pyobo 0.12.0__py3-none-any.whl → 0.12.1__py3-none-any.whl

{pyobo-0.12.0.dist-info → pyobo-0.12.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.0
+Version: 0.12.1
 Summary: A python package for handling and generating OBO
 Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
 Author: Charles Tapley Hoyt
@@ -37,7 +37,7 @@ Requires-Dist: humanize
 Requires-Dist: tabulate
 Requires-Dist: cachier
 Requires-Dist: pystow>=0.7.0
-Requires-Dist: bioversions>=0.7.0
+Requires-Dist: bioversions>=0.8.0
 Requires-Dist: bioregistry>=0.12.7
 Requires-Dist: bioontologies>=0.7.1
 Requires-Dist: ssslm>=0.0.13
@@ -45,7 +45,7 @@ Requires-Dist: zenodo-client>=0.3.6
 Requires-Dist: class-resolver>=0.6.0
 Requires-Dist: psycopg2-binary
 Requires-Dist: pydantic>=2.0
-Requires-Dist: curies>=0.10.10
+Requires-Dist: curies>=0.10.13
 Requires-Dist: python-dateutil
 Requires-Dist: networkx>=3.4
 Requires-Dist: drugbank-downloader
@@ -55,14 +55,8 @@ Requires-Dist: clinicaltrials-downloader>=0.0.2
 Requires-Dist: nih-reporter-downloader>=0.0.1
 Requires-Dist: typing-extensions
 Requires-Dist: rdflib
-Requires-Dist: sphinx>=8 ; extra == 'docs'
-Requires-Dist: sphinx-rtd-theme>=3.0 ; extra == 'docs'
-Requires-Dist: sphinx-click ; extra == 'docs'
-Requires-Dist: sphinx-automodapi ; extra == 'docs'
 Requires-Dist: ssslm[gilda] ; extra == 'gilda'
 Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
-Requires-Dist: pytest ; extra == 'tests'
-Requires-Dist: coverage[toml] ; extra == 'tests'
 Maintainer: Charles Tapley Hoyt
 Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 Requires-Python: >=3.10
@@ -71,10 +65,8 @@ Project-URL: Documentation, https://pyobo.readthedocs.io
 Project-URL: Funding, https://github.com/sponsors/cthoyt
 Project-URL: Homepage, https://github.com/biopragmatics/pyobo
 Project-URL: Repository, https://github.com/biopragmatics/pyobo.git
-Provides-Extra: docs
 Provides-Extra: gilda
 Provides-Extra: gilda-slim
-Provides-Extra: tests
 Description-Content-Type: text/markdown
 
 <!--
@@ -120,14 +112,7 @@ identifiers. It also means all identifiers are strings, no exceptions.
 
 Note! The first time you run these, they have to download and cache all
 resources. We're not in the business of redistributing data, so all scripts
-should be completely reproducible. There's some AWS tools for
-hosting/downloading pre-compiled versions in `pyobo.aws` if you don't have time
-for that.
-
-Note! PyOBO can perform grounding in a limited number of cases, but it is _not_
-a general solution for named entity recognition (NER) or grounding. It's
-suggested to check `Gilda <https://github.com/indralab/gilda>`\_ for a
-no-nonsense solution.
+should be completely reproducible.
 
 ### Mapping Identifiers and CURIEs
 
@@ -136,19 +121,11 @@ Get mapping of ChEBI identifiers to names:
 ```python
 import pyobo
 
-chebi_id_to_name = pyobo.get_id_name_mapping('chebi')
+chebi_id_to_name = pyobo.get_id_name_mapping("chebi")
+assert "fluazifop-P-butyl" == chebi_id_to_name["132964"]
 
-name = chebi_id_to_name['132964']
-assert name == 'fluazifop-P-butyl'
-```
-
-Or, you don't have time for two lines:
-
-```python
-import pyobo
-
-name = pyobo.get_name('chebi', '132964')
-assert name == 'fluazifop-P-butyl'
+# or more directly
+assert "fluazifop-P-butyl" == pyobo.get_name("chebi", "132964")
 ```
 
 Get reverse mapping of ChEBI names to identifiers:
@@ -156,10 +133,8 @@ Get reverse mapping of ChEBI names to identifiers:
 ```python
 import pyobo
 
-chebi_name_to_id = pyobo.get_name_id_mapping('chebi')
-
-identifier = chebi_name_to_id['fluazifop-P-butyl']
-assert identifier == '132964'
+chebi_name_to_id = pyobo.get_name_id_mapping("chebi")
+assert "132964" == chebi_name_to_id["fluazifop-P-butyl"]
 ```
 
 Maybe you live in CURIE world and just want to normalize something like
@@ -168,8 +143,7 @@ Maybe you live in CURIE world and just want to normalize something like
 ```python
 import pyobo
 
-name = pyobo.get_name_by_curie('CHEBI:132964')
-assert name == 'fluazifop-P-butyl'
+assert "fluazifop-P-butyl" == pyobo.get_name_by_curie("CHEBI:132964")
 ```
 
 Sometimes you accidentally got an old CURIE. It can be mapped to the more recent
@@ -181,11 +155,11 @@ from pyobo import Reference
 
 # Look up DNA-binding transcription factor activity (go:0003700)
 # based on an old id
-primary_curie = pyobo.get_primary_curie('go:0001071')
-assert primary_curie == 'go:0003700'
+primary_curie = pyobo.get_primary_curie("go:0001071")
+assert primary_curie == "go:0003700"
 
 # If it's already the primary, it just gets returned
-assert Reference.from_curie('go:0003700') == pyobo.get_primary_curie('go:0003700')
+assert Reference.from_curie("go:0003700") == pyobo.get_primary_curie("go:0003700")
 ```
 
 ### Mapping Species
@@ -196,11 +170,10 @@ WikiPathway identifiers to species (as NCBI taxonomy identifiers):
 ```python
 import pyobo
 
-wikipathways_id_to_species = pyobo.get_id_species_mapping('wikipathways')
+wikipathways_id_to_species = pyobo.get_id_species_mapping("wikipathways")
 
 # Apoptosis (Homo sapiens)
-taxonomy_id = wikipathways_id_to_species['WP254']
-assert taxonomy_id == '9606'
+assert "9606" == wikipathways_id_to_species["WP254"]
 ```
 
 Or, you don't have time for two lines:
@@ -209,8 +182,8 @@ Or, you don't have time for two lines:
 import pyobo
 
 # Apoptosis (Homo sapiens)
-taxonomy_id = pyobo.get_species('wikipathways', 'WP254')
-assert taxonomy_id == '9606'
+taxonomy_id = pyobo.get_species("wikipathways", "WP254")
+assert taxonomy_id == "9606"
 ```
 
 ### Grounding
@@ -222,13 +195,13 @@ it up and its preferred label.
 ```python
 import pyobo
 
-reference = pyobo.ground('chebi', 'Fusilade II')
-assert reference.prefix == 'chebi'
-assert reference.identifier == '132964'
-assert reference.name == 'fluazifop-P-butyl'
+reference = pyobo.ground("chebi", "Fusilade II")
+assert reference.prefix == "chebi"
+assert reference.identifier == "132964"
+assert reference.name == "fluazifop-P-butyl"
 
 # When failure happens...
-reference = pyobo.ground('chebi', 'Definitely not a real name')
+reference = pyobo.ground("chebi", "Definitely not a real name")
 assert reference is None
 ```
 
@@ -240,10 +213,10 @@ false positives in case of conflicts):
 import pyobo
 
 # looking for phenotypes/pathways
-reference = pyobo.ground(['efo', 'go'], 'ERAD')
-assert reference.prefix == 'go'
-assert reference.identifier == '0030433'
-assert reference.name == 'ubiquitin-dependent ERAD pathway'
+reference = pyobo.ground(["efo", "go"], "ERAD")
+assert reference.prefix == "go"
+assert reference.identifier == "0030433"
+assert reference.name == "ubiquitin-dependent ERAD pathway"
 ```
 
 ### Cross-referencing
@@ -253,10 +226,10 @@ Get xrefs from ChEBI to PubChem:
 ```python
 import pyobo
 
-chebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs('chebi', 'pubchem.compound')
+chebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs("chebi", "pubchem.compound")
 
-pubchem_compound_id = chebi_id_to_pubchem_compound_id['132964']
-assert pubchem_compound_id == '3033674'
+pubchem_compound_id = chebi_id_to_pubchem_compound_id["132964"]
+assert pubchem_compound_id == "3033674"
 ```
 
 If you don't have time for two lines:
@@ -264,8 +237,8 @@ If you don't have time for two lines:
 ```python
 import pyobo
 
-pubchem_compound_id = pyobo.get_xref('chebi', '132964', 'pubchem.compound')
-assert pubchem_compound_id == '3033674'
+pubchem_compound_id = pyobo.get_xref("chebi", "132964", "pubchem.compound")
+assert pubchem_compound_id == "3033674"
 ```
 
 Get xrefs from Entrez to HGNC, but they're only available through HGNC, so you
@@ -274,13 +247,13 @@ need to flip them:
 ```python
 import pyobo
 
-hgnc_id_to_ncbigene_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene')
+hgnc_id_to_ncbigene_id = pyobo.get_filtered_xrefs("hgnc", "ncbigene")
 ncbigene_id_to_hgnc_id = {
   ncbigene_id: hgnc_id
   for hgnc_id, ncbigene_id in hgnc_id_to_ncbigene_id.items()
 }
-mapt_hgnc = ncbigene_id_to_hgnc_id['4137']
-assert mapt_hgnc == '6893'
+mapt_hgnc = ncbigene_id_to_hgnc_id["4137"]
+assert mapt_hgnc == "6893"
 ```
 
 Since this is a common pattern, there's a keyword argument `flip` that does this
@@ -289,9 +262,9 @@ for you:
 ```python
 import pyobo
 
-ncbigene_id_to_hgnc_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene', flip=True)
-mapt_hgnc_id = ncbigene_id_to_hgnc_id['4137']
-assert mapt_hgnc_id == '6893'
+ncbigene_id_to_hgnc_id = pyobo.get_filtered_xrefs("hgnc", "ncbigene", flip=True)
+mapt_hgnc_id = ncbigene_id_to_hgnc_id["4137"]
+assert mapt_hgnc_id == "6893"
 ```
 
 If you don't have time for two lines (I admit this one is a bit confusing) and
@@ -300,8 +273,8 @@ need to flip it:
 ```python
 import pyobo
 
-hgnc_id = pyobo.get_xref('hgnc', '4137', 'ncbigene', flip=True)
-assert hgnc_id == '6893'
+hgnc_id = pyobo.get_xref("hgnc", "4137", "ncbigene", flip=True)
+assert hgnc_id == "6893"
 ```
 
 ### Properties
@@ -313,11 +286,11 @@ basis.
 import pyobo
 
 # I don't make the rules. I wouldn't have chosen this as the key for this property. It could be any string
-chebi_smiles_property = 'http://purl.obolibrary.org/obo/chebi/smiles'
-chebi_id_to_smiles = pyobo.get_filtered_properties_mapping('chebi', chebi_smiles_property)
+chebi_smiles_property = "http://purl.obolibrary.org/obo/chebi/smiles"
+chebi_id_to_smiles = pyobo.get_filtered_properties_mapping("chebi", chebi_smiles_property)
 
-smiles = chebi_id_to_smiles['132964']
-assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
+smiles = chebi_id_to_smiles["132964"]
+assert smiles == "C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F"
 ```
 
 If you don't have time for two lines:
@@ -325,8 +298,8 @@ If you don't have time for two lines:
 ```python
 import pyobo
 
-smiles = pyobo.get_property('chebi', '132964', 'http://purl.obolibrary.org/obo/chebi/smiles')
-assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
+smiles = pyobo.get_property("chebi", "132964", "http://purl.obolibrary.org/obo/chebi/smiles")
+assert smiles == "C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F"
 ```
 
 ### Hierarchy
@@ -338,12 +311,12 @@ import pyobo
 from pyobo import Reference
 
 # check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process
-assert Reference.from_curie('go:0008219') in pyobo.get_ancestors('go', '0006915')
+assert Reference.from_curie("go:0008219") in pyobo.get_ancestors("go", "0006915")
 
 # check that go:0070246 ! natural killer cell apoptotic process is a
 # descendant of go:0006915 ! apoptotic process
-apopototic_process_descendants = pyobo.get_descendants('go', '0006915')
-assert Reference.from_curie('go:0070246') in apopototic_process_descendants
+apopototic_process_descendants = pyobo.get_descendants("go", "0006915")
+assert Reference.from_curie("go:0070246") in apopototic_process_descendants
 ```
 
 Get the sub-hierarchy below a given node:
@@ -353,11 +326,11 @@ import pyobo
 from pyobo import Reference
 
 # get the descendant graph of go:0006915 ! apoptotic process
-apopototic_process_subhierarchy = pyobo.get_subhierarchy('go', '0006915')
+apopototic_process_subhierarchy = pyobo.get_subhierarchy("go", "0006915")
 
 # check that go:0070246 ! natural killer cell apoptotic process is a
 # descendant of go:0006915 ! apoptotic process through the subhierarchy
-assert Reference.from_curie('go:0070246') in apopototic_process_subhierarchy
+assert Reference.from_curie("go:0070246") in apopototic_process_subhierarchy
 ```
 
 Get a hierarchy with properties preloaded in the node data dictionaries:
@@ -366,12 +339,12 @@ Get a hierarchy with properties preloaded in the node data dictionaries:
 import pyobo
 from pyobo import Reference
 
-prop = 'http://purl.obolibrary.org/obo/chebi/smiles'
-chebi_hierarchy = pyobo.get_hierarchy('chebi', properties=[prop])
+prop = "http://purl.obolibrary.org/obo/chebi/smiles"
+chebi_hierarchy = pyobo.get_hierarchy("chebi", properties=[prop])
 
-assert Reference.from_curie('chebi:132964') in chebi_hierarchy
-assert prop in chebi_hierarchy.nodes['chebi:132964']
-assert chebi_hierarchy.nodes['chebi:132964'][prop] == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
+assert Reference.from_curie("chebi:132964") in chebi_hierarchy
+assert prop in chebi_hierarchy.nodes["chebi:132964"]
+assert chebi_hierarchy.nodes["chebi:132964"][prop] == "C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F"
 ```
 
 ### Relations
@@ -381,9 +354,9 @@ way)
 
 ```python
 >>> import pyobo
->>> human_mapt_hgnc_id = '6893'
->>> mouse_mapt_mgi_id = '97180'
->>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping('hgnc', 'ro:HOM0000017', 'mgi')
+>>> human_mapt_hgnc_id = "6893"
+>>> mouse_mapt_mgi_id = "97180"
+>>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping("hgnc", "ro:HOM0000017", "mgi")
 >>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]
 ```
 
@@ -392,9 +365,9 @@ If you want to do it in one line, use:
 ```python
 
 >>> import pyobo
->>> human_mapt_hgnc_id = '6893'
->>> mouse_mapt_mgi_id = '97180'
->>> assert mouse_mapt_mgi_id == pyobo.get_relation('hgnc', 'ro:HOM0000017', 'mgi', human_mapt_hgnc_id)
+>>> human_mapt_hgnc_id = "6893"
+>>> mouse_mapt_mgi_id = "97180"
+>>> assert mouse_mapt_mgi_id == pyobo.get_relation("hgnc", "ro:HOM0000017", "mgi", human_mapt_hgnc_id)
 ```
 
 ### Writings Tests that Use PyOBO
@@ -410,8 +383,8 @@ import pyobo
 from pyobo.mocks import get_mock_id_name_mapping
 
 mock_id_name_mapping = get_mock_id_name_mapping({
-  'chebi': {
-      '132964': 'fluazifop-P-butyl',
+  "chebi": {
+      "132964": "fluazifop-P-butyl",
   },
 })
 
@@ -419,33 +392,21 @@ class MyTestCase(unittest.TestCase):
   def my_test(self):
       with mock_id_name_mapping:
           # use functions directly, or use your functions that wrap them
-          pyobo.get_name('chebi', '1234')
+          pyobo.get_name("chebi", "1234")
 ```
 
-## Curation of the Bioregistry
+## Preprocessing CURIEs, URIs, and unqualified identifiers
 
 In order to normalize references and identify resources, PyOBO uses the
 [Bioregistry](https://github.com/bioregistry/bioregistry). It used to be a part
 of PyOBO, but has since been externalized for more general reuse.
 
 At
-[src/pyobo/registries/metaregistry.json](https://github.com/pyobo/pyobo/blob/master/src/pyobo/registries/metaregistry.json)
-is the curated "metaregistry". This is a source of information that contains all
-sorts of fixes for missing/wrong information in MIRIAM, OLS, and OBO Foundry;
-entries that don't appear in any of them; additional synonym information for
-each namespace/prefix; rules for normalizing xrefs and CURIEs, etc.
-
-Other entries in the metaregistry:
-
-- The `"remappings"->"full"` entry is a dictionary from strings that might
-  follow `xref:` in a given OBO file that need to be completely replaced, due to
-  incorrect formatting
-- The `"remappings"->"prefix"` entry contains a dictionary of prefixes for xrefs
-  that need to be remapped. Several rules, for example, remove superfluous
-  spaces that occur inside CURIEs or and others address instances of the GOGO
-  issue.
-- The `"blacklists"` entry contains rules for throwing out malformed xrefs based
-  on full string, just prefix, or just suffix.
+[src/pyobo/identifier_utils/preprocessing.json](https://github.com/pyobo/pyobo/blob/master/src/pyobo/src/pyobo/identifier_utils/preprocessing.json)
+is the curated set of pre-processing rules. These are used in combination with
+the `curies` package to do pre-processing steps on CURIEs, URIs, and unqualified
+identifiers beyond what is possible with the Bioregistry. See
+https://curies.readthedocs.io/en/latest/preprocessing.html.
 
 ## Troubleshooting
 

{pyobo-0.12.0.dist-info → pyobo-0.12.1.dist-info}/RECORD

@@ -1,12 +1,12 @@
 pyobo/plugins.py,sha256=c04afe369c99ed9eae12bd2e18334e7972ce199a2419b166a377becf63cd2893,1232
-pyobo/getters.py,sha256=2c692998854debb077a34760e2137a384538f67ab26223528ac61ef2f6f75db0,18190
-pyobo/gilda_utils.py,sha256=d2f9a9cdc55aac31f9e0c22ff74b189733b767b78f6c30d40efd6d103c024cc5,4726
-pyobo/.DS_Store,sha256=3be251abc9bfef0098dacb54b161230be447594c210a59c77bc5761c3b891943,8196
-pyobo/version.py,sha256=2eea47b601dcb6b0c7680274221cb4f6a81e95fc7937aaf8db8352966358f692,926
+pyobo/getters.py,sha256=68c8982ac868863e73d1428bcdb82dfdfd0d9397e25d9dc2e0eca05d9b9d566a,17366
+pyobo/gilda_utils.py,sha256=b9384002b00b48dcc98be86b47d954bed41c8b9548c380aaab62fa9ad929d0aa,1990
+pyobo/.DS_Store,sha256=00b8c741cd5b001c03c1a582f55bfbcda0ad16f0e55019d64f93241b74991980,8196
+pyobo/version.py,sha256=dab7f9a58f271077f9eb69671bc8ff659ad64f36f418250a964fa030d634373d,926
 pyobo/ner/__init__.py,sha256=0199b704f1235184d521069034823c3d9960ff6756205c299649b87a4bbd4041,153
 pyobo/ner/api.py,sha256=b34309833eac8f5dea881d531323bf682f35d377e09d807066ba1183282964dc,2167
 pyobo/ner/normalizer.py,sha256=4e90d93801877f72f2fab8069db986e79cc749533a068a8b07a9d7c9e37cb9c2,954
-pyobo/obographs.py,sha256=0736a4446a4f4f824fb42383e96c8853d50b6d1bbbb52c889f543b372d87e286,4189
+pyobo/obographs.py,sha256=f4d9904d939afd04b29b42aa40acbaf6ec9d4a8f2eb3e1dc714b051b1025c41e,4239
 pyobo/resource_utils.py,sha256=6e5a1229b1df30bcf4841f009213247cb386ab0e85c8ef02114e8b360d0f54c9,4406
 pyobo/resources/goc.py,sha256=6b7e352d9a7e00e08c92588a65d283be09ab5dac9fc4e9780e14b130b64ce5ba,2550
 pyobo/resources/goc.tsv,sha256=5bb98b945fbc9e0876e2a921f328a72f8b44f5686037e341fc8432b1a1d0d616,9081
@@ -22,46 +22,45 @@ pyobo/__init__.py,sha256=0d90185e6e3aa041ccc27c68226c45e456e39369328e3db17706d65
 pyobo/utils/iter.py,sha256=ad845b6da1491f131a134c94fab419a026a0608aed7afd3db98d26c4591fe736,1524
 pyobo/utils/misc.py,sha256=99d1f6e88b48d3f0cdbd7fff8a908556bf949278fcf0ef639e5cc8a421d0f4db,2684
 pyobo/utils/ndex_utils.py,sha256=128902592d345ab93fe32f2575e42e53269a0bac8dcc18370da81497e2767336,2326
-pyobo/utils/io.py,sha256=fd1b02443f0e834fe96b8656ff3baa1bca336a18f11802b74aaacb33308236c0,4214
-pyobo/utils/cache.py,sha256=f23601b67c7435ea37cd5bea6caec120e69455cfebfe9b65b65d7527c58b6253,3088
+pyobo/utils/io.py,sha256=fa0cb5a8633a6c9fb95eb2f74e08fbf69acc4fc229b89c18dd233921b80378a9,5100
+pyobo/utils/cache.py,sha256=136ccd03b82afd534699a36bad129e5f3e73aba5c3184fb93d5a24af30d99227,3098
 pyobo/utils/__init__.py,sha256=08035263cbc6abfeaff2b5a159121d9e4f96a392c0d91f568e0d67a9b5aa2cec,17
-pyobo/utils/path.py,sha256=e77ded1aa51869bf941fa250d6306fbdfbe30bf712954ebecb830130539ca62c,3486
-pyobo/cli/database.py,sha256=7b954538c4e643e606150462447645b2f7d10f0b1ae859d76e141e3e35255bfe,11012
+pyobo/utils/path.py,sha256=cc37f10de8e0ef90a6063cc2b1c5d1b0993e41649536f04bfddc892d61a3bc4f,3398
+pyobo/cli/database.py,sha256=e880ac2c78bd437d73c99cea5c44938129852571bca35e2ab0cc7de195851ce6,11963
 pyobo/cli/lookup.py,sha256=1b11bbe771979c345ff8df494562919900b95e237c7c437997595ee42de31c76,9163
 pyobo/cli/__init__.py,sha256=a5388bbb38e3a62d0febdc958d0da413a9c152666e6059ea74934364b0e482f9,71
-pyobo/cli/database_utils.py,sha256=aef42d7d5e561cf2a765cececd0fd8c1750a20739c3294d0b3df6e595322d195,5793
+pyobo/cli/database_utils.py,sha256=8d0eea4a0fa8664f90f910b5db536451ba9778d8342bc7d5f7a8a05da2b7adae,5540
 pyobo/cli/cli.py,sha256=ca057c8505fa7f40730ac0aa0a77e033e30ede9074a145f0b70d7b5f622aa2bd,2939
 pyobo/cli/utils.py,sha256=9e6b57b311b44d61088e321efa387f6aacebd3d6d337bf8d1c589fb871b3304d,1738
 pyobo/struct/__init__.py,sha256=fb813dfa7de27f195c07cd5311de78403b03dfbf0a183995c8fb448033ace311,1444
 pyobo/struct/typedef.py,sha256=fd94429e28efcdf7bbeba4b1729fa66af5f64c34e49437d82e4b3e5a457d064d,12099
 pyobo/struct/struct_utils.py,sha256=7b8bfd7a322f34cf1436b83c8eab983944651ba467923045bf61ecc245800d2c,39164
 pyobo/struct/utils.py,sha256=ce4a4e138d894087e4374adce6a34434ad375482a691fff9eed1e88cc24aef56,906
-pyobo/struct/reference.py,sha256=e54972991dc195149ab3e1dc154a47629adc16361eb6800bbf18a123cdeca51c,11715
+pyobo/struct/reference.py,sha256=4fc7d3b665cd18c8dfbbb2b8b49de4bc30a8e101d14ff26bf5f88e9c562bc2d3,11735
 pyobo/struct/vocabulary.py,sha256=56e0f6770cf7da2d6f1221e3fc8261f1c07dc8358a1f3dfb487894a25b1ed133,4335
 pyobo/struct/functional/dsl.py,sha256=780b4e5616b8dc823cee610945a95ffa109aa43287992dd4dd51511c461f96fb,101183
 pyobo/struct/functional/__init__.py,sha256=d536edb7fe86a1aad19607df3dea62b49dd0b4bb2b30f31b8431a842700a499e,32
 pyobo/struct/functional/obo_to_functional.py,sha256=785c46fdb00dc45f3903f67ad24ae4fcb6d187ce48208373fc9d42833a85f6b8,13273
 pyobo/struct/functional/utils.py,sha256=73e5c6d9227b0a162dcfb294dcad05f93ea870c8d87af7a2d16c6591f9249ad1,3487
 pyobo/struct/functional/macros.py,sha256=cc654f131fa685d4afc87d8c7b5e8565da1b789dd5d73045a77b3e033a8ced52,13785
-pyobo/struct/functional/ontology.py,sha256=64620cc1c1df919835a4a48342f62d1fdfa7067bb40e45da0169632aee4ff6c1,9245
-pyobo/struct/struct.py,sha256=d057dc0ccc6f153b9984770013ee7a8d1227029e29b957224ef10cfdcf787f05,87231
+pyobo/struct/functional/ontology.py,sha256=bc610a206c5f502cc658cbf7dcaa9caeb112a596ab1cb07fcbd571c8a6da2894,9331
+pyobo/struct/struct.py,sha256=29b77204d903a948aff74f93aa043e5421cc932c22a893e70dbfd3f27b911fb7,89480
 pyobo/ssg/index.html,sha256=da62c16a198f7ad2468599c5d7e4da4d7b81e02a18a25a59da741a579746e676,4346
 pyobo/ssg/typedef.html,sha256=2ab76acc1eb18edebcf5b1b7dc3dba00bfb5d49aef36e124a3134d23e106f938,2038
 pyobo/ssg/base.html,sha256=fef95d5026be80bd984cd63a1a002ec4d4f74e06840f9f39bc5feaed3aeb8d8b,2844
 pyobo/ssg/__init__.py,sha256=8500042e3156fe3acd5fd5546b0ed52038d842150389c512b3e99267302f152a,5224
 pyobo/ssg/term.html,sha256=b522c82774980d37ad2bd8361280cacaee1a1dc855a351145e4fda62119e38aa,3869
-pyobo/reader.py,sha256=76eff0c23950346e12f9a9c88422b6b4b9cb4dabb080eff154bd197b1900792c,52486
+pyobo/reader.py,sha256=6fc2522a89772b718eaa6278e2abc7d5ca536378b537992b34bfe12bcfd10d72,52246
 pyobo/identifier_utils/relations/data_rdfs.json,sha256=6e3a7166d7b78385afac626c987b8024dfdc83f7dac6a21af6d08bedab8776a4,86
 pyobo/identifier_utils/relations/__init__.py,sha256=2961f492b8530a678a9e010887b5530c3de1cc2df8f294e210a18dbb748d01db,159
 pyobo/identifier_utils/relations/data.json,sha256=88b6ce5fb632faa389b512b68f1b73acdd54b552a1aaa8043430eb5e0020a0bc,113169
 pyobo/identifier_utils/relations/api.py,sha256=c625bca0f09379ba7ef544d05aaf4b998ee9798945a90f3b98b6d763ef9d36df,5764
 pyobo/identifier_utils/relations/data_rdf.json,sha256=4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945,2
 pyobo/identifier_utils/relations/data_owl.json,sha256=a70fe8850a0b32f0ca5f9358085a340297a3464d7ba61e83333fe69d6ae4c826,1066
-pyobo/identifier_utils/__init__.py,sha256=8aa8cd780d13c8af054ff96ed098d618775d9dd1bbfb1c1a537e67e8e6fb80d4,894
-pyobo/identifier_utils/model.py,sha256=569c9198397cbed31544662fb9ed19da901062ec5ccb26a35f3dc303cec0f96a,5103
-pyobo/identifier_utils/api.py,sha256=2e114f702188838057122114cca344a8f5371d13d90f386dbbbc4c2630caa062,9001
-pyobo/identifier_utils/preprocessing.py,sha256=7a0f7ab6d8dc85b0b185b88a9bd4c01ad6a49f4b76faaf8fbdeceee86806e6ea,1845
-pyobo/identifier_utils/preprocessing.json,sha256=9298fbec6148b4987edce3e931190f8a1f5fdd727aa239b8fcf59fbed9f1212f,32710
+pyobo/identifier_utils/__init__.py,sha256=865d3a02c3a6d38ff13d4e30685a60368c4a7823397f93e609c2ad356c5d46a3,749
+pyobo/identifier_utils/api.py,sha256=310bf6e0ac55882b9bbf179b1628bfc70797ae419a962ea6e1e3cdf48e8e5c26,9212
+pyobo/identifier_utils/preprocessing.py,sha256=67c9109c1a4ba1f5f45368516563a044e38d4095799b520519a57044230d5fd7,618
+pyobo/identifier_utils/preprocessing.json,sha256=e84f2ed9bb4f2a92c83845daf739f4052d7a615bfc6c13dcc54845a306916627,34821
 pyobo/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
 pyobo/sources/signor/download.py,sha256=ae40c954403a95dd33e221b5e2d30e70072e4658d043d48024068b75ac5a833f,1053
 pyobo/sources/signor/__init__.py,sha256=6de6ff151aaca2a2d5317b437916405dff5783d50120704ed39b8f53df0d6a32,139
@@ -101,7 +100,7 @@ pyobo/sources/drugbank/drugbank.py,sha256=eb2fc65b2d43ac54c0c81fefb0701b13264110
 pyobo/sources/rgd.py,sha256=46020f5933a846a7575ffdd8330ddde8df560d16872c9475f204da59cfdbce4e,5316
 pyobo/sources/__init__.py,sha256=94db6754ef36ea969a347c2ae38ff9eddb44dbe177ce06d9f93e5432592bc404,4630
 pyobo/sources/pharmgkb/pharmgkb_pathway.py,sha256=3eb66d425b46ff38f3be9f8aeb7291c3e22ac49b4eef25f74e703ff68fb270e7,2042
-pyobo/sources/pharmgkb/pharmgkb_gene.py,sha256=848aa319c348e7eb84341183294d08000c36b54cd1a692fbbc5b833d087d092b,4102
+pyobo/sources/pharmgkb/pharmgkb_gene.py,sha256=04c3c39bc0d900491e8d7d827cd0c17c898f2ea17d4a645544822373647413e1,4049
 pyobo/sources/pharmgkb/__init__.py,sha256=25df339dedc6617df9ba4a80ef2b5b620b2425ab900893cc3f4de8e5c3557a20,443
 pyobo/sources/pharmgkb/pharmgkb_chemical.py,sha256=698096d364d5cc0c59e659dee428eb4fb5224818fa0b567a30173a9dc9ff229c,3142
 pyobo/sources/pharmgkb/pharmgkb_variant.py,sha256=1a1f5f34895446614589cf9f4307bfe9218a316dee21018a4610b4b6fb163ad0,2873
@@ -112,7 +111,7 @@ pyobo/sources/pathbank.py,sha256=496e2611d5825f6319606d55269f322c4cf206efce99a65
 pyobo/sources/gwascentral/gwascentral_phenotype.py,sha256=4af302177b18a9cdc5e6735709fefa033221353ebdf191c79d3a4ed0819fb7ca,1788
 pyobo/sources/gwascentral/__init__.py,sha256=55d1c8801551fb7e81ee02ee851e175795179ff120359d3e8b583d36384e8d8d,231
 pyobo/sources/gwascentral/gwascentral_study.py,sha256=bddb3b20e2374cc3ff14601aba36c17466897d46f1d086bf75ecf62992263bd9,2657
-pyobo/sources/omim_ps.py,sha256=1a09fbded65dc3e85697692552dcf3a5c643ef27677d17bd8b316afc28606c08,1249
+pyobo/sources/omim_ps.py,sha256=692cb56e44090b2c600d87c0ef0a71a13b77750faa3e40886385f9dbf7a51c76,1432
 pyobo/sources/selventa/schem.py,sha256=bea37f6bf34b7ac863fb6751b997a57ce2c943977253766085f49122af441550,1162
 pyobo/sources/selventa/sdis.py,sha256=b3169dde3868d74ab6a12ce3c820e419605884ac2ccbf8da4bec0f24ac1c2e75,1287
 pyobo/sources/selventa/__init__.py,sha256=7082039562fdce72f6af4699209dabd4537734cf62a3be30f877b67a0cc9c17f,254
@@ -177,12 +176,12 @@ pyobo/sources/complexportal.py,sha256=78ec7567393ccc33cfd43acadb2392bf5f22f6933a
 pyobo/sources/credit.py,sha256=7643164ed0aa81333dd2415af23ec170fc94efc89b1656ea2d7f66551b6aff9a,1795
 pyobo/sources/chebi.py,sha256=f9ffd7c812ce1e80b6b86aaef14cd0dc780095ba80866efe014bded072b44ce0,1202
 pyobo/sources/ror.py,sha256=212fca52d31e2a002776b6cb8e17282bc8a5a7e8ce7a20f0cc64f2e51f5c2309,8882
-pyobo/sources/flybase.py,sha256=91fca7e65e559a67b9766d42bfbca52856397ecc76395083c232ac0f12c63669,5747
-pyobo/sources/cgnc.py,sha256=c241687df2adcf1eb690d25e8892d7d89d752b797fd716e7d52d26d136215fbc,2215
+pyobo/sources/flybase.py,sha256=8144b7f4d17fa9cef6dd1d9201b85062a3e0e943a2c0ac0f5e15d0d49c02ebc4,5666
+pyobo/sources/cgnc.py,sha256=5e5c2aaa325cec1f7bdf9dbe020691a3c95acd79ca7fffc9555e2575f1899754,2299
 pyobo/api/species.py,sha256=631cc978295fb8a23ea6360ba6ee7bf7b8dd0dec93917a6340381d99cf4c2b0a,2376
 pyobo/api/metadata.py,sha256=b2d25a897fe5ef1d11d55efb4cdc07bcfb6892e67e128a9bf473112fbd0d896b,1029
 pyobo/api/combine.py,sha256=ed3f108fc5b5c164352a0289b0ed641511d9c6441cadf28cd6106b86a1ec1245,1106
-pyobo/api/properties.py,sha256=2fa0be64bf85d2453a8020f93f142db2678d3e2bb4cb9de7d99f244b998c1acf,6949
+pyobo/api/properties.py,sha256=6d85af1ebd5b7f4c5d232323faab9d8f8a11a419eab0a86eca36052b22b2f778,6914
 pyobo/api/relations.py,sha256=6dfda59d8ae2c3addb816d7dad2b97856916c6f2e6114f7a774bfcaff1c25747,5859
 pyobo/api/__init__.py,sha256=259870a4519a6baa5df1180378837e67c688e8ecbe46e9a3d4a90e6435c79e1d,2955
 pyobo/api/edges.py,sha256=4849b6809c7a2e83a48571a3d75578dae2e0e0589d15af6326a5bd1f39e57f09,1974
@@ -190,13 +189,13 @@ pyobo/api/hierarchy.py,sha256=37f27381f08a3c859adb4a1d46132fa60889a5ccce8867620d
 pyobo/api/names.py,sha256=2f620187285c1fccbeac23708d624bc374ec1e9d6abce65ebf5eb4f9c63070b8,10673
 pyobo/api/utils.py,sha256=ae8d2274e48d129a0d3520e48ba462af066afff928c9fcd231f569c4b322bcf5,5429
 pyobo/api/typedefs.py,sha256=1d3ba2d2497f5442f18238b4bdf06bf8d046df3aeba4253cb66b9039258ae9fc,1262
-pyobo/api/xrefs.py,sha256=f681b01b7772e1d97ad329cc5dbddddcf4bb7a297a802bb4c6204f0b0e3619b5,5309
+pyobo/api/xrefs.py,sha256=9d62cbb761b36957e780d0546ce3154a33a90ae6be23bbbedadba8c735c6aab0,5242
 pyobo/api/alts.py,sha256=478b3162574616f2827bd73107f80f5dfdaf5971eaf6c6813109109dba89e522,3032
 pyobo/__main__.py,sha256=70e610d8e10bc45fbd4fa9ee67dc672d2bbd6cb1e4e9e8a7aec4a8cfb11c0fd3,83
 pyobo/reader_utils.py,sha256=5324154d08576e167d7c28b3660dbaa394e67878acf7ea9930abd0170201460a,4423
 pyobo/mocks.py,sha256=8f9e392bd3ff0cfb0306e6070eb8724cb8e694fa0d951744b5c4652e15e56d72,2440
-pyobo-0.12.0.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
-pyobo-0.12.0.dist-info/WHEEL,sha256=75a1e6cb20cd73e6878351e9e19d65d3d1832ba44f36116fe21a93d222c5897a,79
-pyobo-0.12.0.dist-info/entry_points.txt,sha256=00d833beec05ffdff58a90a8c49b5b04ce80e22d8c92ddfd80c3f340eea1bc6b,42
-pyobo-0.12.0.dist-info/METADATA,sha256=3279dbc737f1a343a764ca3e2295ff4118fd6568de059f23cffb08a985e388e8,23685
-pyobo-0.12.0.dist-info/RECORD,,
+pyobo-0.12.1.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
+pyobo-0.12.1.dist-info/WHEEL,sha256=1c77bbda0b527f376a68ced20cbc1aac3efc7bc4d7c10cc4323a905ef79ae8db,78
+pyobo-0.12.1.dist-info/entry_points.txt,sha256=00d833beec05ffdff58a90a8c49b5b04ce80e22d8c92ddfd80c3f340eea1bc6b,42
+pyobo-0.12.1.dist-info/METADATA,sha256=891eda0af949aecf1dc5064aaba32edf807fc6ec4d43d7eebd8b0af65dc3b388,22299
+pyobo-0.12.1.dist-info/RECORD,,

{pyobo-0.12.0.dist-info → pyobo-0.12.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: uv 0.6.16
+Generator: uv 0.7.2
 Root-Is-Purelib: true
 Tag: py3-none-any