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API Reference

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Important update

The APIs described below are out-of-date and will not be supported soon. For the up-to-date APIs, please refer to the our preprint at BioRxiv (Supplementary Table 4):

FinaleDB: a browser and database of cell-free DNA fragmentation patterns Haizi Zheng, Michelle S Zhu, Yaping Liu bioRxiv 2020.08.18.255885; doi: https://doi.org/10.1101/2020.08.18.255885arrow-up-right

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Authentication

Currently, FinaleDB doesn't require authentication to use its API.

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FinaleDB summary

GET http://finaledb.research.cchmc.org/api/v1/summary

This endpoint returns you a summary report about FinaleDB.

{
    "http://localhost:5000/samples?frag_num=38084192,38084196": 2579,
    "sampleCnt": 2505,
    "instrument": {
        "NextSeq 500": 141,
        "HiSeq 4000": 5,
        "NovaSeq 6000": 3
    },
    "disease": {
        "Colorectal cancer": 48,
        "Liver cancer": 93,
        "Ovarian cancer": 30,
        "Hepatitis B": 67
    },
    "tissue": {
        "urine": 139
    },
    "assay": {
        "WGS": 2572,
        "WXS": 7
    }
}

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Make queries

GET http://finaledb.research.cchmc.org/api/v1/seqrun

Returns a list of records matching filters and queries terms specified by this API. Example: the following request will blindly return the first 5 records in the dataset: http://finaledb.research.cchmc.org/api/v1/seqrun?limit=5

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Query Parameters

Name
Type
Description

offset

integer

Specify the offset of the returned items

limit

integer

Return entries associated with certain samples.

disease

string

Return entries associated with the specified pathological condition

tissue

string

Return entries associated with the specified tissue.

ID

string

Database entry ID

frag_num

string

Format: min_value,max_value. For example: frag_num=38713820,38713890. Return entries with the number of fragments between the range.

instrument

boolean

Return entries sequenced by the specified sequencing instrument.

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