DevelopmentalStage

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

  1. Human Developmental Stages

  2. Mouse Developmental Stages

Here we show how to access and search DevelopmentalStage 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:

developmentalstages = bt.DevelopmentalStage.public(organism="human")
developmentalstages
PublicOntology
Entity: DevelopmentalStage
Organism: human
Source: hsapdv, 2020-03-10
#terms: 243

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

df = developmentalstages.df()
df.head()
name definition synonyms parents
ontology_id
HsapDv:0000000 human life cycle stage A Spatiotemporal Region Encompassing Some Part... developmental stage []
HsapDv:0000001 human life cycle Temporal Interval That Defines Human Life From... None [HsapDv:0000000]
HsapDv:0000002 embryonic human stage Prenatal Stage That Starts With Fertilization ... None [HsapDv:0000000]
HsapDv:0000003 Carnegie stage 01 Embryonic Stage Defined By A Fertilized Oocyte... CS01 [HsapDv:0000000]
HsapDv:0000004 cleavage stage Early Stage Of Carnegie Stage 02 Consisting Of... None [HsapDv:0000000]

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 = developmentalstages.lookup()

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

lookup.organogenesis_stage
DevelopmentalStage(ontology_id='HsapDv:0000015', name='organogenesis stage', definition='Embryonic Stage At Which The Ectoderm, Endoderm, And Mesoderm Develop Into The Internal Organs Of The Organism.', synonyms=None, parents=array(['HsapDv:0000000'], 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["organogenesis stage"]
DevelopmentalStage(ontology_id='HsapDv:0000015', name='organogenesis stage', definition='Embryonic Stage At Which The Ectoderm, Endoderm, And Mesoderm Develop Into The Internal Organs Of The Organism.', synonyms=None, parents=array(['HsapDv:0000000'], dtype=object))

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

lookup = developmentalstages.lookup(developmentalstages.ontology_id)
lookup.hsapdv_0000015
DevelopmentalStage(ontology_id='HsapDv:0000015', name='organogenesis stage', definition='Embryonic Stage At Which The Ectoderm, Endoderm, And Mesoderm Develop Into The Internal Organs Of The Organism.', synonyms=None, parents=array(['HsapDv:0000000'], dtype=object))

Search terms

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

developmentalstages.search("organogenesis").head(3)
ontology_id definition synonyms parents __ratio__
name
organogenesis stage HsapDv:0000015 Embryonic Stage At Which The Ectoderm, Endoder... None [HsapDv:0000000] 95.000000
morula stage HsapDv:0000205 The Morula Stage Is The Later Part Of Carnegie... None [HsapDv:0000000] 40.000000
80 year-old and over human stage HsapDv:0000095 Aged Stage That Refers To An Adult Who Is Over... None [HsapDv:0000000] 39.461538

By default, search also covers synonyms:

developmentalstages.search("developmental stage").head(3)
ontology_id definition synonyms parents __ratio__
name
human life cycle stage HsapDv:0000000 A Spatiotemporal Region Encompassing Some Part... developmental stage [] 100.000000
prenatal stage HsapDv:0000045 Prenatal Stage That Starts With Fertilization ... None [HsapDv:0000000] 72.727273
fetal stage HsapDv:0000037 Prenatal Stage That Starts With The Fully Form... None [HsapDv:0000000] 66.666667

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

developmentalstages.search("developmental stage", synonyms_field=None).head(3)
ontology_id definition synonyms parents __ratio__
name
prenatal stage HsapDv:0000045 Prenatal Stage That Starts With Fertilization ... None [HsapDv:0000000] 72.727273
fetal stage HsapDv:0000037 Prenatal Stage That Starts With The Fully Form... None [HsapDv:0000000] 66.666667
adolescent stage HsapDv:0000086 Mature Stage That Refers To An Adolescent Who ... 13-18 years [HsapDv:0000000] 62.857143

Search another field (default is .name):

developmentalstages.search(
    "Prenatal Stage That Starts With Fertilization",
    field=developmentalstages.definition,
).head()
ontology_id name synonyms parents __ratio__
definition
Prenatal Stage That Starts With Fertilization And Ends At Birth. HsapDv:0000045 prenatal stage None [HsapDv:0000000] 83.333333
Prenatal Stage That Starts With The Fully Formed Embryo And Ends At Birth. HsapDv:0000037 fetal stage None [HsapDv:0000000] 64.406780
Human Developmental Stage That Refers To An Adult Who Is Over 19. HsapDv:0000087 human adult stage 19+ years [HsapDv:0000000] 51.376147
Human Developmental Stage That Refers To A Sexually Mature Human. HsapDv:0000204 mature stage None [HsapDv:0000000] 51.376147
Adult Stage That Refers To An Adult Who Is Over 45. HsapDv:0000091 human late adulthood stage 45+ years [HsapDv:0000000] 50.526316

Standardize DevelopmentalStage identifiers

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

df_orig = pd.DataFrame(
    index=[
        "blastula stage",
        "Carnegie stage 03",
        "neurula stage",
        "organogenesis stage",
        "This developmentalstage does not exist",
    ]
)
df_orig
blastula stage
Carnegie stage 03
neurula stage
organogenesis stage
This developmentalstage does not exist

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

validated = developmentalstages.validate(df_orig.index, developmentalstages.name)
df_orig.index[~validated]
4 terms (80.00%) are validated
1 term (20.00%) is not validated: This developmentalstage does not exist
Index(['This developmentalstage does not exist'], dtype='object')

Ontology source versions

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

bt.PublicSource.filter(entity="DevelopmentalStage").df()
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
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 2024-06-19 23:14:43.640679+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 2024-06-19 23:14:43.640781+00:00

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

public_source = bt.PublicSource.filter(
    source="hsapdv", version="2020-03-10", organism="human"
).one()
developmentalstages= bt.DevelopmentalStage.public(public_source=public_source)
developmentalstages
PublicOntology
Entity: DevelopmentalStage
Organism: human
Source: hsapdv, 2020-03-10
#terms: 243

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 2024-06-19 23:14:43.633921+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 2024-06-19 23:14:43.634460+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 2024-06-19 23:14:43.634557+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 2024-06-19 23:14:43.634654+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 2024-06-19 23:14:43.634750+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 2024-06-19 23:14:43.634846+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 2024-06-19 23:14:43.634944+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 2024-06-19 23:14:43.635343+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 2024-06-19 23:14:43.635731+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 2024-06-19 23:14:43.636031+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 2024-06-19 23:14:43.636233+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 2024-06-19 23:14:43.636426+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 2024-06-19 23:14:43.636524+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 2024-06-19 23:14:43.636619+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 2024-06-19 23:14:43.636715+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 2024-06-19 23:14:43.637192+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 2024-06-19 23:14:43.637670+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 2024-06-19 23:14:43.638168+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 2024-06-19 23:14:43.638843+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 2024-06-19 23:14:43.639132+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 2024-06-19 23:14:43.639514+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 2024-06-19 23:14:43.639706+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 2024-06-19 23:14:43.639997+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 2024-06-19 23:14:43.640094+00:00
67 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai None 1 2024-06-19 23:14:43.640389+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 2024-06-19 23:14:43.640486+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 2024-06-19 23:14:43.640679+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 2024-06-19 23:14:43.640781+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 2024-06-19 23:14:43.642901+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 2024-06-19 23:14:43.643010+00:00