cthoyt

Hierarchical Synonym Type Demo

This demonstration goes along with information-artifact-ontology/ontology-metadata#194 to show what happens when ROBOT tries to convert an ontology that has hierarchical synonym type properties.

Unfortunately, it doesn't appear to write the child property in OBO. This is probably because the parser only looks for direct children of oboInOwl:SynonymTypeProperty

cthoyt

import bioregistry
import quickstatements_client
import sssom
from curies.dataframe import filter_df_by_curies, filter_df_by_prefixes
from quickstatements_client import Line, Qualifier, TextLine, TextQualifier
from sssom import MappingSetDataFrame


def open_quickstatements_tab(msdf: MappingSetDataFrame) -> None:
    """Create a QuickStatements tab from mappings."""

cthoyt

cthoyt

# /// script
# requires-python = ">=3.11"
# dependencies = [
#     "clinicaltrials-downloader>=0.0.2",
#     "pyobo[grounding]",
#     "tabulate",
#     "pystow",
#     "click",
# ]
#

cthoyt

# /// script
# requires-python = ">=3.11"
# dependencies = [
#     "beautifulsoup4",
#     "requests",
#     "yt-dlp",
# ]
# ///

"""Download chapters from Wind and Truth.

cthoyt

import json

import bioregistry

if __name__ == "__main__":
    r = json.load(open("mismatch.json"))
    with open("mismatches.sssom.tsv", "w") as file:
        print(
            "subject_id",
            "subject_label",

cthoyt

from typing import Any

from snapquery.snapquery_core import QueryName, NamedQueryManager, QueryBundle

#: See documentation at https://snapquery.bitplan.com/docs
API_ENDPOINT_FMT = "https://snapquery.bitplan.com/api/query/{domain}/{namespace}/{name}"

type Result = dict[str, Any]
type Results = list[Result]

cthoyt

import bioregistry
from pydantic.functional_validators import AfterValidator


def validate_local_identifier(prefix: str) -> AfterValidator:
    """Make a validator function based on a Bioregistry prefix.

    Example usage:

    .. code-block:: python

cthoyt

from tabulate import tabulate

import bioregistry

if __name__ == "__main__":
    rows = []
    for resource in bioregistry.resources():
        if resource.is_deprecated():
            continue
        if resource.get_contact():

cthoyt

import requests
from dateutil.parser import parse

res_json = requests.get(
  f'https://pypi.org/pypi/bioregistry/json', 
  headers={'Accept': 'application/json'}
).json()

releases = {
    parse(data[0]['upload_time']): version