DevelopmentalStage

lamindb provides access to the following public DevelopmentalStage 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

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:

developmentalstages = bt.DevelopmentalStage.public(organism="human")
developmentalstages
 connected lamindb: testuser1/test-public-ontologies
PublicOntology
Entity: DevelopmentalStage
Organism: human
Source: hsapdv, 2024-05-28
#terms: 259

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

df = developmentalstages.df()
df.head()
name definition synonyms parents
ontology_id
HsapDv:0000000 life cycle stage A Spatiotemporal Region Encompassing Some Part... developmental stage []
HsapDv:0000001 life cycle Temporal Interval That Defines Human Life From... None [HsapDv:0000000]
HsapDv:0000002 embryonic stage Prenatal Stage That Starts With Fertilization ... None [HsapDv:0000000, HsapDv:0000045, HsapDv:0000001]
HsapDv:0000003 Carnegie stage 01 Embryonic Stage Defined By A Fertilized Oocyte... CS01 [HsapDv:0000000, HsapDv:0000002, HsapDv:000004...
HsapDv:0000004 cleavage stage Early Stage Of Carnegie Stage 02 Consisting Of... None []

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', 'HsapDv:0000002', 'HsapDv:0000045',
       'HsapDv:0000001'], 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', 'HsapDv:0000002', 'HsapDv:0000045',
       'HsapDv:0000001'], 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', 'HsapDv:0000002', 'HsapDv:0000045',
       'HsapDv:0000001'], dtype=object))

Search terms

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

developmentalstages.search("organogenesis").head(3)
name definition synonyms parents
ontology_id
HsapDv:0000015 organogenesis stage Embryonic Stage At Which The Ectoderm, Endoder... None [HsapDv:0000000, HsapDv:0000002, HsapDv:000004...
HsapDv:0000016 Carnegie stage 09 Organogenesis Stage During Which Somites 1-3 A... CS09 [HsapDv:0000000, HsapDv:0000015, HsapDv:000000...
HsapDv:0000017 Carnegie stage 10 Organogenesis Stage During Which Somites 4-12 ... CS10 [HsapDv:0000000, HsapDv:0000015, HsapDv:000000...

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

developmentalstages.search("developmental stage").head(3)
name definition synonyms parents
ontology_id
HsapDv:0000000 life cycle stage A Spatiotemporal Region Encompassing Some Part... developmental stage []
HsapDv:0000020 Carnegie stage 13 Organogenesis Developmental Stage During Which... CS13 [HsapDv:0000000, HsapDv:0000015, HsapDv:000000...
HsapDv:0000031 Carnegie stage 05a Carnegie Developmental Stage 5 Defined By A So... CS05a [HsapDv:0000000, HsapDv:0000009, HsapDv:000000...

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

developmentalstages.search(
    "Prenatal Stage That Starts With Fertilization",
    field=developmentalstages.definition,
).head()
name definition synonyms parents
ontology_id
HsapDv:0000002 embryonic stage Prenatal Stage That Starts With Fertilization ... None [HsapDv:0000000, HsapDv:0000045, HsapDv:0000001]
HsapDv:0000045 prenatal stage Prenatal Stage That Starts With Fertilization ... None [HsapDv:0000000, HsapDv:0000001]

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]
! 1 unique 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.Source.filter(entity="bionty.DevelopmentalStage").df()
Hide code cell output
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_code
id
99 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 2025-03-10 13:25:14.952000+00:00 1 None 1
100 7Zm9hzpv bionty.DevelopmentalStage human hsapdv False False Human Developmental Stages http://aber-owl.net/media/ontologies/HSAPDV/11... None https://github.com/obophenotype/developmental-... 1 None 2020-03-10 None 2025-03-10 13:25:14.952000+00:00 1 None 1
101 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 2025-03-10 13:25:14.952000+00:00 1 None 1
102 6vJmiDf8 bionty.DevelopmentalStage mouse mmusdv False False Mouse Developmental Stages http://aber-owl.net/media/ontologies/MMUSDV/9/... None https://github.com/obophenotype/developmental-... 1 None 2020-03-10 None 2025-03-10 13:25:14.952000+00:00 1 None 1
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.DevelopmentalStage", 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_code
id
99 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 2025-03-10 13:25:14.952000+00:00 1 None 1
101 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 2025-03-10 13:25:14.952000+00:00 1 None 1

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

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

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 space_id dataframe_artifact_id version run_id created_at created_by_id _aux _branch_code
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 2025-03-10 13:25:14.948000+00:00 1 None 1
6 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 2025-03-10 13:25:14.948000+00:00 1 None 1
7 6s9nV6xh bionty.Organism fungi ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/fungi/releas... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
8 2PmTrc8x bionty.Organism metazoa ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/metazoa/rele... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
9 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 2025-03-10 13:25:14.948000+00:00 1 None 1
10 4tsksCMX bionty.Organism all ncbitaxon False True NCBItaxon Ontology s3://bionty-assets/df_all__ncbitaxon__2023-06-... None https://github.com/obophenotype/ncbitaxon 1 None 2023-06-20 None 2025-03-10 13:25:14.948000+00:00 1 None 1
11 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 2025-03-10 13:25:14.948000+00:00 1 None 1
15 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 2025-03-10 13:25:14.948000+00:00 1 None 1
19 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 2025-03-10 13:25:14.948000+00:00 1 None 1
22 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 2025-03-10 13:25:14.948000+00:00 1 None 1
25 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 2025-03-10 13:25:14.948000+00:00 1 None 1
28 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 2025-03-10 13:25:14.948000+00:00 1 None 1
29 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 2025-03-10 13:25:14.948000+00:00 1 None 1
30 6LyRtvz8 bionty.CellLine all clo False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... None https://bioportal.bioontology.org/ontologies/CLO 1 None 2022-03-21 None 2025-03-10 13:25:14.948000+00:00 1 None 1
32 3Uw2Va7a 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 2024-08-16 None 2025-03-10 13:25:14.948000+00:00 1 None 1
41 MUtAGdL4 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 2024-08-07 None 2025-03-10 13:25:14.948000+00:00 1 None 1
50 4a3ejKuf bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org 1 None 2024-08-06 None 2025-03-10 13:25:14.948000+00:00 1 None 1
59 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 2025-03-10 13:25:14.952000+00:00 1 None 1
67 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 2025-03-10 13:25:14.952000+00:00 1 None 1
75 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 2025-03-10 13:25:14.952000+00:00 1 None 1
80 4t7QibxO bionty.Phenotype mammalian mp False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... None https://github.com/mgijax/mammalian-phenotype-... 1 None 2024-06-18 None 2025-03-10 13:25:14.952000+00:00 1 None 1
83 sqPX2b7b bionty.Phenotype zebrafish zp False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... None https://github.com/obophenotype/zebrafish-phen... 1 None 2024-04-18 None 2025-03-10 13:25:14.952000+00:00 1 None 1
87 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 2025-03-10 13:25:14.952000+00:00 1 None 1
89 7Ent3V2y bionty.Pathway all go False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... None http://geneontology.org 1 None 2024-06-17 None 2025-03-10 13:25:14.952000+00:00 1 None 1
94 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 2025-03-10 13:25:14.952000+00:00 1 None 1
95 ugaIoIlj Drug all dron False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... None https://bioportal.bioontology.org/ontologies/DRON 1 None 2024-08-05 None 2025-03-10 13:25:14.952000+00:00 1 None 1
99 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 2025-03-10 13:25:14.952000+00:00 1 None 1
101 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 2025-03-10 13:25:14.952000+00:00 1 None 1
103 MJRqduf9 bionty.Ethnicity human hancestro False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... None https://github.com/EBISPOT/hancestro 1 None 3.0 None 2025-03-10 13:25:14.952000+00:00 1 None 1
104 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 2025-03-10 13:25:14.952000+00:00 1 None 1