pyobo 0.12.1__py3-none-any.whl → 0.12.3__py3-none-any.whl

pyobo/identifier_utils/preprocessing.py

@@ -1,27 +0,0 @@
-"""Load the manually curated metaregistry."""
-
-from functools import lru_cache
-from pathlib import Path
-
-from curies.preprocessing import PreprocessingRules, _load_rules
-
-from ..resources.goc import load_goc_map
-
-__all__ = [
-    "get_rules",
-]
-
-HERE = Path(__file__).parent.resolve()
-RULES_PATH = HERE.joinpath("preprocessing.json")
-
-
-@lru_cache(1)
-def get_rules() -> PreprocessingRules:
-    """Get the CURIE/URI string preprocessing rules."""
-    rules = _load_rules(RULES_PATH)
-    rules.rewrites.full.update(load_goc_map())
-    return rules
-
-
-if __name__ == "__main__":
-    PreprocessingRules.lint_file(RULES_PATH)

pyobo/obographs.py

@@ -1,147 +0,0 @@
-"""Convert PyOBO into OBO Graph."""
-
-from __future__ import annotations
-
-import logging
-from collections.abc import Iterable
-
-import bioregistry
-from bioontologies.obograph import (
-    Definition,
-    Edge,
-    Graph,
-    GraphDocument,
-    Meta,
-    Node,
-    Synonym,
-    Xref,
-)
-from bioontologies.robot import ParseResults
-from tqdm import tqdm
-
-from pyobo.struct import Obo, OBOLiteral, Reference, Term
-from pyobo.struct.typedef import definition_source, is_a
-
-__all__ = [
-    "graph_from_obo",
-    "parse_results_from_obo",
-]
-
-logger = logging.getLogger(__name__)
-
-
-def parse_results_from_obo(obo: Obo) -> ParseResults:
-    """Get parse results from an OBO graph."""
-    graph = graph_from_obo(obo)
-    return ParseResults(graph_document=GraphDocument(graphs=[graph]))
-
-
-def graph_from_obo(obo: Obo, use_tqdm: bool = True) -> Graph:
-    """Get an OBO Graph object from a PyOBO object."""
-    nodes: list[Node] = []
-    edges: list[Edge] = []
-    for term in tqdm(
-        obo,
-        disable=not use_tqdm,
-        unit="term",
-        unit_scale=True,
-        desc=f"[{obo._prefix_version}] to OBO Graph JSON",
-    ):
-        nodes.append(_get_class_node(term))
-        edges.extend(_iter_edges(term))
-    return Graph(
-        id=bioregistry.get_bioregistry_iri("bioregistry", obo.ontology),
-        prefix=obo.ontology,
-        meta=_get_meta(obo),
-        nodes=nodes,
-        edges=edges,
-        standardized=True,  # from construction :)
-    )
-
-
-def _get_meta(obo: Obo) -> Meta:
-    return Meta(
-        version=obo.data_version,
-    )
-
-
-def _get_class_node(term: Term) -> Node:
-    if term.provenance or term.definition:
-        definition = Definition.from_parsed(
-            value=term.definition, references=_prep_prov(term.provenance)
-        )
-    else:
-        definition = None
-    xrefs = [
-        Xref.from_parsed(
-            predicate=Reference.from_reference(mapping_predicate),
-            value=Reference.from_reference(mapping_object),
-        )
-        for mapping_predicate, mapping_object in term.get_mappings(
-            include_xrefs=True, add_context=False
-        )
-    ]
-    synonyms = [
-        Synonym.from_parsed(
-            name=synonym.name,
-            predicate=Reference.from_reference(synonym.predicate),
-            synonym_type=Reference.from_reference(synonym.type) if synonym.type else None,
-            references=_prep_prov(synonym.provenance),
-        )
-        for synonym in term.synonyms
-    ]
-
-    meta = Meta(
-        definition=definition,
-        xrefs=xrefs,
-        synonyms=synonyms,
-        basicPropertyValues=None,  # TODO properties
-        deprecated=term.is_obsolete or False,
-    )
-    return Node(
-        # FIXME do expansion same as for OFN
-        id=f"https://bioregistry.io/{term.curie}",
-        lbl=term.name,
-        meta=meta,
-        type="CLASS",
-        reference=Reference.from_reference(term.reference),
-        standardized=True,
-    )
-
-
-def _prep_prov(provenance):
-    rv = []
-    for x in provenance:
-        match x:
-            case Reference():
-                rv.append(Reference.from_reference(x))
-            case OBOLiteral():
-                logger.debug("not implemented to convert literal provenance")
-                continue
-    return rv
-
-
-def _iter_edges(term: Term) -> Iterable[Edge]:
-    for parent in term.parents:
-        yield Edge.from_parsed(
-            Reference.from_reference(term.reference),
-            Reference.from_reference(is_a.reference),
-            Reference.from_reference(parent),
-        )
-
-    for typedef, targets in term.relationships.items():
-        for target in targets:
-            yield Edge.from_parsed(
-                Reference.from_reference(term.reference),
-                Reference.from_reference(typedef),
-                Reference.from_reference(target),
-            )
-
-    for provenance_reference in term.provenance:
-        if isinstance(provenance_reference, Reference):
-            yield Edge.from_parsed(
-                Reference.from_reference(term.reference),
-                Reference.from_reference(definition_source.reference),
-                Reference.from_reference(provenance_reference),
-            )
-    # TODO also look through xrefs and seealso to get provenance xrefs?

pyobo/resources/goc.py

@@ -1,75 +0,0 @@
-"""Get GOC to ORCID CURIE mappings.
-
-Due to historical reasons, the Gene Ontology and related resources use an internal
-curator identifier space ``GOC`` instead of ORCID. This namespace is partially mapped to
-ORCID and is version controlled `here
-<https://raw.githubusercontent.com/geneontology/go-site/refs/heads/master/metadata/users.yaml>`_.
-
-This module loads that namespace and uses :mod:`orcid_downloader` to try and add
-additional ORCID groundings. Then, this module is loaded in PyOBO's custom CURIE upgrade
-system so GOC CURIEs are seamlessly replaced with ORCID CURIEs, when possible.
-
-.. seealso::
-
-    https://github.com/geneontology/go-ontology/issues/22551
-"""
-
-import csv
-from pathlib import Path
-
-__all__ = ["load_goc_map"]
-
-URL = "https://raw.githubusercontent.com/geneontology/go-site/refs/heads/master/metadata/users.yaml"
-
-HERE = Path(__file__).parent.resolve()
-PATH = HERE.joinpath("goc.tsv")
-
-
-def load_goc_map() -> dict[str, str]:
-    """Get GOC to ORCID mappings."""
-    rv = {}
-    with PATH.open() as f:
-        for goc_curie, _, orcid, *_ in csv.reader(f, delimiter="\t"):
-            rv[goc_curie] = f"orcid:{orcid}"
-            rv[goc_curie.upper()] = f"orcid:{orcid}"
-    return rv
-
-
-def main() -> None:
-    """Generate GOC to ORCID mappings."""
-    import orcid_downloader
-    import requests
-    import yaml
-    from tqdm import tqdm
-
-    columns = ["curie", "name", "orcid", "guessed"]
-    res = requests.get(URL, timeout=5)
-    records = yaml.safe_load(res.text)
-    with PATH.open("w") as file:
-        print(*columns, sep="\t", file=file)
-        for record in tqdm(records, unit="person"):
-            goc_curie = record.get("xref")
-            if goc_curie is None or not goc_curie.startswith("GOC:"):
-                continue
-
-            guessed = False
-            nickname = record["nickname"]
-            uri = record.get("uri", "")
-            if not uri:
-                continue
-            if "orcid.org" in uri:
-                orcid = uri.removeprefix("https://orcid.org/").removeprefix("https://orcid.org/")
-            if "orcid.org" not in uri:
-                orcid = orcid_downloader.ground_researcher_unambiguous(nickname)
-                if not orcid:
-                    tqdm.write(f"Could not guess ORCID for {nickname}")
-                    continue
-
-                tqdm.write(f"Check if https://orcid.org/{orcid} is correct for {nickname}")
-                guessed = True
-
-            print(goc_curie, nickname, orcid, guessed, sep="\t", file=file)
-
-
-if __name__ == "__main__":
-    main()

pyobo/resources/goc.tsv

@@ -1,188 +0,0 @@
-curie	name	orcid	guessed
-GOC:jk	Jim Knowles	0009-0009-5100-2472	True
-GOC:amu	Anushya Muruganujan	0000-0001-7169-5864	True
-GOC:pt	Paul Thomas	0000-0002-9074-3507	False
-GOC:hm	Huaiyu Mi	0000-0001-8721-202X	False
-GOC:sjc	Seth Carbon	0000-0001-8244-1536	False
-GOC:jnx	Jeremy Nguyen Xuan	0000-0002-4301-0968	True
-GOC:anm	Anna Melidoni	0000-0002-2535-883X	True
-GOC:ml2	Mike Livstone	0000-0001-5386-5823	True
-GOC:hd	Heiko Dietze	0000-0003-0234-1688	False
-GOC:dp	Dexter Pratt	0000-0002-1471-9513	True
-GOC:di	Diane Inglis	0000-0003-3166-4638	False
-GOC:cy	Courtland Yockey	0000-0003-4917-3490	True
-GOC:hal	Hadil Alrohaif	0000-0002-6980-6972	True
-GOC:jbu	Jessica Buxton	0000-0002-0918-9335	False
-GOC:kom	Klaus Mitchell	0000-0001-9510-5320	False
-GOC:nc	Nancy Campbell	0000-0001-9995-0839	False
-GOC:rl	Ruth Lovering	0000-0002-9791-0064	False
-GOC:vk	Varsha Khodiyar	0000-0002-2743-6918	True
-GOC:amm	Anna Maria Masci	0000-0003-1940-6740	True
-GOC:dsd	David S. Dougall	0000-0002-9043-2709	True
-GOC:pf	Petra Fey	0000-0002-4532-2703	False
-GOC:pg	Pascale Gaudet	0000-0003-1813-6857	False
-GOC:rjd	Robert Dodson	0000-0002-2757-5950	False
-GOC:jh2	Jim Hu	0000-0001-9016-2684	False
-GOC:nv	Nicole Vasilevsky	0000-0001-5208-3432	True
-GOC:ha	Helen Attrill	0000-0003-3212-6364	False
-GOC:hb	Heather Butler	0000-0003-4454-4889	True
-GOC:mc	Marta Costa	0000-0001-5948-3092	False
-GOC:ma	Michael Ashburner	0000-0002-6962-2807	False
-GOC:dos	David Osumi-Sutherland	0000-0002-7073-9172	False
-GOC:sart	Susan Tweedie	0000-0003-1818-8243	False
-GOC:mb	Matt Berriman	0000-0002-9581-0377	False
-GOC:bf	Rebecca Foulger	0000-0001-8682-8754	False
-GOC:ceb	Cath Brooksbank	0000-0001-9395-7001	False
-GOC:jid	Jennifer Deegan (nee Clark)	0000-0001-9227-417X	False
-GOC:jl	Jane Lomax	0000-0001-8865-4321	False
-GOC:mec	Melanie Courtot	0000-0002-9551-6370	False
-GOC:pr	Paola Roncaglia	0000-0002-2825-0621	False
-GOC:als	Alice Dashow	0000-0003-3829-1600	False
-GOC:es	Elena Speretta	0000-0003-1506-7438	False
-GOC:gg	George Georghiou	0000-0001-5067-3199	False
-GOC:hbye	Hema Bye-A-Jee	0000-0003-2464-7688	False
-GOC:pm	Prudence Mutowo	0000-0002-4646-4172	True
-GOC:rph	Rachael Huntley	0000-0001-6718-3559	False
-GOC:yaf	Yasmin Alam-Faruque	0000-0001-8902-0232	True
-GOC:bhm	Birgit Meldal	0000-0003-4062-6158	False
-GOC:imk	Ingrid Keseler	0000-0003-1738-6117	True
-GOC:dph	David Hill	0000-0001-7476-6306	False
-GOC:tfm	Terry Meehan	0000-0003-1980-3228	True
-GOC:ajp	Tony Planchart	0000-0001-8691-8856	False
-GOC:dms	Dmitry Sitnikov	0000-0003-3394-9805	False
-GOC:smb	Sue Bello	0000-0003-4606-0597	False
-GOC:hjd	Harold Drabkin	0000-0003-2689-5511	False
-GOC:ln	Li Ni	0000-0002-9796-7693	False
-GOC:jab	Judith Blake	0000-0001-8522-334X	False
-GOC:crds	Claudia Rato da Silva	0000-0002-3971-046X	True
-GOC:tw	Trish Whetzel	0000-0002-3458-4839	True
-GOC:rv	Randi Vita	0000-0001-8957-7612	True
-GOC:ml	Magdalen Lindeberg	0000-0001-6386-4066	True
-GOC:gvg	George Gkoutos	0000-0002-2061-091X	True
-GOC:al	Antonia Lock	0000-0003-1179-5999	False
-GOC:jb	Jurg Bahler	0000-0003-4036-1532	True
-GOC:mah	Midori Harris	0000-0003-4148-4606	False
-GOC:vw	Val Wood	0000-0001-6330-7526	False
-GOC:lc	Laurel Cooper	0000-0002-6379-8932	False
-GOC:rw	Ramona Walls	0000-0001-8815-0078	True
-GOC:cna	Cecilia Arighi	0000-0002-0803-4817	True
-GOC:bj	Bijay Jassal	0000-0002-5039-5405	True
-GOC:mg2	Marc Gillespie	0000-0002-5766-1702	True
-GOC:pde	Peter D'Eustachio	0000-0002-5494-626X	False
-GOC:phg	Phani Garapati	0000-0003-0941-2207	False
-GOC:sj	Steven Jupe	0000-0001-5807-0069	True
-GOC:vs	Veronica Shamovsky	0000-0002-2187-2241	True
-GOC:jsg	John Garavelli	0000-0002-4131-735X	True
-GOC:sjw	Shur-Jen Wang	0000-0001-5256-8683	True
-GOC:sl	Stan Laulederkind	0000-0001-5356-4174	False
-GOC:st	Simon Twigger	0000-0001-5659-3632	True
-GOC:vp	Victoria Petri	0000-0002-5540-8498	True
-GOC:cb	Colin Batchelor	0000-0001-5985-7429	True
-GOC:cjm	Chris Mungall	0000-0002-6601-2165	False
-GOC:clt	Chandra Theesfeld	0000-0002-8379-6600	False
-GOC:dgf	Dianna Fisk	0000-0003-4929-9472	False
-GOC:ew	Edith Wong	0000-0001-9799-5523	False
-GOC:elh	Eurie Hong	0000-0002-1775-4998	False
-GOC:jd	Janos Demeter	0000-0002-7301-8055	False
-GOC:jh	Jodi Hirschman	0000-0001-8850-9925	False
-GOC:krc	Karen Christie	0000-0001-5501-853X	False
-GOC:mcc	Maria Costanzo	0000-0001-9043-693X	False
-GOC:rb	Rama Balakrishnan	0000-0003-2468-9933	False
-GOC:rn	Rob Nash	0000-0002-3726-7441	False
-GOC:se	Stacia Engel	0000-0001-5472-917X	False
-GOC:ssd	Selina Dwight	0000-0002-8546-7798	False
-GOC:dw	Dani Welter	0000-0003-1058-2668	False
-GOC:ask	A. S. Karthikeyan	0000-0003-0065-0217	True
-GOC:ct	Christopher Tissier	0000-0002-0693-3202	True
-GOC:dhl	Donghui Li	0000-0003-3335-4537	False
-GOC:ds	David Swarbreck	0000-0002-5453-1013	True
-GOC:kad	Kate Dreher	0000-0003-4652-4398	False
-GOC:tb	Tanya Berardini	0000-0002-3837-8864	False
-GOC:dh	Dan Haft	0000-0001-8101-4938	True
-GOC:lh	Linda Hannick	0000-0002-8018-8466	False
-GOC:ef	Erika Feltrin	0000-0002-9899-7456	False
-GOC:lm	Lorenza Mittempergher	0000-0003-3425-3965	True
-GOC:ar	Alan Ruttenberg	0000-0002-1604-3078	True
-GOC:hw	Heather Wick	0000-0003-0961-0377	True
-GOC:pad	Paul Denny	0000-0003-4659-6893	False
-GOC:mat	Mathew Tata	0000-0002-0960-5677	True
-GOC:aa	Andrea Auchincloss	0000-0002-5297-5390	True
-GOC:ae	Anne Estreicher	0000-0001-6828-2508	True
-GOC:ab	Alan Bridge	0000-0003-2148-9135	False
-GOC:ans	Andre Stutz	0000-0002-7175-2168	True
-GOC:ag	Arnaud Gos	0000-0002-5018-1378	True
-GOC:cr2	Catherine Rivoire	0000-0002-5979-8382	True
-GOC:ch	Chantal Hulo	0000-0001-8176-7999	True
-GOC:dl2	Damien Lieberherr	0000-0002-9724-1710	True
-GOC:ecu	Elena Cibrian-Uhalte	0000-0002-0987-9862	False
-GOC:fj	Florence Jungo	0000-0002-7456-8390	True
-GOC:gc	Gayatri Chavali	0000-0001-8575-1847	True
-GOC:gk	Guillaume Keller	0000-0001-9497-8269	True
-GOC:ip	Ivo Pedruzzi	0000-0001-8561-7170	True
-GOC:kd	Kirill Degtyarenko	0000-0003-0058-650X	True
-GOC:klp	Klemens Pichler	0000-0001-6099-8931	False
-GOC:ka	Kristian Axelsen	0000-0003-3889-2879	True
-GOC:mf	Marc Feuermann	0000-0002-4187-2863	False
-GOC:mt	Michael Tognolli	0000-0002-5278-3321	True
-GOC:mm2	Michele Magrane	0000-0003-3544-996X	True
-GOC:pm2	Patrick Masson	0000-0001-7646-0052	False
-GOC:pdr	Paula Duek Roggli	0000-0002-0819-0473	True
-GOC:pga	Penelope Garmiri	0000-0002-2283-2575	False
-GOC:plm	Philippe Le Mercier	0000-0001-8528-090X	True
-GOC:reh	Reija Hieta	0000-0001-5724-6253	True
-GOC:so	Sandra Orchard	0000-0002-8878-3972	True
-GOC:sp	Sylvain Poux	0000-0001-7299-6685	False
-GOC:ss	Shyamala Sundaram	0000-0003-4209-460X	True
-GOC:uh	Ursula Hinz	0000-0002-2365-2234	True
-GOC:wmc	Wei Mun Chan	0000-0002-9971-813X	True
-GOC:nhn	Nevila Hyka-Nouspikel	0000-0001-7855-209X	True
-GOC:jc	Jonas Cicenas	0000-0002-9365-1843	True
-GOC:gap	Ghislaine Argoud-Puy	0000-0002-2979-8613	False
-GOC:ppm	Pablo Porras Millan	0000-0002-8429-8793	True
-GOC:dsz	Dora Szakonyi	0000-0002-9189-629X	True
-GOC:dr	Daniela Raciti	0000-0002-4945-5837	False
-GOC:kmv	Kimberly Van Auken	0000-0002-1706-4196	False
-GOC:rk	Ranjana Kishore	0000-0002-1478-7671	False
-GOC:dgh	Doug Howe	0000-0001-5831-7439	False
-GOC:dsf	David Fashena	0000-0001-9656-0683	False
-GOC:cvs	Ceri Van Slyke	0000-0002-2244-7917	False
-GOC:sr	Sridhar Ramachandran	0000-0002-2246-3722	False
-GOC:ymb	Yvonne M Bradford	0000-0002-9900-7880	False
-GOC:sat	Sabrina Toro	0000-0002-4142-7153	False
-GOC:ksf	Ken Frazer	0000-0002-6889-0711	False
-GOC:lrz	Leyla Ruzicka	0000-0002-1009-339X	False
-GOC:ejs	Erik Segerdell	0000-0002-9611-1279	True
-GOC:lb	Lionel Breuza	0000-0002-8075-8625	False
-GOC:mh	Melissa Haendel	0000-0001-9114-8737	False
-GOC:mag	Marion Gremse	0000-0003-0350-6392	True
-GOC:hp	Helen Parkinson	0000-0003-3035-4195	True
-GOC:sk	Scott Kalberer	0000-0003-2101-2484	True
-GOC:md	Mickael Desvaux	0000-0003-2986-6417	True
-GOC:expert_db	Dominique Bergmann	0000-0003-0873-3543	True
-GOC:expert_ks	Kevin Struhl	0000-0002-4181-7856	True
-GOC:expert_jwt	Jeremy Thorner	0000-0002-2583-500X	True
-GOC:expert_mm	Michael Melkonian	0000-0002-5911-6548	True
-GOC:expert_pt	Philippa Talmud	0000-0002-5560-1933	True
-GOC:expert_rsh	R. Scott Hawley	0000-0002-6478-0494	True
-GOC:expert_tf	Tim Formosa	0000-0002-8477-2483	True
-GOC:jal	Jamie A. Lee	0000-0001-6182-2372	True
-GOC:mmt	Monica Munoz-Torres	0000-0001-8430-6039	False
-GOC:at	Anne Thessen	0000-0002-2908-3327	False
-GOC:ga	Giulia Antonazzo	0000-0003-0086-5621	False
-GOC:ani	Anne Niknejad	0000-0003-3308-6245	True
-GOC:pvn	Pim van Nierop	0000-0003-0593-3443	False
-GOC:add	Alexander Diehl	0000-0001-9990-8331	False
-GOC:pj	Pankaj Jaiswal	0000-0002-1005-8383	False
-GOC:rz	Rossana Zaru	0000-0002-3358-4423	False
-GOC:lr	Leonore Reiser	0000-0003-0073-0858	False
-GOC:mcc2	Marcus Chibucos	0000-0001-9586-0780	False
-GOC:das	Debby Siegele	0000-0001-8935-0696	False
-GOC:bc	Barbara Kramarz	0000-0002-3898-1727	False
-GOC:lnp	Livia Perfetto	0000-0003-4392-8725	False
-GOC:ach	Achchuthan Shanmugasundram	0000-0003-2349-6929	False
-GOC:mch	Marie-Claire Harrison	0000-0002-3013-9906	False
-GOC:mlg	Michelle Gwinn Giglio	0000-0001-7628-5565	False
-GOC:jja	Josh Jaffery	0000-0002-1965-6945	True
-GOC:tc	Teresa Chu	0000-0003-4172-1966	True
-GOC:apd	Allan P Davis	0000-0002-5741-7128	False
-GOC:sjm	Steven Marygold	0000-0003-2759-266X	False