05-01 18:49:19.738123+00:00 1
33 3V9D Disease human True doid Human Disease Ontology 2023-03-31 http://purl.obolibrary.org/obo/doid/releases/2... 64f083a1e47867c307c8eae308afc3bb https://disease-ontology.org 2024-05-01 18:49:19.738467+00:00 2024-05-01 18:49:19.738476+00:00 1
39 6fKX ExperimentalFactor all True efo The Experimental Factor Ontology 3.57.0 http://www.ebi.ac.uk/efo/releases/v3.57.0/efo.owl 2ecafc69b3aba7bdb31ad99438505c05 https://bioportal.bioontology.org/ontologies/EFO 2024-05-01 18:49:19.739086+00:00 2024-05-01 18:49:19.739095+00:00 1
41 6jHz Phenotype human True hp Human Phenotype Ontology 2023-06-17 https://github.com/obophenotype/human-phenotyp... 65e8d96bc81deb893163927063b10c06 https://hpo.jax.org 2024-05-01 18:49:19.739264+00:00 2024-05-01 18:49:19.739273+00:00 1
44 4q5A Phenotype mammalian True mp Mammalian Phenotype Ontology 2023-05-31 https://github.com/mgijax/mammalian-phenotype-... be89052cf6d9c0b6197038fe347ef293 https://github.com/mgijax/mammalian-phenotype-... 2024-05-01 18:49:19.739531+00:00 2024-05-01 18:49:19.739540+00:00 1
45 6Czy Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2022-12-17 https://github.com/obophenotype/zebrafish-phen... 03430b567bf153216c0fa4c3440b3b24 https://github.com/obophenotype/zebrafish-phen... 2024-05-01 18:49:19.739618+00:00 2024-05-01 18:49:19.739627+00:00 1
47 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 2024-05-01 18:49:19.739794+00:00 2024-05-01 18:49:19.739803+00:00 1
48 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org 2024-05-01 18:49:19.739882+00:00 2024-05-01 18:49:19.739892+00:00 1
50 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai 2024-05-01 18:49:19.740066+00:00 2024-05-01 18:49:19.740075+00:00 1
51 3TI0 Drug all True dron Drug Ontology 2023-03-10 https://data.bioontology.org/ontologies/DRON/s... 75e86011158fae76bb46d96662a33ba3 https://bioportal.bioontology.org/ontologies/DRON 2024-05-01 18:49:19.740154+00:00 2024-05-01 18:49:19.740163+00:00 1
52 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-... 2024-05-01 18:49:19.740241+00:00 2024-05-01 18:49:19.740250+00:00 1
53 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-... 2024-05-01 18:49:19.740329+00:00 2024-05-01 18:49:19.740339+00:00 1
54 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 2024-05-01 18:49:19.740418+00:00 2024-05-01 18:49:19.740427+00:00 1
55 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... 2024-05-01 18:49:19.740506+00:00 2024-05-01 18:49:19.740514+00:00 1