Manage biological registries¶

This guide shows how to manage metadata for basic biological entities based on plugin bionty.

# !pip install 'lamindb[bionty]'
!lamin init --storage ./test-registries --modules bionty

import lamindb as ln
import bionty as bt

→ connected lamindb: testuser1/test-registries

Seed registries with public ontologies¶

Let’s first populate our CellType registry with the configured public ontology (Cell Ontology):

# check configured public ontology
bt.Source.filter(entity="bionty.CellType", currently_used=True).one()

Source(uid='3Uw2', entity='bionty.CellType', organism='all', name='cl', version='2024-08-16', in_db=False, currently_used=True, description='Cell Ontology', url='http://purl.obolibrary.org/obo/cl/releases/2024-08-16/cl.owl', md5='', source_website='https://obophenotype.github.io/cell-ontology', created_by_id=1, space_id=1, created_at=2025-01-12 14:03:47 UTC)

# populate the database with the public ontology
bt.CellType.import_source()

This is now your in-house CellType registry:

# all public cell types are now available in LaminDB
bt.CellType.df()

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	uid	name	ontology_id	abbr	synonyms	description	space_id	source_id	run_id	created_at	created_by_id	aux	_branch_code
id
2959	77KNSTIT	cycling neuroblast (sensu Vertebrata)	CL:4047005	None	proliferating neuroblast (sensu Vertebrata)	A(N) Neuroblast (Sensu Vertebrata) That Is Cyc...	1	32	None	2025-01-12 14:03:57.347239+00:00	1	None	1
2958	tEH7Cu81	cycling type EC enteroendocrine cell	CL:4047004	None	proliferating type EC enteroendocrine cell	A(N) Type Ec Enteroendocrine Cell That Is Cycl...	1	32	None	2025-01-12 14:03:57.347169+00:00	1	None	1
2957	5CQynGea	cycling plasma cell	CL:4047003	None	proliferating plasma cell	A(N) Plasma Cell That Is Cycling.	1	32	None	2025-01-12 14:03:57.347100+00:00	1	None	1
2956	d8qkyh5t	cycling glial cell	CL:4047002	None	proliferating glial cell	A(N) Glial Cell That Is Cycling.	1	32	None	2025-01-12 14:03:57.347030+00:00	1	None	1
2955	4C2F94cV	cycling stromal cell	CL:4047001	None	proliferating stromal cell	A(N) Stromal Cell That Is Cycling.	1	32	None	2025-01-12 14:03:57.346961+00:00	1	None	1
...	...	...	...	...	...	...	...	...	...	...	...	...	...
2864	4efKc9o9	retinal astrocyte	CL:4033015	None	None	A Star-Shaped Glial Cell That Is Part Of Some ...	1	32	None	2025-01-12 14:03:57.336935+00:00	1	None	1
2863	6zbMPCM6	peg cell	CL:4033014	None	FTE stem-like cell\|fallopian tube epithelial s...	A Small, Narrow, Peg-Shaped Epithelial Cell Wi...	1	32	None	2025-01-12 14:03:57.336865+00:00	1	None	1
2862	3VV9jqFH	suprabasal keratinocyte	CL:4033013	None	None	A Keratinocyte Of The Epidermis Suprabasal Lay...	1	32	None	2025-01-12 14:03:57.336795+00:00	1	None	1
2861	3olktS6h	smooth muscle cell of large intestine smooth m...	CL:4033012	None	None	A(N) Smooth Muscle Cell That Is Part Of A(N) L...	1	32	None	2025-01-12 14:03:57.336721+00:00	1	None	1
2860	1poo3P4b	smooth muscle cell of large intestine smooth m...	CL:4033011	None	None	A(N) Smooth Muscle Cell That Is Part Of A(N) L...	1	32	None	2025-01-12 14:03:57.336651+00:00	1	None	1

100 rows × 13 columns

# similarly, let's populate the Gene registry with human and mouse genes
bt.Gene.import_source(organism="human")
bt.Gene.import_source(organism="mouse")

Access records in in-house registries¶

Search key words:

bt.CellType.search("gamma-delta T").df().head(2)

	uid	name	ontology_id	abbr	synonyms	description	space_id	source_id	run_id	created_at	created_by_id	aux	_branch_code
id
780	1HuNn2EP	gamma-delta T cell	CL:0000798	None	gamma-delta T-cell\|gamma-delta T lymphocyte\|ga...	A T Cell That Expresses A Gamma-Delta T Cell R...	1	32	None	2025-01-12 14:03:57.090716+00:00	1	None	1
781	70lHcCNw	immature gamma-delta T cell	CL:0000799	None	immature gamma-delta T lymphocyte\|immature gam...	A Gamma-Delta T Cell That Has An Immature Phen...	1	32	None	2025-01-12 14:03:57.090785+00:00	1	None	1

Or look up with auto-complete:

cell_types = bt.CellType.lookup()
hsc_record = cell_types.hematopoietic_stem_cell
hsc_record

CellType(uid='2U8xapxu', name='hematopoietic stem cell', ontology_id='CL:0000037', synonyms='hemopoietic stem cell|blood forming stem cell', description='A Stem Cell From Which All Cells Of The Lymphoid And Myeloid Lineages Develop, Including Blood Cells And Cells Of The Immune System. Hematopoietic Stem Cells Lack Cell Markers Of Effector Cells (Lin-Negative). Lin-Negative Is Defined By Lacking One Or More Of The Following Cell Surface Markers: Cd2, Cd3 Epsilon, Cd4, Cd5 ,Cd8 Alpha Chain, Cd11B, Cd14, Cd19, Cd20, Cd56, Ly6G, Ter119.', created_by_id=1, space_id=1, source_id=32, created_at=2025-01-12 14:03:56 UTC)

Filter by fields and relationships:

gdt_cell = bt.CellType.get(ontology_id="CL:0000798", created_by__handle="testuser1")
gdt_cell

CellType(uid='1HuNn2EP', name='gamma-delta T cell', ontology_id='CL:0000798', synonyms='gamma-delta T-cell|gamma-delta T lymphocyte|gammadelta T cell|gamma-delta T-lymphocyte', description='A T Cell That Expresses A Gamma-Delta T Cell Receptor Complex.', created_by_id=1, space_id=1, source_id=32, created_at=2025-01-12 14:03:57 UTC)

View the ontological hierarchy:

gdt_cell.view_parents()  # pass with_children=True to also view children

_images/263a9f9f74a548ea1b204bbe59b2b306f2a462ef89dc238e1ad3eaa22404a8f0.svg

Or access the parents and children directly:

gdt_cell.parents.df()

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	uid	name	ontology_id	abbr	synonyms	description	space_id	source_id	run_id	created_at	created_by_id	aux	_branch_code
id
83	22LvKd01	T cell	CL:0000084	None	T-cell\|T-lymphocyte\|T lymphocyte	A Type Of Lymphocyte Whose Defining Characteri...	1	32	None	2025-01-12 14:03:56.940242+00:00	1	None	1

gdt_cell.children.df()

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	uid	name	ontology_id	abbr	synonyms	description	space_id	source_id	run_id	created_at	created_by_id	aux	_branch_code
id
781	70lHcCNw	immature gamma-delta T cell	CL:0000799	None	immature gamma-delta T lymphocyte\|immature gam...	A Gamma-Delta T Cell That Has An Immature Phen...	1	32	None	2025-01-12 14:03:57.090785+00:00	1	None	1
782	3W6NKGpW	mature gamma-delta T cell	CL:0000800	None	mature gamma-delta T-lymphocyte\|mature gamma-d...	A Gamma-Delta T Cell That Has A Mature Phenoty...	1	32	None	2025-01-12 14:03:57.093882+00:00	1	None	1
1465	26icgrTr	gamma-delta thymocyte	CL:0002405	None	gd thymocyte\|gammadelta thymocyte	A Post-Natal Thymocyte Expressing Components O...	1	32	None	2025-01-12 14:03:57.171465+00:00	1	None	1
2921	5XXsI4tm	cycling gamma-delta T cell	CL:4033072	None	proliferating gamma-delta T cell	A(N) Gamma-Delta T Cell That Is Cycling.	1	32	None	2025-01-12 14:03:57.344569+00:00	1	None	1

It is also possible to recursively query parents or children, getting direct parents (children), their parents, and so forth.

gdt_cell.query_parents().df()

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	uid	name	ontology_id	abbr	synonyms	description	space_id	source_id	run_id	created_at	created_by_id	aux	_branch_code
id
83	22LvKd01	T cell	CL:0000084	None	T-cell\|T-lymphocyte\|T lymphocyte	A Type Of Lymphocyte Whose Defining Characteri...	1	32	None	2025-01-12 14:03:56.940242+00:00	1	None	1
822	2Jgr5Xx4	mononuclear cell	CL:0000842	None	mononuclear leukocyte	A Leukocyte With A Single Non-Segmented Nucleu...	1	32	None	2025-01-12 14:03:57.096776+00:00	1	None	1
214	2K93w3xO	motile cell	CL:0000219	None	None	A Cell That Moves By Its Own Activities.	1	32	None	2025-01-12 14:03:57.028514+00:00	1	None	1
221	2cXC7cgF	single nucleate cell	CL:0000226	None	None	A Cell With A Single Nucleus.	1	32	None	2025-01-12 14:03:57.029047+00:00	1	None	1
721	3VEAlFdi	leukocyte	CL:0000738	None	white blood cell\|leucocyte	An Achromatic Cell Of The Myeloid Or Lymphoid ...	1	32	None	2025-01-12 14:03:57.086551+00:00	1	None	1
967	4Ilrnj9U	hematopoietic cell	CL:0000988	None	haematopoietic cell\|hemopoietic cell\|haemopoie...	A Cell Of A Hematopoietic Lineage.	1	32	None	2025-01-12 14:03:57.113585+00:00	1	None	1
250	4WnpvUTH	eukaryotic cell	CL:0000255	None	None	Any Cell That Only Exists In Eukaryota.	1	32	None	2025-01-12 14:03:57.031133+00:00	1	None	1
1	4bKGljt0	cell	CL:0000000	None	None	A Material Entity Of Anatomical Origin (Part O...	1	32	None	2025-01-12 14:03:56.929868+00:00	1	None	1
529	X6c7osZ5	lymphocyte	CL:0000542	None	None	A Lymphocyte Is A Leukocyte Commonly Found In ...	1	32	None	2025-01-12 14:03:57.063364+00:00	1	None	1
1303	u3sr1Gdf	nucleate cell	CL:0002242	None	None	A Cell Containing At Least One Nucleus.	1	32	None	2025-01-12 14:03:57.153504+00:00	1	None	1

gdt_cell.query_children().df()

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	uid	name	ontology_id	abbr	synonyms	description	space_id	source_id	run_id	created_at	created_by_id	aux	_branch_code
id
1190	1DEERh4L	CD27-negative gamma-delta T cell	CL:0002125	None	gammadelta-17 cells	A Circulating Gamma-Delta T Cell That Expresse...	1	32	None	2025-01-12 14:03:57.139025+00:00	1	None	1
1572	1jlK4jJ9	Vgamma5-positive CD8alpha alpha positive gamma...	CL:0002513	None	tgd.vg5+.IEL	A Cd8Alpha Alpha Positive Gamma-Delta Intraepi...	1	32	None	2025-01-12 14:03:57.185761+00:00	1	None	1
785	1mNzVotO	CD4-negative CD8-negative gamma-delta intraepi...	CL:0000803	None	CD4-positive, gamma-delta intraepithelial T-ce...	A Gamma-Delta Intraepithelial T Cell That Has ...	1	32	None	2025-01-12 14:03:57.094127+00:00	1	None	1
895	1tYOPZxH	dendritic epidermal T cell	CL:0000916	None	dendritic epidermal T lymphocyte\|DETC\|dendriti...	A Mature Gamma-Delta T Cell Located In The Epi...	1	32	None	2025-01-12 14:03:57.105152+00:00	1	None	1
1465	26icgrTr	gamma-delta thymocyte	CL:0002405	None	gd thymocyte\|gammadelta thymocyte	A Post-Natal Thymocyte Expressing Components O...	1	32	None	2025-01-12 14:03:57.171465+00:00	1	None	1
1475	2SYX59uO	immature Vgamma1.1-positive, Vdelta6.3-positiv...	CL:0002415	None	immature Vg1.1+Vd6.3+ T cell	A Vgamma1.1-Positive, Vdelta6.3-Positive Thymo...	1	32	None	2025-01-12 14:03:57.172171+00:00	1	None	1
783	2xXcHDQq	gamma-delta intraepithelial T cell	CL:0000801	None	gamma-delta intraepithelial T-cell\|gamma-delta...	A Mature Gamma-Delta T Cell That Is Found In T...	1	32	None	2025-01-12 14:03:57.093979+00:00	1	None	1
1468	3ABJ1l1O	immature Vgamma2-negative thymocyte	CL:0002408	None	None	A Double Negative Post-Natal Thymocyte That Ha...	1	32	None	2025-01-12 14:03:57.171676+00:00	1	None	1
782	3W6NKGpW	mature gamma-delta T cell	CL:0000800	None	mature gamma-delta T-lymphocyte\|mature gamma-d...	A Gamma-Delta T Cell That Has A Mature Phenoty...	1	32	None	2025-01-12 14:03:57.093882+00:00	1	None	1
1191	3efemme8	CD25-positive, CD27-positive immature gamma-de...	CL:0002126	None	None	A Cd25-Positive, Cd27-Positive Immature Gamma-...	1	32	None	2025-01-12 14:03:57.139094+00:00	1	None	1
1473	4cYNDr25	mature Vgamma1.1-positive, Vdelta6.3-negative ...	CL:0002413	None	None	A Vgamma1.1-Positive, Vdelta6.3-Negative Thymo...	1	32	None	2025-01-12 14:03:57.172030+00:00	1	None	1
1466	4hrSce5T	immature Vgamma2-positive thymocyte	CL:0002406	None	None	A Double Negative Post-Natal Thymocyte That Ha...	1	32	None	2025-01-12 14:03:57.171536+00:00	1	None	1
2921	5XXsI4tm	cycling gamma-delta T cell	CL:4033072	None	proliferating gamma-delta T cell	A(N) Gamma-Delta T Cell That Is Cycling.	1	32	None	2025-01-12 14:03:57.344569+00:00	1	None	1
1474	5pDjyjfF	immature Vgamma1.1-positive, Vdelta6.3-negativ...	CL:0002414	None	None	A Vgamma1.1-Positive, Vdelta6.3-Negative Thymo...	1	32	None	2025-01-12 14:03:57.172101+00:00	1	None	1
1471	64PCjpkJ	Vgamma1.1-positive, Vdelta6.3-negative thymocyte	CL:0002411	None	Vg1.1-positive, Vd6.3-negative T cell	A Gamma-Delta Receptor That Expresses Vgamma1....	1	32	None	2025-01-12 14:03:57.171886+00:00	1	None	1
1476	6JxpxGgM	mature Vgamma1.1-positive, Vdelta6.3-positive ...	CL:0002416	None	mature Vg1.1+Vd6.3+ T cell	A Vgamma1.1-Positive, Vdelta6.3-Positive Thymo...	1	32	None	2025-01-12 14:03:57.172242+00:00	1	None	1
1469	6RBJq86b	mature Vgamma2-negative thymocyte	CL:0002409	None	Vgamma2-negative	A Thymocyte That Has A T Cell Receptor Consist...	1	32	None	2025-01-12 14:03:57.171746+00:00	1	None	1
784	6fdlvmJ3	CD8-alpha alpha positive, gamma-delta intraepi...	CL:0000802	None	CD8-positive, gamma-delta intraepithelial T-ly...	A Gamma-Delta Intraepithelial T Cell That Has ...	1	32	None	2025-01-12 14:03:57.094054+00:00	1	None	1
1472	6vYlL7zk	Vgamma1.1-positive, Vdelta6.3-positive thymocyte	CL:0002412	None	Vg1.1+Vd6.3+ T cell	A Gamma-Delta Receptor That Expresses Vgamma1....	1	32	None	2025-01-12 14:03:57.171959+00:00	1	None	1
781	70lHcCNw	immature gamma-delta T cell	CL:0000799	None	immature gamma-delta T lymphocyte\|immature gam...	A Gamma-Delta T Cell That Has An Immature Phen...	1	32	None	2025-01-12 14:03:57.090785+00:00	1	None	1
1467	76CEFg3A	mature Vgamma2-positive thymocyte	CL:0002407	None	Vgamma2-positive	A Thymocyte That Has A T Cell Receptor Consist...	1	32	None	2025-01-12 14:03:57.171606+00:00	1	None	1
1189	7MDv71IV	CD27-positive gamma-delta T cell	CL:0002124	None	gammadelta27-positive\|gd27-positive	A Circulating Gamma-Delta T Cell That Is Cd27-...	1	32	None	2025-01-12 14:03:57.138955+00:00	1	None	1
1573	E2koIf0l	Vgamma5-negative CD8alpha alpha positive gamma...	CL:0002514	None	tgd.vg5-.IEL	A Cd8Alpha Alpha Positive Gamma-Delta Intraepi...	1	32	None	2025-01-12 14:03:57.185831+00:00	1	None	1

You can construct custom hierarchies of records:

# register a new cell type
my_celltype = bt.CellType(name="my new T-cell subtype").save()
# specify "gamma-delta T cell" as a parent
my_celltype.parents.add(gdt_cell)

# visualize hierarchy
gdt_cell.view_parents(distance=2, with_children=True)

_images/51eb98c9316f1423c5b0161ea9f9de70d0902cf75e644f8b690c3092240f704b.svg

Create records from values¶

When accessing datasets, one often encounters bulk references to entities that might be corrupted or standardized using different standardization schemes.

Let’s consider an example based on an AnnData object, in the cell_type annotations of this AnnData object, we find 4 references to cell types:

adata = ln.core.datasets.anndata_with_obs()
adata.obs.cell_type.value_counts()

We’d like to load the corresponding records in our in-house registry to annotate a dataset.

To this end, you’ll typically use from_values, which will both validate & retrieve records that match the values.

cell_types = bt.CellType.from_values(adata.obs.cell_type)
cell_types

Logging informed us that 3 cell types were validated. Since we loaded these records at the same time, we could readily use them to annotate a dataset.

Alternatively, we can retrieve records based on ontology ids:

adata.obs.cell_type_id.unique().tolist()

bt.CellType.from_values(adata.obs.cell_type_id, field=bt.CellType.ontology_id)

Validate & standardize¶

Simple validation of an iterable of values works like so:

bt.CellType.validate(["fat cell", "blood forming stem cell"])

Because these values don’t comply with the registry, they’re not validated!

You can easily convert these values to validated standardized names based on synonyms like so:

bt.CellType.standardize(["fat cell", "blood forming stem cell"])

Alternatively, you can use .from_values(), which will only ever return validated records and automatically standardize under-the-hood:

bt.CellType.from_values(["fat cell", "blood forming stem cell"])

If you are now sure what to do, use .inspect() to get instructions:

bt.CellType.inspect(["fat cell", "blood forming stem cell"]);

We can also add new synonyms to a record like so:

hsc_record.add_synonym("HSC")

And when we encounter this synonym as a value, it will now be standardized using synonyms-lookup, and mapped on the correct registry record:

bt.CellType.standardize(["HSC"])

A special synonym is .abbr (short for abbreviation), which has its own field and can be assigned via:

hsc_record.set_abbr("HSC")

You can create a lookup object from the .abbr field:

cell_types = bt.CellType.lookup("abbr")
hsc = cell_types.hsc
hsc

The same workflow works for all of bionty’s registries.

Manage registries across organisms¶

Several registries are organism-aware (has a .organism field), for instance, Gene.

In this case, API calls that interact with multi-organism registries require an organism argument when there’s ambiguity.

For instance, when validating gene symbols:

bt.Gene.validate(["TCF7", "ABC1"], organism="human")

In contrary, working with Ensembl Gene IDs doesn’t require passing organism, as there’s no ambiguity:

bt.Gene.validate(
    ["ENSG00000000419", "ENSMUSG00002076988"], field=bt.Gene.ensembl_gene_id
)

array([ True,  True])

When working with the same organism throughout your analysis/workflow, you can omit the organism argument by configuring it globally:

bt.settings.organism = "mouse"
bt.Gene.from_source(symbol="Ap5b1")

Gene(uid='3b8mHb0MRal4', symbol='Ap5b1', ensembl_gene_id='ENSMUSG00000049562', ncbi_gene_ids='381201', biotype='protein_coding', synonyms='Gm962', description='adaptor-related protein complex 5, beta 1 subunit ', created_by_id=1, space_id=1, source_id=15, organism_id=2, created_at=2025-01-12 14:06:12 UTC)

Track underlying ontology source versions¶

Under-the-hood, source ontology versions are automatically tracked for each registry:

bt.Source.filter(currently_used=True).df()

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	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	33TU	bionty.Organism	vertebrates	ensembl	False	True	Ensembl	https://ftp.ensembl.org/pub/release-112/specie...	0ec37e77f4bc2d0b0b47c6c62b9f122d	https://www.ensembl.org	1	None	release-112	None	2025-01-12 14:03:47.555530+00:00	1	None	1
6	6bbV	bionty.Organism	bacteria	ensembl	False	True	Ensembl	https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte...	ee28510ed5586ea7ab4495717c96efc8	https://www.ensembl.org	1	None	release-57	None	2025-01-12 14:03:47.556061+00:00	1	None	1
7	6s9n	bionty.Organism	fungi	ensembl	False	True	Ensembl	http://ftp.ensemblgenomes.org/pub/fungi/releas...	dbcde58f4396ab8b2480f7fe9f83df8a	https://www.ensembl.org	1	None	release-57	None	2025-01-12 14:03:47.556148+00:00	1	None	1
8	2PmT	bionty.Organism	metazoa	ensembl	False	True	Ensembl	http://ftp.ensemblgenomes.org/pub/metazoa/rele...	424636a574fec078a61cbdddb05f9132	https://www.ensembl.org	1	None	release-57	None	2025-01-12 14:03:47.556237+00:00	1	None	1
9	7GPH	bionty.Organism	plants	ensembl	False	True	Ensembl	https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant...	eadaa1f3e527e4c3940c90c7fa5c8bf4	https://www.ensembl.org	1	None	release-57	None	2025-01-12 14:03:47.556325+00:00	1	None	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	1	None	2023-06-20	None	2025-01-12 14:03:47.556427+00:00	1	None	1
11	4UGN	bionty.Gene	human	ensembl	False	True	Ensembl	s3://bionty-assets/df_human__ensembl__release-...	4ccda4d88720a326737376c534e8446b	https://www.ensembl.org	1	None	release-112	None	2025-01-12 14:03:47.556519+00:00	1	None	1
15	4r4f	bionty.Gene	mouse	ensembl	False	True	Ensembl	s3://bionty-assets/df_mouse__ensembl__release-...	519cf7b8acc3c948274f66f3155a3210	https://www.ensembl.org	1	None	release-112	None	2025-01-12 14:03:47.556871+00:00	1	None	1
19	4RPA	bionty.Gene	saccharomyces cerevisiae	ensembl	False	True	Ensembl	s3://bionty-assets/df_saccharomyces cerevisiae...	11775126b101233525a0a9e2dd64edae	https://www.ensembl.org	1	None	release-112	None	2025-01-12 14:03:47.557220+00:00	1	None	1
22	3EYy	bionty.Protein	human	uniprot	False	True	Uniprot	s3://bionty-assets/df_human__uniprot__2024-03_...	b5b9e7645065b4b3187114f07e3f402f	https://www.uniprot.org	1	None	2024-03	None	2025-01-12 14:03:47.557494+00:00	1	None	1
25	01RW	bionty.Protein	mouse	uniprot	False	True	Uniprot	s3://bionty-assets/df_mouse__uniprot__2024-03_...	b1b6a196eb853088d36198d8e3749ec4	https://www.uniprot.org	1	None	2024-03	None	2025-01-12 14:03:47.557758+00:00	1	None	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	1	None	2.0	None	2025-01-12 14:03:47.558027+00:00	1	None	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	1	None	2.0	None	2025-01-12 14:03:47.558115+00:00	1	None	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	1	None	2022-03-21	None	2025-01-12 14:03:47.558202+00:00	1	None	1
32	3Uw2	bionty.CellType	all	cl	True	True	Cell Ontology	http://purl.obolibrary.org/obo/cl/releases/202...		https://obophenotype.github.io/cell-ontology	1	None	2024-08-16	None	2025-01-12 14:03:47.558378+00:00	1	None	1
41	MUtA	bionty.Tissue	all	uberon	False	True	Uberon multi-species anatomy ontology	http://purl.obolibrary.org/obo/uberon/releases...		http://obophenotype.github.io/uberon	1	None	2024-08-07	None	2025-01-12 14:03:47.559205+00:00	1	None	1
50	4a3e	bionty.Disease	all	mondo	False	True	Mondo Disease Ontology	http://purl.obolibrary.org/obo/mondo/releases/...		https://mondo.monarchinitiative.org	1	None	2024-08-06	None	2025-01-12 14:03:47.560008+00:00	1	None	1
59	4ksw	bionty.Disease	human	doid	False	True	Human Disease Ontology	http://purl.obolibrary.org/obo/doid/releases/2...	bbefd72247d638edfcd31ec699947407	https://disease-ontology.org	1	None	2024-05-29	None	2025-01-12 14:03:47.564309+00:00	1	None	1
67	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	1	None	3.70.0	None	2025-01-12 14:03:47.565002+00:00	1	None	1
74	48fB	bionty.Phenotype	human	hp	False	True	Human Phenotype Ontology	https://github.com/obophenotype/human-phenotyp...	e0f2e534eb2ad44a4d45573ef27b508f	https://hpo.jax.org	1	None	2024-04-26	None	2025-01-12 14:03:47.565602+00:00	1	None	1
79	4t7Q	bionty.Phenotype	mammalian	mp	False	True	Mammalian Phenotype Ontology	https://github.com/mgijax/mammalian-phenotype-...	795d8378fe48ec13b41d01a86dd1c86c	https://github.com/mgijax/mammalian-phenotype-...	1	None	2024-06-18	None	2025-01-12 14:03:47.566017+00:00	1	None	1
82	sqPX	bionty.Phenotype	zebrafish	zp	False	True	Zebrafish Phenotype Ontology	https://github.com/obophenotype/zebrafish-phen...	2231ebaa95becf8ff34a33c95a8d4350	https://github.com/obophenotype/zebrafish-phen...	1	None	2024-04-18	None	2025-01-12 14:03:47.566265+00:00	1	None	1
86	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	1	None	2024-03-28	None	2025-01-12 14:03:47.566608+00:00	1	None	1
88	7Ent	bionty.Pathway	all	go	False	True	Gene Ontology	https://data.bioontology.org/ontologies/GO/sub...	7fa7ade5e3e26eab3959a7e4bc89ad4f	http://geneontology.org	1	None	2024-06-17	None	2025-01-12 14:03:47.566773+00:00	1	None	1
93	3rm9	BFXPipeline	all	lamin	False	True	Bioinformatics Pipeline	s3://bionty-assets/df_all__lamin__1.0.0__BFXpi...		https://lamin.ai	1	None	1.0.0	None	2025-01-12 14:03:47.567187+00:00	1	None	1
94	ugaI	Drug	all	dron	False	True	Drug Ontology	https://data.bioontology.org/ontologies/DRON/s...		https://bioportal.bioontology.org/ontologies/DRON	1	None	2024-08-05	None	2025-01-12 14:03:47.567270+00:00	1	None	1
98	1GbF	bionty.DevelopmentalStage	human	hsapdv	False	True	Human Developmental Stages	https://github.com/obophenotype/developmental-...		https://github.com/obophenotype/developmental-...	1	None	2024-05-28	None	2025-01-12 14:03:47.567617+00:00	1	None	1
100	10va	bionty.DevelopmentalStage	mouse	mmusdv	False	True	Mouse Developmental Stages	https://github.com/obophenotype/developmental-...		https://github.com/obophenotype/developmental-...	1	None	2024-05-28	None	2025-01-12 14:03:47.567782+00:00	1	None	1
102	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	1	None	3.0	None	2025-01-12 14:03:47.567953+00:00	1	None	1
103	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...	1	None	2023-09	None	2025-01-12 14:03:47.568038+00:00	1	None	1

Each record is linked to a versioned public source (if it was created from public):

hepatocyte = bt.CellType.get(name="hepatocyte")
hepatocyte.source

Create records from specific source¶

By default, new records are imported or created from the "currently_used" public sources which are configured during the instance initialization, e.g.:

bt.Source.filter(entity="bionty.Phenotype", currently_used=True).df()

Show code cell output 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
74	48fB	bionty.Phenotype	human	hp	False	True	Human Phenotype Ontology	https://github.com/obophenotype/human-phenotyp...	e0f2e534eb2ad44a4d45573ef27b508f	https://hpo.jax.org	1	None	2024-04-26	None	2025-01-12 14:03:47.565602+00:00	1	None	1
79	4t7Q	bionty.Phenotype	mammalian	mp	False	True	Mammalian Phenotype Ontology	https://github.com/mgijax/mammalian-phenotype-...	795d8378fe48ec13b41d01a86dd1c86c	https://github.com/mgijax/mammalian-phenotype-...	1	None	2024-06-18	None	2025-01-12 14:03:47.566017+00:00	1	None	1
82	sqPX	bionty.Phenotype	zebrafish	zp	False	True	Zebrafish Phenotype Ontology	https://github.com/obophenotype/zebrafish-phen...	2231ebaa95becf8ff34a33c95a8d4350	https://github.com/obophenotype/zebrafish-phen...	1	None	2024-04-18	None	2025-01-12 14:03:47.566265+00:00	1	None	1
86	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	1	None	2024-03-28	None	2025-01-12 14:03:47.566608+00:00	1	None	1

Sometimes, the default source doesn’t contain the ontology term you are looking for.

You can then specify to create a record from a non-default source. For instance, we can use the ncbitaxon ontology:

source = bt.Source.get(entity="bionty.Organism", name="ncbitaxon")
source

Source(uid='4tsk', entity='bionty.Organism', organism='all', name='ncbitaxon', version='2023-06-20', in_db=False, currently_used=True, description='NCBItaxon Ontology', url='s3://bionty-assets/df_all__ncbitaxon__2023-06-20__Organism.parquet', md5='00d97ba65627f1cd65636d2df22ea76c', source_website='https://github.com/obophenotype/ncbitaxon', created_by_id=1, space_id=1, created_at=2025-01-12 14:03:47 UTC)

# validate against the NCBI Taxonomy
bt.Organism.validate(
    ["iris setosa", "iris versicolor", "iris virginica"], source=source
)

records = bt.Organism.from_values(
    ["iris setosa", "iris versicolor", "iris virginica"], source=source
)

# since we didn't seed the Organism registry with the NCBITaxon public ontology
# we need to save the records to the database
ln.save(records)

# now we can query a iris organism and view its parents and children
iris = bt.Organism.get(name="iris")
iris.view_parents(with_children=True)