obophenotype / obophenotype/uberon
Deconvolute non-standard prefixes
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tech
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- Emacs Lisp
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Description
The following prefixes show up in various places in UBERON but they are not in the Bioregistry, based on the OQUAT analysis in https://biopragmatics.github.io/oquat/unknowns/source/uberon and https://biopragmatics.github.io/oquat/invalids/source/uberon:
Generated by the following code:
from tabulate import tabulate
from collections import Counter
import requests
def main():
url = "https://raw.githubusercontent.com/biopragmatics/oquat/main/results/uberon.json"
data = requests.get(url).json()
counter = Counter()
examples = {}
for data in data["results"].values():
for key in ["synonym_pack", "prov_pack", "xref_pack"]:
for prefix, uri_to_value_dict in data[key]["unknown_prefixes"].items():
counter[prefix] += len(uri_to_value_dict)
examples[prefix] = list(uri_to_value_dict.items())[0]
rows = [(prefix, count, *examples[prefix]) for prefix, count in counter.most_common()]
print(
tabulate(
rows, headers=["prefix", "count", "example_node", "example_val"], tablefmt="github"
)
)
if __name__ == "__main__":
main()
Any help figuring out what these are and how they're used would be appreciated!
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