Register LNPs from Benchling¶

# pip install git+https://github.com/laminlabs/sentseqdb.git
import lamindb as ln
import sentseqdb as sq
from sentseqdb.benchling import BenchlingConnector

→ connected lamindb: testuser1/test-sentseqdb

Initialize the BenchlingConnector¶

from benchling_sdk.benchling import Benchling
from benchling_sdk.auth.client_credentials_oauth2 import ClientCredentialsOAuth2
import os

# create a benchling object
benchling = Benchling(
    url="https://navatx.benchling.com/",
    auth_method=ClientCredentialsOAuth2(
        client_id=os.environ["BENCHLING_CLIENT_ID"],
        client_secret=os.environ["BENCHLING_CLIENT_SECRET"],
    ),
)
connector = BenchlingConnector(benchling)

Get a record from Benchling¶

# Benchling id of a record
uid = "bfi_JXLZkNm4"
orm = sq.LNPFormulation

benchling_record = connector.get(uid, orm)
benchling_record.to_dict()

{'url': '/navatx_org/f/lib_6o0vJed2-registry/bfi_JXLZkNm4-asu-2-1-55-001/edit',
 'aliases': [],
 'apiURL': 'https://navatx.benchling.com/api/v2/custom-entities/bfi_JXLZkNm4',
 'archiveRecord': None,
 'authors': [{'handle': 'njustice', 'id': 'ent_opnJziEm', 'name': ''}],
 'createdAt': '2024-05-10T06:49:00.230799+00:00',
 'creator': {'handle': 'njustice', 'id': 'ent_opnJziEm', 'name': ''},
 'customFields': {'original LNP result ID': {'value': '3d430cd7-b475-4405-8c21-6f6feb23aca4'},
  'original entry of LNP result': {'value': 'EXP24000102'},
  'original mrna container ID': {'value': 'con_jN64CCvg'},
  'original mrna tube barcode': {'value': 'TUBE1806'}},
 'entityRegistryId': 'LNP_Form3668',
 'fields': {'5th Lipid Component Lot': {'displayValue': None,
   'isMulti': False,
   'textValue': None,
   'type': 'entity_link',
   'value': None},
  'Barcode': {'displayValue': 'GCTCAGCCTA',
   'isMulti': False,
   'textValue': 'GCTCAGCCTA',
   'type': 'entity_link',
   'value': 'seq_umV7zs9O'},
  'Cholesterol Lot': {'displayValue': 'Cholesterol-LOT001',
   'isMulti': False,
   'textValue': 'Cholesterol-LOT001',
   'type': 'entity_link',
   'value': 'mol_T0WRBAzR'},
  'Formulation Process': {'displayValue': 'Legacy Spark',
   'isMulti': False,
   'textValue': 'Legacy Spark',
   'type': 'entity_link',
   'value': 'bfi_u3wGuqKP'},
  'Ionizable Lipid Lot': {'displayValue': 'NAVA-101-LOT001',
   'isMulti': False,
   'textValue': 'NAVA-101-LOT001',
   'type': 'entity_link',
   'value': 'mol_iMmkNmWo'},
  'LNP Identity': {'displayValue': 'ASU-2.1.55',
   'isMulti': False,
   'textValue': 'ASU-2.1.55',
   'type': 'entity_link',
   'value': 'bfi_2sqCPJJV'},
  'Notes': {'displayValue': 'created as part of may 2024 data migration',
   'isMulti': False,
   'textValue': 'created as part of may 2024 data migration',
   'type': 'long_text',
   'value': 'created as part of may 2024 data migration'},
  'PEG Lot': {'displayValue': '14:0 PEG2000 PE-LOT001',
   'isMulti': False,
   'textValue': '14:0 PEG2000 PE-LOT001',
   'type': 'entity_link',
   'value': 'mol_imgZb5OV'},
  'Phospholipid Lot': {'displayValue': 'DSPC-LOT001',
   'isMulti': False,
   'textValue': 'DSPC-LOT001',
   'type': 'entity_link',
   'value': 'mol_gXfrJUeH'},
  'Study': {'displayValue': None,
   'isMulti': False,
   'textValue': None,
   'type': 'entity_link',
   'value': None},
  'Targeting Epitope Lot': {'displayValue': None,
   'isMulti': False,
   'textValue': None,
   'type': 'entity_link',
   'value': None},
  'mRNA Lot': {'displayValue': 'Dual_HA_Batch5',
   'isMulti': False,
   'textValue': 'Dual_HA_Batch5',
   'type': 'entity_link',
   'value': 'bfi_4VJpk1gB'},
  'sgRNA Lot': {'displayValue': None,
   'isMulti': False,
   'textValue': None,
   'type': 'entity_link',
   'value': None}},
 'folderId': 'lib_MLtpK6QT',
 'id': 'bfi_JXLZkNm4',
 'modifiedAt': '2024-09-28T12:32:37.387142+00:00',
 'name': 'ASU-2.1.55-001',
 'registrationOrigin': {'originEntryId': None,
  'registeredAt': '2024-05-10T06:49:00.230799+00:00'},
 'registryId': 'src_8XcPMnUA',
 'schema': {'id': 'ts_SKDXt9OA', 'name': 'LNP Formulation'},
 'webURL': 'https://navatx.benchling.com/navatx_org/f/lib_6o0vJed2-registry/bfi_JXLZkNm4-asu-2-1-55-001/edit'}

Register an LNPFormulation record in LaminDB¶

This automatically populates all related records.

lamindb_record = connector.save_to_lamindb(benchling_record)

! Field lot_number not found in CompoundLot, skipping

! Field molecular_weight not found in CompoundLot, skipping

! Field sku_catalog_ not found in CompoundLot, skipping

! Field formulation_process not found in LNPFormulation, skipping

! Field lot_number not found in CompoundLot, skipping

! Field molecular_weight not found in CompoundLot, skipping

! Field sku_catalog_ not found in CompoundLot, skipping

! Field cargo_targeting_epitope_ratio not found in LNPIdentity, skipping

! Field n_p_ratio not found in LNPIdentity, skipping

! Field mrna not found in LNPIdentity, skipping

! Field sgrna not found in LNPIdentity, skipping

! Field lot_number not found in CompoundLot, skipping

! Field molecular_weight not found in CompoundLot, skipping

! Field sku_catalog_ not found in CompoundLot, skipping

! Field lot_number not found in CompoundLot, skipping

! Field molecular_weight not found in CompoundLot, skipping

! Field sku_catalog_ not found in CompoundLot, skipping

! Field notes not found in mRNAlot, skipping

! Field plasmid not found in mRNAlot, skipping

! Field plasmid_lot not found in mRNAlot, skipping

! Field synthesis_protocols not found in mRNAlot, skipping

! Field n3_utr not found in mRNA, skipping

! Field n5_utr not found in mRNA, skipping

! Field plasmid not found in mRNA, skipping

Check direct fields:

lamindb_record.uid

'bfi_JXLZkNm4'

lamindb_record.name

'ASU-2.1.55-001'

lamindb_record.notes

'created as part of may 2024 data migration'

Check related records:

lamindb_record.lnp_identity

LNPIdentity(uid='bfi_2sqCPJJV', name='ASU-2.1.55', ionizable_lipid_mole_=45.0, cholesterol_mole_=44.0, peg_lipid_mole_=2.0, phospholipid_mole_=9.0, space_id=1, ionizable_lipid_id_id=2, cholesterol_id_id=1, peg_lipid_id_id=3, phospholipid_id_id=4)

lamindb_record.cholesterol_lot

CompoundLot(uid='mol_T0WRBAzR', name='Cholesterol-LOT001', vendor='Avanti Lipids', formula_mass=386.664, initial_nmr='[]', initial_lcms='[]', reaction_path='[]', additional_attachments='[]', space_id=1, compound_id=1)

lamindb_record.peg_lot

CompoundLot(uid='mol_imgZb5OV', name='14:0 PEG2000 PE-LOT001', vendor='Avanti Polar Lipids', formula_mass=2693.32, initial_nmr='[]', initial_lcms='[]', reaction_path='[]', additional_attachments='[]', space_id=1, compound_id=3)

lamindb_record.phospholipid_lot

CompoundLot(uid='mol_gXfrJUeH', name='DSPC-LOT001', vendor='Avanti Lipids', formula_mass=790.145, initial_nmr='[]', initial_lcms='[]', reaction_path='[]', additional_attachments='[]', space_id=1, compound_id=4)

lamindb_record.barcode

Barcode(uid='seq_umV7zs9O', name='GCTCAGCCTA', space_id=1)

Check all added records in LaminDB:

ln.view(modules="sentseqdb")

ADTBarcodes

	uid	name	concentration	clone	species_reactivity	payload_sentseq_align	space_id	_aux	_branch_code
id
1	seq_oigcgwiR	aVHH-isotype	None	Rabbit IgG control	sfso_N2OJeFSS	None	1	None	1

Barcode

	uid	name	description	space_id	_aux	_branch_code
id
1	seq_umV7zs9O	GCTCAGCCTA	None	1	None	1

Compound

	uid	name	type	number_of_ionizable_amines	structure	has_this_lipid_been_previously_screened	design_series	design_set	space_id	_aux	_branch_code
id
4	mol_EGPd7ouY	DSPC	sfso_ptdVXfbi	NaN	['72dee15c-fa38-4a8b-a4f2-2e9b02c68538']	None	sfso_DdB7k1wm	N/A	1	None	1
3	mol_1oHdLCNI	14:0 PEG2000 PE	sfso_zZeX1DAt	NaN	['a0453622-5b01-4320-aa4d-72207ac83af2']	None	sfso_DdB7k1wm	N/A	1	None	1
2	mol_PcjiZpzx	PME-002-191	sfso_WnhcaabR	2.0	['3c5b726e-d3e8-447d-ae48-b18d46841741']	sfso_HbjQc34F	sfso_7l71Cx9A	Maleimides	1	None	1
1	mol_OEAHjTyc	Cholesterol	sfso_rA0D4rtZ	NaN	['cbcd28ab-a82b-4101-a92b-713c23b15894']	None	sfso_DdB7k1wm	N/A	1	None	1

CompoundLot

	uid	name	vendor	formula_mass	salt	initial_nmr	initial_lcms	purity_	total_synthesis_amount_mg	reaction_path	additional_attachments	vendor_and_sku_catalog_	vendor_lot	space_id	compound_id	_aux	_branch_code
id
4	mol_gXfrJUeH	DSPC-LOT001	Avanti Lipids	790.145	None	[]	[]	None	None	[]	[]	None	None	1	4	None	1
3	mol_imgZb5OV	14:0 PEG2000 PE-LOT001	Avanti Polar Lipids	2693.320	None	[]	[]	None	None	[]	[]	None	None	1	3	None	1
2	mol_iMmkNmWo	NAVA-101-LOT001	None	774.360	None	['00a1b548-6313-4c80-8cc8-50f9d51ea0c7']	[]	None	None	[]	[]	None	None	1	2	None	1
1	mol_T0WRBAzR	Cholesterol-LOT001	Avanti Lipids	386.664	None	[]	[]	None	None	[]	[]	None	None	1	1	None	1

HTObarcodes

	uid	name	antibody	concentration	clone	species_reactivity	space_id	_aux	_branch_code
id
1	seq_3zTG56qb	DEPRICATED Mouse HTO 1	H-2	1.0	M1/42	sfso_30Eey9Vx	1	None	1

LNPFormulation

	uid	name	notes	space_id	lnp_identity_id	ionizable_lipid_lot_id	cholesterol_lot_id	peg_lot_id	phospholipid_lot_id	n5th_lipid_component_lot_id	targeting_epitope_lot_id	mrna_lot_id	sgrna_lot_id	barcode_id	study_id	_aux	_branch_code
id
1	bfi_JXLZkNm4	ASU-2.1.55-001	created as part of may 2024 data migration	1	1	2	1	3	4	None	None	1	None	1	None	None	1

LNPIdentity

	uid	name	lnp_number	chemical_class	screen_number	iteration_number	ionizable_lipid_mole_	cholesterol_mole_	peg_lipid_mole_	phospholipid_mole_	n5th_lipid_component_mole_	lipid_rna_mass_ratio	space_id	ionizable_lipid_id_id	cholesterol_id_id	peg_lipid_id_id	phospholipid_id_id	n5th_lipid_component_id_id	targeting_epitope_identity_id	_aux	_branch_code
id
1	bfi_2sqCPJJV	ASU-2.1.55	None	None	None	None	45.0	44.0	2.0	9.0	None	None	1	2	1	3	4	None	None	None	1

mRNA

	uid	name	description	cleancap	notes	space_id	_aux	_branch_code
id
1	seq_dvBAh0Yt	Dual_HA_aVHH_mRNA	None	None	None	1	None	1

mRNAlot

	uid	name	manufacture_date	vendor	vendor_lot	space_id	mrna_id	_aux	_branch_code
id
1	bfi_4VJpk1gB	Dual_HA_Batch5	None	None	None	1	1	None	1

Bionty registries¶

Create a Bionty record from public ontology:

import bionty as bt

tissue = bt.Tissue.from_source(name="brain")
tissue.save()

Tissue(uid='1fIFAQJY', name='brain', ontology_id='UBERON:0000955', description='The Brain Is The Center Of The Nervous System In All Vertebrate, And Most Invertebrate, Animals. Some Primitive Animals Such As Jellyfish And Starfish Have A Decentralized Nervous System Without A Brain, While Sponges Lack Any Nervous System At All. In Vertebrates, The Brain Is Located In The Head, Protected By The Skull And Close To The Primary Sensory Apparatus Of Vision, Hearing, Balance, Taste, And Smell[Wp].', space_id=1, created_by_id=1, source_id=41, created_at=2025-03-11 14:49:48 UTC)

sq_tissue = sq.Tissue(bionty_id=tissue.id, uid=tissue.uid, name=tissue.name).save()

sq_tissue.bionty

Tissue(uid='1fIFAQJY', name='brain', ontology_id='UBERON:0000955', description='The Brain Is The Center Of The Nervous System In All Vertebrate, And Most Invertebrate, Animals. Some Primitive Animals Such As Jellyfish And Starfish Have A Decentralized Nervous System Without A Brain, While Sponges Lack Any Nervous System At All. In Vertebrates, The Brain Is Located In The Head, Protected By The Skull And Close To The Primary Sensory Apparatus Of Vision, Hearing, Balance, Taste, And Smell[Wp].', space_id=1, created_by_id=1, source_id=41, created_at=2025-03-11 14:49:48 UTC)