The metadata for CRISPR pertubation

[dahw0706]

Hi, we are conducting some analysis using the CRISPR pertubation dataset and wonder if there is a way to retrieve the detail informaiton (ex. disease, cell line, pert time) from individual CRISPR pertubation data. It seems there is only metadata of small molecule pertubation metadata available from download page. Thanks!

[jeevangelista]

Hi @dahw0706, We don't have the metadata for the CRISPR signatures on the download page at the moment, we'll work on making this information more accessible. Meanwhile, you can query the API to get this information:

import json
import time
limit = 5000
skip = 0

payload = {
    "limit": limit,
    "fields": ["meta"]
}
metadata = []
while True:
    payload["skip"] = skip
    # the UUID is the id of the CRISPR daataset
    res = requests.get("https://maayanlab.cloud/sigcom-lincs/metadata-api/libraries/96c7b8c5-1eca-5764-88e4-e4ccaee6603f/signatures?filter=%s"%json.dumps(payload))
    time.sleep(1)
    if not res.ok:
        break
    else:
        signatures = res.json()
        metadata = metadata + signatures
        skip = skip + limit
        if len(signatures) < limit:
            break

It should return a list with the information you are requesting

{
    "meta": {
        "md5": "41c9bfbd5049e0ec8d3b6a6242bb383f",
        "doid": "DOID:2526",
        "sha256": "f223ca7d3cd7e36eeb3ef5a718543abce8e5e9f5e5d0bf0c8c06aa001d3ea058",
        "tissue": "prostate gland",
        "anatomy": "UBERON:0002367",
        "cmap_id": "XPR036_PC3.311B_96H:M10",
        "disease": "prostate adenocarcinoma",
        "version": 1,
        "filename": "L1000_LINCS_DCIC_XPR036_PC3.311B_96H_M10_PAK2.tsv",
        "local_id": "XPR036_PC3.311B_96H_M10_PAK2",
        "cell_line": "PC3",
        "pert_name": "PAK2",
        "pert_time": "96 h",
        "pert_type": "CRISPR Knockout",
        "$validator": "https://raw.githubusercontent.com/MaayanLab/sigcom-lincs/main/validators/l1000_signatures.json",
        "data_level": 5,
        "creation_time": "2021-05-25",
        "persistent_id": "https://lincs-dcic.s3.amazonaws.com/LINCS-sigs-2021/cd/xpr/L1000_LINCS_DCIC_XPR036_PC3.311B_96H_M10_PAK2.tsv",
        "size_in_bytes": 217281,
        "$download_counter": 1,
        "uncompressed_size_in_bytes": 217281
    }
}

[dahw0706]

Hi, @jeevangelista. Thanks for the reply and information. It is quite helpful. Again, really appreciate the work and the data shared by the lab/team!