Register CellTypist vocabulary

Cell types classify cells based on public and private knowledge from studying transcription, morphology, function & other properties. Established cell types have well-characterized markers and properties; however, cell subtypes and states are continuously being discovered, refined and better understood.

In this notebook, we register the immune cell type vocabulary from CellTypist, a computational tool used for cell type classification in scRNA-seq data.

Setup

!lamin init --storage ./celltypist --schema bionty

Show code cell output Hide code cell output

💡 creating schemas: core==0.47.5 bionty==0.30.4 
✅ saved: User(id='DzTjkKse', handle='testuser1', email='testuser1@lamin.ai', name='Test User1', updated_at=2023-09-06 17:04:10)
✅ saved: Storage(id='YJb8nhK4', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/celltypist', type='local', updated_at=2023-09-06 17:04:10, created_by_id='DzTjkKse')

✅ loaded instance: testuser1/celltypist
💡 did not register local instance on hub (if you want, call `lamin register`)

Show code cell content Hide code cell content

# filter warnings from celltypist
import warnings

warnings.filterwarnings("ignore", message=".*The 'nopython' keyword.*")

import lamindb as ln
import lnschema_bionty as lb
import celltypist
import pandas as pd

lb.settings.species = "human"  # globally set species

✅ loaded instance: testuser1/celltypist (lamindb 0.52.2)

ln.track()

💡 notebook imports: celltypist==1.6.0 lamindb==0.52.2 lnschema_bionty==0.30.4 pandas==2.0.3

✅ saved: Transform(id='s5mkN5NQ1ttIz8', name='Register CellTypist vocabulary', short_name='celltypist', version='0', type=notebook, updated_at=2023-09-06 17:04:16, created_by_id='DzTjkKse')

✅ saved: Run(id='5PuM1cFWcnKKyAHMQ5qN', run_at=2023-09-06 17:04:16, transform_id='s5mkN5NQ1ttIz8', created_by_id='DzTjkKse')

Access CellTypist records

As a first step we will read in CellTypist’s immune cell encyclopedia

description = "CellTypist Pan Immune Atlas v2: basic cell type information"
celltypist_source_v2_url = "https://github.com/Teichlab/celltypist_wiki/raw/main/atlases/Pan_Immune_CellTypist/v2/tables/Basic_celltype_information.xlsx"

# our source data
celltypist_file = ln.File.filter(description=description).one_or_none()

if celltypist_file is None:
    celltypist_df = pd.read_excel(celltypist_source_v2_url)
    celltypist_file = ln.File(celltypist_df).save()
else:
    celltypist_df = celltypist_file.load().head()

💡 file will be copied to default storage upon `save()` with key `None` ('.lamindb/KN63c410DhShGB9C6V6a.parquet')

💡 data is a dataframe, consider using .from_df() to link column names as features

✅ storing file 'KN63c410DhShGB9C6V6a' at '.lamindb/KN63c410DhShGB9C6V6a.parquet'

It provides an ontology_id of the public Cell Ontology for the majority of records.

celltypist_df.head()

	High-hierarchy cell types	Low-hierarchy cell types	Description	Cell Ontology ID	Curated markers
0	B cells	B cells	B lymphocytes with diverse cell surface immuno...	CL:0000236	CD79A, MS4A1, CD19
1	B cells	Follicular B cells	resting mature B lymphocytes found in the prim...	CL:0000843	CXCR5, TNFRSF13B, CD22
2	B cells	Proliferative germinal center B cells	proliferating germinal center B cells	CL:0000844	MKI67, SUGCT, AICDA
3	B cells	Germinal center B cells	proliferating mature B cells that undergo soma...	CL:0000844	POU2AF1, CD40, SUGCT
4	B cells	Memory B cells	long-lived mature B lymphocytes which are form...	CL:0000787	CR2, CD27, MS4A1

The “Cell Ontology ID” is associated with multiple “Low-hierarchy cell types”:

celltypist_df.set_index(["Cell Ontology ID", "Low-hierarchy cell types"]).head(10)

		High-hierarchy cell types	Description	Curated markers
Cell Ontology ID	Low-hierarchy cell types
CL:0000236	B cells	B cells	B lymphocytes with diverse cell surface immuno...	CD79A, MS4A1, CD19
CL:0000843	Follicular B cells	B cells	resting mature B lymphocytes found in the prim...	CXCR5, TNFRSF13B, CD22
CL:0000844	Proliferative germinal center B cells	B cells	proliferating germinal center B cells	MKI67, SUGCT, AICDA
	Germinal center B cells	B cells	proliferating mature B cells that undergo soma...	POU2AF1, CD40, SUGCT
CL:0000787	Memory B cells	B cells	long-lived mature B lymphocytes which are form...	CR2, CD27, MS4A1
	Age-associated B cells	B cells	CD11c+ T-bet+ memory B cells associated with a...	FCRL2, ITGAX, TBX21
CL:0000788	Naive B cells	B cells	mature B lymphocytes which express cell-surfac...	IGHM, IGHD, TCL1A
CL:0000818	Transitional B cells	B cells	immature B cell precursors in the bone marrow ...	CD24, MYO1C, MS4A1
CL:0000817	Large pre-B cells	B-cell lineage	proliferative B lymphocyte precursors derived ...	MME, CD24, MKI67
	Small pre-B cells	B-cell lineage	non-proliferative B lymphocyte precursors deri...	MME, CD24, IGLL5

Validate CellTypist records

For any cell type record that can be validated against the public Cell Ontology, we’d like to ensure that it’s actually validated.

This will avoid that we’ll refer to the same cell type with different identifiers.

We need a Bionty object for this:

bionty = lb.CellType.bionty()

bionty

CellType
Species: all
Source: cl, 2023-04-20
#terms: 2862

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

We can now validate the "Cell Ontology ID" column

When should I use inspect() and when validate()?

inspect() gives us more logging than validate() but runs a bit slower.

Hence, we’ll use inspect if we suspect validation won’t pass and we want to debug why to curate data.

bionty.inspect(celltypist_df["Cell Ontology ID"], bionty.ontology_id);

✅ 68 terms (100.00%) are validated for ontology_id

This looks good!

But when inspecting the names, most of them don’t validate:

bionty.inspect(celltypist_df["Low-hierarchy cell types"], bionty.name);

✅ 1 term (1.00%) is validated for name

❗ 97 terms (99.00%) are not validated for name: B cells, Follicular B cells, Proliferative germinal center B cells, Germinal center B cells, Memory B cells, Age-associated B cells, Naive B cells, Transitional B cells, Large pre-B cells, Small pre-B cells, Pre-pro-B cells, Pro-B cells, Cycling B cells, Cycling DCs, Cycling gamma-delta T cells, Cycling monocytes, Cycling NK cells, Cycling T cells, DC, DC1, ...

💡    detected 9 terms with synonyms: DC1, DC2, ETP, CMP, ELP, GMP, ILC2, ILC3, pDC

💡 →  standardize terms via .standardize()

A search tells us that terms that are named in plural in Cell Typist occur with a name in singular in the Cell Ontology:

celltypist_df["Low-hierarchy cell types"][0]

'B cells'

bionty.search(celltypist_df["Low-hierarchy cell types"][0]).head(2)

	ontology_id	definition	synonyms	parents	__agg__	__ratio__
name
B cell	CL:0000236	A Lymphocyte Of B Lineage That Is Capable Of B...	B-cell|B lymphocyte|B-lymphocyte	[CL:0000945]	b cell	92.307692
cell	CL:0000000	A Material Entity Of Anatomical Origin (Part O...	None	[]	cell	90.000000

Let’s try to strip "s" and inspect if more names are now validated. Yes, there are!

bionty.inspect(
    [i.rstrip("s") for i in celltypist_df["Low-hierarchy cell types"]],
    bionty.name,
);

✅ 5 terms (5.10%) are validated for name

❗ 93 terms (94.90%) are not validated for name: Follicular B cell, Proliferative germinal center B cell, Germinal center B cell, Memory B cell, Age-associated B cell, Naive B cell, Transitional B cell, Large pre-B cell, Small pre-B cell, Pre-pro-B cell, Pro-B cell, Cycling B cell, Cycling DC, Cycling gamma-delta T cell, Cycling monocyte, Cycling NK cell, Cycling T cell, DC, DC1, DC2, ...

💡    detected 34 terms with inconsistent casing/synonyms: Follicular B cell, Germinal center B cell, Memory B cell, Naive B cell, Transitional B cell, Small pre-B cell, Pro-B cell, DC1, DC2, Endothelial cell, Epithelial cell, Erythrocyte, ETP, Fibroblast, Granulocyte, Neutrophil, CMP, ELP, GMP, ILC2, ...

💡 →  standardize terms via .standardize()

Every “low-hierarchy cell type” has an ontology id and most “high-hierarchy cell types” also appear as “low-hierarchy cell types” in the Cell Typist table. Four, however, don’t, and therefore don’t have an ontology ID.

high_terms = celltypist_df["High-hierarchy cell types"].unique()
low_terms = celltypist_df["Low-hierarchy cell types"].unique()

high_terms_nonval = set(high_terms).difference(low_terms)
high_terms_nonval

{'B-cell lineage', 'Cycling cells', 'Erythroid', 'T cells'}

Register CellTypist records

Let’s first add the “High-hierarchy cell types” as a column "parent".

This enables LaminDB to populate the parents and children fields, which will enable you to query for hierarchical relationships.

celltypist_df["parent"] = celltypist_df.pop("High-hierarchy cell types")

# if high and low terms are the same, no parents
celltypist_df.loc[
    (celltypist_df["parent"] == celltypist_df["Low-hierarchy cell types"]), "parent"
] = None

# rename columns, drop markers
celltypist_df.drop(columns=["Curated markers"], inplace=True)
celltypist_df.rename(
    columns={"Low-hierarchy cell types": "name", "Cell Ontology ID": "ontology_id"},
    inplace=True,
)
celltypist_df.columns = celltypist_df.columns.str.lower()

celltypist_df.head(2)

	name	description	ontology_id	parent
0	B cells	B lymphocytes with diverse cell surface immuno...	CL:0000236	None
1	Follicular B cells	resting mature B lymphocytes found in the prim...	CL:0000843	B cells

Now, let’s create records from the public ontology:

public_records = lb.CellType.from_values(
    celltypist_df.ontology_id, lb.CellType.ontology_id
)

✅ created 68 CellType records from Bionty matching ontology_id: 'CL:0000236', 'CL:0000843', 'CL:0000844', 'CL:0000787', 'CL:0000788', 'CL:0000818', 'CL:0000817', 'CL:0002046', 'CL:0000826', 'CL:0001056', 'CL:0000798', 'CL:0000576', 'CL:0000623', 'CL:0000084', 'CL:0000990', 'CL:0000840', 'CL:0001029', 'CL:0002489', 'CL:0000809', 'CL:0000553', ...

Let’s now amend public ontology records so that they maintain additional annotations that Cell Typist might have.

records_names = {}
public_records_dict = {r.ontology_id: r for r in public_records}

for _, row in celltypist_df.iterrows():
    name = row["name"]
    ontology_id = row["ontology_id"]
    public_record = public_records_dict[ontology_id]

    # if both name and ontology_id match public record, use public record
    if name.lower() == public_record.name.lower():
        records_names[name] = public_record
        continue
    else:  # when ontology_id matches the public record and name doesn't match
        # if singular form of the Celltypist name matches public name
        if name.lower().rstrip("s") == public_record.name.lower():
            # add the Celltypist name to the synonyms of the public ontology record
            public_record.add_synonym(name)
            records_names[name] = public_record
            continue
        if public_record.synonyms is not None:
            synonyms = [s.lower() for s in public_record.synonyms.split("|")]
            # if any of the public matches celltypist name
            if any(
                [
                    i.lower() in {name.lower(), name.lower().rstrip("s")}
                    for i in synonyms
                ]
            ):
                # add the Celltypist name to the synonyms of the public ontology record
                public_record.add_synonym(name)
                records_names[name] = public_record
                continue

        # create a record only based on Celltypist metadata
        records_names[name] = lb.CellType(
            name=name, ontology_id=ontology_id, description=row.description
        )

You can see certain records are created by adding the Celltypist name to the synonyms of the public record:

records_names["GMP"]

CellType(id='f5eAsw0p', name='granulocyte monocyte progenitor cell', ontology_id='CL:0000557', synonyms='colony forming unit granulocyte macrophage|granulocyte/monocyte precursor|granulocyte/monocyte progenitor|GMP|granulocyte-macrophage progenitor|CFU-GM', description='A Hematopoietic Progenitor Cell That Is Committed To The Granulocyte And Monocyte Lineages. These Cells Are Cd123-Positive, And Do Not Express Gata1 Or Gata2 But Do Express C/Ebpa, And Pu.1.', bionty_source_id='haF7', created_by_id='DzTjkKse')

Other records are created based on Celltypist metadata:

records_names["Age-associated B cells"]

CellType(id='00ieV0IG', name='Age-associated B cells', ontology_id='CL:0000787', description='CD11c+ T-bet+ memory B cells associated with autoimmunity and aging', created_by_id='DzTjkKse')

Let’s save them to our database:

records = set(records_names.values())

ln.save(records)

Show code cell output Hide code cell output

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='ePsFBu6n', name='transitional stage B cell', ontology_id='CL:0000818', synonyms='transitional stage B lymphocyte|transitional stage B-lymphocyte|transitional B cell|transitional stage B-cell|Transitional B cells', description='An Immature B Cell Of An Intermediate Stage Between The Pre-B Cell Stage And The Mature Naive Stage With The Phenotype Surface Igm-Positive And Cd19-Positive, And Are Subject To The Process Of B Cell Selection. A Transitional B Cell Migrates From The Bone Marrow Into The Peripheral Circulation, And Then To The Spleen.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0001201'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='CIS4VJI0', name='B cell, CD19-positive', ontology_id='CL:0001201', synonyms='CD19+ B cell|B lymphocyte, CD19-positive|B-lymphocyte, CD19-positive|CD19-positive B cell|B-cell, CD19-positive', description='A B Cell That Is Cd19-Positive.', updated_at=2023-09-06 17:04:21, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='64kIG7So', name='gamma-delta T cell', ontology_id='CL:0000798', synonyms='gamma-delta T-lymphocyte|gamma-delta T-cell|gamma-delta T lymphocyte|gamma-delta T cells|gammadelta T cell', description='A T Cell That Expresses A Gamma-Delta T Cell Receptor Complex.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='X458vtJX', name='naive B cell', ontology_id='CL:0000788', synonyms='naive B-lymphocyte|naive B lymphocyte|naive B-cell|Naive B cells', description='A Naive B Cell Is A Mature B Cell That Has The Phenotype Surface Igd-Positive, Surface Igm-Positive, Cd20-Positive, Cd27-Negative And That Has Not Yet Been Activated By Antigen In The Periphery.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000785'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='0I51jgPp', name='mature B cell', ontology_id='CL:0000785', synonyms='mature B lymphocyte|mature B-cell|mature B-lymphocyte', description='A B Cell That Is Mature, Having Left The Bone Marrow. Initially, These Cells Are Igm-Positive And Igd-Positive, And They Can Be Activated By Antigen.', updated_at=2023-09-06 17:04:22, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='S4Urkinl', name='macrophage', ontology_id='CL:0000235', synonyms='histiocyte|Macrophages', description='A Mononuclear Phagocyte Present In Variety Of Tissues, Typically Differentiated From Monocytes, Capable Of Phagocytosing A Variety Of Extracellular Particulate Material, Including Immune Complexes, Microorganisms, And Dead Cells.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000766'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='40onq0tm', name='myeloid leukocyte', ontology_id='CL:0000766', description='A Cell Of The Monocyte, Granulocyte, Or Mast Cell Lineage.', updated_at=2023-09-06 17:04:24, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000738'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='MkrH0gsX', 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.', updated_at=2023-09-06 17:04:25, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000988'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='Q0aQr5JB', name='hematopoietic cell', ontology_id='CL:0000988', synonyms='haematopoietic cell|hemopoietic cell|haemopoietic cell', description='A Cell Of A Hematopoietic Lineage.', updated_at=2023-09-06 17:04:26, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 2 CellType records from Bionty matching ontology_id: 'CL:0002371', 'CL:0000548'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='H0taCt24', name='animal cell', ontology_id='CL:0000548', synonyms='metazoan cell', description='A Native Cell That Is Part Of Some Metazoa.', updated_at=2023-09-06 17:04:27, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000255'

💡 also saving parents of CellType(id='QMAH6IlS', name='somatic cell', ontology_id='CL:0002371', description='A Cell Of An Organism That Does Not Pass On Its Genetic Material To The Organism'S Offspring (I.E. A Non-Germ Line Cell).', updated_at=2023-09-06 17:04:27, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ loaded 1 CellType record matching ontology_id: 'CL:0000548'

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000003'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='VT73gpK2', name='native cell', ontology_id='CL:0000003', description='A Cell That Is Found In A Natural Setting, Which Includes Multicellular Organism Cells 'In Vivo' (I.E. Part Of An Organism), And Unicellular Organisms 'In Environment' (I.E. Part Of A Natural Environment).', updated_at=2023-09-06 17:04:30, bionty_source_id='haF7', created_by_id='DzTjkKse')

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

💡 also saving parents of CellType(id='XjG8T0GY', name='fibroblast', ontology_id='CL:0000057', synonyms='Fibroblasts', description='A Connective Tissue Cell Which Secretes An Extracellular Matrix Rich In Collagen And Other Macromolecules. Flattened And Irregular In Outline With Branching Processes; Appear Fusiform Or Spindle-Shaped.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0002320'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='4zAzIMBQ', name='connective tissue cell', ontology_id='CL:0002320', description='A Cell Of The Supporting Or Framework Tissue Of The Body, Arising Chiefly From The Embryonic Mesoderm And Including Adipose Tissue, Cartilage, And Bone.', updated_at=2023-09-06 17:04:32, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='FMTngXKK', name='follicular B cell', ontology_id='CL:0000843', synonyms='Follicular B cells|follicular B lymphocyte|Fo B cell|Fo B-cell|follicular B-lymphocyte|follicular B-cell', description='A Resting Mature B Cell That Has The Phenotype Igm-Positive, Igd-Positive, Cd23-Positive And Cd21-Positive, And Found In The B Cell Follicles Of The White Pulp Of The Spleen Or The Corticol Areas Of The Peripheral Lymph Nodes. This Cell Type Is Also Described As Being Cd19-Positive, B220-Positive, Aa4-Negative, Cd43-Negative, And Cd5-Negative.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='YN0gzDt3', name='Kupffer cell', ontology_id='CL:0000091', synonyms='Kupffer cells|von Kupffer cell|hepatic macrophage|stellate cell of von Kupffer|macrophagocytus stellatus|littoral cell of hepatic sinusoid|liver macrophage', description='A Tissue-Resident Macrophage Of The Reticuloendothelial System Found On The Luminal Surface Of The Hepatic Sinusoids Involved In Erythrocyte Clearance. Markers Include F4/80+, Cd11B-Low, Cd68-Positive, Sialoadhesin-Positive, Cd163/Srcr-Positive. Irregular, With Long Processes Including Lamellipodia Extending Into The Sinusoid Lumen, Have Flattened Nucleus With Cytoplasm Containing Characteristic Invaginations Of The Plasma Membrane (Vermiform Bodies); Lie Within The Sinusoid Lumen Attached To The Endothelial Surface; Derived From The Bone Marrow, Form A Major Part Of The Body'S Mononuclear Phagocyte System.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000864'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='pXnRaLwJ', name='tissue-resident macrophage', ontology_id='CL:0000864', synonyms='resting histiocyte|fixed macrophage', description='A Macrophage Constitutively Resident In A Particular Tissue Under Non-Inflammatory Conditions, And Capable Of Phagocytosing A Variety Of Extracellular Particulate Material, Including Immune Complexes, Microorganisms, And Dead Cells.', updated_at=2023-09-06 17:04:34, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='YzV7Qgmj', name='monocyte', ontology_id='CL:0000576', synonyms='Monocytes', description='Myeloid Mononuclear Recirculating Leukocyte That Can Act As A Precursor Of Tissue Macrophages, Osteoclasts And Some Populations Of Tissue Dendritic Cells.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='ppLUhJWx', name='non-classical monocyte', ontology_id='CL:0000875', synonyms='patrolling monocyte|Non-classical monocytes|resident monocyte', description='A Type Of Monocyte Characterized By Low Expression Of Ccr2, Low Responsiveness To Monocyte Chemoattractant Ccl2/Mcp1, Low Phagocytic Activity, And Decrease Size Relative To Classical Monocytes, But Increased Co-Stimulatory Activity. May Also Play A Role In Tissue Repair.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='b5k0suF0', name='erythrocyte', ontology_id='CL:0000232', synonyms='RBC|Erythrocytes|red blood cell', description='A Red Blood Cell. In Mammals, Mature Erythrocytes Are Biconcave Disks Containing Hemoglobin Whose Function Is To Transport Oxygen.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='Iywg7lUq', name='early lymphoid progenitor', ontology_id='CL:0000936', synonyms='ELP|lymphoid-primed multipotent progenitor|LMPP', description='A Lymphoid Progenitor Cell That Is Found In Bone Marrow, Gives Rise To B Cells, T Cells, Natural Killer Cells And Dendritic Cells, And Has The Phenotype Lin-Negative, Kit-Positive, Sca-1-Positive, Flt3-Positive, Cd34-Positive, Cd150 Negative, And Glya-Negative.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='NJ07Q1hX', name='plasmablast', ontology_id='CL:0000980', synonyms='CD27-positive, CD38-positive, CD20-negative B cell|Plasmablasts', description='An Activated Mature (Naive Or Memory) B Cell That Is Secreting Immunoglobulin, Typified By Being Cd27-Positive, Cd38-Positive, Cd138-Negative.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='4fOuOYtl', name='endothelial cell', ontology_id='CL:0000115', synonyms='Endothelial cells|endotheliocyte', description='An Endothelial Cell Comprises The Outermost Layer Or Lining Of Anatomical Structures And Can Be Squamous Or Cuboidal. In Mammals, Endothelial Cell Has Vimentin Filaments And Is Derived From The Mesoderm.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 2 CellType records from Bionty matching ontology_id: 'CL:0000213', 'CL:0002078'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='AHV57RuN', name='lining cell', ontology_id='CL:0000213', synonyms='boundary cell', description='A Cell Within An Epithelial Cell Sheet Whose Main Function Is To Act As An Internal Or External Covering For A Tissue Or An Organism.', updated_at=2023-09-06 17:04:35, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000215'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='gON03kRx', name='barrier cell', ontology_id='CL:0000215', description='A Cell Whose Primary Function Is To Prevent The Transport Of Stuff Across Compartments.', updated_at=2023-09-06 17:04:36, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='nGEtVlKq', name='meso-epithelial cell', ontology_id='CL:0002078', synonyms='epithelial mesenchymal cell', description='Epithelial Cell Derived From Mesoderm Or Mesenchyme.', updated_at=2023-09-06 17:04:35, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='xfxkvliE', name='granulocyte', ontology_id='CL:0000094', synonyms='granular leucocyte|Granulocytes|granular leukocyte|polymorphonuclear leukocyte', description='A Leukocyte With Abundant Granules In The Cytoplasm.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='0JvRwfVm', name='plasma cell', ontology_id='CL:0000786', synonyms='plasma B cell|plasmacyte|plasma B-cell|plasmocyte|Plasma cells', description='A Terminally Differentiated, Post-Mitotic, Antibody Secreting Cell Of The B Cell Lineage With The Phenotype Cd138-Positive, Surface Immunonoglobulin-Negative, And Mhc Class Ii-Negative. Plasma Cells Are Oval Or Round With Extensive Rough Endoplasmic Reticulum, A Well-Developed Golgi Apparatus, And A Round Nucleus Having A Characteristic Cartwheel Heterochromatin Pattern And Are Devoted To Producing Large Amounts Of Immunoglobulin.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000946'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='hFMWJcWc', name='antibody secreting cell', ontology_id='CL:0000946', description='A Lymphocyte Of B Lineage That Is Devoted To Secreting Large Amounts Of Immunoglobulin.', updated_at=2023-09-06 17:04:37, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000945'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='Z0yFV7vU', name='lymphocyte of B lineage', ontology_id='CL:0000945', description='A Lymphocyte Of B Lineage With The Commitment To Express An Immunoglobulin Complex.', updated_at=2023-09-06 17:04:39, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ 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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='g8slxY8X', 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.', updated_at=2023-09-06 17:04:40, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='i20ionW5', name='mast cell', ontology_id='CL:0000097', synonyms='Mast cells|histaminocyte|labrocyte|mastocyte', description='A Cell That Is Found In Almost All Tissues Containing Numerous Basophilic Granules And Capable Of Releasing Large Amounts Of Histamine And Heparin Upon Activation. Progenitors Leave Bone Marrow And Mature In Connective And Mucosal Tissue. Mature Mast Cells Are Found In All Tissues, Except The Bloodstream. Their Phenotype Is Cd117-High, Cd123-Negative, Cd193-Positive, Cd200R3-Positive, And Fceri-High. Stem-Cell Factor (Kit-Ligand; Scf) Is The Main Controlling Signal Of Their Survival And Development.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ loaded 1 CellType record matching ontology_id: 'CL:0000766'

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0002274'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='70wMh2r7', name='histamine secreting cell', ontology_id='CL:0002274', description='A Cell Type That Secretes Histamine.', updated_at=2023-09-06 17:04:41, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000457'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='TpKvGjqi', name='biogenic amine secreting cell', ontology_id='CL:0000457', updated_at=2023-09-06 17:04:42, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000151'

💡 also saving parents of CellType(id='Z7uMAWUF', name='regulatory T cell', ontology_id='CL:0000815', synonyms='regulatory T-lymphocyte|regulatory T lymphocyte|Treg|regulatory T-cell|Regulatory T cells', description='A T Cell Which Regulates Overall Immune Responses As Well As The Responses Of Other T Cell Subsets Through Direct Cell-Cell Contact And Cytokine Release.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0002419'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='2C5PhwrW', name='mature T cell', ontology_id='CL:0002419', synonyms='mature T-cell|CD3e-positive T cell', description='A T Cell That Expresses A T Cell Receptor Complex And Has Completed T Cell Selection.', updated_at=2023-09-06 17:04:45, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='8lTrmDbK', name='neutrophil', ontology_id='CL:0000775', synonyms='neutrocyte|neutrophil leukocyte|neutrophil leucocyte|neutrophilic leukocyte|Neutrophils|neutrophilic leucocyte', description='Any Of The Immature Or Mature Forms Of A Granular Leukocyte That In Its Mature Form Has A Nucleus With Three To Five Lobes Connected By Slender Threads Of Chromatin, And Cytoplasm Containing Fine Inconspicuous Granules And Stainable By Neutral Dyes.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='l0R9X3Bs', name='promyelocyte', ontology_id='CL:0000836', synonyms='Promyelocytes', description='A Precursor In The Granulocytic Series, Being A Cell Intermediate In Development Between A Myeloblast And Myelocyte, That Has Distinct Nucleoli, A Nuclear-To-Cytoplasmic Ratio Of 5:1 To 3:1, And Containing A Few Primary Cytoplasmic Granules. Markers For This Cell Are Fucosyltransferase Fut4-Positive, Cd33-Positive, Integrin Alpha-M-Negative, Low Affinity Immunoglobulin Gamma Fc Region Receptor Iii-Negative, And Cd24-Negative.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0002191'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='odstSt5D', name='granulocytopoietic cell', ontology_id='CL:0002191', description='A Cell Involved In The Formation Of A Granulocyte.', updated_at=2023-09-06 17:04:46, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000839'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='Q0v4wWyZ', name='myeloid lineage restricted progenitor cell', ontology_id='CL:0000839', description='A Progenitor Cell Restricted To The Myeloid Lineage.', updated_at=2023-09-06 17:04:47, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0002031'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='xl6RtpG9', name='hematopoietic lineage restricted progenitor cell', ontology_id='CL:0002031', description='A Hematopoietic Progenitor Cell That Is Capable Of Developing Into Only One Lineage Of Hematopoietic Cells.', updated_at=2023-09-06 17:04:48, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ loaded 1 CellType record matching ontology_id: 'CL:0000988'

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0008001'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='0d3ym06W', name='hematopoietic precursor cell', ontology_id='CL:0008001', description='Any Hematopoietic Cell That Is A Precursor Of Some Other Hematopoietic Cell Type.', updated_at=2023-09-06 17:04:50, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='P6E7yrc7', name='epithelial cell', ontology_id='CL:0000066', synonyms='Epithelial cells|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.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='67zMsufW', name='memory B cell', ontology_id='CL:0000787', synonyms='memory B-cell|memory B lymphocyte|memory B-lymphocyte|Memory B cells', description='A Memory B Cell Is A Mature B Cell That Is Long-Lived, Readily Activated Upon Re-Encounter Of Its Antigenic Determinant, And Has Been Selected For Expression Of Higher Affinity Immunoglobulin. This Cell Type Has The Phenotype Cd19-Positive, Cd20-Positive, Mhc Class Ii-Positive, And Cd138-Negative.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='cx8VcggA', name='B cell', ontology_id='CL:0000236', synonyms='B-cell|B lymphocyte|B-lymphocyte|B cells', description='A Lymphocyte Of B Lineage That Is Capable Of B Cell Mediated Immunity.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='f5eAsw0p', name='granulocyte monocyte progenitor cell', ontology_id='CL:0000557', synonyms='colony forming unit granulocyte macrophage|granulocyte/monocyte precursor|granulocyte/monocyte progenitor|GMP|granulocyte-macrophage progenitor|CFU-GM', description='A Hematopoietic Progenitor Cell That Is Committed To The Granulocyte And Monocyte Lineages. These Cells Are Cd123-Positive, And Do Not Express Gata1 Or Gata2 But Do Express C/Ebpa, And Pu.1.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0002032'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='JYQl3RX8', name='hematopoietic oligopotent progenitor cell', ontology_id='CL:0002032', description='A Hematopoietic Oligopotent Progenitor Cell That Has The Ability To Differentiate Into Limited Cell Types But Lacks Lineage Cell Markers And Self Renewal Capabilities.', updated_at=2023-09-06 17:04:51, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='loo3Xanl', name='common myeloid progenitor', ontology_id='CL:0000049', synonyms='CMP|common myeloid precursor', description='A Progenitor Cell Committed To Myeloid Lineage, Including The Megakaryocyte And Erythroid Lineages.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='Q2BH279Q', name='classical monocyte', ontology_id='CL:0000860', synonyms='Classical monocytes|inflammatory monocyte', description='A Monocyte That Responds Rapidly To Microbial Stimuli By Secreting Cytokines And Antimicrobial Factors And Which Is Characterized By High Expression Of Ccr2 In Both Rodents And Humans, Negative For The Lineage Markers Cd3, Cd19, And Cd20, And Of Larger Size Than Non-Classical Monocytes.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='g2Rk2xkb', name='myelocyte', ontology_id='CL:0002193', synonyms='Myelocytes', description='A Cell Type That Is The First Of The Maturation Stages Of The Granulocytic Leukocytes Normally Found In The Bone Marrow. Granules Are Seen In The Cytoplasm. The Nuclear Material Of The Myelocyte Is Denser Than That Of The Myeloblast But Lacks A Definable Membrane. The Cell Is Flat And Contains Increasing Numbers Of Granules As Maturation Progresses.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='nd6Qaf38', name='Hofbauer cell', ontology_id='CL:3000001', synonyms='Hofbauer cells', description='Oval Eosinophilic Histiocytes With Granules And Vacuoles Found In Placenta, Which Are Of Mesenchymal Origin, In Mesoderm Of The Chorionic Villus, Particularly Numerous In Early Pregnancy.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='TENASE93', name='alveolar macrophage', ontology_id='CL:0000583', synonyms='dust cell|Alveolar macrophages', description='A Tissue-Resident Macrophage Found In The Alveoli Of The Lungs. Ingests Small Inhaled Particles Resulting In Degradation And Presentation Of The Antigen To Immunocompetent Cells. Markers Include F4/80-Positive, Cd11B-/Low, Cd11C-Positive, Cd68-Positive, Sialoadhesin-Positive, Dectin-1-Positive, Mr-Positive, Cx3Cr1-Negative.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ loaded 1 CellType record matching ontology_id: 'CL:0000864'

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:1001603'

💡 also saving parents of CellType(id='RSjQq98q', name='pro-B cell', ontology_id='CL:0000826', synonyms='pro-B-lymphocyte|progenitor B-cell|progenitor B cell|progenitor B-lymphocyte|pro-B lymphocyte|progenitor B lymphocyte|pro-B-cell|Pro-B cells', description='A Progenitor Cell Of The B Cell Lineage, With Some Lineage Specific Activity Such As Early Stages Of Recombination Of B Cell Receptor Genes, But Not Yet Fully Committed To The B Cell Lineage Until The Expression Of Pax5 Occurs.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000838'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='vQ9N8BKH', name='lymphoid lineage restricted progenitor cell', ontology_id='CL:0000838', description='A Progenitor Cell Restricted To The Lymphoid Lineage.', updated_at=2023-09-06 17:04:54, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='3rJgLble', name='conventional dendritic cell', ontology_id='CL:0000990', synonyms='cDC|type 1 DC|DC1|dendritic reticular cell', description='Conventional Dendritic Cell Is A Dendritic Cell That Is Cd11C-High.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

✅ created 1 CellType record from Bionty matching ontology_id: 'CL:0000451'

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

💡 you can switch this off via: lb.settings.auto_save_parents = False

💡 also saving parents of CellType(id='9JGbXeUA', name='dendritic cell', ontology_id='CL:0000451', description='A Cell Of Hematopoietic Origin, Typically Resident In Particular Tissues, Specialized In The Uptake, Processing, And Transport Of Antigens To Lymph Nodes For The Purpose Of Stimulating An Immune Response Via T Cell Activation. These Cells Are Lineage Negative (Cd3-Negative, Cd19-Negative, Cd34-Negative, And Cd56-Negative).', updated_at=2023-09-06 17:04:55, bionty_source_id='haF7', created_by_id='DzTjkKse')

💡 also saving parents of CellType(id='uMLhrmbZ', name='germinal center B cell', ontology_id='CL:0000844', synonyms='GC B cell|Germinal center B cells|germinal center B-lymphocyte|GC B-lymphocyte|germinal center B lymphocyte|GC B lymphocyte|germinal center B-cell|GC B-cell', description='A Rapidly Cycling Mature B Cell That Has Distinct Phenotypic Characteristics And Is Involved In T-Dependent Immune Responses And Located Typically In The Germinal Centers Of Lymph Nodes. This Cell Type Expresses Ly77 After Activation.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

Add parent-child relationship of the records from Celltypist

We still need to add the renaming 4 High hierarchy terms:

list(high_terms_nonval)

['Cycling cells', 'B-cell lineage', 'Erythroid', 'T cells']

Let’s get the top hits from a search:

for term in list(high_terms_nonval):
    print(f"Term: {term}")
    display(bionty.search(term).head(1))

Term: Cycling cells

	ontology_id	definition	synonyms	parents	__agg__	__ratio__
name
type G enteroendocrine cell	CL:0000508	An Endocrine Cell Found In The Pyloric Gland M...	G cell	[CL:0000509, CL:0000164, CL:0000506]	type g enteroendocrine cell	90.0

Term: B-cell lineage

	ontology_id	definition	synonyms	parents	__agg__	__ratio__
name
cell	CL:0000000	A Material Entity Of Anatomical Origin (Part O...	None	[]	cell	90.0

Term: Erythroid

	ontology_id	definition	synonyms	parents	__agg__	__ratio__
name
erythroid progenitor cell	CL:0000038	A Progenitor Cell Committed To The Erythroid L...	None	[CL:0000839, CL:0000764]	erythroid progenitor cell	90.0

Term: T cells

	ontology_id	definition	synonyms	parents	__agg__	__ratio__
name
T cell	CL:0000084	A Type Of Lymphocyte Whose Defining Characteri...	T-lymphocyte|T-cell|T lymphocyte	[CL:0000542]	t cell	92.307692

So we decide to:

• Add the “T cells” to the synonyms of the public “T cell” record

• Create the remaining 3 terms only using their names (we think “B cell flow” shouldn’t be identified with “B cell”)

for name in high_terms_nonval:
    if name == "T cells":
        record = lb.CellType.from_bionty(name="T cell")
        record.add_synonym(name)
        record.save()
    else:
        record = lb.CellType(name=name)
        record.save()
    records_names[name] = record

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

	id	synonyms	__ratio__
name
Cycling B cells	ibzfn1zQ		95.0
Cycling T cells	TTziQpub		95.0
Cycling NK cells	rC47wc9h		95.0
cell	Ry0JGwSD		90.0
Tcm/Naive helper T cells	qlqe2Fe3		85.5
CRTAM+ gamma-delta T cells	pYHfZPub		85.5
Cycling gamma-delta T cells	mI0t06Vi		85.5
Follicular helper T cells	Z40YuehV		85.5
Memory CD4+ cytotoxic T cells	lgyyreJJ		85.5
Proliferative germinal center B cells	TC2eLf0p		85.5
B cell	cx8VcggA	B-cell|B lymphocyte|B-lymphocyte|B cells	85.5
Tem/Effector helper T cells PD1+	LIJ5jLyj		85.5
Tcm/Naive cytotoxic T cells	6KPuL5ry		85.5
Tem/Temra cytotoxic T cells	Qr0e8qFx		85.5
Tem/Trm cytotoxic T cells	ZpMndkcZ		85.5
germinal center B cell	uMLhrmbZ	GC B cell|Germinal center B cells|germinal cen...	85.5
natural killer cell	qzbC18BN	NK cells|NK cell	85.5
Tem/Effector helper T cells	E6PjRrZr		85.5
Age-associated B cells	00ieV0IG		85.5
transitional stage B cell	ePsFBu6n	transitional stage B lymphocyte|transitional s...	85.5

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

	id	synonyms	__ratio__
name
B cell	cx8VcggA	B-cell|B lymphocyte|B-lymphocyte|B cells	90.0
cell	Ry0JGwSD		90.0
B cell, CD19-positive	CIS4VJI0	CD19+ B cell|B lymphocyte, CD19-positive|B-lym...	85.5
alveolar macrophage	TENASE93	dust cell|Alveolar macrophages	85.5
conventional dendritic cell	3rJgLble	cDC|type 1 DC|DC1|dendritic reticular cell	85.5
follicular B cell	FMTngXKK	Follicular B cells|follicular B lymphocyte|Fo ...	85.5
germinal center B cell	uMLhrmbZ	GC B cell|Germinal center B cells|germinal cen...	85.5
meso-epithelial cell	nGEtVlKq	epithelial mesenchymal cell	85.5
natural killer cell	qzbC18BN	NK cells|NK cell	85.5
plasmablast	NJ07Q1hX	CD27-positive, CD38-positive, CD20-negative B ...	85.5

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

	id	synonyms	__ratio__
name
Mid erythroid	lveE8XKg		95.0
Early erythroid	MiIxaBcE		90.0
Late erythroid	NY6Iq1SQ		90.0
Megakaryocyte-erythroid-mast cell progenitor	rDuO4MVx		90.0

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

💡 also saving parents of CellType(id='BxNjby0x', name='T cell', ontology_id='CL:0000084', synonyms='T-lymphocyte|T lymphocyte|T-cell|T cells', description='A Type Of Lymphocyte Whose Defining Characteristic Is The Expression Of A T Cell Receptor Complex.', updated_at=2023-09-06 17:04:56, bionty_source_id='haF7', created_by_id='DzTjkKse')

Now let’s add the parent records:

for _, row in celltypist_df.iterrows():
    record = records_names[row["name"]]
    if row["parent"] is not None:
        parent_record = records_names[row["parent"]]
        record.parents.add(parent_record)

Access the registry

The previously added CellTypist ontology registry is now available in LaminDB. To retrieve the full ontology table as a Pandas DataFrame we can use .filter:

lb.CellType.filter().df()

	name	ontology_id	abbr	synonyms	description	bionty_source_id	updated_at	created_by_id
id
TTziQpub	Cycling T cells	CL:0000084	None	None	proliferating T lymphocytes	None	2023-09-06 17:04:20	DzTjkKse
ePsFBu6n	transitional stage B cell	CL:0000818	None	transitional stage B lymphocyte|transitional s...	An Immature B Cell Of An Intermediate Stage Be...	haF7	2023-09-06 17:04:20	DzTjkKse
64kIG7So	gamma-delta T cell	CL:0000798	None	gamma-delta T-lymphocyte|gamma-delta T-cell|ga...	A T Cell That Expresses A Gamma-Delta T Cell R...	haF7	2023-09-06 17:04:20	DzTjkKse
pYHfZPub	CRTAM+ gamma-delta T cells	CL:0000798	None	None	CRTAM+ IKZF2+ ITGAD+ gamma-delta T cells that ...	None	2023-09-06 17:04:20	DzTjkKse
QD3kFUXo	MEMP	CL:0000050	None	None	shared progenitors which are derived from comm...	None	2023-09-06 17:04:20	DzTjkKse
...	...	...	...	...	...	...	...	...
9JGbXeUA	dendritic cell	CL:0000451	None	None	A Cell Of Hematopoietic Origin, Typically Resi...	haF7	2023-09-06 17:04:55	DzTjkKse
VXEM4KvL	Cycling cells	None	None	None	None	None	2023-09-06 17:04:55	DzTjkKse
scntm1BL	B-cell lineage	None	None	None	None	None	2023-09-06 17:04:55	DzTjkKse
Icirho5C	Erythroid	None	None	None	None	None	2023-09-06 17:04:55	DzTjkKse
BxNjby0x	T cell	CL:0000084	None	T-lymphocyte|T lymphocyte|T-cell|T cells	A Type Of Lymphocyte Whose Defining Characteri...	haF7	2023-09-06 17:04:56	DzTjkKse

132 rows × 8 columns

This enables us to look for cell types by creating a lookup object from our new CellType registry.

db_lookup = lb.CellType.lookup()

db_lookup.memory_b_cell

CellType(id='67zMsufW', name='memory B cell', ontology_id='CL:0000787', synonyms='memory B-cell|memory B lymphocyte|memory B-lymphocyte|Memory B cells', description='A Memory B Cell Is A Mature B Cell That Is Long-Lived, Readily Activated Upon Re-Encounter Of Its Antigenic Determinant, And Has Been Selected For Expression Of Higher Affinity Immunoglobulin. This Cell Type Has The Phenotype Cd19-Positive, Cd20-Positive, Mhc Class Ii-Positive, And Cd138-Negative.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')

See cell type hierarchy:

db_lookup.memory_b_cell.view_parents()

Access parents of a record:

db_lookup.memory_b_cell.parents.list()

[CellType(id='0I51jgPp', name='mature B cell', ontology_id='CL:0000785', synonyms='mature B lymphocyte|mature B-cell|mature B-lymphocyte', description='A B Cell That Is Mature, Having Left The Bone Marrow. Initially, These Cells Are Igm-Positive And Igd-Positive, And They Can Be Activated By Antigen.', updated_at=2023-09-06 17:04:22, bionty_source_id='haF7', created_by_id='DzTjkKse'),
 CellType(id='cx8VcggA', name='B cell', ontology_id='CL:0000236', synonyms='B-cell|B lymphocyte|B-lymphocyte|B cells', description='A Lymphocyte Of B Lineage That Is Capable Of B Cell Mediated Immunity.', updated_at=2023-09-06 17:04:20, bionty_source_id='haF7', created_by_id='DzTjkKse')]

# clean up test instance
!lamin delete --force celltypist
!rm -r ./celltypist

Show code cell output Hide code cell output

💡 deleting instance testuser1/celltypist

✅     deleted instance settings file: /home/runner/.lamin/instance--testuser1--celltypist.env

✅     instance cache deleted
✅     deleted '.lndb' sqlite file
❗     consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/celltypist