Manage biological registries¶

Registries manage the formalized knowledge & experimental design that anchor dry & wetlab work.

In LaminDB, registries are standard SQL tables, equipped with mechanisms that avoid typos & duplicated data.

In addition, LaminDB makes it easy to import records from public biological ontologies, based on plug-in bionty.

In this notebook, you’ll see how to manage an in-house ontology anchored in public knowledge.

(If you also manage experimental design through registries, you can access all metadata through one API and store it in one simple SQL database.)

Setup¶

Let us create an instance that has bionty mounted, which extends to include biological registries:

!lamin init --storage ./test-registries --schema bionty

import lamindb as ln
import bionty as bt

ln.connect("test-registries")
ln.settings.verbosity = "info"

💡 connected lamindb: testuser1/test-registries

Let’s pre-populate the cell type registry with a few records:

bt.Organism.from_public(name="human").save()
bt.CellType.from_public(name="T cell").save()
bt.CellType(name="my T cell subtype").save()

Show code cell output Hide code cell output

✅ created 1 Organism record from Bionty matching name: 'human'

✅ created 1 CellType record from Bionty matching name: 'T cell'

💡 also saving parents of CellType(uid='22LvKd01', name='T cell', ontology_id='CL:0000084', synonyms='T-lymphocyte|T lymphocyte|T-cell', description='A Type Of Lymphocyte Whose Defining Characteristic Is The Expression Of A T Cell Receptor Complex.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:45 UTC')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000542'

❗ now recursing through parents: this only happens once, but is much slower than bulk saving

💡 also saving parents of CellType(uid='X6c7osZ5', name='lymphocyte', ontology_id='CL:0000542', description='A Lymphocyte Is A Leukocyte Commonly Found In The Blood And Lymph That Has The Characteristics Of A Large Nucleus, A Neutral Staining Cytoplasm, And Prominent Heterochromatin.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:45 UTC')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000842'

💡 also saving parents of CellType(uid='2Jgr5Xx4', name='mononuclear cell', ontology_id='CL:0000842', synonyms='mononuclear leukocyte', description='A Leukocyte With A Single Non-Segmented Nucleus In The Mature Form.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:46 UTC')

✅ created 2 CellType records from Bionty matching ontology_id: 'CL:0000738', 'CL:0000226'

💡 also saving parents of CellType(uid='3VEAlFdi', name='leukocyte', ontology_id='CL:0000738', synonyms='white blood cell|leucocyte', description='An Achromatic Cell Of The Myeloid Or Lymphoid Lineages Capable Of Ameboid Movement, Found In Blood Or Other Tissue.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:46 UTC')

✅ created 4 CellType records from Bionty matching ontology_id: 'CL:0000255', 'CL:0000219', 'CL:0002242', 'CL:0000988'

💡 also saving parents of CellType(uid='4WnpvUTH', name='eukaryotic cell', ontology_id='CL:0000255', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:47 UTC')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000000'

💡 also saving parents of CellType(uid='2K93w3xO', name='motile cell', ontology_id='CL:0000219', description='A Cell That Moves By Its Own Activities.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:47 UTC')

💡 also saving parents of CellType(uid='u3sr1Gdf', name='nucleate cell', ontology_id='CL:0002242', description='A Cell Containing At Least One Nucleus.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:47 UTC')

💡 also saving parents of CellType(uid='4Ilrnj9U', name='hematopoietic cell', ontology_id='CL:0000988', synonyms='haematopoietic cell|hemopoietic cell|haemopoietic cell', description='A Cell Of A Hematopoietic Lineage.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:47 UTC')

💡 also saving parents of CellType(uid='2cXC7cgF', name='single nucleate cell', ontology_id='CL:0000226', description='A Cell With A Single Nucleus.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:46 UTC')

❗ records with similar names exist! did you mean to load one of them?

	uid	name	ontology_id	abbr	synonyms	description	public_source_id	run_id	created_by_id	updated_at
id
1	22LvKd01	T cell	CL:0000084	None	T-lymphocyte\|T lymphocyte\|T-cell	A Type Of Lymphocyte Whose Defining Characteri...	29	None	1	2024-05-25 15:24:45.203755+00:00
2	X6c7osZ5	lymphocyte	CL:0000542	None	None	A Lymphocyte Is A Leukocyte Commonly Found In ...	29	None	1	2024-05-25 15:24:45.768171+00:00
3	2Jgr5Xx4	mononuclear cell	CL:0000842	None	mononuclear leukocyte	A Leukocyte With A Single Non-Segmented Nucleu...	29	None	1	2024-05-25 15:24:46.249787+00:00
4	3VEAlFdi	leukocyte	CL:0000738	None	white blood cell\|leucocyte	An Achromatic Cell Of The Myeloid Or Lymphoid ...	29	None	1	2024-05-25 15:24:46.811211+00:00
5	2cXC7cgF	single nucleate cell	CL:0000226	None	None	A Cell With A Single Nucleus.	29	None	1	2024-05-25 15:24:46.811366+00:00

Access records in public ontologies¶

We start with a public ontology for cell types.

.public() gives you access to the ReferenceTable, a class for accessing public ontologies.

ReferenceTable provides simple access to standardized public ontologies that Lamin hosts for reliable and performant access. For most ReferenceTable objects, you can access the underlying ontology through Pronto.

Let’s create a ReferenceTable object:

public = bt.CellType.public()

public

PublicOntology
Entity: CellType
Organism: all
Source: cl, 2024-02-13
#terms: 2918

We can use it to search the public ontology against cell types:

public.search("gamma delta T cell").head(3)

Show code cell output Hide code cell output

	ontology_id	definition	synonyms	parents	__ratio__
name
gamma-delta T cell	CL:0000798	A T Cell That Expresses A Gamma-Delta T Cell R...	gammadelta T cell\|gamma-delta T-cell\|gamma-del...	[CL:0000084]	100.000000
CD27-negative gamma-delta T cell	CL:0002125	A Circulating Gamma-Delta T Cell That Expresse...	gammadelta-17 cells	[CL:0000800]	86.486486
mature gamma-delta T cell	CL:0000800	A Gamma-Delta T Cell That Has A Mature Phenoty...	mature gamma-delta T-lymphocyte\|mature gamma-d...	[CL:0002419, CL:0000798]	83.720930

And we can also use it to look up cell types with auto-complete:

lookup = public.lookup()
lookup.gamma_delta_t_cell

Create records in in-house ontologies¶

We can now create a record for our in-house SQL registry by passing the result of the lookup in the public ontology to the CellType constructor:

gdt_cell = bt.CellType(lookup.gamma_delta_t_cell)
gdt_cell

Show code cell output Hide code cell output

❗ records with similar names exist! did you mean to load one of them?

	uid	name	ontology_id	abbr	synonyms	description	public_source_id	run_id	created_by_id	updated_at
id
1	22LvKd01	T cell	CL:0000084	None	T-lymphocyte\|T lymphocyte\|T-cell	A Type Of Lymphocyte Whose Defining Characteri...	29	None	1	2024-05-25 15:24:45.203755+00:00
3	2Jgr5Xx4	mononuclear cell	CL:0000842	None	mononuclear leukocyte	A Leukocyte With A Single Non-Segmented Nucleu...	29	None	1	2024-05-25 15:24:46.249787+00:00
4	3VEAlFdi	leukocyte	CL:0000738	None	white blood cell\|leucocyte	An Achromatic Cell Of The Myeloid Or Lymphoid ...	29	None	1	2024-05-25 15:24:46.811211+00:00
5	2cXC7cgF	single nucleate cell	CL:0000226	None	None	A Cell With A Single Nucleus.	29	None	1	2024-05-25 15:24:46.811366+00:00
6	4WnpvUTH	eukaryotic cell	CL:0000255	None	None	None	29	None	1	2024-05-25 15:24:47.374869+00:00

CellType(uid='1HuNn2EP', name='gamma-delta T cell', ontology_id='CL:0000798', synonyms='gammadelta T cell|gamma-delta T-cell|gamma-delta T lymphocyte|gamma-delta T-lymphocyte', created_by_id=1, public_source_id=29)

(Alternatively, we could construct the gamma delta T cell via from_public(), which is synonyms-aware.)

bt.CellType.from_public(ontology_id="CL:0000798")

When we save this record to the registry, logging informs us that we’re also saving parent ontological terms:

gdt_cell.save()

View the ontological hierarchy:

gdt_cell.view_parents()

_images/abfd2e62cbde35910b09380a9851547aff2cf029c2a35a8e0286f57741ad7ea4.svg

Or access the parents directly:

gdt_cell.parents.df()

Show code cell output Hide code cell output

	uid	name	ontology_id	abbr	synonyms	description	public_source_id	run_id	created_by_id	updated_at
id
1	22LvKd01	T cell	CL:0000084	None	T-lymphocyte\|T lymphocyte\|T-cell	A Type Of Lymphocyte Whose Defining Characteri...	29	None	1	2024-05-25 15:24:45.203755+00:00

You can construct custom hierarchies of terms by specifying parents:

my_celltype = bt.CellType.filter(name="my T cell subtype").one()
my_celltype.parents.add(gdt_cell)

gdt_cell.view_parents(distance=2, with_children=True)

_images/d489b6fee84c2d1771a61acdca4a5302fdb608708cf47967f9f25b7e2d739a40.svg

This cell type and all its parents can now be queried & searched in the registry using bionty.CellType.filter and bionty.CellType.search.

Load records for values in data sources¶

When accessing data sources, 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 ontology to annotate a dataset.

To this end, you’ll typically use from_values, which will both validate & load 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 create entries 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)

If we’re happy with cell_types records, we save them to the registry:

ln.save(cell_types)

Show code cell output Hide code cell output

❗ now recursing through parents: this only happens once, but is much slower than bulk saving

💡 also saving parents of 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, public_source_id=29, updated_at='2024-05-25 15:24:51 UTC')

✅ created 3 CellType records from Bionty matching ontology_id: 'CL:0008001', 'CL:0000723', 'CL:0011026'

💡 also saving parents of CellType(uid='5M0BT5FC', name='hematopoietic precursor cell', ontology_id='CL:0008001', description='Any Hematopoietic Cell That Is A Precursor Of Some Other Hematopoietic Cell Type.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:51 UTC')

💡 also saving parents of CellType(uid='2Dvf9ly5', name='somatic stem cell', ontology_id='CL:0000723', description='A Stem Cell That Can Give Rise To Cell Types Of The Body Other Than Those Of The Germ-Line.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:51 UTC')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000034'

💡 also saving parents of CellType(uid='jxDD8ajD', name='stem cell', ontology_id='CL:0000034', synonyms='animal stem cell', description='A Relatively Undifferentiated Cell That Retains The Ability To Divide And Proliferate Throughout Life To Provide Progenitor Cells That Can Differentiate Into Specialized Cells.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:52 UTC')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0011115'

💡 also saving parents of CellType(uid='5J0ndawv', name='precursor cell', ontology_id='CL:0011115', description='A Cell That, By Division Or Terminal Differentiation, Can Give Rise To Other Cell Types.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:52 UTC')

💡 also saving parents of CellType(uid='5fX4hLCd', name='progenitor cell', ontology_id='CL:0011026', description='A Precursor Cell That Has A Tendency To Differentiate Into A Specific Type Of Cell. They Are Descendants Of Stem Cells, Only They Are More Constrained In Their Differentiation Potential Or Capacity For Self-Renewal, And Are Often More Limited In Both Senses.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:51 UTC')

💡 also saving parents of CellType(uid='7hggmgo1', name='hepatocyte', ontology_id='CL:0000182', description='The Main Structural Component Of The Liver. They Are Specialized Epithelial Cells That Are Organized Into Interconnected Plates Called Lobules. Majority Of Cell Population Of Liver, Polygonal In Shape, Arranged In Plates Or Trabeculae Between Sinusoids; May Have Single Nucleus Or Binucleated.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:51 UTC')

✅ created 2 CellType records from Bionty matching ontology_id: 'CL:0000066', 'CL:0000417'

💡 also saving parents of CellType(uid='68LNvDH7', name='epithelial cell', ontology_id='CL:0000066', synonyms='epitheliocyte', description='A Cell That Is Usually Found In A Two-Dimensional Sheet With A Free Surface. The Cell Has A Cytoskeleton That Allows For Tight Cell To Cell Contact And For Cell Polarity Where Apical Part Is Directed Towards The Lumen And The Basal Part To The Basal Lamina.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:53 UTC')

💡 also saving parents of CellType(uid='M3aRHlL9', name='endopolyploid cell', ontology_id='CL:0000417', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:53 UTC')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000412'

💡 also saving parents of CellType(uid='1035XQsH', name='polyploid cell', ontology_id='CL:0000412', description='A Cell That Contains More Than Two Haploid Sets Of Chromosomes.', created_by_id=1, public_source_id=29, updated_at='2024-05-25 15:24:53 UTC')

Now, let’s inspect our in-house registry:

bt.CellType.df()

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	uid	name	ontology_id	abbr	synonyms	description	public_source_id	run_id	created_by_id	updated_at
id
22	1035XQsH	polyploid cell	CL:0000412	None	None	A Cell That Contains More Than Two Haploid Set...	29.0	None	1	2024-05-25 15:24:53.804293+00:00
21	M3aRHlL9	endopolyploid cell	CL:0000417	None	None	None	29.0	None	1	2024-05-25 15:24:53.205099+00:00
20	68LNvDH7	epithelial cell	CL:0000066	None	epitheliocyte	A Cell That Is Usually Found In A Two-Dimensio...	29.0	None	1	2024-05-25 15:24:53.204950+00:00
19	5J0ndawv	precursor cell	CL:0011115	None	None	A Cell That, By Division Or Terminal Different...	29.0	None	1	2024-05-25 15:24:52.701730+00:00
18	jxDD8ajD	stem cell	CL:0000034	None	animal stem cell	A Relatively Undifferentiated Cell That Retain...	29.0	None	1	2024-05-25 15:24:52.090949+00:00
17	5fX4hLCd	progenitor cell	CL:0011026	None	None	A Precursor Cell That Has A Tendency To Differ...	29.0	None	1	2024-05-25 15:24:51.609438+00:00
16	2Dvf9ly5	somatic stem cell	CL:0000723	None	None	A Stem Cell That Can Give Rise To Cell Types O...	29.0	None	1	2024-05-25 15:24:51.609277+00:00
15	5M0BT5FC	hematopoietic precursor cell	CL:0008001	None	None	Any Hematopoietic Cell That Is A Precursor Of ...	29.0	None	1	2024-05-25 15:24:51.609133+00:00
14	7hggmgo1	hepatocyte	CL:0000182	None	None	The Main Structural Component Of The Liver. Th...	29.0	None	1	2024-05-25 15:24:51.012960+00:00
13	2U8xapxu	hematopoietic stem cell	CL:0000037	None	hemopoietic stem cell\|blood forming stem cell	A Stem Cell From Which All Cells Of The Lympho...	29.0	None	1	2024-05-25 15:24:51.012800+00:00
12	1HuNn2EP	gamma-delta T cell	CL:0000798	None	gammadelta T cell\|gamma-delta T-cell\|gamma-del...	None	29.0	None	1	2024-05-25 15:24:49.228238+00:00
11	2eNGzkOc	my T cell subtype	None	None	None	None	NaN	None	1	2024-05-25 15:24:47.938469+00:00
10	4bKGljt0	cell	CL:0000000	None	None	A Material Entity Of Anatomical Origin (Part O...	29.0	None	1	2024-05-25 15:24:47.836592+00:00
9	4Ilrnj9U	hematopoietic cell	CL:0000988	None	haematopoietic cell\|hemopoietic cell\|haemopoie...	A Cell Of A Hematopoietic Lineage.	29.0	None	1	2024-05-25 15:24:47.375295+00:00
8	u3sr1Gdf	nucleate cell	CL:0002242	None	None	A Cell Containing At Least One Nucleus.	29.0	None	1	2024-05-25 15:24:47.375159+00:00
7	2K93w3xO	motile cell	CL:0000219	None	None	A Cell That Moves By Its Own Activities.	29.0	None	1	2024-05-25 15:24:47.375019+00:00
6	4WnpvUTH	eukaryotic cell	CL:0000255	None	None	None	29.0	None	1	2024-05-25 15:24:47.374869+00:00
5	2cXC7cgF	single nucleate cell	CL:0000226	None	None	A Cell With A Single Nucleus.	29.0	None	1	2024-05-25 15:24:46.811366+00:00
4	3VEAlFdi	leukocyte	CL:0000738	None	white blood cell\|leucocyte	An Achromatic Cell Of The Myeloid Or Lymphoid ...	29.0	None	1	2024-05-25 15:24:46.811211+00:00
3	2Jgr5Xx4	mononuclear cell	CL:0000842	None	mononuclear leukocyte	A Leukocyte With A Single Non-Segmented Nucleu...	29.0	None	1	2024-05-25 15:24:46.249787+00:00
2	X6c7osZ5	lymphocyte	CL:0000542	None	None	A Lymphocyte Is A Leukocyte Commonly Found In ...	29.0	None	1	2024-05-25 15:24:45.768171+00:00
1	22LvKd01	T cell	CL:0000084	None	T-lymphocyte\|T lymphocyte\|T-cell	A Type Of Lymphocyte Whose Defining Characteri...	29.0	None	1	2024-05-25 15:24:45.203755+00:00

Access records in in-house ontologies¶

Search:

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

Show code cell output Hide code cell output

	uid	name	ontology_id	abbr	synonyms	description	public_source_id	run_id	created_by_id	updated_at
id
1	22LvKd01	T cell	CL:0000084	None	T-lymphocyte\|T lymphocyte\|T-cell	A Type Of Lymphocyte Whose Defining Characteri...	29.0	None	1	2024-05-25 15:24:45.203755+00:00
3	2Jgr5Xx4	mononuclear cell	CL:0000842	None	mononuclear leukocyte	A Leukocyte With A Single Non-Segmented Nucleu...	29.0	None	1	2024-05-25 15:24:46.249787+00:00

Or look up with auto-complete:

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

hsc_record

Validate & standardize¶

Simple validation of an iterable of values works like so:

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

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

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

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

hsc_record.add_synonym("HSCs")

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(["HSCs"])

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 organism¶

Most registries are organism-aware, for instance, Gene:

bt.Gene.from_public(symbol="TCF7", organism="human")

✅ created 1 Gene record from Bionty matching symbol: 'TCF7'

Gene(uid='7IkHKPl0ScQR', symbol='TCF7', ensembl_gene_id='ENSG00000081059', ncbi_gene_ids='6932', biotype='protein_coding', description='transcription factor 7 ', synonyms='TCF-1', created_by_id=1, organism_id=1, public_source_id=11)

Similarly, API calls that interact with multi-organism registries accept a organism argument, e.g.:

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

And 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_public(symbol="Ap5b1")

✅ created 1 Gene record from Bionty matching symbol: 'Ap5b1'

Gene(uid='3b8mHb0MRal4', symbol='Ap5b1', ensembl_gene_id='ENSMUSG00000049562', ncbi_gene_ids='381201', biotype='protein_coding', description='adaptor-related protein complex 5, beta 1 subunit ', synonyms='Gm962', created_by_id=1, organism_id=2, public_source_id=15)

Track underlying ontology versions¶

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

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

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	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	2024-05-25 15:24:41.968790+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	2024-05-25 15:24:41.969621+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	2024-05-25 15:24:41.969774+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	2024-05-25 15:24:41.969927+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	2024-05-25 15:24:41.970081+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	2024-05-25 15:24:41.970232+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	2024-05-25 15:24:41.970385+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	2024-05-25 15:24:41.970990+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	2024-05-25 15:24:41.971594+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	2024-05-25 15:24:41.972045+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	2024-05-25 15:24:41.972347+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	2024-05-25 15:24:41.972649+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	2024-05-25 15:24:41.972799+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	2024-05-25 15:24:41.972949+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	2024-05-25 15:24:41.973099+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	2024-05-25 15:24:41.973874+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	2024-05-25 15:24:41.974629+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	2024-05-25 15:24:41.975381+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	2024-05-25 15:24:41.976431+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	2024-05-25 15:24:41.976884+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	2024-05-25 15:24:41.977501+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	2024-05-25 15:24:41.977806+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	2024-05-25 15:24:41.978258+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	2024-05-25 15:24:41.978407+00:00
67	3rm9	BFXPipeline	all	True	lamin	Bioinformatics Pipeline	1.0.0	s3://bionty-assets/bfxpipelines.json	a7eff57a256994692fba46e0199ffc94	https://lamin.ai	None	1	2024-05-25 15:24:41.978859+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	2024-05-25 15:24:41.979010+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	2024-05-25 15:24:41.979316+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	2024-05-25 15:24:41.979465+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	2024-05-25 15:24:41.982456+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	2024-05-25 15:24:41.982620+00:00

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

hepatocyte = bt.CellType.filter(name="hepatocyte").one()
hepatocyte.public_source

Create records from specific public ontologies¶

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

bt.Phenotype.public()

bt.Phenotype.sources(currently_used=True).df()

Show code cell output 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
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	2024-05-25 15:24:41.976884+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	2024-05-25 15:24:41.977501+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	2024-05-25 15:24:41.977806+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	2024-05-25 15:24:41.978258+00:00

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, instead of using untyped labels for iris organisms as Tutorial: Features & labels, we can use the ncbitaxon ontology:

public_source = bt.PublicSource.filter(entity="Organism", source="ncbitaxon").one()
iris_setosa = bt.Organism.from_public(name="iris setosa", public_source=public_source)
iris_setosa.save()

Analogously, you can pass public_source to bulk-create records from a non-default source:

records = bt.Organism.from_values(
    ["iris setosa", "iris versicolor", "iris virginica"], public_source=public_source
)
ln.save(records)
iris_setosa.parents.get(name="iris").view_parents(with_children=True)