diff --git a/build.py b/build.py index 5cfafde..184f56f 100644 --- a/build.py +++ b/build.py @@ -24,24 +24,24 @@ from textwrap import dedent from typing import TypedDict +import bioontologies.version +import bioregistry +import bioregistry.version import click import pystow.utils import yaml +from bioontologies.robot import convert from more_click import verbose_option from tabulate import tabulate from tqdm import tqdm from tqdm.contrib.logging import logging_redirect_tqdm from typing_extensions import NotRequired + import pyobo.constants import pyobo.version from pyobo import Obo from pyobo.sources import ontology_resolver -import bioontologies.version -import bioregistry -import bioregistry.version -from bioontologies.robot import convert - BASE_PURL = "https://w3id.org/biopragmatics/resources" HERE = Path(__file__).parent.resolve() DATA = HERE.joinpath("docs", "_data") @@ -163,15 +163,19 @@ def _get_summary(obo: Obo) -> dict: len(values) for term in terms for values in term.relationships.values() ), "properties": sum( - len(values) for term in terms for values in term.properties.values() + len(values) + for term in terms + for dd in [term.annotations_literal, term.annotations_object] + for values in dd.values() ), "synonyms": sum(len(term.synonyms) for term in terms), - "xrefs": sum(len(term.xrefs) for term in terms), + "mappings": sum(len(term.get_mappings(include_xrefs=True)) for term in terms), "alts": sum(len(term.alt_ids) for term in terms), "parents": sum(len(term.parents) for term in terms), "references": sum(len(term.provenance) for term in terms), "definitions": sum(term.definition is not None for term in terms), "version": obo.data_version, + "license": bioregistry.get_license(obo.ontology), } return rv @@ -253,7 +257,7 @@ def _make( _write_nodes(names_path, obo, prefix) _, rv["nodes"] = _prepare_artifact(prefix, names_path, has_version, ".tsv.gz") - sssom_df = pyobo.get_sssom_df(obo, names=False) + sssom_df = pyobo.get_mappings_df(obo, names=False) sssom_df.to_csv(sssom_path, sep="\t", index=False) _, rv["sssom"] = _prepare_artifact(prefix, sssom_path, has_version, ".sssom.tsv.gz") @@ -306,20 +310,25 @@ def _make( # Write a README file, so anyone who navigates there can see what's going on summary = sorted((k, v) for k, v in rv["summary"].items() if k != "version") - text = dedent(f"""\ + text = ( + dedent(f"""\ # {bioregistry.get_name(prefix)} {bioregistry.get_description(prefix)} +**License**: {bioregistry.get_license(prefix) or '_unlicensed_'} + ## PURLs -{tabulate(purls_table_rows, headers=['Artifact', 'Download PURL', 'Versioned Download PURL'], tablefmt="github")} +{tabulate(purls_table_rows, headers=['Artifact', 'Download PURL', 'Latest Versioned Download PURL'], tablefmt="github")} ## Summary {tabulate(summary, headers=['field', 'count'], tablefmt='github')} """).strip() + + "\n" + ) readme_path.write_text(text) return rv @@ -330,8 +339,8 @@ def _make( @click.option("-m", "--minimum") @click.option("--no-convert", is_flag=True) @click.option("-x", "--xvalue", help="Select a specific ontology", multiple=True) -@click.option("-w", "--no-force", is_flag=True) -def main(minimum: str | None, xvalue: list[str], no_convert: bool, no_force: bool): +@click.option("--force/--no-force") +def main(minimum: str | None, xvalue: list[str], no_convert: bool, force: bool): """Build the PyOBO examples.""" if xvalue: for prefix in xvalue: @@ -345,6 +354,10 @@ def main(minimum: str | None, xvalue: list[str], no_convert: bool, no_force: boo else: prefixes = PREFIXES + for prefix in prefixes: + if not bioregistry.get_license(prefix): + click.secho(f"missing license for `{prefix}`", fg="yellow") + it = [(prefix, ontology_resolver.lookup(prefix)) for prefix in prefixes] it = tqdm(it, desc="Making OBO examples") @@ -359,7 +372,7 @@ def main(minimum: str | None, xvalue: list[str], no_convert: bool, no_force: boo prefix=prefix, module=cls, do_convert=not no_convert, - no_force=no_force, + no_force=not force, ) except Exception as e: tqdm.write(click.style(f"[{prefix}] {e}", fg="red")) diff --git a/docs/_data/manifest.yml b/docs/_data/manifest.yml index 07b697f..06fb4af 100644 --- a/docs/_data/manifest.yml +++ b/docs/_data/manifest.yml @@ -1,4 +1,4 @@ -date: '2024-11-04' +date: '2024-11-26' resources: cgnc: nodes: @@ -24,14 +24,14 @@ resources: summary: alts: 0 definitions: 0 + mappings: 41332 parents: 0 - properties: 0 + properties: 41332 references: 0 - relations: 67353 + relations: 26021 synonyms: 27221 terms: 26021 version: null - xrefs: 41332 complexportal: nodes: gzipped: false @@ -66,14 +66,14 @@ resources: summary: alts: 0 definitions: 4841 + mappings: 9863 parents: 0 - properties: 0 + properties: 19802 references: 12655 - relations: 24643 + relations: 4841 synonyms: 12156 terms: 4841 version: '2024-09-08' - xrefs: 9865 dictybase.gene: nodes: gzipped: false @@ -98,6 +98,7 @@ resources: summary: alts: 0 definitions: 0 + mappings: 0 parents: 0 properties: 0 references: 0 @@ -105,7 +106,6 @@ resources: synonyms: 16000 terms: 14222 version: null - xrefs: 0 drugcentral: nodes: gzipped: false @@ -140,14 +140,14 @@ resources: summary: alts: 0 definitions: 3267 + mappings: 76519 parents: 0 - properties: 8620 + properties: 17913 references: 0 - relations: 9293 + relations: 0 synonyms: 19053 terms: 4995 version: '54' - xrefs: 76519 eccode: nodes: gzipped: false @@ -168,11 +168,11 @@ resources: version_iri: https://w3id.org/biopragmatics/resources/eccode/2024-10-02/eccode.json version_path: eccode/2024-10-02/eccode.json owl: - gzipped: true - iri: https://w3id.org/biopragmatics/resources/eccode/eccode.owl.gz - path: eccode/eccode.owl.gz - version_iri: https://w3id.org/biopragmatics/resources/eccode/2024-10-02/eccode.owl.gz - version_path: eccode/2024-10-02/eccode.owl.gz + gzipped: false + iri: https://w3id.org/biopragmatics/resources/eccode/eccode.owl + path: eccode/eccode.owl + version_iri: https://w3id.org/biopragmatics/resources/eccode/2024-10-02/eccode.owl + version_path: eccode/2024-10-02/eccode.owl sssom: gzipped: false iri: https://w3id.org/biopragmatics/resources/eccode/eccode.sssom.tsv @@ -182,14 +182,14 @@ resources: summary: alts: 0 definitions: 0 + mappings: 0 parents: 7244 - properties: 0 + properties: 254949 references: 0 - relations: 259726 + relations: 4777 synonyms: 10465 terms: 8736 version: '2024-10-02' - xrefs: 0 flybase: nodes: gzipped: false @@ -224,6 +224,7 @@ resources: summary: alts: 0 definitions: 35702 + mappings: 0 parents: 35298 properties: 0 references: 0 @@ -231,7 +232,48 @@ resources: synonyms: 24869 terms: 35702 version: '2024_05' - xrefs: 0 + gtdb: + nodes: + gzipped: true + iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.tsv.gz + path: gtdb/gtdb.tsv.gz + version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.tsv.gz + version_path: gtdb/220/gtdb.tsv.gz + obo: + gzipped: true + iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.obo.gz + path: gtdb/gtdb.obo.gz + version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.obo.gz + version_path: gtdb/220/gtdb.obo.gz + obograph: + gzipped: false + iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.json + path: gtdb/gtdb.json + version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.json + version_path: gtdb/220/gtdb.json + owl: + gzipped: false + iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.owl + path: gtdb/gtdb.owl + version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.owl + version_path: gtdb/220/gtdb.owl + sssom: + gzipped: false + iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.sssom.tsv + path: gtdb/gtdb.sssom.tsv + version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.sssom.tsv + version_path: gtdb/220/gtdb.sssom.tsv + summary: + alts: 0 + definitions: 0 + mappings: 596859 + parents: 3581154 + properties: 4178013 + references: 0 + relations: 0 + synonyms: 0 + terms: 4178013 + version: '220' hgnc: nodes: gzipped: false @@ -266,14 +308,14 @@ resources: summary: alts: 0 definitions: 43882 + mappings: 260015 parents: 43882 - properties: 44134 + properties: 295301 references: 34994 - relations: 402851 + relations: 151684 synonyms: 105217 terms: 43882 version: '2024-10-01' - xrefs: 260015 hgnc.genegroup: nodes: gzipped: false @@ -308,6 +350,7 @@ resources: summary: alts: 0 definitions: 730 + mappings: 0 parents: 1885 properties: 0 references: 1612 @@ -315,7 +358,6 @@ resources: synonyms: 1160 terms: 1815 version: '2024-10-01' - xrefs: 0 interpro: nodes: gzipped: false @@ -350,6 +392,7 @@ resources: summary: alts: 0 definitions: 0 + mappings: 0 parents: 8976 properties: 46035 references: 0 @@ -357,7 +400,6 @@ resources: synonyms: 0 terms: 46035 version: '102.0' - xrefs: 0 kegg.genome: nodes: gzipped: false @@ -392,6 +434,7 @@ resources: summary: alts: 0 definitions: 0 + mappings: 0 parents: 0 properties: 0 references: 0 @@ -399,7 +442,6 @@ resources: synonyms: 0 terms: 10682 version: '112.0' - xrefs: 0 mesh: nodes: gzipped: false @@ -434,6 +476,7 @@ resources: summary: alts: 0 definitions: 30613 + mappings: 0 parents: 42021 properties: 0 references: 0 @@ -441,39 +484,48 @@ resources: synonyms: 634143 terms: 354471 version: '2024' - xrefs: 0 mgi: nodes: gzipped: false iri: https://w3id.org/biopragmatics/resources/mgi/mgi.tsv path: mgi/mgi.tsv + version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.tsv + version_path: mgi/6.24/mgi.tsv obo: gzipped: true iri: https://w3id.org/biopragmatics/resources/mgi/mgi.obo.gz path: mgi/mgi.obo.gz + version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.obo.gz + version_path: mgi/6.24/mgi.obo.gz obograph: gzipped: true iri: https://w3id.org/biopragmatics/resources/mgi/mgi.json.gz path: mgi/mgi.json.gz + version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.json.gz + version_path: mgi/6.24/mgi.json.gz owl: gzipped: true iri: https://w3id.org/biopragmatics/resources/mgi/mgi.owl.gz path: mgi/mgi.owl.gz + version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.owl.gz + version_path: mgi/6.24/mgi.owl.gz sssom: gzipped: false iri: https://w3id.org/biopragmatics/resources/mgi/mgi.sssom.tsv path: mgi/mgi.sssom.tsv + version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.sssom.tsv + version_path: mgi/6.24/mgi.sssom.tsv summary: alts: 0 - definitions: 719749 + definitions: 719756 + mappings: 168405 parents: 0 - properties: 0 + properties: 111831 references: 0 - relations: 1042386 - synonyms: 259738 - terms: 719749 - version: null - xrefs: 168405 + relations: 930562 + synonyms: 259761 + terms: 719756 + version: '6.24' mirbase: nodes: gzipped: false @@ -508,6 +560,7 @@ resources: summary: alts: 0 definitions: 38589 + mappings: 8814 parents: 0 properties: 0 references: 0 @@ -515,7 +568,6 @@ resources: synonyms: 1441 terms: 38589 version: '22.1' - xrefs: 8814 mirbase.family: nodes: gzipped: false @@ -550,6 +602,7 @@ resources: summary: alts: 0 definitions: 0 + mappings: 0 parents: 0 properties: 0 references: 0 @@ -557,7 +610,6 @@ resources: synonyms: 0 terms: 19907 version: '22.1' - xrefs: 0 mirbase.mature: nodes: gzipped: false @@ -592,6 +644,7 @@ resources: summary: alts: 0 definitions: 0 + mappings: 0 parents: 0 properties: 0 references: 0 @@ -599,7 +652,6 @@ resources: synonyms: 7179 terms: 49168 version: '22.1' - xrefs: 0 npass: nodes: gzipped: false @@ -634,6 +686,7 @@ resources: summary: alts: 0 definitions: 0 + mappings: 103085 parents: 0 properties: 0 references: 0 @@ -641,7 +694,6 @@ resources: synonyms: 22501 terms: 96420 version: '2.0' - xrefs: 103085 pathbank: nodes: gzipped: false @@ -676,14 +728,14 @@ resources: summary: alts: 0 definitions: 0 + mappings: 110242 parents: 0 - properties: 110242 + properties: 220484 references: 0 - relations: 2565795 + relations: 2455553 synonyms: 0 terms: 110242 version: '2.0' - xrefs: 110242 pfam: nodes: gzipped: false @@ -718,6 +770,7 @@ resources: summary: alts: 0 definitions: 23794 + mappings: 0 parents: 10923 properties: 0 references: 0 @@ -725,7 +778,6 @@ resources: synonyms: 0 terms: 23794 version: '37.1' - xrefs: 0 pfam.clan: nodes: gzipped: false @@ -760,6 +812,7 @@ resources: summary: alts: 0 definitions: 0 + mappings: 0 parents: 0 properties: 0 references: 0 @@ -767,7 +820,6 @@ resources: synonyms: 0 terms: 751 version: '37.1' - xrefs: 0 pombase: nodes: gzipped: false @@ -802,14 +854,14 @@ resources: summary: alts: 0 definitions: 12684 + mappings: 0 parents: 12684 - properties: 12684 + properties: 23473 references: 0 - relations: 23473 + relations: 12684 synonyms: 2620 terms: 12684 version: '2024-11-01' - xrefs: 0 reactome: nodes: gzipped: false @@ -844,6 +896,7 @@ resources: summary: alts: 0 definitions: 0 + mappings: 0 parents: 22675 properties: 0 references: 0 @@ -851,49 +904,48 @@ resources: synonyms: 0 terms: 22537 version: '90' - xrefs: 0 rgd: nodes: gzipped: false iri: https://w3id.org/biopragmatics/resources/rgd/rgd.tsv path: rgd/rgd.tsv - version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.tsv - version_path: rgd/2024-10-25/rgd.tsv + version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.tsv + version_path: rgd/2024-11-22/rgd.tsv obo: gzipped: false iri: https://w3id.org/biopragmatics/resources/rgd/rgd.obo path: rgd/rgd.obo - version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.obo - version_path: rgd/2024-10-25/rgd.obo + version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.obo + version_path: rgd/2024-11-22/rgd.obo obograph: gzipped: false iri: https://w3id.org/biopragmatics/resources/rgd/rgd.json path: rgd/rgd.json - version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.json - version_path: rgd/2024-10-25/rgd.json + version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.json + version_path: rgd/2024-11-22/rgd.json owl: gzipped: true iri: https://w3id.org/biopragmatics/resources/rgd/rgd.owl.gz path: rgd/rgd.owl.gz - version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.owl.gz - version_path: rgd/2024-10-25/rgd.owl.gz + version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.owl.gz + version_path: rgd/2024-11-22/rgd.owl.gz sssom: gzipped: false iri: https://w3id.org/biopragmatics/resources/rgd/rgd.sssom.tsv path: rgd/rgd.sssom.tsv - version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.sssom.tsv - version_path: rgd/2024-10-25/rgd.sssom.tsv + version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.sssom.tsv + version_path: rgd/2024-11-22/rgd.sssom.tsv summary: alts: 0 - definitions: 50930 + definitions: 51054 + mappings: 103906 parents: 0 - properties: 0 - references: 124411 - relations: 141023 - synonyms: 139111 + properties: 79013 + references: 124654 + relations: 61331 + synonyms: 139322 terms: 61331 - version: '2024-10-25' - xrefs: 104518 + version: '2024-11-22' rhea: nodes: gzipped: false @@ -928,98 +980,98 @@ resources: summary: alts: 0 definitions: 0 + mappings: 19627 parents: 69210 - properties: 0 + properties: 165016 references: 0 - relations: 762437 + relations: 597421 synonyms: 0 terms: 67880 version: '135' - xrefs: 19627 sgd: nodes: gzipped: false iri: https://w3id.org/biopragmatics/resources/sgd/sgd.tsv path: sgd/sgd.tsv - version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-3-1/sgd.tsv - version_path: sgd/R64-3-1/sgd.tsv + version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-5-1/sgd.tsv + version_path: sgd/R64-5-1/sgd.tsv obo: gzipped: false iri: https://w3id.org/biopragmatics/resources/sgd/sgd.obo path: sgd/sgd.obo - version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-3-1/sgd.obo - version_path: sgd/R64-3-1/sgd.obo + version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-5-1/sgd.obo + version_path: sgd/R64-5-1/sgd.obo obograph: gzipped: false iri: https://w3id.org/biopragmatics/resources/sgd/sgd.json path: sgd/sgd.json - version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-3-1/sgd.json - version_path: sgd/R64-3-1/sgd.json + version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-5-1/sgd.json + version_path: sgd/R64-5-1/sgd.json owl: gzipped: false iri: https://w3id.org/biopragmatics/resources/sgd/sgd.owl path: sgd/sgd.owl - version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-3-1/sgd.owl - version_path: sgd/R64-3-1/sgd.owl + version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-5-1/sgd.owl + version_path: sgd/R64-5-1/sgd.owl sssom: gzipped: false iri: https://w3id.org/biopragmatics/resources/sgd/sgd.sssom.tsv path: sgd/sgd.sssom.tsv - version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-3-1/sgd.sssom.tsv - version_path: sgd/R64-3-1/sgd.sssom.tsv + version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-5-1/sgd.sssom.tsv + version_path: sgd/R64-5-1/sgd.sssom.tsv summary: alts: 0 definitions: 6600 + mappings: 0 parents: 0 properties: 0 references: 0 relations: 6600 synonyms: 11109 terms: 6600 - version: R64-3-1 - xrefs: 0 + version: R64-5-1 slm: nodes: gzipped: true iri: https://w3id.org/biopragmatics/resources/slm/slm.tsv.gz path: slm/slm.tsv.gz - version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-04/slm.tsv.gz - version_path: slm/2024-11-04/slm.tsv.gz + version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-26/slm.tsv.gz + version_path: slm/2024-11-26/slm.tsv.gz obo: gzipped: true iri: https://w3id.org/biopragmatics/resources/slm/slm.obo.gz path: slm/slm.obo.gz - version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-04/slm.obo.gz - version_path: slm/2024-11-04/slm.obo.gz + version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-26/slm.obo.gz + version_path: slm/2024-11-26/slm.obo.gz obograph: gzipped: true iri: https://w3id.org/biopragmatics/resources/slm/slm.json.gz path: slm/slm.json.gz - version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-04/slm.json.gz - version_path: slm/2024-11-04/slm.json.gz + version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-26/slm.json.gz + version_path: slm/2024-11-26/slm.json.gz owl: gzipped: true iri: https://w3id.org/biopragmatics/resources/slm/slm.owl.gz path: slm/slm.owl.gz - version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-04/slm.owl.gz - version_path: slm/2024-11-04/slm.owl.gz + version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-26/slm.owl.gz + version_path: slm/2024-11-26/slm.owl.gz sssom: gzipped: false iri: https://w3id.org/biopragmatics/resources/slm/slm.sssom.tsv path: slm/slm.sssom.tsv - version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-04/slm.sssom.tsv - version_path: slm/2024-11-04/slm.sssom.tsv + version_iri: https://w3id.org/biopragmatics/resources/slm/2024-11-26/slm.sssom.tsv + version_path: slm/2024-11-26/slm.sssom.tsv summary: alts: 0 definitions: 0 + mappings: 635636 parents: 0 - properties: 2150101 + properties: 2781459 references: 10101 - relations: 631358 + relations: 0 synonyms: 1344722 terms: 779249 - version: '2024-11-04' - xrefs: 635637 + version: '2024-11-26' uniprot: nodes: gzipped: false @@ -1054,99 +1106,99 @@ resources: summary: alts: 0 definitions: 0 + mappings: 315074 parents: 0 - properties: 572214 + properties: 5249411 references: 1136558 - relations: 5712898 + relations: 1035701 synonyms: 0 terms: 572214 version: '2024_05' - xrefs: 315074 wikipathways: nodes: gzipped: false iri: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.tsv path: wikipathways/wikipathways.tsv - version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241010/wikipathways.tsv - version_path: wikipathways/20241010/wikipathways.tsv + version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241110/wikipathways.tsv + version_path: wikipathways/20241110/wikipathways.tsv obo: gzipped: false iri: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.obo path: wikipathways/wikipathways.obo - version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241010/wikipathways.obo - version_path: wikipathways/20241010/wikipathways.obo + version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241110/wikipathways.obo + version_path: wikipathways/20241110/wikipathways.obo obograph: gzipped: false iri: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.json path: wikipathways/wikipathways.json - version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241010/wikipathways.json - version_path: wikipathways/20241010/wikipathways.json + version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241110/wikipathways.json + version_path: wikipathways/20241110/wikipathways.json owl: gzipped: false iri: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.owl path: wikipathways/wikipathways.owl - version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241010/wikipathways.owl - version_path: wikipathways/20241010/wikipathways.owl + version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241110/wikipathways.owl + version_path: wikipathways/20241110/wikipathways.owl sssom: gzipped: false iri: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.sssom.tsv path: wikipathways/wikipathways.sssom.tsv - version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241010/wikipathways.sssom.tsv - version_path: wikipathways/20241010/wikipathways.sssom.tsv + version_iri: https://w3id.org/biopragmatics/resources/wikipathways/20241110/wikipathways.sssom.tsv + version_path: wikipathways/20241110/wikipathways.sssom.tsv summary: alts: 0 definitions: 0 + mappings: 0 parents: 0 properties: 0 references: 0 - relations: 73311 + relations: 74581 synonyms: 0 - terms: 1852 - version: '20241010' - xrefs: 0 + terms: 1861 + version: '20241110' zfin: nodes: gzipped: false iri: https://w3id.org/biopragmatics/resources/zfin/zfin.tsv path: zfin/zfin.tsv - version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-03/zfin.tsv - version_path: zfin/2024-11-03/zfin.tsv + version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-25/zfin.tsv + version_path: zfin/2024-11-25/zfin.tsv obo: gzipped: false iri: https://w3id.org/biopragmatics/resources/zfin/zfin.obo path: zfin/zfin.obo - version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-03/zfin.obo - version_path: zfin/2024-11-03/zfin.obo + version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-25/zfin.obo + version_path: zfin/2024-11-25/zfin.obo obograph: gzipped: true iri: https://w3id.org/biopragmatics/resources/zfin/zfin.json.gz path: zfin/zfin.json.gz - version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-03/zfin.json.gz - version_path: zfin/2024-11-03/zfin.json.gz + version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-25/zfin.json.gz + version_path: zfin/2024-11-25/zfin.json.gz owl: gzipped: true iri: https://w3id.org/biopragmatics/resources/zfin/zfin.owl.gz path: zfin/zfin.owl.gz - version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-03/zfin.owl.gz - version_path: zfin/2024-11-03/zfin.owl.gz + version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-25/zfin.owl.gz + version_path: zfin/2024-11-25/zfin.owl.gz sssom: gzipped: false iri: https://w3id.org/biopragmatics/resources/zfin/zfin.sssom.tsv path: zfin/zfin.sssom.tsv - version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-03/zfin.sssom.tsv - version_path: zfin/2024-11-03/zfin.sssom.tsv + version_iri: https://w3id.org/biopragmatics/resources/zfin/2024-11-25/zfin.sssom.tsv + version_path: zfin/2024-11-25/zfin.sssom.tsv summary: - alts: 27962 - definitions: 33491 - parents: 191967 - properties: 0 + alts: 27970 + definitions: 33519 + mappings: 24764 + parents: 192543 + properties: 24764 references: 0 - relations: 289713 + relations: 265547 synonyms: 0 - terms: 191967 - version: '2024-11-03' - xrefs: 24745 + terms: 192543 + version: '2024-11-25' versions: - bioontologies: 0.5.2-dev-3e46aa69 - bioregistry: 0.11.24-dev-9900364b - pyobo: 0.11.1-dev-b4a18517 + bioontologies: 0.5.1-b6c7106b + bioregistry: 0.11.27-dev-712ef19f + pyobo: 0.12.0-dev-b6c7106b