Frequently Asked Questions

Codebook

How do you perform the Base62 encoding for species

See below an example of a Python code to create the encoding for species

 #!/usr/bin/env python3
import sys

ALPHABET = '0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz'
BASE = len(ALPHABET)  # 62
MAX_VALUE = BASE ** 2  # 3844

def encode_base62(num: int) -> str:
    """
    Encode an integer in the range [0, 3843] to a 2-character Base62 string.
    """
    if not (0 <= num < MAX_VALUE):
        raise ValueError(f'Number out of range (0 ≤ num < {MAX_VALUE}), got {num}')
    high = num // BASE
    low = num % BASE
    return ALPHABET[high] + ALPHABET[low]

def main():
    for n in range(MAX_VALUE):
        print(f'{n}\t{encode_base62(n)}')

if __name__ == '__main__':
    main()

last change 2025-08-01 by Manuel Rueda

For condition do I need to encode to ICD-10 before ClariD-Tools?

Yes, Clarid-Tools reads ICD-10 diagnoses codes. Take look to this documentation).

last change 2025-07-21 by Manuel Rueda

Can I include multiple ICD-10 diagnose codes?

Yes.

• Command-line: --condition C22.1,C22.2 (comma separated)
• Bulk (CSV): Separate them by ; (semicolon)

The maximum is set with the parameter --max-conditions that defaults to 10. We reserve 2 chars for that field so the limit will be 99 conditions.

last change 2025-08-10 by Manuel Rueda

Which ICD-10 code should I use when no specific disease is available?

Since we rely on ICD-10 coding, we have selected code Z00.00 ("Encounter for general adult medical examination without abnormal findings").

If you believe there's a more appropriate code for this context, please feel free to suggest it .

last change 2025-08-10 by Manuel Rueda

General

How do I cite clarid-tools?

You can cite the Clarid-Tools paper. Thx!

Citation

Manuel Ruedan and Ivo G. Gut (2025). ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration. Submitted.