BE-dataHIVE API (1.0.0)

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E-mail: lucas.schneider@cs.ox.ac.uk License: Apache 2.0

BE-dataHIVE - Base Editing Data API. Python wrapper for the API is available on Github.

Studies

Provides an overview of the included studies

query Parameters

id	string study id of interest
year	integer [ 0 .. 2022 ] publication year of study
base-editor	string base editors covered by publication supplied as tuple ('ABE'), ('CBE') or ('ABE, CBE') or any combination

Responses

Response samples

Content type

application/json

[{"id": 1,
"title": "Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning",
"authors": "Arbab et al.",
"year": 2020,
"journal": "Cell",
"citations": 56,
"data": "38,538 total pairs of sgRNAs and target sequences integrated into three mammalian cell types",
"model": "BE-Hive",
"base_editors": "ABE, CBE",
"prediction_score": "Editing Efficiency R= 0.70, Editing Outcome R= 0.90",
"description": "Develop the BE-Hive machine learning model to predict base editing efficiency and editing patterns",
"study_link": "https://www.sciencedirect.com/science/article/pii/S0092867420306322",
"links": "Paper: https://www.sciencedirect.com/science/article/pii/S0092867420306322  Software: https://www.crisprbehive.design/  Code: https://github.com/maxwshen/lib-dataprocessing, https://github.com/maxwshen/lib-analysis  Data: 10.6084/m9.figshare.10673816, 10.6084/m9.figshare.10678097"
}
]

Efficiency

Base editing efficiency data

Retrieves base editing efficiency data. Please batch requests via limit and offset parameters when querying the full database.

query Parameters

limit	integer limit
offset	integer offset
id	integer id
original_id	string original study id (e.g., 1_BE4_ontargetpos_editpos6_mES_AID)
study_id	integer study id of interest
gRNA	string guide RNA
sequence	string target sequence
full_context_sequence	string full context sequence of the target - this includes more bases than the sequence field
pam_sequence	string PAM sequence (e.g., GGG)
grna_sequence_match	boolean flag indicating if gRNA matches a sequence in the target exactly
cell	string cell line (e.g., HEK293T, U2OS, mES, K562)
base-editor	string base editor (e.g., AID, ABE)

Responses

Response samples

Content type

application/json

[{"id": 0,
"original_id": "1_BE4_ontargetpos_editpos6_mES_AID",
"grna": "GCATCCGCGTGAGAACCGCA",
"pam_sequence": "GGG",
"sequence": "ACCAAGGGCTGCATCCGCGTGAGAACCGCAGGGAGCAGCT",
"full_context_sequence": "AACCAAGGGCTGCATCCGCGTGAGAACCGCAGGGAGCAGCTGGGGAGGGGACCTAG",
"full_context_sequence_padded": "NNNNNNNNNNNNNNNNNNNNNNNNNNAACCAAGGGCTGCATCCGCGTGAGAACCGCAGGGAGCAGCTGGGGAGGGGACCTAGNNNNNNNNNNNNN",
"protospace_position": 11,
"pam_index": 31,
"grna_sequence_match": true,
"cell": "mES",
"base_editor": "AID",
"total_count_reported_efficiency": 995,
"edited_count_reported_efficiency": 849,
"total_count": 996,
"edited_count": 849,
"efficiency_full_grna_reported": 0.852409639,
"editing_windows_3_10_efficiency_reported": 0,
"efficiency_full_grna_calculated": 0,
"editing_windows_3_10_efficiency_calculated": 0,
"energy_1": 0,
"energy_2": 0,
"energy_3": 0,
"energy_4": 0,
"energy_5": 0,
"energy_6": 0,
"energy_7": 15.8321002,
"energy_8": 21.26733113,
"energy_9": 46.60733113,
"energy_10": 18.1321002,
"energy_11": 23.56733113,
"energy_12": 48.90733113,
"energy_13": 0,
"energy_14": 0,
"energy_15": 0,
"energy_16": 0,
"energy_17": 0,
"energy_18": 0,
"energy_19": -6.575230939,
"energy_20": -1.14,
"energy_21": 24.2,
"energy_22": -4.275230939,
"energy_23": 1.16,
"energy_24": 26.5,
"free_energy": -2.3,
"melt_temperature_grna": 60.38281374,
"melt_temperature_target": 60.38281374,
"study_id": 1,
"one_hot_grna": "numpy array encoded as bytestring",
"one_hot_pam_sequence": "numpy array encoded as bytestring",
"one_hot_sequence": "numpy array encoded as bytestring",
"one_hot_full_context_sequence": "numpy array encoded as bytestring",
"one_hot_full_context_sequence_padded": "numpy array encoded as bytestring",
"hilbert_curve_grna": "numpy array encoded as bytestring",
"hilbert_curve_pam_sequence": "numpy array encoded as bytestring",
"hilbert_curve_sequence": "numpy array encoded as bytestring",
"hilbert_curve_full_context_sequence": "numpy array encoded as bytestring",
"hilbert_curve_full_context_sequence_padded": "numpy array encoded as bytestring"
}
]

Bystander

Base editing bystander data

Retrieves base editing bystander data. Please batch requests via limit and offset parameters when querying the full database.

query Parameters

limit	integer limit
offset	integer offset
id	integer id
original_id	string original study id (e.g., 1_BE4_ontargetpos_editpos6_mES_AID)
study_id	integer study id of interest
gRNA	string guide RNA
sequence	string target sequence
full_context_sequence	string full context sequence of the target - this includes more bases than the sequence field
pam_sequence	string PAM sequence (e.g., GGG)
grna_sequence_match	boolean flag indicating if gRNA matches a sequence in the target exactly
cell	string cell line (e.g., HEK293T, U2OS, mES, K562)
base-editor	string base editor (e.g., AID, ABE)

Responses

Response samples

Content type

application/json

[{"id": 0,
"original_id": "1_BE4_ontargetpos_editpos6_mES_AID",
"grna": "GCATCCGCGTGAGAACCGCA",
"pam_sequence": "GGG",
"sequence": "ACCAAGGGCTGCATCCGCGTGAGAACCGCAGGGAGCAGCT",
"full_context_sequence": "AACCAAGGGCTGCATCCGCGTGAGAACCGCAGGGAGCAGCTGGGGAGGGGACCTAG",
"full_context_sequence_padded": "NNNNNNNNNNNNNNNNNNNNNNNNNNAACCAAGGGCTGCATCCGCGTGAGAACCGCAGGGAGCAGCTGGGGAGGGGACCTAGNNNNNNNNNNNNN",
"protospace_position": 11,
"pam_index": 31,
"grna_sequence_match": true,
"cell": "mES",
"base_editor": "AID",
"total_count": 996,
"edited_count": 849,
"Position_-11": 0,
"Position_-10": 0,
"Position_-9": 0,
"Position_-8": 0,
"Position_-7": 0,
"Position_-6": 0.997644287,
"Position_-5": 0,
"Position_-4": 0,
"Position_-3": 0,
"Position_-2": 0,
"Position_-1": 1,
"Position_0": 0.939929329,
"Position_1": 0,
"Position_2": 1,
"Position_3": 1,
"Position_4": 0,
"Position_5": 0,
"Position_6": 0.96819788,
"Position_7": 1,
"Position_8": 0,
"Position_9": 1,
"Position_10": 0,
"Position_11": 0,
"Position_12": 0,
"Position_13": 0,
"Position_14": 0,
"Position_15": 0,
"Position_16": 0,
"Position_17": 0.001177856,
"Position_18": 1,
"Position_19": 0,
"Position_20": 1,
"Position_21": 0,
"Position_22": 0,
"Position_23": 0,
"Position_24": 0,
"Position_25": 0,
"Position_26": 0,
"Position_27": 0,
"Position_28": 0,
"Position_29": 0,
"Position_30": 0,
"Position_-11 A": 0,
"Position_-11 T": 0,
"Position_-11 C": 0,
"Position_-11 G": 0,
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"Position_-10 G": 0,
"Position_-9 A": 0.852409639,
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"Position_-7 G": 0,
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"Position_-6 T": 0.080321285,
"Position_-6 C": 0.770080321,
"Position_-6 G": 0,
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"Position_-4 G": 0,
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"Position_-3 T": 0,
"Position_-3 C": 0,
"Position_-3 G": 0,
"Position_-2 A": 0,
"Position_-2 T": 0,
"Position_-2 C": 0,
"Position_-2 G": 0,
"Position_-1 A": 0,
"Position_-1 T": 0,
"Position_-1 C": 0,
"Position_-1 G": 0.852409639,
"Position_0 A": 0,
"Position_0 T": 0.051204819,
"Position_0 C": 0.801204819,
"Position_0 G": 0,
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"Position_1 T": 0,
"Position_1 G": 0,
"Position_1 C": 0,
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"Position_2 G": 0,
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"Position_5 C": 0.852409639,
"Position_5 G": 0,
"Position_6 A": 0,
"Position_6 T": 0.825301205,
"Position_6 C": 0.027108434,
"Position_6 G": 0,
"Position_7 A": 0,
"Position_7 T": 0.790160643,
"Position_7 C": 0.062248996,
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"Position_8 G": 0,
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"Position_9 C": 0.124497992,
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"Position_12 A": 0.852409639,
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"Position_13 G": 0.852409639,
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"Position_14 C": 0,
"Position_14 G": 0,
"Position_15 A": 0.852409639,
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"Position_25 A": 0,
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"Position_25 C": 0,
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"Position_29 T": 0,
"Position_29 C": 0.852409639,
"Position_29 G": 0,
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"Position_30 T": 0.852409639,
"Position_30 C": 0,
"Position_30 G": 0,
"energy_1": 0,
"energy_2": 0,
"energy_3": 0,
"energy_4": 0,
"energy_5": 0,
"energy_6": 0,
"energy_7": 15.8321002,
"energy_8": 21.26733113,
"energy_9": 46.60733113,
"energy_10": 18.1321002,
"energy_11": 23.56733113,
"energy_12": 48.90733113,
"energy_13": 0,
"energy_14": 0,
"energy_15": 0,
"energy_16": 0,
"energy_17": 0,
"energy_18": 0,
"energy_19": -6.575230939,
"energy_20": -1.14,
"energy_21": 24.2,
"energy_22": -4.275230939,
"energy_23": 1.16,
"energy_24": 26.5,
"free_energy": -2.3,
"melt_temperature_grna": 60.38281374,
"melt_temperature_target": 60.38281374,
"study_id": 1,
"one_hot_grna": "numpy array encoded as bytestring",
"one_hot_pam_sequence": "numpy array encoded as bytestring",
"one_hot_sequence": "numpy array encoded as bytestring",
"one_hot_full_context_sequence": "numpy array encoded as bytestring",
"one_hot_full_context_sequence_padded": "numpy array encoded as bytestring",
"hilbert_curve_grna": "numpy array encoded as bytestring",
"hilbert_curve_pam_sequence": "numpy array encoded as bytestring",
"hilbert_curve_sequence": "numpy array encoded as bytestring",
"hilbert_curve_full_context_sequence": "numpy array encoded as bytestring",
"hilbert_curve_full_context_sequence_padded": "numpy array encoded as bytestring"
}
]