CellTypist

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

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✅ saved: User(id='DzTjkKse', handle='testuser1', email='testuser1@lamin.ai', name='Test User1', updated_at=2023-10-01 16:39:44)
✅ saved: Storage(id='cHssT2iR', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/celltypist', type='local', updated_at=2023-10-01 16:39:45, created_by_id='DzTjkKse')

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

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# 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 0.54.4)

2023-10-01 16:39:48,259:INFO - Failed to extract font properties from /usr/share/fonts/truetype/noto/NotoColorEmoji.ttf: In FT2Font: Can not load face (unknown file format; error code 0x2)

2023-10-01 16:39:49,033:INFO - generated new fontManager

ln.track()

💡 notebook imports: celltypist==1.6.1 lamindb==0.54.4 lnschema_bionty==0.31.2 pandas==1.5.3

💡 Transform(id='s5mkN5NQ1ttIz8', name='CellTypist', short_name='celltypist', version='0', type=notebook, updated_at=2023-10-01 16:39:51, created_by_id='DzTjkKse')

💡 Run(id='kAu6iLAD3XW4M0Jmob2j', run_at=2023-10-01 16:39:51, 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()

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);

This looks good!

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

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

❗ 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
)

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='granulocyte/monocyte precursor|colony forming unit granulocyte macrophage|GMP|granulocyte-macrophage progenitor|granulocyte/monocyte 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='sXSM', 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)

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

Add parent-child relationship of the records from Celltypist

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

list(high_terms_nonval)

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

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: 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

Term: Cycling cells

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

Term: B-cell lineage

	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	90.0

Term: Erythroid

	ontology_id	definition	synonyms	parents	__agg__	__ratio__
name
CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell	CL:0002005	A Megakaryocyte Erythroid Progenitor Cell Is C...	None	[CL:0000050]	cd34-positive, cd38-positive megakaryocyte ery...	90.0

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 NK cells	rC47wc9h		95.0
Cycling T cells	TTziQpub		95.0
cell	Ry0JGwSD		90.0

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

	id	synonyms	__ratio__
name
B cell	cx8VcggA	B lymphocyte|B-lymphocyte|B-cell|B cells	90.0
cell	Ry0JGwSD		90.0

❗ 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
Megakaryocyte-erythroid-mast cell progenitor	rDuO4MVx		90.0
Late erythroid	NY6Iq1SQ		90.0

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
dOvgklmm	Cycling monocytes	CL:0000576	None	None	proliferating monocytes	None	2023-10-01 16:39:54	DzTjkKse
NyvLMjOH	MNP	CL:0000113	None	None	mononuclear phagocytes including dendritic cel...	None	2023-10-01 16:39:54	DzTjkKse
ibzfn1zQ	Cycling B cells	CL:0000236	None	None	proliferating B lymphocytes	None	2023-10-01 16:39:54	DzTjkKse
Jg7rWWSY	ILC1	CL:0001077	None	None	innate lymphoid cell subpopulation I that is n...	None	2023-10-01 16:39:54	DzTjkKse
YzV7Qgmj	monocyte	CL:0000576	None	Monocytes	Myeloid Mononuclear Recirculating Leukocyte Th...	sXSM	2023-10-01 16:39:54	DzTjkKse
...	...	...	...	...	...	...	...	...
wVT2qeb9	secretory cell	CL:0000151	None	None	A Cell That Specializes In Controlled Release ...	sXSM	2023-10-01 16:40:18	DzTjkKse
BxNjby0x	T cell	CL:0000084	None	T cells|T-lymphocyte|T-cell|T lymphocyte	A Type Of Lymphocyte Whose Defining Characteri...	sXSM	2023-10-01 16:40:19	DzTjkKse
ZOKQrYVY	Cycling cells	None	None	None	None	None	2023-10-01 16:40:19	DzTjkKse
TOSCffRH	B-cell lineage	None	None	None	None	None	2023-10-01 16:40:19	DzTjkKse
PHmBAiqv	Erythroid	None	None	None	None	None	2023-10-01 16:40:19	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 lymphocyte|Memory B cells|memory B-lymphocyte|memory B-cell', 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=2023-10-01 16:39:54, bionty_source_id='sXSM', 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=2023-10-01 16:40:03, bionty_source_id='sXSM', created_by_id='DzTjkKse'),
 CellType(id='cx8VcggA', name='B cell', ontology_id='CL:0000236', synonyms='B lymphocyte|B-lymphocyte|B-cell|B cells', description='A Lymphocyte Of B Lineage That Is Capable Of B Cell Mediated Immunity.', updated_at=2023-10-01 16:39:54, bionty_source_id='sXSM', created_by_id='DzTjkKse')]

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

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💡 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