From 4a16dec73819f549190d4399eaddb0d8a9f138a4 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 10 Feb 2025 17:59:35 -0800 Subject: [PATCH 1/3] Added association-graphs command --- .../AdHoc/Summarizing-with-LLMs.ipynb | 438 ++ docs/examples/AdHoc/index.rst | 10 + docs/examples/Commands/index.rst | 1 + docs/examples/OntologyEditorsGuide/index.rst | 9 + docs/examples/index.rst | 2 + poetry.lock | 4338 ++++++++++------- pyproject.toml | 2 + src/oaklib/cli.py | 280 +- src/oaklib/conf/obograph-style.json | 20 + src/oaklib/datamodels/obograph.py | 1095 ++--- src/oaklib/datamodels/obograph.yaml | 7 + src/oaklib/datamodels/vocabulary.py | 1 + .../amigo/amigo_implementation.py | 12 +- .../obograph/obograph_implementation.py | 10 +- .../uniprot/uniprot_implementation.py | 2 + .../association_provider_interface.py | 12 + .../interfaces/basic_ontology_interface.py | 2 + src/oaklib/interfaces/obograph_interface.py | 26 +- src/oaklib/io/obograph_writer.py | 42 +- src/oaklib/io/streaming_writer.py | 11 + src/oaklib/query.py | 85 +- src/oaklib/selector.py | 3 + .../associations/association_queries.py | 48 + .../metrics/text_content_analysis.py | 6 +- src/oaklib/utilities/obograph_utils.py | 59 +- 25 files changed, 3948 insertions(+), 2573 deletions(-) create mode 100644 docs/examples/AdHoc/Summarizing-with-LLMs.ipynb create mode 100644 docs/examples/AdHoc/index.rst create mode 100644 docs/examples/OntologyEditorsGuide/index.rst create mode 100644 src/oaklib/utilities/associations/association_queries.py diff --git a/docs/examples/AdHoc/Summarizing-with-LLMs.ipynb b/docs/examples/AdHoc/Summarizing-with-LLMs.ipynb new file mode 100644 index 000000000..980026048 --- /dev/null +++ b/docs/examples/AdHoc/Summarizing-with-LLMs.ipynb @@ -0,0 +1,438 @@ +{ + "cells": [ + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "# Summarizing with LLMs\n", + "\n", + "This notebook demonstrates how to summarize the output of LLMs using the [datasette LLM command line tool](https://llm.datasette.io/en/stable/).\n", + "\n", + "See also:\n", + "\n", + "- [How to use LLMs with OAK](https://incatools.github.io/ontology-access-kit/howtos/use-llms.html\n" + ], + "id": "7373e90b82b3695e" + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "## Install the LLM command line tool\n", + "\n", + "```\n", + "pip install llm\n", + "```\n", + "\n", + "You may also want to install plugins for your models of choice:\n", + "\n", + "```\n", + "pip install llm-deepseek\n", + "```" + ], + "id": "7e17ec75eca57b86" + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "## Summarize outputs\n", + "\n", + "You can redirect any output you like to `llm`. For example, consider this OAK query to get definition of all kinds of hearts in Uberon:" + ], + "id": "be5a6ffbc0277213" + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2025-02-08T02:23:24.381674Z", + "start_time": "2025-02-08T02:23:19.484155Z" + } + }, + "cell_type": "code", + "source": "!runoak -i sqlite:obo:uberon definitions .sub \"circulatory organ\"", + "id": "65ca9da0284cc307", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "id\tlabel\tdefinition\r\n", + "UBERON:0000948\theart\tA myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.\r\n", + "UBERON:0007100\tprimary circulatory organ\tA hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].\r\n", + "UBERON:0015202\tlymph heart\tA circulatory organ that is reponsible for pumping lymph throughout the body.\r\n", + "UBERON:0015227\tperistaltic circulatory vessel\tA vessel down which passes a wave of muscular contraction, that forces the flow of haemolymphatic fluid.\r\n", + "UBERON:0015228\tcirculatory organ\tA hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.\r\n", + "UBERON:0015229\taccessory circulatory organ\tA circulatory organ that is not responsible for primary circulation.\r\n", + "UBERON:0015230\tdorsal vessel heart\tThe caudal, pulsatile region of the dorsal vessel of the arthropod circulatory system.\r\n", + "UBERON:0034961\tembryonic lymph heart\tA lymph heart that is part of an embryo.\r\n", + "UBERON:0034962\tcopulatory lymph heart\tA lymph heart that assists in the return of lymph from the penis to the venous system.\r\n", + "UBERON:0036259\tcardial lymph propulsor\tA lymphatic propulsor that lies tightly against the truncus arteriosus, the major outflow tract of the amphibian heart.\r\n", + "UBERON:0034959\tright lymph heart\tNone\r\n", + "UBERON:0034960\tleft lymph heart\tNone\r\n" + ] + } + ], + "execution_count": 1 + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2025-02-08T02:24:35.943675Z", + "start_time": "2025-02-08T02:24:22.150332Z" + } + }, + "cell_type": "code", + "source": "!runoak -i sqlite:obo:uberon definitions .sub \"circulatory organ\" | llm -m 4o -s \"give a summary of these terms and critical comments on definitions\"", + "id": "bd010c282460f7a0", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "The terms provided mainly describe various structures within the circulatory system, both in vertebrates and invertebrates, with a focus on definitions from anatomical and biological perspectives. Here is a summary of the terms along with critical comments on their definitions:\r\n", + "\r\n", + "1. **Heart (UBERON:0000948):** Defined as a myogenic muscular organ in vertebrates, responsible for circulating blood through cardiac muscle chambers. The term appropriately highlights the heart’s primary function and structural characteristics.\r\n", + "\r\n", + "2. **Primary Circulatory Organ (UBERON:0007100):** Described as a hollow, muscular organ that maintains blood circulation through rhythmic contractions. The definition is clear, albeit a bit redundant with the general concept of a \"heart.\"\r\n", + "\r\n", + "3. **Lymph Heart (UBERON:0015202):** Defined as an organ pumping lymph throughout the body. The definition clearly states its function, but it might benefit from specifying its presence in particular animal groups.\r\n", + "\r\n", + "4. **Peristaltic Circulatory Vessel (UBERON:0015227):** A vessel where muscular contractions propel fluid, specifically haemolymph. The definition is clear, but could use more context or examples of organisms in which such structures are found.\r\n", + "\r\n", + "5. **Circulatory Organ (UBERON:0015228):** Broadly covers any hollow, muscular organ aiding blood, lymph, or fluid circulation. The examples provided enhance understanding, though the broad nature of the definition might necessitate more clarity or distinction between types.\r\n", + "\r\n", + "6. **Accessory Circulatory Organ (UBERON:0015229):** An organ not primarily responsible for circulation, suggesting a supportive role. This generally makes sense, but would benefit from specific examples for clarity.\r\n", + "\r\n", + "7. **Dorsal Vessel Heart (UBERON:0015230):** Describes the pulsatile region of the arthropod dorsal vessel, indicating its role in the circulatory system. The definition is precise for those familiar with arthropod anatomy but could confuse those without such background.\r\n", + "\r\n", + "8. **Embryonic Lymph Heart (UBERON:0034961):** Specifies a lymph heart within an embryo. This is straightforward, however, further description of its role during development could enhance understanding.\r\n", + "\r\n", + "9. **Copulatory Lymph Heart (UBERON:0034962):** Involves lymph return from the penis to the venous system. The definition is clear, yet specialized, relevant mostly to anatomy involving reproductive systems.\r\n", + "\r\n", + "10. **Cardial Lymph Propulsor (UBERON:0036259):** A lymph structure associated with the amphibian heart’s major outflow tract. The definition is precise for specific studies of amphibian physiology.\r\n", + "\r\n", + "11. **Right Lymph Heart (UBERON:0034959) & Left Lymph Heart (UBERON:0034960):** These terms lack definitions, which raises questions about their specific roles and anatomical details; adding definitions would improve completeness and understanding.\r\n", + "\r\n", + "Critical observations indicate that many definitions would benefit from contextual enlargement or specification of their presence and role in different species, enhancing educational value. Furthermore, terms without definitions need elaboration for comprehensive utility.\r\n" + ] + } + ], + "execution_count": 2 + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "## Templates\n", + "\n", + "The llm tool allows you to define templates.\n", + "\n", + "`llm templates edit summarize-definitions` \n", + "\n", + "Then in your editor:\n", + "\n", + "```yaml\n", + "system: give a summary of these terms and critical comments on definitions\n", + "```" + ], + "id": "ddab5a52efb184b1" + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2025-02-08T02:27:39.062864Z", + "start_time": "2025-02-08T02:27:22.621187Z" + } + }, + "cell_type": "code", + "source": "!runoak -i sqlite:obo:uberon definitions .sub \"circulatory organ\" | llm -m 4o -t summarize-definitions\n", + "id": "a7dc56ace685baa7", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "The dataset provides definitions for various types of circulatory organs and structures within the UBERON ontology, which is a comprehensive multi-species anatomy ontology encompassing multiple biological domains. Here is a summary of each term included:\r\n", + "\r\n", + "1. **Heart (UBERON:0000948)**: Described as a myogenic muscular organ within the vertebrate cardiovascular system. It is the primary circulatory organ that functions by moving blood throughout the body via chambers of cardiac muscle.\r\n", + "\r\n", + "2. **Primary Circulatory Organ (UBERON:0007100)**: A hollow, muscular organ that maintains blood circulation through rhythmic contractions. The definition is adapted from the Gene Ontology (GO).\r\n", + "\r\n", + "3. **Lymph Heart (UBERON:0015202)**: A circulatory organ tasked with pumping lymphatic fluid throughout the body. It serves a function analogous to the heart but specific to lymph circulation.\r\n", + "\r\n", + "4. **Peristaltic Circulatory Vessel (UBERON:0015227)**: Described as a vessel in which muscular contractions send waves that propel haemolymphatic fluid forward, common in certain invertebrates.\r\n", + "\r\n", + "5. **Circulatory Organ (UBERON:0015228)**: This broader category includes any hollow, muscular organ that contributes to the circulation of blood, lymph, or their analogs. Examples include the vertebrate heart, ascidian peristaltic heart, the insect dorsal vessel, and a reptile's lymph heart.\r\n", + "\r\n", + "6. **Accessory Circulatory Organ (UBERON:0015229)**: Any circulatory organ that does not play the primary role in circulation, implying a supportive or secondary role.\r\n", + "\r\n", + "7. **Dorsal Vessel Heart (UBERON:0015230)**: A section of the dorsal vessel in arthropods, it is characterized as pulsatile, assisting in their circulatory system.\r\n", + "\r\n", + "8. **Embryonic Lymph Heart (UBERON:0034961)**: A lymph heart that is active during the embryonic stage of development.\r\n", + "\r\n", + "9. **Copulatory Lymph Heart (UBERON:0034962)**: A specialized lymph heart aiding in returning lymph from the penis to the venous system.\r\n", + "\r\n", + "10. **Cardial Lymph Propulsor (UBERON:0036259)**: Positioned closely against the truncus arteriosus in amphibians, it helps propel lymphatic fluid, acting near the heart's outflow tract.\r\n", + "\r\n", + "11. **Right Lymph Heart (UBERON:0034959)** and **Left Lymph Heart (UBERON:0034960)**: These entries lack defined descriptions in the dataset, suggesting they might represent specific anatomical structures known in certain species but not yet fully characterized in this context.\r\n", + "\r\n", + "**Critical Comments on Definitions:**\r\n", + "\r\n", + "- **Incompleteness and Specificity:** Some entries, like the right and left lymph heart, are missing definitions, which indicate a need for further research or input in these areas. Definitions should be expanded to clarify their unique roles or confirm their existence in various species.\r\n", + "\r\n", + "- **Overlap and Clarity:** There is potential overlap in the definitions of terms like \"circulatory organ\" and \"primary circulatory organ,\" which might cause confusion regarding their distinct functionalities and hierarchies. It would be beneficial to delineate these more clearly within the ontology.\r\n", + "\r\n", + "- **Use of Examples and Context:** The use of examples, such as the mention of ascidians and insects in the circulatory organ definition, enriches understanding but might require caveats for context-specific interpretations.\r\n", + "\r\n", + "Overall, while the given definitions are fairly descriptive of the various components of circulatory systems across different organisms, further refinement and detail, particularly where missing or vague, could improve comprehensiveness and usability in biological research and applications.\r\n" + ] + } + ], + "execution_count": 3 + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": [ + "## Gene summaries\n", + "\n", + "Create a template for summarizing gene annotations:\n", + "\n", + "`llm templates edit summarize-gaf-for-gene` \n", + "\n", + "```yaml\n", + "system: I will provide you with GAF for a gene. Summarize the function of the gene.\n", + " Give a one short description a biologist would understand.\n", + " You may weave together multiple terms where there is redundancy.\n", + " You should aim to be faithful to the GAF, but be aware that mistakes and over-annotation happens.\n", + " If you see things that are unlikely, you can omit these.\n", + " You may also produce some commentary at the end\n", + " (e.g. 'the GAF showed annotation to X but this contradicts what is known about the gene')\n", + " Do not focus on the evidence, or names, or IDs, or metadata about the annotation,\n", + " just write the biological narrative.\n", + " The exception is if this is really relevant (e.g. you may call into question a very old annotation if it\n", + " does not make sense).\n", + " Be aware that historically there has been over-annotation with experimental codes, for example, phenotypes from downstream effects.\n", + " These are less relevant, and you should focus on the core activity, cellular process, and localization.\n", + " You may however choose to briefly summarize phenotypic annotations (e.g. the role of G in process P has downstream effects E1, ...).\n", + " Use your judgment to explain the story biologically rather than simply regurgitating terms.\n", + " Note that the IBA code (inferred from biological ancestor) reflects high quality annotations in many species because these terms\n", + " have been reviewed in a phylogenetic context and checked for over-annotation.\n", + " But note that IBAs may sometimes be less complete, especially for organism-specific knowledge.\n", + " Use your own biological knowledge.\n", + " If aspects of the model are not clear, or you think there are errors, then at the end of your summary report on problems or anything that was not clear.\n", + "```" + ], + "id": "8d110396a9060620" + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2025-02-11T01:31:44.007957Z", + "start_time": "2025-02-11T01:31:39.246698Z" + } + }, + "cell_type": "code", + "source": "!runoak -i amigo:NCBITaxon:9606 associations -p i,p -H --expand GO:0009229 ", + "id": "4e3830b8ff13215b", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "# Query IDs: GO:0009229\r\n", + "# Ontology closure predicates: rdfs:subClassOf, BFO:0000050\r\n", + "#\r\n", + "# The results include a round of expansion\r\n", + "#\r\n", + "subject\tpredicate\tobject\tproperty_values\tsubject_label\tpredicate_label\tobject_label\tnegated\tpublications\tevidence_type\tsupporting_objects\tprimary_knowledge_source\taggregator_knowledge_source\tsubject_closure\tsubject_closure_label\tobject_closure\tobject_closure_label\tcomments\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0009229\t\tSLC19A3\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0009229\t\tTPK1\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000041\tIEA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0009229\t\tTPK1\tNone\tthiamine diphosphate biosynthetic process\tFalse\tPMID:11342111\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0009229\t\tTPK1\tNone\tthiamine diphosphate biosynthetic process\tFalse\tPMID:38547260\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0009229\t\tTPK1\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0009229\t\tSLC25A19\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0009229\t\tSLC19A2\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0009229\t\tTHTPA\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005515\t\tSLC19A3\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0015234\t\tSLC19A3\tNone\tthiamine transmembrane transporter activity\tFalse\tGO_REF:0000024\tISS\t\tBHF-UCL\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0015234\t\tSLC19A3\tNone\tthiamine transmembrane transporter activity\tFalse\tReactome:R-HSA-199626\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0009229\t\tSLC19A3\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0015888\t\tSLC19A3\tNone\tthiamine transport\tFalse\tPMID:11731220\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0015888\t\tSLC19A3\tNone\tthiamine transport\tFalse\tPMID:33008889\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0015888\t\tSLC19A3\tNone\tthiamine transport\tFalse\tPMID:35512554\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0015888\t\tSLC19A3\tNone\tthiamine transport\tFalse\tPMID:35724964\tIMP\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0031923\t\tSLC19A3\tNone\tpyridoxine transport\tFalse\tPMID:33008889\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0031923\t\tSLC19A3\tNone\tpyridoxine transport\tFalse\tPMID:35512554\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0031923\t\tSLC19A3\tNone\tpyridoxine transport\tFalse\tPMID:35724964\tIMP\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0031923\t\tSLC19A3\tNone\tpyridoxine transport\tFalse\tPMID:36456177\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0042723\t\tSLC19A3\tNone\tthiamine-containing compound metabolic process\tFalse\tReactome:R-HSA-196819\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0071934\t\tSLC19A3\tNone\tthiamine transmembrane transport\tFalse\tGO_REF:0000024\tISS\t\tBHF-UCL\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005886\t\tSLC19A3\tNone\tplasma membrane\tFalse\tReactome:R-HSA-199626\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0016020\t\tSLC19A3\tNone\tmembrane\tFalse\tPMID:11136550\tNAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0005886\t\tSLC19A3\tNone\tplasma membrane\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0055085\t\tSLC19A3\tNone\ttransmembrane transport\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BZV2\tbiolink:related_to\tGO:0015234\t\tSLC19A3\tNone\tthiamine transmembrane transporter activity\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0004788\t\tTPK1\tNone\tthiamine diphosphokinase activity\tFalse\tPMID:11342111\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0004788\t\tTPK1\tNone\tthiamine diphosphokinase activity\tFalse\tPMID:38547260\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0005515\t\tTPK1\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0005524\t\tTPK1\tNone\tATP binding\tFalse\tGO_REF:0000043\tIEA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0016301\t\tTPK1\tNone\tkinase activity\tFalse\tGO_REF:0000043\tIEA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0030975\t\tTPK1\tNone\tthiamine binding\tFalse\tGO_REF:0000002\tIEA\t\tInterPro\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0042802\t\tTPK1\tNone\tidentical protein binding\tFalse\tPMID:25502805\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0042802\t\tTPK1\tNone\tidentical protein binding\tFalse\tPMID:29892012\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0042802\t\tTPK1\tNone\tidentical protein binding\tFalse\tPMID:31515488\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0042802\t\tTPK1\tNone\tidentical protein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0141200\t\tTPK1\tNone\tUTP thiamine diphosphokinase activity\tFalse\tPMID:38547260\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0006772\t\tTPK1\tNone\tthiamine metabolic process\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0009229\t\tTPK1\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000041\tIEA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0009229\t\tTPK1\tNone\tthiamine diphosphate biosynthetic process\tFalse\tPMID:11342111\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0009229\t\tTPK1\tNone\tthiamine diphosphate biosynthetic process\tFalse\tPMID:38547260\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0010510\t\tTPK1\tNone\tregulation of acetyl-CoA biosynthetic process from pyruvate\tFalse\tPMID:38547260\tIMP\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0005829\t\tTPK1\tNone\tcytosol\tFalse\tReactome:R-HSA-196761\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0004788\t\tTPK1\tNone\tthiamine diphosphokinase activity\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9H3S4\tbiolink:related_to\tGO:0009229\t\tTPK1\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:not\tGO:0030233\t\tSLC25A19\tNone\tdeoxynucleotide transmembrane transporter activity\tTrue\tPMID:15539640\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:not\tGO:0030233\t\tSLC25A19\tNone\tdeoxynucleotide transmembrane transporter activity\tTrue\tPMID:17035501\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:not\tGO:0030302\t\tSLC25A19\tNone\tdeoxynucleotide transport\tTrue\tPMID:15539640\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0015297\t\tSLC25A19\tNone\tantiporter activity\tFalse\tGO_REF:0000043\tIEA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0030233\t\tSLC25A19\tNone\tdeoxynucleotide transmembrane transporter activity\tFalse\tPMID:11226231\tTAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0090422\t\tSLC25A19\tNone\tthiamine pyrophosphate transmembrane transporter activity\tFalse\tPMID:17035501\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0090422\t\tSLC25A19\tNone\tthiamine pyrophosphate transmembrane transporter activity\tFalse\tReactome:R-HSA-8875838\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0009229\t\tSLC25A19\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0030302\t\tSLC25A19\tNone\tdeoxynucleotide transport\tFalse\tPMID:11226231\tNAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0030974\t\tSLC25A19\tNone\tthiamine pyrophosphate transmembrane transport\tFalse\tPMID:17035501\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0042723\t\tSLC25A19\tNone\tthiamine-containing compound metabolic process\tFalse\tReactome:R-HSA-196819\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0005634\t\tSLC25A19\tNone\tnucleus\tFalse\tPMID:21630459\tHDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0005739\t\tSLC25A19\tNone\tmitochondrion\tFalse\tGO_REF:0000052\tIDA\t\tHPA\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0005739\t\tSLC25A19\tNone\tmitochondrion\tFalse\tGO_REF:0000052\tIDA\t\tHPA\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0005739\t\tSLC25A19\tNone\tmitochondrion\tFalse\tGO_REF:0000052\tIDA\t\tHPA\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0005739\t\tSLC25A19\tNone\tmitochondrion\tFalse\tPMID:15539640\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0005739\t\tSLC25A19\tNone\tmitochondrion\tFalse\tPMID:31506564\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0005739\t\tSLC25A19\tNone\tmitochondrion\tFalse\tPMID:34800366\tHTP\t\tFlyBase\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0005743\t\tSLC25A19\tNone\tmitochondrial inner membrane\tFalse\tReactome:R-HSA-8875838\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0030974\t\tSLC25A19\tNone\tthiamine pyrophosphate transmembrane transport\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0015234\t\tSLC25A19\tNone\tthiamine transmembrane transporter activity\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9HC21\tbiolink:related_to\tGO:0005743\t\tSLC25A19\tNone\tmitochondrial inner membrane\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0005515\t\tSLC19A2\tNone\tprotein binding\tFalse\tPMID:21836059\tIPI\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0005515\t\tSLC19A2\tNone\tprotein binding\tFalse\tPMID:21836059\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0008517\t\tSLC19A2\tNone\tfolic acid transmembrane transporter activity\tFalse\tPMID:10542220\tNAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015234\t\tSLC19A2\tNone\tthiamine transmembrane transporter activity\tFalse\tGO_REF:0000024\tISS\t\tBHF-UCL\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015234\t\tSLC19A2\tNone\tthiamine transmembrane transporter activity\tFalse\tPMID:10542220\tTAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015234\t\tSLC19A2\tNone\tthiamine transmembrane transporter activity\tFalse\tPMID:21836059\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015234\t\tSLC19A2\tNone\tthiamine transmembrane transporter activity\tFalse\tReactome:R-HSA-199626\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0007283\t\tSLC19A2\tNone\tspermatogenesis\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0009229\t\tSLC19A2\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015884\t\tSLC19A2\tNone\tfolic acid transport\tFalse\tGO_REF:0000108\tIEA\t\tGOC\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015888\t\tSLC19A2\tNone\tthiamine transport\tFalse\tPMID:10391222\tIMP\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015888\t\tSLC19A2\tNone\tthiamine transport\tFalse\tPMID:10542220\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015888\t\tSLC19A2\tNone\tthiamine transport\tFalse\tPMID:10542220\tNAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015888\t\tSLC19A2\tNone\tthiamine transport\tFalse\tPMID:33008889\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015888\t\tSLC19A2\tNone\tthiamine transport\tFalse\tPMID:35512554\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015888\t\tSLC19A2\tNone\tthiamine transport\tFalse\tPMID:35724964\tIMP\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0031923\t\tSLC19A2\tNone\tpyridoxine transport\tFalse\tPMID:33008889\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0031923\t\tSLC19A2\tNone\tpyridoxine transport\tFalse\tPMID:35512554\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0042723\t\tSLC19A2\tNone\tthiamine-containing compound metabolic process\tFalse\tReactome:R-HSA-196819\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0071934\t\tSLC19A2\tNone\tthiamine transmembrane transport\tFalse\tGO_REF:0000024\tISS\t\tBHF-UCL\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0005886\t\tSLC19A2\tNone\tplasma membrane\tFalse\tPMID:21836059\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0005886\t\tSLC19A2\tNone\tplasma membrane\tFalse\tReactome:R-HSA-199626\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0016020\t\tSLC19A2\tNone\tmembrane\tFalse\tPMID:10542220\tNAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0005886\t\tSLC19A2\tNone\tplasma membrane\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015888\t\tSLC19A2\tNone\tthiamine transport\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0015234\t\tSLC19A2\tNone\tthiamine transmembrane transporter activity\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:O60779\tbiolink:related_to\tGO:0055085\t\tSLC19A2\tNone\ttransmembrane transport\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0000287\t\tTHTPA\tNone\tmagnesium ion binding\tFalse\tGO_REF:0000024\tISS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0005515\t\tTHTPA\tNone\tprotein binding\tFalse\tPMID:32296183\tIPI\t\tIntAct\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0016787\t\tTHTPA\tNone\thydrolase activity\tFalse\tPMID:11827967\tTAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0050333\t\tTHTPA\tNone\tthiamine triphosphate phosphatase activity\tFalse\tPMID:11827967\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0006091\t\tTHTPA\tNone\tgeneration of precursor metabolites and energy\tFalse\tPMID:11827967\tNAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0006772\t\tTHTPA\tNone\tthiamine metabolic process\tFalse\tPMID:11827967\tTAS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0009229\t\tTHTPA\tNone\tthiamine diphosphate biosynthetic process\tFalse\tGO_REF:0000107\tIEA\t\tEnsembl\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0016311\t\tTHTPA\tNone\tdephosphorylation\tFalse\tPMID:11827967\tIDA\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0042357\t\tTHTPA\tNone\tthiamine diphosphate metabolic process\tFalse\tGO_REF:0000024\tISS\t\tUniProt\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0005829\t\tTHTPA\tNone\tcytosol\tFalse\tReactome:R-HSA-965067\tTAS\t\tReactome\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0000287\t\tTHTPA\tNone\tmagnesium ion binding\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0050333\t\tTHTPA\tNone\tthiamine triphosphate phosphatase activity\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n", + "UniProtKB:Q9BU02\tbiolink:related_to\tGO:0042357\t\tTHTPA\tNone\tthiamine diphosphate metabolic process\tFalse\tGO_REF:0000033\tIBA\t\tGO_Central\tinfores:go\t\t\t\t\t\r\n" + ] + } + ], + "execution_count": 8 + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2025-02-11T01:58:57.530226Z", + "start_time": "2025-02-11T01:58:38.140634Z" + } + }, + "cell_type": "code", + "source": "!runoak -i amigo:NCBITaxon:9606 associations -p i,p -H --expand GO:0009229 | llm -m 4o -t summarize-gaf-for-gene", + "id": "c1b7855cebdc47ca", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "The gene products associated with the thiamine diphosphate biosynthetic process (GO:0009229) involve several proteins including SLC19A3, TPK1, SLC25A19, SLC19A2, and THTPA, each contributing to the synthesis and transport of thiamine-related compounds in different capacities.\r\n", + "\r\n", + "SLC19A3 is primarily involved in the transport of thiamine and pyridoxine across the plasma membrane, displaying thiamine transmembrane transporter activity. It facilitates thiamine transmembrane transport and is located on the plasma membrane. This protein also plays a role in thiamine transport in general, contributing to the overall metabolic process of thiamine-containing compounds.\r\n", + "\r\n", + "TPK1 (thiamine pyrophosphate kinase) catalyzes the ATP-dependent phosphorylation of thiamine to form thiamine diphosphate, which is the active form of thiamine used as a coenzyme in various enzymatic reactions. It has been detected in the cytosol and also possesses kinase and ATP binding activity.\r\n", + "\r\n", + "SLC25A19 is responsible for the transmembrane transport of thiamine pyrophosphate into mitochondria. It shows activity as a thiamine pyrophosphate transmembrane transporter, indicating its critical role in mitochondrial functions related to thiamine metabolism. This protein is associated with the mitochondrial inner membrane, further evidencing its role in mitochondrial transport processes.\r\n", + "\r\n", + "SLC19A2 serves as both a thiamine and folic acid transporter at the plasma membrane, contributing to the transport of these vitamins into cells, supporting both thiamine and folic acid metabolic processes.\r\n", + "\r\n", + "THTPA functions in the conversion of thiamine triphosphate to thiamine diphosphate, acting as a thiamine triphosphate phosphatase. Involved in broad thiamine metabolic processes, it possesses hydrolase activity, with a focus on dephosphorylation reactions. It has been primarily located in the cytosol.\r\n", + "\r\n", + "Anomalous annotations include SLC19A2 being associated with spermatogenesis, which may not directly relate to its primary functions in vitamin transport. Additionally, some annotations suggest contradictory activities, such as SLC25A19 annotations to deoxynucleotide transport, which have been negated in other studies.\r\n", + "\r\n", + "Overall, these genes coordinate to manage the cellular and systemic availability of thiamine diphosphate, ensuring proper metabolic processes that utilize this crucial co-factor.\r\n" + ] + } + ], + "execution_count": 11 + }, + { + "metadata": {}, + "cell_type": "code", + "outputs": [], + "execution_count": null, + "source": "", + "id": "e8ccdf0b3998b48d" + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/examples/AdHoc/index.rst b/docs/examples/AdHoc/index.rst new file mode 100644 index 000000000..84c00366f --- /dev/null +++ b/docs/examples/AdHoc/index.rst @@ -0,0 +1,10 @@ +.. _ad_hoc_examples: + +Ad Hoc Examples +================ + +.. toctree:: + :maxdepth: 2 + + Summarizing-with-LLMs + Text-Content-Analysis diff --git a/docs/examples/Commands/index.rst b/docs/examples/Commands/index.rst index 833a2b7e2..7cefbec77 100644 --- a/docs/examples/Commands/index.rst +++ b/docs/examples/Commands/index.rst @@ -8,6 +8,7 @@ Commands Apply Associations + Crawl DiffViaMappings Disjoints Enrichment diff --git a/docs/examples/OntologyEditorsGuide/index.rst b/docs/examples/OntologyEditorsGuide/index.rst new file mode 100644 index 000000000..e8b759b8c --- /dev/null +++ b/docs/examples/OntologyEditorsGuide/index.rst @@ -0,0 +1,9 @@ +.. _ontology_editing_examples: + +Ontology Editing Examples +================ + +.. toctree:: + :maxdepth: 2 + + Edit-File-Examples diff --git a/docs/examples/index.rst b/docs/examples/index.rst index 8c24a257d..4f1947740 100644 --- a/docs/examples/index.rst +++ b/docs/examples/index.rst @@ -12,3 +12,5 @@ All the examples here are Jupyter notebooks that can be run interactively. Ontologies/index Adapters/index Interfaces/index + OntologyEditorsGraph/index + AdHoc/index diff --git a/poetry.lock b/poetry.lock index 3974c8f8b..13c2e2126 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand. 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= true, markers = "extra == \"format-nongpl\""} -isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} -jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""} +fqdn = [ + {version = "*", optional = true, markers = "extra == \"format\""}, + {version = "*", optional = true, markers = "extra == \"format-nongpl\""}, +] +idna = [ + {version = "*", optional = true, markers = "extra == \"format\""}, + {version = "*", optional = true, markers = "extra == \"format-nongpl\""}, +] +isoduration = [ + {version = "*", optional = true, markers = "extra == \"format\""}, + {version = "*", optional = true, markers = "extra == \"format-nongpl\""}, +] +jsonpointer = [ + {version = ">1.13", optional = true, markers = "extra == \"format\""}, + {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""}, +] jsonschema-specifications = ">=2023.03.6" referencing = ">=0.28.4" -rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} +rfc3339-validator = [ + {version = "*", optional = true, markers = "extra == \"format\""}, + {version = "*", optional = true, markers = "extra == \"format-nongpl\""}, +] rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""} rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""} rpds-py = ">=0.7.1" -uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} +uri-template = [ + {version = "*", optional = true, markers = "extra == \"format\""}, + {version = "*", optional = true, markers = "extra == \"format-nongpl\""}, +] webcolors = [ {version = ">=1.11", optional = true, markers = "extra == \"format\""}, {version = ">=24.6.0", optional = true, markers = "extra == \"format-nongpl\""}, @@ -2368,6 +2727,8 @@ version = "2024.10.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" optional = false python-versions = ">=3.9" +groups = ["main", "dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jsonschema_specifications-2024.10.1-py3-none-any.whl", hash = "sha256:a09a0680616357d9a0ecf05c12ad234479f549239d0f5b55f3deea67475da9bf"}, {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"}, @@ -2382,6 +2743,8 @@ version = "1.1.1" description = "Jupyter metapackage. Install all the Jupyter components in one go." optional = false python-versions = "*" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter-1.1.1-py2.py3-none-any.whl", hash = "sha256:7a59533c22af65439b24bbe60373a4e95af8f16ac65a6c00820ad378e3f7cc83"}, {file = "jupyter-1.1.1.tar.gz", hash = "sha256:d55467bceabdea49d7e3624af7e33d59c37fff53ed3a350e1ac957bed731de7a"}, @@ -2401,6 +2764,8 @@ version = "8.6.3" description = "Jupyter protocol implementation and client libraries" optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"}, {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"}, @@ -2424,6 +2789,8 @@ version = "6.6.3" description = "Jupyter terminal console" optional = false python-versions = ">=3.7" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_console-6.6.3-py3-none-any.whl", hash = "sha256:309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485"}, {file = "jupyter_console-6.6.3.tar.gz", hash = "sha256:566a4bf31c87adbfadf22cdf846e3069b59a71ed5da71d6ba4d8aaad14a53539"}, @@ -2448,6 +2815,8 @@ version = "5.7.2" description = "Jupyter core package. A base package on which Jupyter projects rely." optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"}, {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"}, @@ -2464,17 +2833,20 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout" [[package]] name = "jupyter-events" -version = "0.10.0" +version = "0.12.0" description = "Jupyter Event System library" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ - {file = "jupyter_events-0.10.0-py3-none-any.whl", hash = "sha256:4b72130875e59d57716d327ea70d3ebc3af1944d3717e5a498b8a06c6c159960"}, - {file = "jupyter_events-0.10.0.tar.gz", hash = "sha256:670b8229d3cc882ec782144ed22e0d29e1c2d639263f92ca8383e66682845e22"}, + {file = "jupyter_events-0.12.0-py3-none-any.whl", hash = "sha256:6464b2fa5ad10451c3d35fabc75eab39556ae1e2853ad0c0cc31b656731a97fb"}, + {file = "jupyter_events-0.12.0.tar.gz", hash = "sha256:fc3fce98865f6784c9cd0a56a20644fc6098f21c8c33834a8d9fe383c17e554b"}, ] [package.dependencies] jsonschema = {version = ">=4.18.0", extras = ["format-nongpl"]} +packaging = "*" python-json-logger = ">=2.0.4" pyyaml = ">=5.3" referencing = "*" @@ -2484,7 +2856,7 @@ traitlets = ">=5.3" [package.extras] cli = ["click", "rich"] -docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme", "sphinxcontrib-spelling"] +docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme (>=0.16)", "sphinx (>=8)", "sphinxcontrib-spelling"] test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "pytest-console-scripts", "rich"] [[package]] @@ -2493,6 +2865,8 @@ version = "2.2.5" description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server" optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"}, {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"}, @@ -2504,13 +2878,15 @@ jupyter-server = ">=1.1.2" [[package]] name = "jupyter-server" -version = "2.14.2" +version = "2.15.0" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ - {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"}, - {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"}, + {file = "jupyter_server-2.15.0-py3-none-any.whl", hash = "sha256:872d989becf83517012ee669f09604aa4a28097c0bd90b2f424310156c2cdae3"}, + {file = "jupyter_server-2.15.0.tar.gz", hash = "sha256:9d446b8697b4f7337a1b7cdcac40778babdd93ba614b6d68ab1c0c918f1c4084"}, ] [package.dependencies] @@ -2519,7 +2895,7 @@ argon2-cffi = ">=21.1" jinja2 = ">=3.0.3" jupyter-client = ">=7.4.4" jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" -jupyter-events = ">=0.9.0" +jupyter-events = ">=0.11.0" jupyter-server-terminals = ">=0.4.4" nbconvert = ">=6.4.4" nbformat = ">=5.3.0" @@ -2544,6 +2920,8 @@ version = "0.5.3" description = "A Jupyter Server Extension Providing Terminals." optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_server_terminals-0.5.3-py3-none-any.whl", hash = "sha256:41ee0d7dc0ebf2809c668e0fc726dfaf258fcd3e769568996ca731b6194ae9aa"}, {file = "jupyter_server_terminals-0.5.3.tar.gz", hash = "sha256:5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269"}, @@ -2559,13 +2937,15 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (> [[package]] name = "jupyterlab" -version = "4.2.5" +version = "4.3.5" description = "JupyterLab computational environment" optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ - {file = "jupyterlab-4.2.5-py3-none-any.whl", hash = "sha256:73b6e0775d41a9fee7ee756c80f58a6bed4040869ccc21411dc559818874d321"}, - {file = "jupyterlab-4.2.5.tar.gz", hash = "sha256:ae7f3a1b8cb88b4f55009ce79fa7c06f99d70cd63601ee4aa91815d054f46f75"}, + {file = "jupyterlab-4.3.5-py3-none-any.whl", hash = "sha256:571bbdee20e4c5321ab5195bc41cf92a75a5cff886be5e57ce78dfa37a5e9fdb"}, + {file = "jupyterlab-4.3.5.tar.gz", hash = "sha256:c779bf72ced007d7d29d5bcef128e7fdda96ea69299e19b04a43635a7d641f9d"}, ] [package.dependencies] @@ -2580,15 +2960,15 @@ jupyter-server = ">=2.4.0,<3" jupyterlab-server = ">=2.27.1,<3" notebook-shim = ">=0.2" packaging = "*" -setuptools = ">=40.1.0" +setuptools = ">=40.8.0" tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""} tornado = ">=6.2.0" traitlets = "*" [package.extras] -dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.3.5)"] -docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<7.3.0)", "sphinx-copybutton"] -docs-screenshots = ["altair (==5.3.0)", "ipython (==8.16.1)", "ipywidgets (==8.1.2)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.1.post2)", "matplotlib (==3.8.3)", "nbconvert (>=7.0.0)", "pandas (==2.2.1)", "scipy (==1.12.0)", "vega-datasets (==0.9.0)"] +dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.6.9)"] +docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<8.1.0)", "sphinx-copybutton"] +docs-screenshots = ["altair (==5.4.1)", "ipython (==8.16.1)", "ipywidgets (==8.1.5)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.2.post3)", "matplotlib (==3.9.2)", "nbconvert (>=7.0.0)", "pandas (==2.2.3)", "scipy (==1.14.1)", "vega-datasets (==0.9.0)"] test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter (>=0.5.3)", "pytest-timeout", "pytest-tornasync", "requests", "requests-cache", "virtualenv"] upgrade-extension = ["copier (>=9,<10)", "jinja2-time (<0.3)", "pydantic (<3.0)", "pyyaml-include (<3.0)", "tomli-w (<2.0)"] @@ -2598,6 +2978,8 @@ version = "0.3.0" description = "Pygments theme using JupyterLab CSS variables" optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyterlab_pygments-0.3.0-py3-none-any.whl", hash = "sha256:841a89020971da1d8693f1a99997aefc5dc424bb1b251fd6322462a1b8842780"}, {file = "jupyterlab_pygments-0.3.0.tar.gz", hash = "sha256:721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d"}, @@ -2609,6 +2991,8 @@ version = "2.27.3" description = "A set of server components for JupyterLab and JupyterLab like applications." optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyterlab_server-2.27.3-py3-none-any.whl", hash = "sha256:e697488f66c3db49df675158a77b3b017520d772c6e1548c7d9bcc5df7944ee4"}, {file = "jupyterlab_server-2.27.3.tar.gz", hash = "sha256:eb36caca59e74471988f0ae25c77945610b887f777255aa21f8065def9e51ed4"}, @@ -2635,6 +3019,8 @@ version = "3.0.13" description = "Jupyter interactive widgets for JupyterLab" optional = false python-versions = ">=3.7" +groups = ["dev"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyterlab_widgets-3.0.13-py3-none-any.whl", hash = "sha256:e3cda2c233ce144192f1e29914ad522b2f4c40e77214b0cc97377ca3d323db54"}, {file = "jupyterlab_widgets-3.0.13.tar.gz", hash = "sha256:a2966d385328c1942b683a8cd96b89b8dd82c8b8f81dda902bb2bc06d46f5bed"}, @@ -2646,6 +3032,8 @@ version = "0.5.0" description = "Schema for the KGCL project." optional = false python-versions = ">=3.8,<4.0" +groups = ["main"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "kgcl_rdflib-0.5.0-py3-none-any.whl", hash = "sha256:214c011eac692384dd18397e455af2a7375f6a2f71fa318df245e8826678f454"}, {file = "kgcl_rdflib-0.5.0.tar.gz", hash = "sha256:19e34690316714b9c500e1749a35d1a0d17282f2a38cd2b1fd3d7d8cf5e6013d"}, @@ -2661,6 +3049,8 @@ version = "0.6.9" description = "Schema for the KGCL project." optional = false python-versions = "<4.0,>=3.9" +groups = ["main"] +markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "kgcl_schema-0.6.9-py3-none-any.whl", hash = "sha256:6acd367a4cd998ec8dfe70987bf797aecce558df86a1395bc8c3e0489f66b9a9"}, {file = "kgcl_schema-0.6.9.tar.gz", hash = "sha256:1bb0f9f13356df7b5c6ba9c73a7124dc897e525af49f40454dafd45bfca021bd"}, @@ -2678,6 +3068,7 @@ version = "1.4.7" description = "A fast implementation of the Cassowary constraint solver" optional = false python-versions = ">=3.8" +groups = ["main", "dev"] files = [ {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8a9c83f75223d5e48b0bc9cb1bf2776cf01563e00ade8775ffe13b0b6e1af3a6"}, {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = 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40505bed1..52662a6d5 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -46,6 +46,7 @@ from oaklib.datamodels.cross_ontology_diff import DiffCategory from oaklib.datamodels.obograph import ( BasicPropertyValue, + Node, Edge, Graph, GraphDocument, @@ -82,7 +83,7 @@ ValidatorInterface, ) from oaklib.interfaces.association_provider_interface import ( - AssociationProviderInterface, + AssociationProviderInterface, SubjectOrObjectRole, ) from oaklib.interfaces.class_enrichment_calculation_interface import ( ClassEnrichmentCalculationInterface, @@ -112,7 +113,7 @@ from oaklib.io.heatmap_writer import HeatmapWriter from oaklib.io.html_writer import HTMLWriter from oaklib.io.obofoundry_markdown_writer import OboFoundryMarkdownWriter -from oaklib.io.obograph_writer import write_graph +from oaklib.io.obograph_writer import write_graph, write_graph_document from oaklib.io.rollup_report_writer import write_report from oaklib.io.streaming_axiom_writer import StreamingAxiomWriter from oaklib.io.streaming_csv_writer import StreamingCsvWriter @@ -131,7 +132,8 @@ from oaklib.io.streaming_yaml_writer import StreamingYamlWriter from oaklib.mappers.ontology_metadata_mapper import OntologyMetadataMapper from oaklib.parsers.association_parser_factory import get_association_parser -from oaklib.query import _process_predicates_arg, curies_from_file, query_terms_iterator +from oaklib.query import process_predicates_arg, curies_from_file, query_terms_iterator +from oaklib.utilities.associations.association_queries import get_association_iterator from oaklib.resource import OntologyResource from oaklib.selector import get_adapter, get_resource_from_shorthand from oaklib.transformers.transformers_factory import ( @@ -180,7 +182,7 @@ graph_to_image, graph_to_tree_display, shortest_paths, - trim_graph, + trim_graph, remove_unlabeled_nodes, ) from oaklib.utilities.publication_utils.pubmed_wrapper import PubmedWrapper from oaklib.utilities.subsets.slimmer_utils import ( @@ -255,17 +257,6 @@ class Direction(Enum): both = "both" -@unique -class SubjectOrObjectRole(Enum): - """ - Role of terms in the term list - """ - - SUBJECT = "subject" - OBJECT = "object" - BOTH = "both" - - @unique class IfAbsent(Enum): """ @@ -1235,7 +1226,7 @@ def term_metadata(terms, predicates, additional_metadata: bool, output_type: str metadata = impl.entity_metadata_map(curie) if predicates: metadata = { - p: metadata.get(p, None) for p in _process_predicates_arg(predicates) + p: metadata.get(p, None) for p in process_predicates_arg(predicates) } writer.emit(metadata) writer.finish() @@ -1534,7 +1525,7 @@ def viz( impl.precompute_lookups() if stylemap is None: stylemap = default_stylemap_path() - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) curies_highlight = None if "@" in terms: ix = terms.index("@") @@ -1712,7 +1703,7 @@ def tree( curies = list(query_terms_iterator(terms, impl)) if stylemap is None: stylemap = default_stylemap_path() - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) if add_mrcas: if isinstance(impl, SemanticSimilarityInterface): curies_to_add = [ @@ -1825,7 +1816,7 @@ def ancestors( graph_traversal_method = GraphTraversalMethod[graph_traversal_method] if graph_traversal_method == GraphTraversalMethod.HOP: impl.precompute_lookups() - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) curies = list(query_terms_iterator(terms, impl)) logging.info(f"Ancestor seed: {curies}") if statistics: @@ -1972,14 +1963,14 @@ def paths( writer.file = sys.stdout if not isinstance(impl, OboGraphInterface): raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") - actual_predicates = _process_predicates_arg( + actual_predicates = process_predicates_arg( predicates, exclude_predicates_str=exclude_predicates, impl=impl ) logging.info(f"Using predicates {actual_predicates}") if predicate_weights: pw = {} for k, v in yaml.safe_load(predicate_weights).items(): - [p] = _process_predicates_arg(k, expected_number=1) + [p] = process_predicates_arg(k, expected_number=1) pw[k] = v else: pw = None @@ -2137,7 +2128,7 @@ def chains( preds = t[1:] if t.endswith("/"): preds = t[0:-1] - actual_preds = _process_predicates_arg(preds, impl=impl) if preds else None + actual_preds = process_predicates_arg(preds, impl=impl) if preds else None blocks.append(set(actual_preds or [])) blocks.append([]) else: @@ -2199,7 +2190,7 @@ def siblings(terms, predicates, output_type: str, output: str): writer = _get_writer(output_type, impl, StreamingInfoWriter) writer.file = output if isinstance(impl, OboGraphInterface): - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) curies = list(query_terms_iterator(terms, impl)) logging.info(f"seed: {curies}") sibs = [] @@ -2254,7 +2245,7 @@ def descendants( graph_traversal_method = GraphTraversalMethod[graph_traversal_method] if not isinstance(impl, OboGraphInterface): raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) curies = list(query_terms_iterator(terms, impl)) result_it = impl.descendants( curies, predicates=actual_predicates, method=graph_traversal_method @@ -2509,7 +2500,7 @@ def extract(terms, predicates, dangling: bool, output, output_type, **kwargs): impl = settings.impl if not isinstance(impl, OboGraphInterface): raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) curies = list(set(query_terms_iterator(terms, impl))) graph = impl.extract_graph(curies, predicates=actual_predicates, dangling=dangling, **kwargs) graph_impl = OboGraphImplementation(obograph_document=GraphDocument(graphs=[graph])) @@ -2568,7 +2559,7 @@ def similarity_pair(terms, predicates, autolabel: bool, output: TextIO, output_t object = list(query_terms_iterator([terms[1]], impl))[0] if not isinstance(impl, SemanticSimilarityInterface): raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) sim = impl.pairwise_similarity(subject, object, predicates=actual_predicates) if autolabel: if not sim.subject_label: @@ -2714,7 +2705,7 @@ def similarity( set2it = list(curies_from_file(file)) else: set2it = query_terms_iterator(terms, impl) - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) for sim in impl.all_by_all_pairwise_similarity( set1it, set2it, @@ -2782,7 +2773,7 @@ def termset_similarity( set2 = list(query_terms_iterator(terms[ix + 1 :], impl)) logging.info(f"Set1={set1}") logging.info(f"Set2={set2}") - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) sim = impl.termset_pairwise_similarity( set1, set2, predicates=actual_predicates, labels=autolabel ) @@ -2831,7 +2822,7 @@ def information_content( writer.file = output if not isinstance(impl, SemanticSimilarityInterface): raise NotImplementedError(f"Cannot execute this with {type(impl)}") - actual_predicates = _process_predicates_arg(predicates) + actual_predicates = process_predicates_arg(predicates) n = 0 logging.info("Fetching ICs...") if terms: @@ -3248,7 +3239,7 @@ def relationships( writer = _get_writer(output_type, impl, StreamingCsvWriter) writer.autolabel = autolabel writer.output = output - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) if not (include_tbox or include_abox): raise ValueError("Cannot exclude both tbox AND abox") if not isinstance(impl, BasicOntologyInterface): @@ -3426,7 +3417,7 @@ def logical_definitions( writer = _get_writer(output_type, impl, StreamingYamlWriter) writer.output = output writer.autolabel = autolabel - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) def _exclude_ldef(ldef: LogicalDefinitionAxiom) -> bool: if actual_predicates: @@ -3551,7 +3542,7 @@ def disjoints( writer = _get_writer(output_type, impl, StreamingYamlWriter) writer.output = output writer.autolabel = autolabel - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) label_fields = [ "classIds", @@ -3707,7 +3698,7 @@ def roots(output: str, output_type: str, predicates: str, has_prefix: str, annot writer.output = output if not isinstance(impl, OboGraphInterface): raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) prefixes = list(has_prefix) if has_prefix else None for curie in impl.roots( actual_predicates, annotated_roots=annotated_roots, id_prefixes=prefixes @@ -3739,7 +3730,7 @@ def leafs(output: str, predicates: str, filter_obsoletes: bool): """ impl = settings.impl if isinstance(impl, OboGraphInterface): - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) for curie in impl.leafs(actual_predicates, filter_obsoletes=filter_obsoletes): print(f"{curie} ! {impl.label(curie)}") else: @@ -3771,7 +3762,7 @@ def singletons(output: str, predicates: str, filter_obsoletes: bool): """ impl = settings.impl if isinstance(impl, OboGraphInterface): - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) for curie in impl.singletons(actual_predicates, filter_obsoletes=filter_obsoletes): print(f"{curie} ! {impl.label(curie)}") else: @@ -4195,7 +4186,7 @@ def expand_subsets(subsets: list, output, predicates): impl = settings.impl # writer = StreamingCsvWriter(output) if isinstance(impl, OboGraphInterface): - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) if not actual_predicates: actual_predicates = [IS_A, PART_OF] impl.enable_transitive_query_cache() @@ -4358,7 +4349,7 @@ def taxon_constraints( impl.subject_graph_traversal_method = GraphTraversalMethod[graph_traversal_method] if not isinstance(impl, TaxonConstraintInterface): raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) impl.precompute_lookups() impl.precompute_direct_constraint_cache() for curie in query_terms_iterator(terms, impl): @@ -4413,7 +4404,7 @@ def apply_taxon_constraints( """ impl = settings.impl - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) impl = settings.impl writer = StreamingYamlWriter(output) curr = None @@ -4568,6 +4559,19 @@ def usages( show_default=True, help="How to interpret query terms.", ) +@click.option( + "--expand/--no-expand", + default=False, + show_default=True, + help="Expand by feeding results into subsequent query", +) +@click.option( + "--header/--no-header", + "-H/--no-H", + default=False, + show_default=True, + help="Show a header", +) @click.argument("terms", nargs=-1) def associations( terms, @@ -4579,6 +4583,8 @@ def associations( output: str, if_absent: bool, set_value: str, + expand: bool, + header: bool, **kwargs, ): """ @@ -4620,11 +4626,20 @@ def associations( writer = _get_writer(output_type, impl, StreamingCsvWriter) writer.autolabel = autolabel writer.output = output - actual_predicates = _process_predicates_arg(predicates, impl=impl) - actual_association_predicates = _process_predicates_arg(association_predicates) + actual_predicates = process_predicates_arg(predicates, impl=impl) + actual_association_predicates = process_predicates_arg(association_predicates) if not isinstance(impl, AssociationProviderInterface): raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") curies = list(query_terms_iterator(terms, impl)) + if header: + writer.emit_header( + f"Query IDs: {', '.join(curies)}", + f"Ontology closure predicates: {', '.join(actual_predicates or [])}", + ) + if expand: + writer.emit_header( + "The results include a round of expansion" + ) qs_it = impl.associations( curies, predicates=actual_association_predicates, @@ -4644,21 +4659,42 @@ def associations( else: logging.info("Using query terms to query both subject and object") it = chain(qs_it, qo_it) + # track which nodes have relationships (used for if_absent) has_relationships = defaultdict(bool) + entities_to_expand = set() for assoc in it: if terms_role is None or terms_role == SubjectOrObjectRole.SUBJECT.value: has_relationships[assoc.subject] = True + entities_to_expand.add(assoc.object) elif terms_role == SubjectOrObjectRole.OBJECT.value: has_relationships[assoc.object] = True + entities_to_expand.add(assoc.subject) else: has_relationships[assoc.subject] = True has_relationships[assoc.object] = True + entities_to_expand.add(assoc.subject) + entities_to_expand.add(assoc.object) if if_absent and if_absent == IfAbsent.absent_only.value: continue writer.emit( assoc, label_fields=["subject", "predicate", "object"], ) + if expand: + logging.info(f"Expanding using {len(entities_to_expand)} nodes") + exp_it = get_association_iterator( + impl, + list(entities_to_expand), + terms_role=SubjectOrObjectRole.SUBJECT.value if terms_role == SubjectOrObjectRole.OBJECT.value else SubjectOrObjectRole.OBJECT.value, + association_predicates=actual_association_predicates, + ontology_predicates=actual_predicates, + **kwargs, + ) + for assoc in exp_it: + writer.emit( + assoc, + label_fields=["subject", "predicate", "object"], + ) if if_absent and if_absent == IfAbsent.absent_only.value: for curie in curies: if not has_relationships[curie]: @@ -4678,6 +4714,148 @@ def associations( _apply_changes(impl, changes) +@main.command() +@predicates_option +@output_type_option +@click.option( + "-o", + "--output", + help="Output file", +) +@click.option( + "--association-predicates", + help="A comma-separated list of predicates for the association relation", +) +@click.option( + "-A", + "--ontology-adapter", + help="Adapter to use for traversing ontology graph", +) +@click.option( + "--gap-fill/--no-gap-fill", + default=False, + show_default=True, + help="Fill in missing nodes", +) +@click.option( + "--terms-role", + "-Q", + type=click.Choice([x.value for x in SubjectOrObjectRole]), + default=SubjectOrObjectRole.OBJECT.value, + show_default=True, + help="How to interpret query terms.", +) +@click.option( + "--view/--no-view", + default=True, + show_default=True, + help="if view is set then open the image after rendering", +) +@stylemap_otion +@stylemap_configure_option +@click.argument("terms", nargs=-1) +def associations_graph( + terms, + predicates: str, + association_predicates: str, + terms_role: str, + gap_fill: bool, + output_type: str, + output: str, + view: bool, + stylemap: str, + ontology_adapter, + **kwargs, +): + """ + Query associations and fill out ontology graph. + + Example: + + runoak -i amigo: associations-graph -p i,p -A sqlite:obo:go -Q subject WB:WBGene00001187 -o gene.json + + This queries for associations whose subject is the gene WBGene00001187 in AmiGO, and uses + the GO ontology to fill out the graph, following is-a and part-of relationships. + + To immediately visualize, add --view to the end: + + runoak -i amigo: associations-graph -p i,p -A sqlite:obo:go -Q subject WB:WBGene00001187 --view + + You can use --gap-fill to trim the graph to only pairwise MRCAs and span the gaps: + + runoak -i amigo: associations-graph -p i,p -A sqlite:obo:go -Q subject WB:WBGene00001187 --gap-fill --view + """ + impl = settings.impl + actual_predicates = process_predicates_arg(predicates, impl=impl) + actual_association_predicates = process_predicates_arg(association_predicates) + if not isinstance(impl, AssociationProviderInterface): + raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") + curies = list(query_terms_iterator(terms, impl)) + # TODO: consider abstracting this into a method + qs_it = impl.associations( + curies, + predicates=actual_association_predicates, + subject_closure_predicates=actual_predicates, + **kwargs, + ) + qo_it = impl.associations( + objects=curies, + predicates=actual_association_predicates, + object_closure_predicates=actual_predicates, + **kwargs, + ) + if terms_role is None or terms_role == SubjectOrObjectRole.SUBJECT.value: + it = qs_it + elif terms_role == SubjectOrObjectRole.OBJECT.value: + it = qo_it + else: + logging.info("Using query terms to query both subject and object") + it = chain(qs_it, qo_it) + node_map = {} + edges = [] + for assoc in it: + node_map[assoc.subject] = Node(id=assoc.subject, lbl=assoc.subject_label) + node_map[assoc.object] = Node(id=assoc.object, lbl=assoc.object_label) + edges.append(Edge(sub=assoc.subject, obj=assoc.object, pred=assoc.predicate)) + logging.info(f"Initial AG, num_nodes={len(node_map)}, num_edges={len(edges)}") + curies = list(node_map.keys()) + if ontology_adapter: + oa = get_adapter(ontology_adapter) + else: + oa = impl + if gap_fill: + if not isinstance(oa, SemanticSimilarityInterface): + raise NotImplementedError(f"{oa} does not implement SemanticSimilarityInterface") + curies_to_add = [ + lca + for s, o, lca in oa.multiset_most_recent_common_ancestors( + curies, predicates=actual_predicates + ) + ] + curies = list(set(curies + curies_to_add)) + logging.info(f"Expanded CURIEs = {curies}") + if not isinstance(oa, SubsetterInterface): + raise NotImplementedError(f"{oa} does not implement SubsetterInterface") + graph = oa.extract_gap_filled_graph(curies, predicates=actual_predicates) + else: + # walk up + if not isinstance(oa, OboGraphInterface): + raise NotImplementedError(f"Cannot execute this using {oa} of type {type(oa)}") + + graph = oa.ancestor_graph(curies, predicates=actual_predicates, method=GraphTraversalMethod.ENTAILMENT) + graph.edges.extend(edges) + existing_nodes = set([node.id for node in graph.nodes]) + for node in node_map.values(): + if node.id not in existing_nodes: + graph.nodes.append(node) + logging.info(f"Final AG, num_nodes={len(graph.nodes)}, num_edges={len(graph.edges)}") + remove_unlabeled_nodes(graph) + gd = GraphDocument(graphs=[graph]) + if stylemap is None: + stylemap = default_stylemap_path() + write_graph_document(gd, output, format=output_type, view=view, stylemap=stylemap, seeds=curies, **kwargs) + + @main.command() @output_option @predicates_option @@ -4785,8 +4963,8 @@ def associations_counts( writer = _get_writer(output_type, impl, StreamingCsvWriter) writer.autolabel = autolabel writer.output = output - actual_predicates = _process_predicates_arg(predicates, impl=impl) - actual_association_predicates = _process_predicates_arg(association_predicates) + actual_predicates = process_predicates_arg(predicates, impl=impl) + actual_association_predicates = process_predicates_arg(association_predicates) if not isinstance(impl, AssociationProviderInterface): raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") curies = list(query_terms_iterator(terms, impl)) @@ -4900,8 +5078,8 @@ def associations_matrix( if main_score_field == "2": main_score_field = "proportion_entity2_subjects_in_entity1" writer.value_field = main_score_field - actual_predicates = _process_predicates_arg(predicates, impl=impl) - actual_association_predicates = _process_predicates_arg(association_predicates) + actual_predicates = process_predicates_arg(predicates, impl=impl) + actual_association_predicates = process_predicates_arg(association_predicates) if not isinstance(impl, AssociationProviderInterface): raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") if "@" in terms: @@ -4989,7 +5167,7 @@ def rollup( secondary_ids = (s[1].split(",") if len(s) > 1 else [] for s in split_ids) objects_dict = dict(zip(primary_ids, secondary_ids, strict=False)) - object_closure_predicates = _process_predicates_arg(predicates, impl=impl) + object_closure_predicates = process_predicates_arg(predicates, impl=impl) groups: List[RollupGroup] = [] for primary, secondaries in objects_dict.items(): @@ -5137,8 +5315,8 @@ def enrichment( """ impl = settings.impl - actual_predicates = _process_predicates_arg(predicates, impl=impl) - actual_association_predicates = _process_predicates_arg(association_predicates) + actual_predicates = process_predicates_arg(predicates, impl=impl) + actual_association_predicates = process_predicates_arg(association_predicates) if sample_file: subjects = list(curies_from_file(sample_file, adapter=impl, allow_labels=allow_labels)) curies = list(query_terms_iterator(terms, impl)) @@ -5236,7 +5414,7 @@ def diff_associations( writer.heterogeneous_keys = True writer.autolabel = autolabel writer.output = output - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) logging.info(f"Fetching parser for {settings.associations_type}") association_parser = get_association_parser(settings.associations_type) if not isinstance(impl, AssociationProviderInterface): @@ -5807,7 +5985,7 @@ def validate_subset( for config in configs: if information_content_adapter: config.ic_score_adapter_name = information_content_adapter - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) if actual_predicates: config.predicates = actual_predicates if exclude_query: @@ -6618,7 +6796,7 @@ def diff_via_mappings( else: logging.info("No term list provided, will compare all mapped terms") entities = None - actual_predicates = _process_predicates_arg(predicates, impl=oi) + actual_predicates = process_predicates_arg(predicates, impl=oi) n = 0 for r in calculate_pairwise_relational_diff( oi, @@ -7272,7 +7450,7 @@ def generate_disjoints( if not isinstance(impl, OboGraphInterface): raise NotImplementedError curies = list(query_terms_iterator(terms, impl)) - actual_predicates = _process_predicates_arg(predicates, impl=impl) + actual_predicates = process_predicates_arg(predicates, impl=impl) if not actual_predicates: actual_predicates = [IS_A] config = DisjointnessInducerConfig( diff --git a/src/oaklib/conf/obograph-style.json b/src/oaklib/conf/obograph-style.json index a1ec750c3..631c08748 100644 --- a/src/oaklib/conf/obograph-style.json +++ b/src/oaklib/conf/obograph-style.json @@ -91,6 +91,26 @@ "color": "green", "penwidth": 3 }, + "biolink:related_to": { + "color": "chartreuse3", + "penwidth": 2, + "arrowhead": "crow", + "label": "Ⓡ" + }, + "obo:chebi#is_conjugate_acid_of": { + "color": "green", + "penwidth": 2, + "arrowhead": "tee", + "arrowtail": "odot", + "label": "⊕⇌⊖" + }, + "obo:chebi#is_conjugate_base_of": { + "color": "red", + "penwidth": 2, + "arrowhead": "odot", + "arrowtail": "tee", + "label": "⊖⇌⊕" + }, "UPHENO:0000001": { "color": "gray", "label": "Ⓐ" diff --git a/src/oaklib/datamodels/obograph.py b/src/oaklib/datamodels/obograph.py index 2776adecc..be46c19f3 100644 --- a/src/oaklib/datamodels/obograph.py +++ b/src/oaklib/datamodels/obograph.py @@ -1,5 +1,5 @@ # Auto generated from obograph.yaml by pythongen.py version: 0.0.1 -# Generation date: 2023-08-29T10:52:15 +# Generation date: 2025-02-05T11:24:54 # Schema: obographs_datamodel # # id: https://github.com/geneontology/obographs @@ -11,30 +11,56 @@ import dataclasses import re from dataclasses import dataclass -from typing import Any, ClassVar, Dict, List, Optional, Union +from datetime import ( + date, + datetime, + time +) +from typing import ( + Any, + ClassVar, + Dict, + List, + Optional, + Union +) -from jsonasobj2 import JsonObj, as_dict +from jsonasobj2 import ( + JsonObj, + as_dict +) from linkml_runtime.linkml_model.meta import ( EnumDefinition, PermissibleValue, - PvFormulaOptions, + PvFormulaOptions ) -from linkml_runtime.linkml_model.types import Boolean, String, Uri from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.utils.dataclass_extensions_376 import ( - dataclasses_init_fn_with_kwargs, -) +from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from linkml_runtime.utils.formatutils import camelcase, sfx, underscore -from linkml_runtime.utils.metamodelcore import URI, Bool, bnode, empty_dict, empty_list +from linkml_runtime.utils.formatutils import ( + camelcase, + sfx, + underscore +) +from linkml_runtime.utils.metamodelcore import ( + bnode, + empty_dict, + empty_list +) from linkml_runtime.utils.slot import Slot from linkml_runtime.utils.yamlutils import ( YAMLRoot, extended_float, extended_int, - extended_str, + extended_str ) -from rdflib import Namespace, URIRef +from rdflib import ( + Namespace, + URIRef +) + +from linkml_runtime.linkml_model.types import Boolean, String, Uri +from linkml_runtime.utils.metamodelcore import Bool, URI metamodel_version = "1.7.0" version = None @@ -43,43 +69,40 @@ dataclasses._init_fn = dataclasses_init_fn_with_kwargs # Namespaces -IAO = CurieNamespace("IAO", "http://purl.obolibrary.org/obo/IAO_") -LINKML = CurieNamespace("linkml", "https://w3id.org/linkml/") -OBOGRAPHS = CurieNamespace("obographs", "https://github.com/geneontology/obographs/") -OIO = CurieNamespace("oio", "http://www.geneontology.org/formats/oboInOwl#") -OWL = CurieNamespace("owl", "http://www.w3.org/2002/07/owl#") -RDF = CurieNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#") -RDFS = CurieNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#") -SDO = CurieNamespace("sdo", "https://schema.org/") -SH = CurieNamespace("sh", "https://w3id.org/shacl/") -SKOS = CurieNamespace("skos", "http://www.w3.org/2004/02/skos/core#") -XSD = CurieNamespace("xsd", "http://www.w3.org/2001/XMLSchema#") +IAO = CurieNamespace('IAO', 'http://purl.obolibrary.org/obo/IAO_') +LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') +OBOGRAPHS = CurieNamespace('obographs', 'https://github.com/geneontology/obographs/') +OIO = CurieNamespace('oio', 'http://www.geneontology.org/formats/oboInOwl#') +OWL = CurieNamespace('owl', 'http://www.w3.org/2002/07/owl#') +RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') +RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#') +SDO = CurieNamespace('sdo', 'https://schema.org/') +SH = CurieNamespace('sh', 'https://w3id.org/shacl/') +SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#') +XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') DEFAULT_ = OBOGRAPHS # Types class XrefString(String): - """A string that is a cross reference to another entity represented in another ontology, vocabulary, database, or website. The string SHOULD be a CURIE or a URL, but this standard relaxes this to a string to support parsing of legacy ontologies that may use other syntaxes. If a CURIE is provided, this SHOULD be registered in a standard registry such as bioregistry.""" - - type_class_uri = XSD.string + """ A string that is a cross reference to another entity represented in another ontology, vocabulary, database, or website. The string SHOULD be a CURIE or a URL, but this standard relaxes this to a string to support parsing of legacy ontologies that may use other syntaxes. If a CURIE is provided, this SHOULD be registered in a standard registry such as bioregistry. """ + type_class_uri = XSD["string"] type_class_curie = "xsd:string" type_name = "XrefString" type_model_uri = OBOGRAPHS.XrefString class OboIdentifierString(String): - """A string that represents an OBO identifier. This MUST be EITHER a PrefixedID (CURIE), an UnprefixedID, or a URI. If the identifier is for a Class, then the identifier MUST be a PrefixedID""" - - type_class_uri = XSD.string + """ A string that represents an OBO identifier. This MUST be EITHER a PrefixedID (CURIE), an UnprefixedID, or a URI. If the identifier is for a Class, then the identifier MUST be a PrefixedID """ + type_class_uri = XSD["string"] type_class_curie = "xsd:string" type_name = "OboIdentifierString" type_model_uri = OBOGRAPHS.OboIdentifierString class SynonymTypeIdentifierString(String): - """A string that represents a synonym type. Note synonym types are distinct from synonym scopes. A synonym type is commonly represented as a plain string such as ABBREVIATION""" - - type_class_uri = XSD.string + """ A string that represents a synonym type. Note synonym types are distinct from synonym scopes. A synonym type is commonly represented as a plain string such as ABBREVIATION """ + type_class_uri = XSD["string"] type_class_curie = "xsd:string" type_name = "SynonymTypeIdentifierString" type_model_uri = OBOGRAPHS.SynonymTypeIdentifierString @@ -106,54 +129,41 @@ class SynonymTypeDefinitionId(OboIdentifierString): pass -@dataclass +@dataclass(repr=False) class GraphDocument(YAMLRoot): """ A graph document is a collection of graphs together with a set of prefixes that apply across all of them """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.GraphDocument + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["GraphDocument"] class_class_curie: ClassVar[str] = "obographs:GraphDocument" class_name: ClassVar[str] = "GraphDocument" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.GraphDocument meta: Optional[Union[dict, "Meta"]] = None - graphs: Optional[ - Union[Dict[Union[str, GraphId], Union[dict, "Graph"]], List[Union[dict, "Graph"]]] - ] = empty_dict() - prefixes: Optional[ - Union[ - Dict[Union[str, PrefixDeclarationPrefix], Union[dict, "PrefixDeclaration"]], - List[Union[dict, "PrefixDeclaration"]], - ] - ] = empty_dict() + graphs: Optional[Union[Dict[Union[str, GraphId], Union[dict, "Graph"]], List[Union[dict, "Graph"]]]] = empty_dict() + prefixes: Optional[Union[Dict[Union[str, PrefixDeclarationPrefix], Union[dict, "PrefixDeclaration"]], List[Union[dict, "PrefixDeclaration"]]]] = empty_dict() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.meta is not None and not isinstance(self.meta, Meta): self.meta = Meta(**as_dict(self.meta)) - self._normalize_inlined_as_list( - slot_name="graphs", slot_type=Graph, key_name="id", keyed=True - ) + self._normalize_inlined_as_list(slot_name="graphs", slot_type=Graph, key_name="id", keyed=True) - self._normalize_inlined_as_dict( - slot_name="prefixes", slot_type=PrefixDeclaration, key_name="prefix", keyed=True - ) + self._normalize_inlined_as_dict(slot_name="prefixes", slot_type=PrefixDeclaration, key_name="prefix", keyed=True) super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class PrefixDeclaration(YAMLRoot): """ A mapping between an individual prefix (e.g. GO) and a namespace (e.g. http://purl.obolibrary.org/obo/GO_) """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SH.PrefixDeclaration + class_class_uri: ClassVar[URIRef] = SH["PrefixDeclaration"] class_class_curie: ClassVar[str] = "sh:PrefixDeclaration" class_name: ClassVar[str] = "PrefixDeclaration" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.PrefixDeclaration @@ -173,59 +183,31 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class Graph(YAMLRoot): """ A graph is a collection of nodes and edges and other axioms that represents a single ontology. """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OWL.Ontology + class_class_uri: ClassVar[URIRef] = OWL["Ontology"] class_class_curie: ClassVar[str] = "owl:Ontology" class_name: ClassVar[str] = "Graph" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.Graph id: Union[str, GraphId] = None lbl: Optional[str] = None - prefixes: Optional[ - Union[ - Dict[Union[str, PrefixDeclarationPrefix], Union[dict, PrefixDeclaration]], - List[Union[dict, PrefixDeclaration]], - ] - ] = empty_dict() - subsetDefinitions: Optional[ - Union[ - Dict[Union[str, SubsetDefinitionId], Union[dict, "SubsetDefinition"]], - List[Union[dict, "SubsetDefinition"]], - ] - ] = empty_dict() - synonymTypeDefinitions: Optional[ - Union[ - Dict[Union[str, SynonymTypeDefinitionId], Union[dict, "SynonymTypeDefinition"]], - List[Union[dict, "SynonymTypeDefinition"]], - ] - ] = empty_dict() + prefixes: Optional[Union[Dict[Union[str, PrefixDeclarationPrefix], Union[dict, PrefixDeclaration]], List[Union[dict, PrefixDeclaration]]]] = empty_dict() + subsetDefinitions: Optional[Union[Dict[Union[str, SubsetDefinitionId], Union[dict, "SubsetDefinition"]], List[Union[dict, "SubsetDefinition"]]]] = empty_dict() + synonymTypeDefinitions: Optional[Union[Dict[Union[str, SynonymTypeDefinitionId], Union[dict, "SynonymTypeDefinition"]], List[Union[dict, "SynonymTypeDefinition"]]]] = empty_dict() meta: Optional[Union[dict, "Meta"]] = None - nodes: Optional[ - Union[Dict[Union[str, NodeId], Union[dict, "Node"]], List[Union[dict, "Node"]]] - ] = empty_dict() + nodes: Optional[Union[Dict[Union[str, NodeId], Union[dict, "Node"]], List[Union[dict, "Node"]]]] = empty_dict() edges: Optional[Union[Union[dict, "Edge"], List[Union[dict, "Edge"]]]] = empty_list() - equivalentNodesSets: Optional[ - Union[Union[dict, "EquivalentNodesSet"], List[Union[dict, "EquivalentNodesSet"]]] - ] = empty_list() - logicalDefinitionAxioms: Optional[ - Union[Union[dict, "LogicalDefinitionAxiom"], List[Union[dict, "LogicalDefinitionAxiom"]]] - ] = empty_list() - domainRangeAxioms: Optional[ - Union[Union[dict, "DomainRangeAxiom"], List[Union[dict, "DomainRangeAxiom"]]] - ] = empty_list() - allValuesFromEdges: Optional[Union[Union[dict, "Edge"], List[Union[dict, "Edge"]]]] = ( - empty_list() - ) - propertyChainAxioms: Optional[ - Union[Union[dict, "PropertyChainAxiom"], List[Union[dict, "PropertyChainAxiom"]]] - ] = empty_list() + equivalentNodesSets: Optional[Union[Union[dict, "EquivalentNodesSet"], List[Union[dict, "EquivalentNodesSet"]]]] = empty_list() + logicalDefinitionAxioms: Optional[Union[Union[dict, "LogicalDefinitionAxiom"], List[Union[dict, "LogicalDefinitionAxiom"]]]] = empty_list() + domainRangeAxioms: Optional[Union[Union[dict, "DomainRangeAxiom"], List[Union[dict, "DomainRangeAxiom"]]]] = empty_list() + allValuesFromEdges: Optional[Union[Union[dict, "Edge"], List[Union[dict, "Edge"]]]] = empty_list() + propertyChainAxioms: Optional[Union[Union[dict, "PropertyChainAxiom"], List[Union[dict, "PropertyChainAxiom"]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -236,88 +218,50 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.lbl is not None and not isinstance(self.lbl, str): self.lbl = str(self.lbl) - self._normalize_inlined_as_dict( - slot_name="prefixes", slot_type=PrefixDeclaration, key_name="prefix", keyed=True - ) + self._normalize_inlined_as_dict(slot_name="prefixes", slot_type=PrefixDeclaration, key_name="prefix", keyed=True) - self._normalize_inlined_as_dict( - slot_name="subsetDefinitions", slot_type=SubsetDefinition, key_name="id", keyed=True - ) + self._normalize_inlined_as_dict(slot_name="subsetDefinitions", slot_type=SubsetDefinition, key_name="id", keyed=True) - self._normalize_inlined_as_dict( - slot_name="synonymTypeDefinitions", - slot_type=SynonymTypeDefinition, - key_name="id", - keyed=True, - ) + self._normalize_inlined_as_dict(slot_name="synonymTypeDefinitions", slot_type=SynonymTypeDefinition, key_name="id", keyed=True) if self.meta is not None and not isinstance(self.meta, Meta): self.meta = Meta(**as_dict(self.meta)) - self._normalize_inlined_as_list( - slot_name="nodes", slot_type=Node, key_name="id", keyed=True - ) + self._normalize_inlined_as_list(slot_name="nodes", slot_type=Node, key_name="id", keyed=True) if not isinstance(self.edges, list): self.edges = [self.edges] if self.edges is not None else [] self.edges = [v if isinstance(v, Edge) else Edge(**as_dict(v)) for v in self.edges] if not isinstance(self.equivalentNodesSets, list): - self.equivalentNodesSets = ( - [self.equivalentNodesSets] if self.equivalentNodesSets is not None else [] - ) - self.equivalentNodesSets = [ - v if isinstance(v, EquivalentNodesSet) else EquivalentNodesSet(**as_dict(v)) - for v in self.equivalentNodesSets - ] + self.equivalentNodesSets = [self.equivalentNodesSets] if self.equivalentNodesSets is not None else [] + self.equivalentNodesSets = [v if isinstance(v, EquivalentNodesSet) else EquivalentNodesSet(**as_dict(v)) for v in self.equivalentNodesSets] if not isinstance(self.logicalDefinitionAxioms, list): - self.logicalDefinitionAxioms = ( - [self.logicalDefinitionAxioms] if self.logicalDefinitionAxioms is not None else [] - ) - self.logicalDefinitionAxioms = [ - v if isinstance(v, LogicalDefinitionAxiom) else LogicalDefinitionAxiom(**as_dict(v)) - for v in self.logicalDefinitionAxioms - ] + self.logicalDefinitionAxioms = [self.logicalDefinitionAxioms] if self.logicalDefinitionAxioms is not None else [] + self.logicalDefinitionAxioms = [v if isinstance(v, LogicalDefinitionAxiom) else LogicalDefinitionAxiom(**as_dict(v)) for v in self.logicalDefinitionAxioms] if not isinstance(self.domainRangeAxioms, list): - self.domainRangeAxioms = ( - [self.domainRangeAxioms] if self.domainRangeAxioms is not None else [] - ) - self.domainRangeAxioms = [ - v if isinstance(v, DomainRangeAxiom) else DomainRangeAxiom(**as_dict(v)) - for v in self.domainRangeAxioms - ] - - if not isinstance(self.allValuesFromEdges, list): - self.allValuesFromEdges = ( - [self.allValuesFromEdges] if self.allValuesFromEdges is not None else [] - ) - self.allValuesFromEdges = [ - v if isinstance(v, Edge) else Edge(**as_dict(v)) for v in self.allValuesFromEdges - ] + self.domainRangeAxioms = [self.domainRangeAxioms] if self.domainRangeAxioms is not None else [] + self.domainRangeAxioms = [v if isinstance(v, DomainRangeAxiom) else DomainRangeAxiom(**as_dict(v)) for v in self.domainRangeAxioms] + + self._normalize_inlined_as_dict(slot_name="allValuesFromEdges", slot_type=Edge, key_name="sub", keyed=False) if not isinstance(self.propertyChainAxioms, list): - self.propertyChainAxioms = ( - [self.propertyChainAxioms] if self.propertyChainAxioms is not None else [] - ) - self.propertyChainAxioms = [ - v if isinstance(v, PropertyChainAxiom) else PropertyChainAxiom(**as_dict(v)) - for v in self.propertyChainAxioms - ] + self.propertyChainAxioms = [self.propertyChainAxioms] if self.propertyChainAxioms is not None else [] + self.propertyChainAxioms = [v if isinstance(v, PropertyChainAxiom) else PropertyChainAxiom(**as_dict(v)) for v in self.propertyChainAxioms] super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class Node(YAMLRoot): """ A node is a class, property, or other entity in an ontology """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = RDF.Resource + class_class_uri: ClassVar[URIRef] = RDF["Resource"] class_class_curie: ClassVar[str] = "rdf:Resource" class_name: ClassVar[str] = "Node" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.Node @@ -349,34 +293,39 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class Edge(YAMLRoot): """ An edge is a simple typed relationship between two nodes. When mapping to OWL, an edge represents either (a) s SubClassOf o (b) s SubClassOf p some o (c) s p o (where s and o are individuals) (d) s SubPropertyOf o (e) s EquivalentTo o (f) s type o """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.Edge + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["Edge"] class_class_curie: ClassVar[str] = "obographs:Edge" class_name: ClassVar[str] = "Edge" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.Edge - sub: Optional[str] = None - pred: Optional[str] = None - obj: Optional[str] = None + sub: str = None + pred: str = None + obj: str = None meta: Optional[Union[dict, "Meta"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.sub is not None and not isinstance(self.sub, str): + if self._is_empty(self.sub): + self.MissingRequiredField("sub") + if not isinstance(self.sub, str): self.sub = str(self.sub) - if self.pred is not None and not isinstance(self.pred, str): + if self._is_empty(self.pred): + self.MissingRequiredField("pred") + if not isinstance(self.pred, str): self.pred = str(self.pred) - if self.obj is not None and not isinstance(self.obj, str): + if self._is_empty(self.obj): + self.MissingRequiredField("obj") + if not isinstance(self.obj, str): self.obj = str(self.obj) if self.meta is not None and not isinstance(self.meta, Meta): @@ -385,16 +334,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class Meta(YAMLRoot): """ A collection of annotations on an entity or ontology or edge or axiom. Metadata typically does not affect the logical interpretation of the container but provides useful information to humans or machines. """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.Meta + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["Meta"] class_class_curie: ClassVar[str] = "obographs:Meta" class_name: ClassVar[str] = "Meta" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.Meta @@ -403,15 +351,9 @@ class Meta(YAMLRoot): version: Optional[str] = None comments: Optional[Union[str, List[str]]] = empty_list() definition: Optional[Union[dict, "DefinitionPropertyValue"]] = None - xrefs: Optional[ - Union[Union[dict, "XrefPropertyValue"], List[Union[dict, "XrefPropertyValue"]]] - ] = empty_list() - synonyms: Optional[ - Union[Union[dict, "SynonymPropertyValue"], List[Union[dict, "SynonymPropertyValue"]]] - ] = empty_list() - basicPropertyValues: Optional[ - Union[Union[dict, "BasicPropertyValue"], List[Union[dict, "BasicPropertyValue"]]] - ] = empty_list() + xrefs: Optional[Union[Union[dict, "XrefPropertyValue"], List[Union[dict, "XrefPropertyValue"]]]] = empty_list() + synonyms: Optional[Union[Union[dict, "SynonymPropertyValue"], List[Union[dict, "SynonymPropertyValue"]]]] = empty_list() + basicPropertyValues: Optional[Union[Union[dict, "BasicPropertyValue"], List[Union[dict, "BasicPropertyValue"]]]] = empty_list() deprecated: Optional[Union[bool, Bool]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -431,26 +373,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.xrefs, list): self.xrefs = [self.xrefs] if self.xrefs is not None else [] - self.xrefs = [ - v if isinstance(v, XrefPropertyValue) else XrefPropertyValue(**as_dict(v)) - for v in self.xrefs - ] + self.xrefs = [v if isinstance(v, XrefPropertyValue) else XrefPropertyValue(**as_dict(v)) for v in self.xrefs] if not isinstance(self.synonyms, list): self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [ - v if isinstance(v, SynonymPropertyValue) else SynonymPropertyValue(**as_dict(v)) - for v in self.synonyms - ] + self.synonyms = [v if isinstance(v, SynonymPropertyValue) else SynonymPropertyValue(**as_dict(v)) for v in self.synonyms] if not isinstance(self.basicPropertyValues, list): - self.basicPropertyValues = ( - [self.basicPropertyValues] if self.basicPropertyValues is not None else [] - ) - self.basicPropertyValues = [ - v if isinstance(v, BasicPropertyValue) else BasicPropertyValue(**as_dict(v)) - for v in self.basicPropertyValues - ] + self.basicPropertyValues = [self.basicPropertyValues] if self.basicPropertyValues is not None else [] + self.basicPropertyValues = [v if isinstance(v, BasicPropertyValue) else BasicPropertyValue(**as_dict(v)) for v in self.basicPropertyValues] if self.deprecated is not None and not isinstance(self.deprecated, Bool): self.deprecated = Bool(self.deprecated) @@ -458,16 +389,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class PropertyValue(YAMLRoot): """ A generic grouping for the different kinds of key-value associations on object. Minimally, a property value has a predicate and a value. It can also have a list of xrefs indicating provenance, as well as a metadata object. """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.PropertyValue + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["PropertyValue"] class_class_curie: ClassVar[str] = "obographs:PropertyValue" class_name: ClassVar[str] = "PropertyValue" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.PropertyValue @@ -502,15 +432,14 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DefinitionPropertyValue(PropertyValue): """ A property value that represents an assertion about the textual definition of an entity """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.DefinitionPropertyValue + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["DefinitionPropertyValue"] class_class_curie: ClassVar[str] = "obographs:DefinitionPropertyValue" class_name: ClassVar[str] = "DefinitionPropertyValue" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.DefinitionPropertyValue @@ -533,24 +462,22 @@ class BasicPropertyValue(PropertyValue): """ A property value that represents an assertion about an entity that is not a definition, synonym, or xref """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.BasicPropertyValue + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["BasicPropertyValue"] class_class_curie: ClassVar[str] = "obographs:BasicPropertyValue" class_name: ClassVar[str] = "BasicPropertyValue" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.BasicPropertyValue -@dataclass +@dataclass(repr=False) class XrefPropertyValue(PropertyValue): """ A property value that represents an assertion about an external reference to an entity """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.XrefPropertyValue + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["XrefPropertyValue"] class_class_curie: ClassVar[str] = "obographs:XrefPropertyValue" class_name: ClassVar[str] = "XrefPropertyValue" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.XrefPropertyValue @@ -564,15 +491,14 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class SynonymPropertyValue(PropertyValue): """ A property value that represents an assertion about a synonym of an entity """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.SynonymPropertyValue + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["SynonymPropertyValue"] class_class_curie: ClassVar[str] = "obographs:SynonymPropertyValue" class_name: ClassVar[str] = "SynonymPropertyValue" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.SynonymPropertyValue @@ -583,9 +509,7 @@ class SynonymPropertyValue(PropertyValue): val: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.synonymType is not None and not isinstance( - self.synonymType, SynonymTypeIdentifierString - ): + if self.synonymType is not None and not isinstance(self.synonymType, SynonymTypeIdentifierString): self.synonymType = SynonymTypeIdentifierString(self.synonymType) if self.isExact is not None and not isinstance(self.isExact, Bool): @@ -600,11 +524,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class SubsetDefinition(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OIO.SubsetProperty + class_class_uri: ClassVar[URIRef] = OIO["SubsetProperty"] class_class_curie: ClassVar[str] = "oio:SubsetProperty" class_name: ClassVar[str] = "SubsetDefinition" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.SubsetDefinition @@ -624,11 +548,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class SynonymTypeDefinition(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OIO.SynonymType + class_class_uri: ClassVar[URIRef] = OIO["SynonymType"] class_class_curie: ClassVar[str] = "oio:SynonymType" class_name: ClassVar[str] = "SynonymTypeDefinition" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.SynonymTypeDefinition @@ -652,16 +576,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class Axiom(YAMLRoot): """ A generic grouping for any OWL axiom or group of axioms that is not captured by existing constructs in this standard. """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OWL.Axiom + class_class_uri: ClassVar[URIRef] = OWL["Axiom"] class_class_curie: ClassVar[str] = "owl:Axiom" class_name: ClassVar[str] = "Axiom" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.Axiom @@ -675,16 +598,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DomainRangeAxiom(Axiom): """ This groups potentially multiple axioms that constrain the usage of a property depending on some combination of domain and range. """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.DomainRangeAxiom + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["DomainRangeAxiom"] class_class_curie: ClassVar[str] = "obographs:DomainRangeAxiom" class_name: ClassVar[str] = "DomainRangeAxiom" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.DomainRangeAxiom @@ -706,26 +628,19 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.rangeClassIds = [self.rangeClassIds] if self.rangeClassIds is not None else [] self.rangeClassIds = [v if isinstance(v, str) else str(v) for v in self.rangeClassIds] - if not isinstance(self.allValuesFromEdges, list): - self.allValuesFromEdges = ( - [self.allValuesFromEdges] if self.allValuesFromEdges is not None else [] - ) - self.allValuesFromEdges = [ - v if isinstance(v, Edge) else Edge(**as_dict(v)) for v in self.allValuesFromEdges - ] + self._normalize_inlined_as_dict(slot_name="allValuesFromEdges", slot_type=Edge, key_name="sub", keyed=False) super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class EquivalentNodesSet(Axiom): """ A clique of nodes that are all mutually equivalent """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OWL.equivalentClass + class_class_uri: ClassVar[URIRef] = OWL["equivalentClass"] class_class_curie: ClassVar[str] = "owl:equivalentClass" class_name: ClassVar[str] = "EquivalentNodesSet" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.EquivalentNodesSet @@ -744,15 +659,14 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class ExistentialRestrictionExpression(YAMLRoot): """ An existential restriction (OWL some values from) expression """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OWL.Restriction + class_class_uri: ClassVar[URIRef] = OWL["Restriction"] class_class_curie: ClassVar[str] = "owl:Restriction" class_name: ClassVar[str] = "ExistentialRestrictionExpression" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.ExistentialRestrictionExpression @@ -770,116 +684,83 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class LogicalDefinitionAxiom(Axiom): """ An axiom that defines a class in terms of a genus or set of genus classes and a set of differentia """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.LogicalDefinitionAxiom + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["LogicalDefinitionAxiom"] class_class_curie: ClassVar[str] = "obographs:LogicalDefinitionAxiom" class_name: ClassVar[str] = "LogicalDefinitionAxiom" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.LogicalDefinitionAxiom - definedClassId: str = None - genusIds: Optional[Union[str, List[str]]] = empty_list() - restrictions: Optional[ - Union[ - Union[dict, ExistentialRestrictionExpression], - List[Union[dict, ExistentialRestrictionExpression]], - ] - ] = empty_list() + definedClassId: Union[str, OboIdentifierString] = None + genusIds: Optional[Union[Union[str, OboIdentifierString], List[Union[str, OboIdentifierString]]]] = empty_list() + restrictions: Optional[Union[Union[dict, ExistentialRestrictionExpression], List[Union[dict, ExistentialRestrictionExpression]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.definedClassId): self.MissingRequiredField("definedClassId") - if not isinstance(self.definedClassId, str): - self.definedClassId = str(self.definedClassId) + if not isinstance(self.definedClassId, OboIdentifierString): + self.definedClassId = OboIdentifierString(self.definedClassId) if not isinstance(self.genusIds, list): self.genusIds = [self.genusIds] if self.genusIds is not None else [] - self.genusIds = [v if isinstance(v, str) else str(v) for v in self.genusIds] + self.genusIds = [v if isinstance(v, OboIdentifierString) else OboIdentifierString(v) for v in self.genusIds] if not isinstance(self.restrictions, list): self.restrictions = [self.restrictions] if self.restrictions is not None else [] - self.restrictions = [ - ( - v - if isinstance(v, ExistentialRestrictionExpression) - else ExistentialRestrictionExpression(**as_dict(v)) - ) - for v in self.restrictions - ] + self.restrictions = [v if isinstance(v, ExistentialRestrictionExpression) else ExistentialRestrictionExpression(**as_dict(v)) for v in self.restrictions] super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DisjointClassExpressionsAxiom(Axiom): """ An axiom that defines a set of classes or class expressions as being mutually disjoint. Formally, there exists no instance that instantiates more that one of the union of classIds and classExpressions. """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.DisjointClassExpressionsAxiom + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["DisjointClassExpressionsAxiom"] class_class_curie: ClassVar[str] = "obographs:DisjointClassExpressionsAxiom" class_name: ClassVar[str] = "DisjointClassExpressionsAxiom" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.DisjointClassExpressionsAxiom - classIds: Optional[Union[str, List[str]]] = empty_list() - classExpressions: Optional[ - Union[ - Union[dict, ExistentialRestrictionExpression], - List[Union[dict, ExistentialRestrictionExpression]], - ] - ] = empty_list() - unionEquivalentTo: Optional[str] = None + classIds: Optional[Union[Union[str, OboIdentifierString], List[Union[str, OboIdentifierString]]]] = empty_list() + classExpressions: Optional[Union[Union[dict, ExistentialRestrictionExpression], List[Union[dict, ExistentialRestrictionExpression]]]] = empty_list() + unionEquivalentTo: Optional[Union[str, OboIdentifierString]] = None unionEquivalentToExpression: Optional[Union[dict, ExistentialRestrictionExpression]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.classIds, list): self.classIds = [self.classIds] if self.classIds is not None else [] - self.classIds = [v if isinstance(v, str) else str(v) for v in self.classIds] + self.classIds = [v if isinstance(v, OboIdentifierString) else OboIdentifierString(v) for v in self.classIds] if not isinstance(self.classExpressions, list): - self.classExpressions = ( - [self.classExpressions] if self.classExpressions is not None else [] - ) - self.classExpressions = [ - ( - v - if isinstance(v, ExistentialRestrictionExpression) - else ExistentialRestrictionExpression(**as_dict(v)) - ) - for v in self.classExpressions - ] - - if self.unionEquivalentTo is not None and not isinstance(self.unionEquivalentTo, str): - self.unionEquivalentTo = str(self.unionEquivalentTo) - - if self.unionEquivalentToExpression is not None and not isinstance( - self.unionEquivalentToExpression, ExistentialRestrictionExpression - ): - self.unionEquivalentToExpression = ExistentialRestrictionExpression( - **as_dict(self.unionEquivalentToExpression) - ) + self.classExpressions = [self.classExpressions] if self.classExpressions is not None else [] + self.classExpressions = [v if isinstance(v, ExistentialRestrictionExpression) else ExistentialRestrictionExpression(**as_dict(v)) for v in self.classExpressions] + + if self.unionEquivalentTo is not None and not isinstance(self.unionEquivalentTo, OboIdentifierString): + self.unionEquivalentTo = OboIdentifierString(self.unionEquivalentTo) + + if self.unionEquivalentToExpression is not None and not isinstance(self.unionEquivalentToExpression, ExistentialRestrictionExpression): + self.unionEquivalentToExpression = ExistentialRestrictionExpression(**as_dict(self.unionEquivalentToExpression)) super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class PropertyChainAxiom(Axiom): """ An axiom that represents an OWL property chain, e.g. R <- R1 o ... o Rn """ - _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = OBOGRAPHS.PropertyChainAxiom + class_class_uri: ClassVar[URIRef] = OBOGRAPHS["PropertyChainAxiom"] class_class_curie: ClassVar[str] = "obographs:PropertyChainAxiom" class_name: ClassVar[str] = "PropertyChainAxiom" class_model_uri: ClassVar[URIRef] = OBOGRAPHS.PropertyChainAxiom @@ -892,12 +773,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.predicateId = str(self.predicateId) if not isinstance(self.chainPredicateIds, list): - self.chainPredicateIds = ( - [self.chainPredicateIds] if self.chainPredicateIds is not None else [] - ) - self.chainPredicateIds = [ - v if isinstance(v, str) else str(v) for v in self.chainPredicateIds - ] + self.chainPredicateIds = [self.chainPredicateIds] if self.chainPredicateIds is not None else [] + self.chainPredicateIds = [v if isinstance(v, str) else str(v) for v in self.chainPredicateIds] super().__post_init__(**kwargs) @@ -907,603 +784,243 @@ class ScopeEnum(EnumDefinitionImpl): """ A vocabulary of terms that can be used to "scope" a synonym """ - hasExactSynonym = PermissibleValue( text="hasExactSynonym", description="The synonym represents the exact meaning of the node.", - meaning=OIO.hasExactSynonym, - ) + meaning=OIO["hasExactSynonym"]) hasNarrowSynonym = PermissibleValue( text="hasNarrowSynonym", description="The synonym represents something narrower in meaning than the node.", - meaning=OIO.hasNarrowSynonym, - ) + meaning=OIO["hasNarrowSynonym"]) hasBroadSynonym = PermissibleValue( text="hasBroadSynonym", description="The synonym represents something broader in meaning than the node.", - meaning=OIO.hasBroadSynonym, - ) + meaning=OIO["hasBroadSynonym"]) hasRelatedSynonym = PermissibleValue( text="hasRelatedSynonym", description="""The synonym represents something closely related in meaning than the node, but in not exact, broad, or narrow.""", - meaning=OIO.hasRelatedSynonym, - ) + meaning=OIO["hasRelatedSynonym"]) _defn = EnumDefinition( name="ScopeEnum", - description='A vocabulary of terms that can be used to "scope" a synonym', + description="A vocabulary of terms that can be used to \"scope\" a synonym", ) - class NodeTypeEnum(EnumDefinitionImpl): """ The main type of a node """ - - CLASS = PermissibleValue(text="CLASS", meaning=OWL.Class) - PROPERTY = PermissibleValue(text="PROPERTY", meaning=RDFS.Property) - INDIVIDUAL = PermissibleValue(text="INDIVIDUAL", meaning=OWL.NamedIndividual) + CLASS = PermissibleValue( + text="CLASS", + meaning=OWL["Class"]) + PROPERTY = PermissibleValue( + text="PROPERTY", + meaning=RDFS["Property"]) + INDIVIDUAL = PermissibleValue( + text="INDIVIDUAL", + meaning=OWL["NamedIndividual"]) _defn = EnumDefinition( name="NodeTypeEnum", description="The main type of a node", ) - class PropertyTypeEnum(EnumDefinitionImpl): """ The node subtype for property nodes """ - - ANNOTATION = PermissibleValue(text="ANNOTATION", meaning=OWL.AnnotationProperty) - OBJECT = PermissibleValue(text="OBJECT", meaning=OWL.ObjectProperty) - DATA = PermissibleValue(text="DATA", meaning=OWL.DatatypeProperty) + ANNOTATION = PermissibleValue( + text="ANNOTATION", + meaning=OWL["AnnotationProperty"]) + OBJECT = PermissibleValue( + text="OBJECT", + meaning=OWL["ObjectProperty"]) + DATA = PermissibleValue( + text="DATA", + meaning=OWL["DatatypeProperty"]) _defn = EnumDefinition( name="PropertyTypeEnum", description="The node subtype for property nodes", ) - # Slots class slots: pass +slots.id = Slot(uri=OBOGRAPHS.id, name="id", curie=OBOGRAPHS.curie('id'), + model_uri=OBOGRAPHS.id, domain=None, range=URIRef) -slots.id = Slot( - uri=OBOGRAPHS.id, - name="id", - curie=OBOGRAPHS.curie("id"), - model_uri=OBOGRAPHS.id, - domain=None, - range=URIRef, -) +slots.sub = Slot(uri=RDF.subject, name="sub", curie=RDF.curie('subject'), + model_uri=OBOGRAPHS.sub, domain=None, range=Optional[str]) -slots.sub = Slot( - uri=RDF.subject, - name="sub", - curie=RDF.curie("subject"), - model_uri=OBOGRAPHS.sub, - domain=None, - range=Optional[str], -) +slots.pred = Slot(uri=RDF.predicate, name="pred", curie=RDF.curie('predicate'), + model_uri=OBOGRAPHS.pred, domain=None, range=Optional[str]) -slots.pred = Slot( - uri=RDF.predicate, - name="pred", - curie=RDF.curie("predicate"), - model_uri=OBOGRAPHS.pred, - domain=None, - range=Optional[str], -) +slots.obj = Slot(uri=RDF.object, name="obj", curie=RDF.curie('object'), + model_uri=OBOGRAPHS.obj, domain=None, range=Optional[str]) -slots.obj = Slot( - uri=RDF.object, - name="obj", - curie=RDF.curie("object"), - model_uri=OBOGRAPHS.obj, - domain=None, - range=Optional[str], -) +slots.val = Slot(uri=RDF.object, name="val", curie=RDF.curie('object'), + model_uri=OBOGRAPHS.val, domain=None, range=Optional[str]) -slots.val = Slot( - uri=RDF.object, - name="val", - curie=RDF.curie("object"), - model_uri=OBOGRAPHS.val, - domain=None, - range=Optional[str], -) +slots.valType = Slot(uri=OBOGRAPHS.valType, name="valType", curie=OBOGRAPHS.curie('valType'), + model_uri=OBOGRAPHS.valType, domain=None, range=Optional[str]) -slots.valType = Slot( - uri=OBOGRAPHS.valType, - name="valType", - curie=OBOGRAPHS.curie("valType"), - model_uri=OBOGRAPHS.valType, - domain=None, - range=Optional[str], -) +slots.lang = Slot(uri=OBOGRAPHS.lang, name="lang", curie=OBOGRAPHS.curie('lang'), + model_uri=OBOGRAPHS.lang, domain=None, range=Optional[str]) -slots.lang = Slot( - uri=OBOGRAPHS.lang, - name="lang", - curie=OBOGRAPHS.curie("lang"), - model_uri=OBOGRAPHS.lang, - domain=None, - range=Optional[str], -) +slots.lbl = Slot(uri=RDFS.label, name="lbl", curie=RDFS.curie('label'), + model_uri=OBOGRAPHS.lbl, domain=None, range=Optional[str]) -slots.lbl = Slot( - uri=RDFS.label, - name="lbl", - curie=RDFS.curie("label"), - model_uri=OBOGRAPHS.lbl, - domain=None, - range=Optional[str], -) +slots.type = Slot(uri=OBOGRAPHS.type, name="type", curie=OBOGRAPHS.curie('type'), + model_uri=OBOGRAPHS.type, domain=None, range=Optional[str]) -slots.type = Slot( - uri=OBOGRAPHS.type, - name="type", - curie=OBOGRAPHS.curie("type"), - model_uri=OBOGRAPHS.type, - domain=None, - range=Optional[str], -) +slots.propertyType = Slot(uri=OBOGRAPHS.propertyType, name="propertyType", curie=OBOGRAPHS.curie('propertyType'), + model_uri=OBOGRAPHS.propertyType, domain=None, range=Optional[Union[str, "PropertyTypeEnum"]]) -slots.propertyType = Slot( - uri=OBOGRAPHS.propertyType, - name="propertyType", - curie=OBOGRAPHS.curie("propertyType"), - model_uri=OBOGRAPHS.propertyType, - domain=None, - range=Optional[Union[str, "PropertyTypeEnum"]], -) +slots.meta = Slot(uri=OBOGRAPHS.meta, name="meta", curie=OBOGRAPHS.curie('meta'), + model_uri=OBOGRAPHS.meta, domain=None, range=Optional[Union[dict, Meta]]) -slots.meta = Slot( - uri=OBOGRAPHS.meta, - name="meta", - curie=OBOGRAPHS.curie("meta"), - model_uri=OBOGRAPHS.meta, - domain=None, - range=Optional[Union[dict, Meta]], -) +slots.definition = Slot(uri=IAO['0000115'], name="definition", curie=IAO.curie('0000115'), + model_uri=OBOGRAPHS.definition, domain=None, range=Optional[Union[dict, DefinitionPropertyValue]]) -slots.definition = Slot( - uri=IAO["0000115"], - name="definition", - curie=IAO.curie("0000115"), - model_uri=OBOGRAPHS.definition, - domain=None, - range=Optional[Union[dict, DefinitionPropertyValue]], -) +slots.basicPropertyValues = Slot(uri=OBOGRAPHS.basicPropertyValues, name="basicPropertyValues", curie=OBOGRAPHS.curie('basicPropertyValues'), + model_uri=OBOGRAPHS.basicPropertyValues, domain=None, range=Optional[Union[Union[dict, BasicPropertyValue], List[Union[dict, BasicPropertyValue]]]]) -slots.basicPropertyValues = Slot( - uri=OBOGRAPHS.basicPropertyValues, - name="basicPropertyValues", - curie=OBOGRAPHS.curie("basicPropertyValues"), - model_uri=OBOGRAPHS.basicPropertyValues, - domain=None, - range=Optional[Union[Union[dict, BasicPropertyValue], List[Union[dict, BasicPropertyValue]]]], -) +slots.comments = Slot(uri=RDFS.comment, name="comments", curie=RDFS.curie('comment'), + model_uri=OBOGRAPHS.comments, domain=None, range=Optional[Union[str, List[str]]]) -slots.comments = Slot( - uri=RDFS.comment, - name="comments", - curie=RDFS.curie("comment"), - model_uri=OBOGRAPHS.comments, - domain=None, - range=Optional[Union[str, List[str]]], -) +slots.version = Slot(uri=OWL.versionInfo, name="version", curie=OWL.curie('versionInfo'), + model_uri=OBOGRAPHS.version, domain=None, range=Optional[str]) -slots.version = Slot( - uri=OWL.versionInfo, - name="version", - curie=OWL.curie("versionInfo"), - model_uri=OBOGRAPHS.version, - domain=None, - range=Optional[str], -) +slots.deprecated = Slot(uri=OWL.deprecated, name="deprecated", curie=OWL.curie('deprecated'), + model_uri=OBOGRAPHS.deprecated, domain=None, range=Optional[Union[bool, Bool]]) -slots.deprecated = Slot( - uri=OWL.deprecated, - name="deprecated", - curie=OWL.curie("deprecated"), - model_uri=OBOGRAPHS.deprecated, - domain=None, - range=Optional[Union[bool, Bool]], -) +slots.subsets = Slot(uri=OIO.inSubset, name="subsets", curie=OIO.curie('inSubset'), + model_uri=OBOGRAPHS.subsets, domain=None, range=Optional[Union[str, List[str]]]) -slots.subsets = Slot( - uri=OIO.inSubset, - name="subsets", - curie=OIO.curie("inSubset"), - model_uri=OBOGRAPHS.subsets, - domain=None, - range=Optional[Union[str, List[str]]], -) +slots.xrefs = Slot(uri=OBOGRAPHS.xrefs, name="xrefs", curie=OBOGRAPHS.curie('xrefs'), + model_uri=OBOGRAPHS.xrefs, domain=None, range=Optional[Union[Union[str, XrefString], List[Union[str, XrefString]]]]) -slots.xrefs = Slot( - uri=OBOGRAPHS.xrefs, - name="xrefs", - curie=OBOGRAPHS.curie("xrefs"), - model_uri=OBOGRAPHS.xrefs, - domain=None, - range=Optional[Union[Union[str, XrefString], List[Union[str, XrefString]]]], -) +slots.nodes = Slot(uri=OBOGRAPHS.nodes, name="nodes", curie=OBOGRAPHS.curie('nodes'), + model_uri=OBOGRAPHS.nodes, domain=None, range=Optional[Union[Dict[Union[str, NodeId], Union[dict, Node]], List[Union[dict, Node]]]]) -slots.nodes = Slot( - uri=OBOGRAPHS.nodes, - name="nodes", - curie=OBOGRAPHS.curie("nodes"), - model_uri=OBOGRAPHS.nodes, - domain=None, - range=Optional[Union[Dict[Union[str, NodeId], Union[dict, Node]], List[Union[dict, Node]]]], -) +slots.edges = Slot(uri=OBOGRAPHS.edges, name="edges", curie=OBOGRAPHS.curie('edges'), + model_uri=OBOGRAPHS.edges, domain=None, range=Optional[Union[Union[dict, Edge], List[Union[dict, Edge]]]]) -slots.edges = Slot( - uri=OBOGRAPHS.edges, - name="edges", - curie=OBOGRAPHS.curie("edges"), - model_uri=OBOGRAPHS.edges, - domain=None, - range=Optional[Union[Union[dict, Edge], List[Union[dict, Edge]]]], -) +slots.equivalentNodesSets = Slot(uri=OBOGRAPHS.equivalentNodesSets, name="equivalentNodesSets", curie=OBOGRAPHS.curie('equivalentNodesSets'), + model_uri=OBOGRAPHS.equivalentNodesSets, domain=None, range=Optional[Union[Union[dict, EquivalentNodesSet], List[Union[dict, EquivalentNodesSet]]]]) -slots.equivalentNodesSets = Slot( - uri=OBOGRAPHS.equivalentNodesSets, - name="equivalentNodesSets", - curie=OBOGRAPHS.curie("equivalentNodesSets"), - model_uri=OBOGRAPHS.equivalentNodesSets, - domain=None, - range=Optional[Union[Union[dict, EquivalentNodesSet], List[Union[dict, EquivalentNodesSet]]]], -) +slots.logicalDefinitionAxioms = Slot(uri=OBOGRAPHS.logicalDefinitionAxioms, name="logicalDefinitionAxioms", curie=OBOGRAPHS.curie('logicalDefinitionAxioms'), + model_uri=OBOGRAPHS.logicalDefinitionAxioms, domain=None, range=Optional[Union[Union[dict, LogicalDefinitionAxiom], List[Union[dict, LogicalDefinitionAxiom]]]]) -slots.logicalDefinitionAxioms = Slot( - uri=OBOGRAPHS.logicalDefinitionAxioms, - name="logicalDefinitionAxioms", - curie=OBOGRAPHS.curie("logicalDefinitionAxioms"), - model_uri=OBOGRAPHS.logicalDefinitionAxioms, - domain=None, - range=Optional[ - Union[Union[dict, LogicalDefinitionAxiom], List[Union[dict, LogicalDefinitionAxiom]]] - ], -) +slots.disjointClassExpressionsAxioms = Slot(uri=OBOGRAPHS.disjointClassExpressionsAxioms, name="disjointClassExpressionsAxioms", curie=OBOGRAPHS.curie('disjointClassExpressionsAxioms'), + model_uri=OBOGRAPHS.disjointClassExpressionsAxioms, domain=None, range=Optional[Union[Union[dict, DisjointClassExpressionsAxiom], List[Union[dict, DisjointClassExpressionsAxiom]]]]) -slots.disjointClassExpressionsAxioms = Slot( - uri=OBOGRAPHS.disjointClassExpressionsAxioms, - name="disjointClassExpressionsAxioms", - curie=OBOGRAPHS.curie("disjointClassExpressionsAxioms"), - model_uri=OBOGRAPHS.disjointClassExpressionsAxioms, - domain=None, - range=Optional[ - Union[ - Union[dict, DisjointClassExpressionsAxiom], - List[Union[dict, DisjointClassExpressionsAxiom]], - ] - ], -) +slots.domainRangeAxioms = Slot(uri=OBOGRAPHS.domainRangeAxioms, name="domainRangeAxioms", curie=OBOGRAPHS.curie('domainRangeAxioms'), + model_uri=OBOGRAPHS.domainRangeAxioms, domain=None, range=Optional[Union[Union[dict, DomainRangeAxiom], List[Union[dict, DomainRangeAxiom]]]]) -slots.domainRangeAxioms = Slot( - uri=OBOGRAPHS.domainRangeAxioms, - name="domainRangeAxioms", - curie=OBOGRAPHS.curie("domainRangeAxioms"), - model_uri=OBOGRAPHS.domainRangeAxioms, - domain=None, - range=Optional[Union[Union[dict, DomainRangeAxiom], List[Union[dict, DomainRangeAxiom]]]], -) +slots.allValuesFromEdges = Slot(uri=OBOGRAPHS.allValuesFromEdges, name="allValuesFromEdges", curie=OBOGRAPHS.curie('allValuesFromEdges'), + model_uri=OBOGRAPHS.allValuesFromEdges, domain=None, range=Optional[Union[Union[dict, Edge], List[Union[dict, Edge]]]]) -slots.allValuesFromEdges = Slot( - uri=OBOGRAPHS.allValuesFromEdges, - name="allValuesFromEdges", - curie=OBOGRAPHS.curie("allValuesFromEdges"), - model_uri=OBOGRAPHS.allValuesFromEdges, - domain=None, - range=Optional[Union[Union[dict, Edge], List[Union[dict, Edge]]]], -) +slots.propertyChainAxioms = Slot(uri=OBOGRAPHS.propertyChainAxioms, name="propertyChainAxioms", curie=OBOGRAPHS.curie('propertyChainAxioms'), + model_uri=OBOGRAPHS.propertyChainAxioms, domain=None, range=Optional[Union[Union[dict, PropertyChainAxiom], List[Union[dict, PropertyChainAxiom]]]]) -slots.propertyChainAxioms = Slot( - uri=OBOGRAPHS.propertyChainAxioms, - name="propertyChainAxioms", - curie=OBOGRAPHS.curie("propertyChainAxioms"), - model_uri=OBOGRAPHS.propertyChainAxioms, - domain=None, - range=Optional[Union[Union[dict, PropertyChainAxiom], List[Union[dict, PropertyChainAxiom]]]], -) +slots.representativeNodeId = Slot(uri=OBOGRAPHS.representativeNodeId, name="representativeNodeId", curie=OBOGRAPHS.curie('representativeNodeId'), + model_uri=OBOGRAPHS.representativeNodeId, domain=None, range=Optional[str]) -slots.representativeNodeId = Slot( - uri=OBOGRAPHS.representativeNodeId, - name="representativeNodeId", - curie=OBOGRAPHS.curie("representativeNodeId"), - model_uri=OBOGRAPHS.representativeNodeId, - domain=None, - range=Optional[str], -) +slots.chainPredicateIds = Slot(uri=OBOGRAPHS.chainPredicateIds, name="chainPredicateIds", curie=OBOGRAPHS.curie('chainPredicateIds'), + model_uri=OBOGRAPHS.chainPredicateIds, domain=None, range=Optional[Union[str, List[str]]]) -slots.chainPredicateIds = Slot( - uri=OBOGRAPHS.chainPredicateIds, - name="chainPredicateIds", - curie=OBOGRAPHS.curie("chainPredicateIds"), - model_uri=OBOGRAPHS.chainPredicateIds, - domain=None, - range=Optional[Union[str, List[str]]], -) +slots.nodeIds = Slot(uri=OBOGRAPHS.nodeIds, name="nodeIds", curie=OBOGRAPHS.curie('nodeIds'), + model_uri=OBOGRAPHS.nodeIds, domain=None, range=Optional[Union[str, List[str]]]) -slots.nodeIds = Slot( - uri=OBOGRAPHS.nodeIds, - name="nodeIds", - curie=OBOGRAPHS.curie("nodeIds"), - model_uri=OBOGRAPHS.nodeIds, - domain=None, - range=Optional[Union[str, List[str]]], -) +slots.fillerId = Slot(uri=OBOGRAPHS.fillerId, name="fillerId", curie=OBOGRAPHS.curie('fillerId'), + model_uri=OBOGRAPHS.fillerId, domain=None, range=Optional[str]) -slots.fillerId = Slot( - uri=OBOGRAPHS.fillerId, - name="fillerId", - curie=OBOGRAPHS.curie("fillerId"), - model_uri=OBOGRAPHS.fillerId, - domain=None, - range=Optional[str], -) +slots.propertyId = Slot(uri=OBOGRAPHS.propertyId, name="propertyId", curie=OBOGRAPHS.curie('propertyId'), + model_uri=OBOGRAPHS.propertyId, domain=None, range=Optional[str]) -slots.propertyId = Slot( - uri=OBOGRAPHS.propertyId, - name="propertyId", - curie=OBOGRAPHS.curie("propertyId"), - model_uri=OBOGRAPHS.propertyId, - domain=None, - range=Optional[str], -) +slots.predicateId = Slot(uri=OBOGRAPHS.predicateId, name="predicateId", curie=OBOGRAPHS.curie('predicateId'), + model_uri=OBOGRAPHS.predicateId, domain=None, range=Optional[str]) -slots.predicateId = Slot( - uri=OBOGRAPHS.predicateId, - name="predicateId", - curie=OBOGRAPHS.curie("predicateId"), - model_uri=OBOGRAPHS.predicateId, - domain=None, - range=Optional[str], -) +slots.domainClassIds = Slot(uri=OBOGRAPHS.domainClassIds, name="domainClassIds", curie=OBOGRAPHS.curie('domainClassIds'), + model_uri=OBOGRAPHS.domainClassIds, domain=None, range=Optional[Union[str, List[str]]]) -slots.domainClassIds = Slot( - uri=OBOGRAPHS.domainClassIds, - name="domainClassIds", - curie=OBOGRAPHS.curie("domainClassIds"), - model_uri=OBOGRAPHS.domainClassIds, - domain=None, - range=Optional[Union[str, List[str]]], -) +slots.rangeClassIds = Slot(uri=OBOGRAPHS.rangeClassIds, name="rangeClassIds", curie=OBOGRAPHS.curie('rangeClassIds'), + model_uri=OBOGRAPHS.rangeClassIds, domain=None, range=Optional[Union[str, List[str]]]) -slots.rangeClassIds = Slot( - uri=OBOGRAPHS.rangeClassIds, - name="rangeClassIds", - curie=OBOGRAPHS.curie("rangeClassIds"), - model_uri=OBOGRAPHS.rangeClassIds, - domain=None, - range=Optional[Union[str, List[str]]], -) +slots.synonyms = Slot(uri=OBOGRAPHS.synonyms, name="synonyms", curie=OBOGRAPHS.curie('synonyms'), + model_uri=OBOGRAPHS.synonyms, domain=None, range=Optional[Union[Union[dict, SynonymPropertyValue], List[Union[dict, SynonymPropertyValue]]]]) -slots.synonyms = Slot( - uri=OBOGRAPHS.synonyms, - name="synonyms", - curie=OBOGRAPHS.curie("synonyms"), - model_uri=OBOGRAPHS.synonyms, - domain=None, - range=Optional[ - Union[Union[dict, SynonymPropertyValue], List[Union[dict, SynonymPropertyValue]]] - ], -) +slots.synonymType = Slot(uri=OBOGRAPHS.synonymType, name="synonymType", curie=OBOGRAPHS.curie('synonymType'), + model_uri=OBOGRAPHS.synonymType, domain=None, range=Optional[Union[str, SynonymTypeIdentifierString]]) -slots.synonymType = Slot( - uri=OBOGRAPHS.synonymType, - name="synonymType", - curie=OBOGRAPHS.curie("synonymType"), - model_uri=OBOGRAPHS.synonymType, - domain=None, - range=Optional[Union[str, SynonymTypeIdentifierString]], -) +slots.isExact = Slot(uri=OBOGRAPHS.isExact, name="isExact", curie=OBOGRAPHS.curie('isExact'), + model_uri=OBOGRAPHS.isExact, domain=None, range=Optional[Union[bool, Bool]]) -slots.isExact = Slot( - uri=OBOGRAPHS.isExact, - name="isExact", - curie=OBOGRAPHS.curie("isExact"), - model_uri=OBOGRAPHS.isExact, - domain=None, - range=Optional[Union[bool, Bool]], -) +slots.graphs = Slot(uri=OBOGRAPHS.graphs, name="graphs", curie=OBOGRAPHS.curie('graphs'), + model_uri=OBOGRAPHS.graphs, domain=None, range=Optional[Union[Dict[Union[str, GraphId], Union[dict, Graph]], List[Union[dict, Graph]]]]) -slots.graphs = Slot( - uri=OBOGRAPHS.graphs, - name="graphs", - curie=OBOGRAPHS.curie("graphs"), - model_uri=OBOGRAPHS.graphs, - domain=None, - range=Optional[Union[Dict[Union[str, GraphId], Union[dict, Graph]], List[Union[dict, Graph]]]], -) +slots.prefixes = Slot(uri=SH.declare, name="prefixes", curie=SH.curie('declare'), + model_uri=OBOGRAPHS.prefixes, domain=None, range=Optional[Union[Dict[Union[str, PrefixDeclarationPrefix], Union[dict, PrefixDeclaration]], List[Union[dict, PrefixDeclaration]]]]) -slots.prefixes = Slot( - uri=SH.declare, - name="prefixes", - curie=SH.curie("declare"), - model_uri=OBOGRAPHS.prefixes, - domain=None, - range=Optional[ - Union[ - Dict[Union[str, PrefixDeclarationPrefix], Union[dict, PrefixDeclaration]], - List[Union[dict, PrefixDeclaration]], - ] - ], -) +slots.synonymTypeDefinitions = Slot(uri=OBOGRAPHS.synonymTypeDefinitions, name="synonymTypeDefinitions", curie=OBOGRAPHS.curie('synonymTypeDefinitions'), + model_uri=OBOGRAPHS.synonymTypeDefinitions, domain=None, range=Optional[Union[Dict[Union[str, SynonymTypeDefinitionId], Union[dict, SynonymTypeDefinition]], List[Union[dict, SynonymTypeDefinition]]]]) -slots.synonymTypeDefinitions = Slot( - uri=OBOGRAPHS.synonymTypeDefinitions, - name="synonymTypeDefinitions", - curie=OBOGRAPHS.curie("synonymTypeDefinitions"), - model_uri=OBOGRAPHS.synonymTypeDefinitions, - domain=None, - range=Optional[ - Union[ - Dict[Union[str, SynonymTypeDefinitionId], Union[dict, SynonymTypeDefinition]], - List[Union[dict, SynonymTypeDefinition]], - ] - ], -) +slots.subsetDefinitions = Slot(uri=OBOGRAPHS.subsetDefinitions, name="subsetDefinitions", curie=OBOGRAPHS.curie('subsetDefinitions'), + model_uri=OBOGRAPHS.subsetDefinitions, domain=None, range=Optional[Union[Dict[Union[str, SubsetDefinitionId], Union[dict, SubsetDefinition]], List[Union[dict, SubsetDefinition]]]]) -slots.subsetDefinitions = Slot( - uri=OBOGRAPHS.subsetDefinitions, - name="subsetDefinitions", - curie=OBOGRAPHS.curie("subsetDefinitions"), - model_uri=OBOGRAPHS.subsetDefinitions, - domain=None, - range=Optional[ - Union[ - Dict[Union[str, SubsetDefinitionId], Union[dict, SubsetDefinition]], - List[Union[dict, SubsetDefinition]], - ] - ], -) +slots.prefixDeclaration__prefix = Slot(uri=SH.prefix, name="prefixDeclaration__prefix", curie=SH.curie('prefix'), + model_uri=OBOGRAPHS.prefixDeclaration__prefix, domain=None, range=URIRef) -slots.prefixDeclaration__prefix = Slot( - uri=SH.prefix, - name="prefixDeclaration__prefix", - curie=SH.curie("prefix"), - model_uri=OBOGRAPHS.prefixDeclaration__prefix, - domain=None, - range=URIRef, -) +slots.prefixDeclaration__namespace = Slot(uri=SH.namespace, name="prefixDeclaration__namespace", curie=SH.curie('namespace'), + model_uri=OBOGRAPHS.prefixDeclaration__namespace, domain=None, range=Optional[Union[str, URI]]) -slots.prefixDeclaration__namespace = Slot( - uri=SH.namespace, - name="prefixDeclaration__namespace", - curie=SH.curie("namespace"), - model_uri=OBOGRAPHS.prefixDeclaration__namespace, - domain=None, - range=Optional[Union[str, URI]], -) +slots.logicalDefinitionAxiom__definedClassId = Slot(uri=OBOGRAPHS.definedClassId, name="logicalDefinitionAxiom__definedClassId", curie=OBOGRAPHS.curie('definedClassId'), + model_uri=OBOGRAPHS.logicalDefinitionAxiom__definedClassId, domain=None, range=Union[str, OboIdentifierString]) -slots.logicalDefinitionAxiom__definedClassId = Slot( - uri=OBOGRAPHS.definedClassId, - name="logicalDefinitionAxiom__definedClassId", - curie=OBOGRAPHS.curie("definedClassId"), - model_uri=OBOGRAPHS.logicalDefinitionAxiom__definedClassId, - domain=None, - range=str, -) +slots.logicalDefinitionAxiom__genusIds = Slot(uri=OBOGRAPHS.genusIds, name="logicalDefinitionAxiom__genusIds", curie=OBOGRAPHS.curie('genusIds'), + model_uri=OBOGRAPHS.logicalDefinitionAxiom__genusIds, domain=None, range=Optional[Union[Union[str, OboIdentifierString], List[Union[str, OboIdentifierString]]]]) -slots.logicalDefinitionAxiom__genusIds = Slot( - uri=OBOGRAPHS.genusIds, - name="logicalDefinitionAxiom__genusIds", - curie=OBOGRAPHS.curie("genusIds"), - model_uri=OBOGRAPHS.logicalDefinitionAxiom__genusIds, - domain=None, - range=Optional[Union[str, List[str]]], -) +slots.logicalDefinitionAxiom__restrictions = Slot(uri=OWL.someValuesFrom, name="logicalDefinitionAxiom__restrictions", curie=OWL.curie('someValuesFrom'), + model_uri=OBOGRAPHS.logicalDefinitionAxiom__restrictions, domain=None, range=Optional[Union[Union[dict, ExistentialRestrictionExpression], List[Union[dict, ExistentialRestrictionExpression]]]]) -slots.logicalDefinitionAxiom__restrictions = Slot( - uri=OWL.someValuesFrom, - name="logicalDefinitionAxiom__restrictions", - curie=OWL.curie("someValuesFrom"), - model_uri=OBOGRAPHS.logicalDefinitionAxiom__restrictions, - domain=None, - range=Optional[ - Union[ - Union[dict, ExistentialRestrictionExpression], - List[Union[dict, ExistentialRestrictionExpression]], - ] - ], -) +slots.disjointClassExpressionsAxiom__classIds = Slot(uri=OBOGRAPHS.classIds, name="disjointClassExpressionsAxiom__classIds", curie=OBOGRAPHS.curie('classIds'), + model_uri=OBOGRAPHS.disjointClassExpressionsAxiom__classIds, domain=None, range=Optional[Union[Union[str, OboIdentifierString], List[Union[str, OboIdentifierString]]]]) -slots.disjointClassExpressionsAxiom__classIds = Slot( - uri=OBOGRAPHS.classIds, - name="disjointClassExpressionsAxiom__classIds", - curie=OBOGRAPHS.curie("classIds"), - model_uri=OBOGRAPHS.disjointClassExpressionsAxiom__classIds, - domain=None, - range=Optional[Union[str, List[str]]], -) +slots.disjointClassExpressionsAxiom__classExpressions = Slot(uri=OBOGRAPHS.classExpressions, name="disjointClassExpressionsAxiom__classExpressions", curie=OBOGRAPHS.curie('classExpressions'), + model_uri=OBOGRAPHS.disjointClassExpressionsAxiom__classExpressions, domain=None, range=Optional[Union[Union[dict, ExistentialRestrictionExpression], List[Union[dict, ExistentialRestrictionExpression]]]]) -slots.disjointClassExpressionsAxiom__classExpressions = Slot( - uri=OBOGRAPHS.classExpressions, - name="disjointClassExpressionsAxiom__classExpressions", - curie=OBOGRAPHS.curie("classExpressions"), - model_uri=OBOGRAPHS.disjointClassExpressionsAxiom__classExpressions, - domain=None, - range=Optional[ - Union[ - Union[dict, ExistentialRestrictionExpression], - List[Union[dict, ExistentialRestrictionExpression]], - ] - ], -) +slots.disjointClassExpressionsAxiom__unionEquivalentTo = Slot(uri=OBOGRAPHS.unionEquivalentTo, name="disjointClassExpressionsAxiom__unionEquivalentTo", curie=OBOGRAPHS.curie('unionEquivalentTo'), + model_uri=OBOGRAPHS.disjointClassExpressionsAxiom__unionEquivalentTo, domain=None, range=Optional[Union[str, OboIdentifierString]]) -slots.disjointClassExpressionsAxiom__unionEquivalentTo = Slot( - uri=OBOGRAPHS.unionEquivalentTo, - name="disjointClassExpressionsAxiom__unionEquivalentTo", - curie=OBOGRAPHS.curie("unionEquivalentTo"), - model_uri=OBOGRAPHS.disjointClassExpressionsAxiom__unionEquivalentTo, - domain=None, - range=Optional[str], -) +slots.disjointClassExpressionsAxiom__unionEquivalentToExpression = Slot(uri=OBOGRAPHS.unionEquivalentToExpression, name="disjointClassExpressionsAxiom__unionEquivalentToExpression", curie=OBOGRAPHS.curie('unionEquivalentToExpression'), + model_uri=OBOGRAPHS.disjointClassExpressionsAxiom__unionEquivalentToExpression, domain=None, range=Optional[Union[dict, ExistentialRestrictionExpression]]) -slots.disjointClassExpressionsAxiom__unionEquivalentToExpression = Slot( - uri=OBOGRAPHS.unionEquivalentToExpression, - name="disjointClassExpressionsAxiom__unionEquivalentToExpression", - curie=OBOGRAPHS.curie("unionEquivalentToExpression"), - model_uri=OBOGRAPHS.disjointClassExpressionsAxiom__unionEquivalentToExpression, - domain=None, - range=Optional[Union[dict, ExistentialRestrictionExpression]], -) +slots.Edge_sub = Slot(uri=RDF.subject, name="Edge_sub", curie=RDF.curie('subject'), + model_uri=OBOGRAPHS.Edge_sub, domain=Edge, range=str) -slots.Meta_xrefs = Slot( - uri=OBOGRAPHS.xrefs, - name="Meta_xrefs", - curie=OBOGRAPHS.curie("xrefs"), - model_uri=OBOGRAPHS.Meta_xrefs, - domain=Meta, - range=Optional[Union[Union[dict, "XrefPropertyValue"], List[Union[dict, "XrefPropertyValue"]]]], -) +slots.Edge_pred = Slot(uri=RDF.predicate, name="Edge_pred", curie=RDF.curie('predicate'), + model_uri=OBOGRAPHS.Edge_pred, domain=Edge, range=str) -slots.DefinitionPropertyValue_val = Slot( - uri=RDF.object, - name="DefinitionPropertyValue_val", - curie=RDF.curie("object"), - model_uri=OBOGRAPHS.DefinitionPropertyValue_val, - domain=DefinitionPropertyValue, - range=Optional[str], -) +slots.Edge_obj = Slot(uri=RDF.object, name="Edge_obj", curie=RDF.curie('object'), + model_uri=OBOGRAPHS.Edge_obj, domain=Edge, range=str) -slots.DefinitionPropertyValue_xrefs = Slot( - uri=OBOGRAPHS.xrefs, - name="DefinitionPropertyValue_xrefs", - curie=OBOGRAPHS.curie("xrefs"), - model_uri=OBOGRAPHS.DefinitionPropertyValue_xrefs, - domain=DefinitionPropertyValue, - range=Optional[Union[Union[str, XrefString], List[Union[str, XrefString]]]], -) +slots.Meta_xrefs = Slot(uri=OBOGRAPHS.xrefs, name="Meta_xrefs", curie=OBOGRAPHS.curie('xrefs'), + model_uri=OBOGRAPHS.Meta_xrefs, domain=Meta, range=Optional[Union[Union[dict, "XrefPropertyValue"], List[Union[dict, "XrefPropertyValue"]]]]) -slots.XrefPropertyValue_val = Slot( - uri=RDF.object, - name="XrefPropertyValue_val", - curie=RDF.curie("object"), - model_uri=OBOGRAPHS.XrefPropertyValue_val, - domain=XrefPropertyValue, - range=Optional[str], -) +slots.DefinitionPropertyValue_val = Slot(uri=RDF.object, name="DefinitionPropertyValue_val", curie=RDF.curie('object'), + model_uri=OBOGRAPHS.DefinitionPropertyValue_val, domain=DefinitionPropertyValue, range=Optional[str]) -slots.SynonymPropertyValue_pred = Slot( - uri=RDF.predicate, - name="SynonymPropertyValue_pred", - curie=RDF.curie("predicate"), - model_uri=OBOGRAPHS.SynonymPropertyValue_pred, - domain=SynonymPropertyValue, - range=Optional[Union[str, "ScopeEnum"]], -) +slots.DefinitionPropertyValue_xrefs = Slot(uri=OBOGRAPHS.xrefs, name="DefinitionPropertyValue_xrefs", curie=OBOGRAPHS.curie('xrefs'), + model_uri=OBOGRAPHS.DefinitionPropertyValue_xrefs, domain=DefinitionPropertyValue, range=Optional[Union[Union[str, XrefString], List[Union[str, XrefString]]]]) -slots.SynonymPropertyValue_val = Slot( - uri=RDF.object, - name="SynonymPropertyValue_val", - curie=RDF.curie("object"), - model_uri=OBOGRAPHS.SynonymPropertyValue_val, - domain=SynonymPropertyValue, - range=Optional[str], -) +slots.XrefPropertyValue_val = Slot(uri=RDF.object, name="XrefPropertyValue_val", curie=RDF.curie('object'), + model_uri=OBOGRAPHS.XrefPropertyValue_val, domain=XrefPropertyValue, range=Optional[str]) + +slots.SynonymPropertyValue_pred = Slot(uri=RDF.predicate, name="SynonymPropertyValue_pred", curie=RDF.curie('predicate'), + model_uri=OBOGRAPHS.SynonymPropertyValue_pred, domain=SynonymPropertyValue, range=Optional[Union[str, "ScopeEnum"]]) + +slots.SynonymPropertyValue_val = Slot(uri=RDF.object, name="SynonymPropertyValue_val", curie=RDF.curie('object'), + model_uri=OBOGRAPHS.SynonymPropertyValue_val, domain=SynonymPropertyValue, range=Optional[str]) diff --git a/src/oaklib/datamodels/obograph.yaml b/src/oaklib/datamodels/obograph.yaml index b7400f763..680bb641d 100644 --- a/src/oaklib/datamodels/obograph.yaml +++ b/src/oaklib/datamodels/obograph.yaml @@ -409,6 +409,13 @@ classes: - pred - obj - meta + slot_usage: + sub: + required: true + pred: + required: true + obj: + required: true Meta: aliases: diff --git a/src/oaklib/datamodels/vocabulary.py b/src/oaklib/datamodels/vocabulary.py index abe678cad..3293c6555 100644 --- a/src/oaklib/datamodels/vocabulary.py +++ b/src/oaklib/datamodels/vocabulary.py @@ -54,6 +54,7 @@ BIOLINK_CATEGORY = "biolink:category" IN_CATEGORY_PREDS = [BIOLINK_CATEGORY, "dbont:category"] +RELATED_TO = "biolink:related_to" OWL_CLASS = "owl:Class" OWL_NAMED_INDIVIDUAL = "owl:NamedIndividual" diff --git a/src/oaklib/implementations/amigo/amigo_implementation.py b/src/oaklib/implementations/amigo/amigo_implementation.py index 2c439ad5d..a10f89291 100644 --- a/src/oaklib/implementations/amigo/amigo_implementation.py +++ b/src/oaklib/implementations/amigo/amigo_implementation.py @@ -12,7 +12,7 @@ from oaklib.datamodels.association import Association, NegatedAssociation from oaklib.datamodels.search import SearchConfiguration -from oaklib.datamodels.vocabulary import IS_A, PART_OF, RDFS_LABEL +from oaklib.datamodels.vocabulary import IS_A, PART_OF, RDFS_LABEL, RELATED_TO from oaklib.interfaces import OboGraphInterface, SearchInterface from oaklib.interfaces.association_provider_interface import ( AssociationProviderInterface, @@ -73,6 +73,11 @@ REFERENCE, ] +def map_predicate(qualifiers: Iterable[str]) -> PRED_CURIE: + for q in qualifiers: + if q != "NOT": + return f"biolink:{q.lower()}" + return RELATED_TO def _fq_element(k, vs): v = " OR ".join([f'"{v}"' for v in vs]) if isinstance(vs, list) else f'"{vs}"' @@ -283,12 +288,13 @@ def associations( # results = solr.search("*:*", rows=1000, **params) for doc in results: cls = Association - if "not" in doc.get(QUALIFIER, []): + quals = set(doc.get(QUALIFIER, [])) + if "not" in quals: cls = NegatedAssociation assoc = cls( subject=_normalize(doc[BIOENTITY]), subject_label=doc[BIOENTITY_LABEL], - # predicate="", + predicate=map_predicate(quals), negated=cls == NegatedAssociation, object=doc[ANNOTATION_CLASS], object_label=doc[ANNOTATION_CLASS_LABEL], diff --git a/src/oaklib/implementations/obograph/obograph_implementation.py b/src/oaklib/implementations/obograph/obograph_implementation.py index 00fced0cb..a1799c52a 100644 --- a/src/oaklib/implementations/obograph/obograph_implementation.py +++ b/src/oaklib/implementations/obograph/obograph_implementation.py @@ -52,6 +52,7 @@ logical_definition_matches, ) from oaklib.utilities.basic_utils import pairs_as_dict +from oaklib.utilities.obograph_utils import load_obograph_document RDFLIB_FORMAT_MAP = { "ttl": "ttl", @@ -61,6 +62,9 @@ "owl": "xml", } +def clean_doc(gd: GraphDocument) -> None: + for g in gd.graphs: + g.nodes = [n for n in g.nodes if n.lbl] @dataclass class OboGraphImplementation( @@ -99,7 +103,8 @@ def __post_init__(self): if self.obograph_document is None: resource = self.resource if resource and resource.local_path: - gd = json_loader.load(str(resource.local_path), target_class=GraphDocument) + gd = load_obograph_document(resource.local_path) + # gd = json_loader.load(str(resource.local_path), target_class=GraphDocument) else: gd = GraphDocument() self.obograph_document = gd @@ -143,6 +148,8 @@ def _all_relationships(self) -> Iterator[RELATIONSHIP]: od = self.obograph_document for g in od.graphs: for e in g.edges: + if not e.pred: + raise ValueError(f"Missing predicate in {e}") yield self._tuple_to_curies((e.sub, e.pred, e.obj)) for ens in g.equivalentNodesSets: for n1 in ens.nodeIds: @@ -411,6 +418,7 @@ def dump(self, path: str = None, syntax: str = "json", **kwargs): logging.info(f"Dumping graph to {path} syntax: {syntax}") if syntax == "json" or syntax == "obojson": if path is None: + clean_doc(self.obograph_document) print(json_dumper.dumps(self.obograph_document)) else: json_dumper.dump(self.obograph_document, to_file=str(path)) diff --git a/src/oaklib/implementations/uniprot/uniprot_implementation.py b/src/oaklib/implementations/uniprot/uniprot_implementation.py index 6f0ebf038..b24fdd82a 100644 --- a/src/oaklib/implementations/uniprot/uniprot_implementation.py +++ b/src/oaklib/implementations/uniprot/uniprot_implementation.py @@ -158,6 +158,8 @@ def relationships( :param include_entailed: TODO :return: """ + from bioservices import UniProt + u = UniProt() exclude_predicates = [ "up:mappedCitation", "up:mappedAnnotation", diff --git a/src/oaklib/interfaces/association_provider_interface.py b/src/oaklib/interfaces/association_provider_interface.py index c720b9501..ff52cc20f 100644 --- a/src/oaklib/interfaces/association_provider_interface.py +++ b/src/oaklib/interfaces/association_provider_interface.py @@ -2,6 +2,7 @@ from abc import ABC from collections import defaultdict from dataclasses import dataclass, field +from enum import unique, Enum from typing import Any, Dict, Iterable, Iterator, List, Optional, Tuple from oaklib.datamodels.association import ( @@ -717,3 +718,14 @@ def normalize_association( strict=normalizer.strict, ) return association + + +@unique +class SubjectOrObjectRole(Enum): + """ + Role of terms in the term list + """ + + SUBJECT = "subject" + OBJECT = "object" + BOTH = "both" diff --git a/src/oaklib/interfaces/basic_ontology_interface.py b/src/oaklib/interfaces/basic_ontology_interface.py index faadc4a5b..8b7e93ca8 100644 --- a/src/oaklib/interfaces/basic_ontology_interface.py +++ b/src/oaklib/interfaces/basic_ontology_interface.py @@ -274,6 +274,8 @@ def uri_to_curie( :param use_uri_fallback: if cannot be contracted, use the URI as a CURIE proxy [default: True] :return: contracted URI, or original URI if no contraction possible """ + if not uri: + raise ValueError("URI cannot be None") rv = self.converter.compress(uri, passthrough=use_uri_fallback) if rv is None and strict: prefix_map_text = "\n".join( diff --git a/src/oaklib/interfaces/obograph_interface.py b/src/oaklib/interfaces/obograph_interface.py index 08b8a048f..11d38ca86 100644 --- a/src/oaklib/interfaces/obograph_interface.py +++ b/src/oaklib/interfaces/obograph_interface.py @@ -16,7 +16,7 @@ Node, SynonymPropertyValue, ) -from oaklib.datamodels.vocabulary import IS_A +from oaklib.datamodels.vocabulary import IS_A, OWL_CLASS from oaklib.interfaces.basic_ontology_interface import ( RELATIONSHIP, BasicOntologyInterface, @@ -221,6 +221,7 @@ def ancestor_graph( self, start_curies: Union[CURIE, List[CURIE]], predicates: List[PRED_CURIE] = None, + method: Optional[GraphTraversalMethod] = None, **kwargs, ) -> Graph: """ @@ -232,6 +233,28 @@ def ancestor_graph( :param predicates: if supplied then only follow edges with these predicates :return: ancestor graph """ + if method and method == GraphTraversalMethod.ENTAILMENT: + ancs = self.ancestors( + start_curies, predicates=predicates, method=method, + ) + node_map = {} + edges = [] + for s, p, o in self.relationships( + subjects=ancs, + predicates=predicates, + ): + node_map[s] = None + node_map[o] = None + edges.append(Edge(sub=s, pred=p, obj=o)) + labels = {k: v for k, v in self.labels(list(node_map.keys()))} + for n in node_map.keys(): + node_map[n] = Node(n, lbl=labels.get(n), type="CLASS") + g = Graph(id="ancestor_graph") + g.nodes = list(node_map.values()) + g.edges = edges + return g + if not isinstance(start_curies, list): + start_curies = [start_curies] key = ( "ancestor_graph", tuple(start_curies), @@ -246,6 +269,7 @@ def ancestor_graph( logging.info( f"Computing ancestor graph for {start_curies} / {predicates} using graph walking" ) + logging.info(f"Walking up from {len(start_curies)} over {predicates}") g = self._graph(walk_up(self, start_curies, predicates=predicates, **kwargs)) if self.transitive_query_cache is not None: self.transitive_query_cache[key] = g diff --git a/src/oaklib/io/obograph_writer.py b/src/oaklib/io/obograph_writer.py index e62f23606..1d2ebbb3d 100644 --- a/src/oaklib/io/obograph_writer.py +++ b/src/oaklib/io/obograph_writer.py @@ -2,7 +2,7 @@ Utilities for writing out obo graphs """ - +import logging from typing import Optional, TextIO, Union from linkml_runtime.dumpers import json_dumper, yaml_dumper @@ -10,14 +10,42 @@ from oaklib import OntologyResource from oaklib.converters.obo_graph_to_cx_converter import OboGraphToCXConverter from oaklib.converters.obo_graph_to_rdf_owl_converter import OboGraphToRdfOwlConverter -from oaklib.datamodels.obograph import Graph +from oaklib.datamodels.obograph import Graph, GraphDocument from oaklib.implementations import ProntoImplementation +from oaklib.utilities.obograph_utils import graph_to_image + +OG_FORMATS = ["json", "yaml", "obojson", "obograph"] +RENDER_FORMATS = ["png", "svg", "dot"] + +logger = logging.getLogger(__name__) + +def write_graph_document( + doc: GraphDocument, + output: Optional[Union[str, TextIO]] = None, + format: str = None, + view: Optional[bool] = None, + **kwargs, +): + logger.info(f"Writing graph document to {output} in format {format} // v={view}") + if view and not format: + format = "png" + if (not format or format in OG_FORMATS) and not view: + if output: + json_dumper.dump(doc, to_file=output, inject_type=False) + else: + print(json_dumper.dumps(doc)) + else: + if len(doc.graphs) != 1: + raise ValueError("Can only write a single graph to a file") + write_graph(doc.graphs[0], output, format, view=view, **kwargs) def write_graph( graph: Graph, output: Optional[Union[str, TextIO]] = None, format: str = None, + view: Optional[bool] = None, + **kwargs, ): """ Writes an obo graph to a file-like object in a specified format @@ -27,7 +55,15 @@ def write_graph( :param format: :return: """ - if format == "json": + if view or format in RENDER_FORMATS: + graph_to_image( + graph, + imgfile=output, + format=format, + view=view, + **kwargs, + ) + elif format in OG_FORMATS: if output: json_dumper.dump(graph, to_file=output, inject_type=False) else: diff --git a/src/oaklib/io/streaming_writer.py b/src/oaklib/io/streaming_writer.py index 1f400ebd5..7957bed37 100644 --- a/src/oaklib/io/streaming_writer.py +++ b/src/oaklib/io/streaming_writer.py @@ -164,3 +164,14 @@ def emit_dict(self, obj: Mapping[str, Any], object_type: Type = None): :return: """ raise NotImplementedError + + def emit_header(self, *header: str): + """ + Emit a header row + + :param header: + :return: + """ + for line in header: + self.line(f"# {line}") + self.line("#") diff --git a/src/oaklib/query.py b/src/oaklib/query.py index f2106249f..426d24586 100644 --- a/src/oaklib/query.py +++ b/src/oaklib/query.py @@ -12,6 +12,7 @@ from typing import IO, Any, Dict, Iterable, Iterator, List, Optional, Tuple, Union import yaml + from pydantic import BaseModel from oaklib import BasicOntologyInterface @@ -36,7 +37,7 @@ RDF_TYPE, RDFS_DOMAIN, RDFS_RANGE, - REGULATES, + REGULATES, SUBPROPERTY_OF, ) from oaklib.interfaces import ( OboGraphInterface, @@ -92,10 +93,15 @@ class Query(BaseModel): >>> from oaklib import get_adapter >>> from oaklib.datamodels.vocabulary import IS_A >>> adapter = get_adapter("sqlite:obo:cl") - >>> neuron_q = ancestor_of("CL:0000540", predicates=[IS_A]) - >>> forebrain_q = ancestor_of("UBERON:0001890", predicates=[IS_A, PART_OF]) + >>> neuron_q = descendant_of("CL:0000540", predicates=[IS_A]) + >>> forebrain_q = descendant_of("UBERON:0001890", predicates=[IS_A, PART_OF]) >>> intersection_q = neuron_q & forebrain_q - >>> assert "CL:1001502" in q.execute(adapter) + >>> for x in sorted(intersection_q.execute(adapter)): + ... print(x, adapter.label(x)) + + ... + CL:1001502 mitral cell + ... The above code is equivalent to: @@ -418,7 +424,7 @@ def onto_query( ... print(x, cl.label(x)) ... - CL:0000749 ON-bipolar cell + CL:0004217 H1 horizontal cell ... @@ -436,7 +442,7 @@ def onto_query( ... print(x, cl.label(x)) ... - CL:0000749 ON-bipolar cell + CL:0004217 H1 horizontal cell ... >>> assert set(both2) == both @@ -518,7 +524,7 @@ def _parse_params(s: str) -> Dict: if k == "p": k = "predicates" if k == "predicates": - v = _process_predicates_arg(v) + v = process_predicates_arg(v) if k == "prefixes": v = v.split(",") d[k] = v @@ -577,7 +583,7 @@ def chain_results(v): logging.debug(f"Predicates: {term}") logging.warning("Deprecated: pass as parameter instead") m = re.match(r"^\.predicates=(\S*)$", term) - predicates = _process_predicates_arg(m.group(1)) + predicates = process_predicates_arg(m.group(1)) elif term == ".and": logging.debug("AND") # boolean term: consume the result of the query and intersect @@ -950,20 +956,80 @@ def _nest_list_of_terms(terms: List[str]) -> Tuple[NESTED_LIST, List[str]]: return nested, [] -def _process_predicates_arg( +def process_predicates_arg( predicates_str: str, expected_number: Optional[int] = None, exclude_predicates_str: Optional[str] = None, impl: Optional[BasicOntologyInterface] = None, ) -> Optional[List[PRED_CURIE]]: + """ + Process a string of predicates into a list of PRED_CURIEs. + + Example: + + >>> process_predicates_arg("FOO:123") + ['FOO:123'] + + >>> process_predicates_arg("i") + ['rdfs:subClassOf'] + + >>> process_predicates_arg("i,p") + ['rdfs:subClassOf', 'BFO:0000050'] + + >>> from oaklib import get_adapter + >>> adapter = get_adapter("sqlite:obo:ro") + >>> process_predicates_arg("i,part of", impl=adapter) + ['rdfs:subClassOf', 'BFO:0000050'] + + Include entailed subproperties: + + >>> for p in sorted(process_predicates_arg("sub(i, connected to)", impl=adapter)): + ... print(p, adapter.label(p)) + + ... + RO:0002103 synapsed by + ... + rdfs:subClassOf None + + + :param predicates_str: + :param expected_number: + :param exclude_predicates_str: + :param impl: + :return: + """ if predicates_str is None and exclude_predicates_str is None: return None + if predicates_str.startswith("sub("): + if not isinstance(impl, OboGraphInterface): + raise ValueError("Must provide an BasicOntologyInterface to use sub()") + + # sub(FOO:123) => FOO:123 + preds = process_predicates_arg( + predicates_str[4:-1], + expected_number=expected_number, + exclude_predicates_str=exclude_predicates_str, + impl=impl, + ) + preds_expanded = set(preds) + # note that RG doesn't pre-computed relation closure; + # use HOP method + for desc_p in impl.descendants( + preds, + predicates=[SUBPROPERTY_OF], + method=GraphTraversalMethod.HOP, + reflexive=True, + ): + preds_expanded.add(desc_p) + return list(preds_expanded) + if predicates_str is None: inputs = [] elif "," in predicates_str: inputs = predicates_str.split(",") else: inputs = predicates_str.split("+") + inputs = [i.strip() for i in inputs] preds = [] for p in inputs: next_preds = _shorthand_to_pred_curie(p) @@ -1028,3 +1094,4 @@ def _shorthand_to_pred_curie(shorthand: str) -> Union[PRED_CURIE, List[PRED_CURI return [IS_A, RDF_TYPE, EQUIVALENT_CLASS, DISJOINT_WITH, RDFS_DOMAIN, RDFS_RANGE] else: return shorthand + diff --git a/src/oaklib/selector.py b/src/oaklib/selector.py index dea4ce77c..5c7da1d90 100644 --- a/src/oaklib/selector.py +++ b/src/oaklib/selector.py @@ -15,6 +15,7 @@ from oaklib.datamodels.input_specification import InputSpecification, Normalizer from oaklib.implementations import GildaImplementation from oaklib.implementations.funowl.funowl_implementation import FunOwlImplementation +from oaklib.implementations.obograph.obograph_implementation import OboGraphImplementation from oaklib.interfaces import OntologyInterface from oaklib.interfaces.association_provider_interface import ( AssociationProviderInterface, @@ -347,6 +348,8 @@ def get_resource_imp_class_from_suffix_descriptor( logging.warning("Using rdflib rdf/xml parser; this behavior may change in future") elif suffix == "ofn": impl_class = FunOwlImplementation + elif suffix == "json": + impl_class = OboGraphImplementation # elif suffix == "obo": # impl_class = SimpleOboImplementation else: diff --git a/src/oaklib/utilities/associations/association_queries.py b/src/oaklib/utilities/associations/association_queries.py new file mode 100644 index 000000000..cec2e84f3 --- /dev/null +++ b/src/oaklib/utilities/associations/association_queries.py @@ -0,0 +1,48 @@ +import itertools +import logging +from typing import List, Optional, Iterator + +from oaklib.datamodels.association import Association +from oaklib.interfaces.association_provider_interface import AssociationProviderInterface, SubjectOrObjectRole +from oaklib.types import CURIE, PRED_CURIE + + +def get_association_iterator( + impl: AssociationProviderInterface, + curies: List[CURIE], + terms_role: Optional[str] = None, + association_predicates: Optional[List[PRED_CURIE]] = None, + ontology_predicates: Optional[List[PRED_CURIE]] = None, + **kwargs, +) -> Iterator[Association]: + """ + Query associations for a list of curies. + + :param impl: + :param curies: Query terms + :param terms_role: are the query terms subjects (e.g. genes; default) or objects (e.g. terms)? + :param association_predicates: if provided, filters the associations by these predicates (e.g. involved-in) + :param ontology_predicates: (recommended) ontology closure predicates + :param kwargs: + :return: + """ + qs_it = impl.associations( + curies, + predicates=association_predicates, + subject_closure_predicates=ontology_predicates, + **kwargs, + ) + qo_it = impl.associations( + objects=curies, + predicates=association_predicates, + object_closure_predicates=ontology_predicates, + **kwargs, + ) + if terms_role is None or terms_role == SubjectOrObjectRole.SUBJECT.value: + it = qs_it + elif terms_role == SubjectOrObjectRole.OBJECT.value: + it = qo_it + else: + logging.info("Using query terms to query both subject and object") + it = itertools.chain(qs_it, qo_it) + return it diff --git a/src/oaklib/utilities/metrics/text_content_analysis.py b/src/oaklib/utilities/metrics/text_content_analysis.py index a0abd23c7..75e64d091 100644 --- a/src/oaklib/utilities/metrics/text_content_analysis.py +++ b/src/oaklib/utilities/metrics/text_content_analysis.py @@ -17,7 +17,7 @@ SUBCLASS_OF, ) from oaklib.implementations import SqlImplementation -from oaklib.query import _process_predicates_arg +from oaklib.query import process_predicates_arg from oaklib.types import PRED_CURIE logger = logging.getLogger(__name__) @@ -61,7 +61,7 @@ def calculate_ontology_text_content( >>> adapter = get_adapter("tests/input/go-nucleus.db") >>> assert isinstance(adapter, SqlImplementation) >>> tc = calculate_ontology_text_content(adapter) - >>> assert 0.5 < tc < 0.8 + >>> assert tc > 0.5 < 0.99 :param adapter: :param predicates: @@ -132,7 +132,7 @@ def main( for input_name in inputs: try: adapter = get_adapter(input_name) - annotation_predicates = _process_predicates_arg(annotation_predicate) + annotation_predicates = process_predicates_arg(annotation_predicate) if not annotation_predicates and default_annotations: annotation_predicates = DEFAULT_ANNOTATION_PREDICATES tc = calculate_ontology_text_content( diff --git a/src/oaklib/utilities/obograph_utils.py b/src/oaklib/utilities/obograph_utils.py index 9be421083..c6ae8cddf 100644 --- a/src/oaklib/utilities/obograph_utils.py +++ b/src/oaklib/utilities/obograph_utils.py @@ -48,14 +48,51 @@ class TreeFormatEnum(Enum): text = "text" -def load_obograph_document(path: str) -> GraphDocument: +def graph_node_ids_from_subject_and_objects(g: Graph) -> List[CURIE]: + node_ids = set() + for edge in g.edges: + node_ids.add(edge.sub) + node_ids.add(edge.obj) + return list(node_ids) + + +def remove_unlabeled_nodes(g: Union[GraphDocument, Graph], rescue_connected_nodes=True) -> None: + if isinstance(g, GraphDocument): + for graph in g.graphs: + remove_unlabeled(graph, rescue_connected_nodes=rescue_connected_nodes) + else: + if rescue_connected_nodes: + rescued = graph_node_ids_from_subject_and_objects(g) + g.nodes = [n for n in g.nodes if n.lbl is not None or n.id in rescued] + else: + g.nodes = [n for n in g.nodes if n.lbl is not None] + +def load_obograph_document(path: Union[str, Path]) -> GraphDocument: """ - Load an OBOGraph document from a file + Load an OBOGraph document from a file. + + Example: + + >>> from oaklib.utilities.obograph_utils import load_obograph_document + >>> doc = load_obograph_document("tests/input/go-nucleus.json") + >>> g = doc.graphs[0] + >>> nucleus_terms = [n for n in g.nodes if n.lbl == "nucleus"] + >>> len(nucleus_terms) + 1 :param path: :return: """ - return json_loader.load(str(path), target_class=GraphDocument) + raw_obj = json.load(open(path)) + if "@type" in raw_obj: + del raw_obj["@type"] + for g in raw_obj["graphs"]: + for n in g["nodes"]: + # workaround for json_loader issue + if len(n.keys()) == 1 and "id" in n: + n["lbl"] = None + return GraphDocument(**raw_obj) + # return json_loader.load(str(path), target_class=GraphDocument) def default_stylemap_path(): @@ -65,7 +102,16 @@ def default_stylemap_path(): def graph_as_dict(graph: Graph) -> Dict[str, Any]: """ - Serialize a graph to a dict. + Serialize graph nodes to a dict. + + Example: + + >>> from oaklib.utilities.obograph_utils import load_obograph_document + >>> doc = load_obograph_document("tests/input/go-nucleus.json") + >>> g = doc.graphs[0] + >>> obj = graph_as_dict(g) + >>> node_map = {n["id"]: n for n in obj["nodes"]} + >>> assert len(node_map) > 20 :param graph: """ @@ -106,6 +152,11 @@ def graph_to_image( """ Renders a graph to png using obographviz. + >>> from oaklib.utilities.obograph_utils import load_obograph_document + >>> doc = load_obograph_document("tests/input/go-nucleus.json") + >>> g = doc.graphs[0] + >>> graph_to_image(g, imgfile="tests/output/go-nucleus-for-g2i.png") + :param graph: OboGraph object to visualize :param seeds: list of node ids to highlight :param configure: yaml string to configure the graph From 7a99c20c3464fec6a3eb7d91ccdbeae5b1baec1e Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 10 Feb 2025 18:00:47 -0800 Subject: [PATCH 2/3] format --- src/oaklib/cli.py | 37 ++++++++++++------- .../amigo/amigo_implementation.py | 2 + .../obograph/obograph_implementation.py | 3 +- .../uniprot/uniprot_implementation.py | 1 + .../association_provider_interface.py | 2 +- src/oaklib/interfaces/obograph_interface.py | 6 ++- src/oaklib/io/obograph_writer.py | 2 + src/oaklib/query.py | 11 +++--- .../associations/association_queries.py | 19 ++++++---- src/oaklib/utilities/obograph_utils.py | 2 +- 10 files changed, 52 insertions(+), 33 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 52662a6d5..de3b75ab4 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -46,12 +46,12 @@ from oaklib.datamodels.cross_ontology_diff import DiffCategory from oaklib.datamodels.obograph import ( BasicPropertyValue, - Node, Edge, Graph, GraphDocument, LogicalDefinitionAxiom, Meta, + Node, PrefixDeclaration, ) from oaklib.datamodels.settings import Settings @@ -83,7 +83,8 @@ ValidatorInterface, ) from oaklib.interfaces.association_provider_interface import ( - AssociationProviderInterface, SubjectOrObjectRole, + AssociationProviderInterface, + SubjectOrObjectRole, ) from oaklib.interfaces.class_enrichment_calculation_interface import ( ClassEnrichmentCalculationInterface, @@ -132,8 +133,7 @@ from oaklib.io.streaming_yaml_writer import StreamingYamlWriter from oaklib.mappers.ontology_metadata_mapper import OntologyMetadataMapper from oaklib.parsers.association_parser_factory import get_association_parser -from oaklib.query import process_predicates_arg, curies_from_file, query_terms_iterator -from oaklib.utilities.associations.association_queries import get_association_iterator +from oaklib.query import curies_from_file, process_predicates_arg, query_terms_iterator from oaklib.resource import OntologyResource from oaklib.selector import get_adapter, get_resource_from_shorthand from oaklib.transformers.transformers_factory import ( @@ -144,6 +144,7 @@ from oaklib.utilities import table_filler from oaklib.utilities.apikey_manager import set_apikey_value from oaklib.utilities.associations.association_differ import AssociationDiffer +from oaklib.utilities.associations.association_queries import get_association_iterator from oaklib.utilities.axioms import ( logical_definition_analyzer, logical_definition_summarizer, @@ -181,8 +182,9 @@ graph_to_d3viz_objects, graph_to_image, graph_to_tree_display, + remove_unlabeled_nodes, shortest_paths, - trim_graph, remove_unlabeled_nodes, + trim_graph, ) from oaklib.utilities.publication_utils.pubmed_wrapper import PubmedWrapper from oaklib.utilities.subsets.slimmer_utils import ( @@ -4637,9 +4639,7 @@ def associations( f"Ontology closure predicates: {', '.join(actual_predicates or [])}", ) if expand: - writer.emit_header( - "The results include a round of expansion" - ) + writer.emit_header("The results include a round of expansion") qs_it = impl.associations( curies, predicates=actual_association_predicates, @@ -4685,7 +4685,11 @@ def associations( exp_it = get_association_iterator( impl, list(entities_to_expand), - terms_role=SubjectOrObjectRole.SUBJECT.value if terms_role == SubjectOrObjectRole.OBJECT.value else SubjectOrObjectRole.OBJECT.value, + terms_role=( + SubjectOrObjectRole.SUBJECT.value + if terms_role == SubjectOrObjectRole.OBJECT.value + else SubjectOrObjectRole.OBJECT.value + ), association_predicates=actual_association_predicates, ontology_predicates=actual_predicates, **kwargs, @@ -4842,7 +4846,9 @@ def associations_graph( if not isinstance(oa, OboGraphInterface): raise NotImplementedError(f"Cannot execute this using {oa} of type {type(oa)}") - graph = oa.ancestor_graph(curies, predicates=actual_predicates, method=GraphTraversalMethod.ENTAILMENT) + graph = oa.ancestor_graph( + curies, predicates=actual_predicates, method=GraphTraversalMethod.ENTAILMENT + ) graph.edges.extend(edges) existing_nodes = set([node.id for node in graph.nodes]) for node in node_map.values(): @@ -4853,7 +4859,9 @@ def associations_graph( gd = GraphDocument(graphs=[graph]) if stylemap is None: stylemap = default_stylemap_path() - write_graph_document(gd, output, format=output_type, view=view, stylemap=stylemap, seeds=curies, **kwargs) + write_graph_document( + gd, output, format=output_type, view=view, stylemap=stylemap, seeds=curies, **kwargs + ) @main.command() @@ -6827,9 +6835,10 @@ def diff_via_mappings( @click.option("--missing-value-token", help="Populate all missing values with this token") @click.option( "--schema", - help=("Path to linkml schema. " - "This is used to infer which fields are identifiers and which are dependent columns, e.g labels" - ), + help=( + "Path to linkml schema. " + "This is used to infer which fields are identifiers and which are dependent columns, e.g labels" + ), ) @click.option( "--delimiter", diff --git a/src/oaklib/implementations/amigo/amigo_implementation.py b/src/oaklib/implementations/amigo/amigo_implementation.py index a10f89291..c5a91c184 100644 --- a/src/oaklib/implementations/amigo/amigo_implementation.py +++ b/src/oaklib/implementations/amigo/amigo_implementation.py @@ -73,12 +73,14 @@ REFERENCE, ] + def map_predicate(qualifiers: Iterable[str]) -> PRED_CURIE: for q in qualifiers: if q != "NOT": return f"biolink:{q.lower()}" return RELATED_TO + def _fq_element(k, vs): v = " OR ".join([f'"{v}"' for v in vs]) if isinstance(vs, list) else f'"{vs}"' return f"{k}:({v})" diff --git a/src/oaklib/implementations/obograph/obograph_implementation.py b/src/oaklib/implementations/obograph/obograph_implementation.py index a1799c52a..b291a15a8 100644 --- a/src/oaklib/implementations/obograph/obograph_implementation.py +++ b/src/oaklib/implementations/obograph/obograph_implementation.py @@ -8,7 +8,6 @@ import sssom_schema as sssom from kgcl_schema.datamodel import kgcl from linkml_runtime.dumpers import json_dumper -from linkml_runtime.loaders import json_loader from oaklib.converters.obo_graph_to_rdf_owl_converter import SCOPE_MAP from oaklib.datamodels import obograph @@ -62,10 +61,12 @@ "owl": "xml", } + def clean_doc(gd: GraphDocument) -> None: for g in gd.graphs: g.nodes = [n for n in g.nodes if n.lbl] + @dataclass class OboGraphImplementation( ValidatorInterface, diff --git a/src/oaklib/implementations/uniprot/uniprot_implementation.py b/src/oaklib/implementations/uniprot/uniprot_implementation.py index b24fdd82a..fb5f9387f 100644 --- a/src/oaklib/implementations/uniprot/uniprot_implementation.py +++ b/src/oaklib/implementations/uniprot/uniprot_implementation.py @@ -159,6 +159,7 @@ def relationships( :return: """ from bioservices import UniProt + u = UniProt() exclude_predicates = [ "up:mappedCitation", diff --git a/src/oaklib/interfaces/association_provider_interface.py b/src/oaklib/interfaces/association_provider_interface.py index ff52cc20f..f26049378 100644 --- a/src/oaklib/interfaces/association_provider_interface.py +++ b/src/oaklib/interfaces/association_provider_interface.py @@ -2,7 +2,7 @@ from abc import ABC from collections import defaultdict from dataclasses import dataclass, field -from enum import unique, Enum +from enum import Enum, unique from typing import Any, Dict, Iterable, Iterator, List, Optional, Tuple from oaklib.datamodels.association import ( diff --git a/src/oaklib/interfaces/obograph_interface.py b/src/oaklib/interfaces/obograph_interface.py index 11d38ca86..8e04065e3 100644 --- a/src/oaklib/interfaces/obograph_interface.py +++ b/src/oaklib/interfaces/obograph_interface.py @@ -16,7 +16,7 @@ Node, SynonymPropertyValue, ) -from oaklib.datamodels.vocabulary import IS_A, OWL_CLASS +from oaklib.datamodels.vocabulary import IS_A from oaklib.interfaces.basic_ontology_interface import ( RELATIONSHIP, BasicOntologyInterface, @@ -235,7 +235,9 @@ def ancestor_graph( """ if method and method == GraphTraversalMethod.ENTAILMENT: ancs = self.ancestors( - start_curies, predicates=predicates, method=method, + start_curies, + predicates=predicates, + method=method, ) node_map = {} edges = [] diff --git a/src/oaklib/io/obograph_writer.py b/src/oaklib/io/obograph_writer.py index 1d2ebbb3d..b9b227b23 100644 --- a/src/oaklib/io/obograph_writer.py +++ b/src/oaklib/io/obograph_writer.py @@ -2,6 +2,7 @@ Utilities for writing out obo graphs """ + import logging from typing import Optional, TextIO, Union @@ -19,6 +20,7 @@ logger = logging.getLogger(__name__) + def write_graph_document( doc: GraphDocument, output: Optional[Union[str, TextIO]] = None, diff --git a/src/oaklib/query.py b/src/oaklib/query.py index 426d24586..f0be754fb 100644 --- a/src/oaklib/query.py +++ b/src/oaklib/query.py @@ -12,7 +12,6 @@ from typing import IO, Any, Dict, Iterable, Iterator, List, Optional, Tuple, Union import yaml - from pydantic import BaseModel from oaklib import BasicOntologyInterface @@ -37,7 +36,8 @@ RDF_TYPE, RDFS_DOMAIN, RDFS_RANGE, - REGULATES, SUBPROPERTY_OF, + REGULATES, + SUBPROPERTY_OF, ) from oaklib.interfaces import ( OboGraphInterface, @@ -1016,9 +1016,9 @@ def process_predicates_arg( # use HOP method for desc_p in impl.descendants( preds, - predicates=[SUBPROPERTY_OF], - method=GraphTraversalMethod.HOP, - reflexive=True, + predicates=[SUBPROPERTY_OF], + method=GraphTraversalMethod.HOP, + reflexive=True, ): preds_expanded.add(desc_p) return list(preds_expanded) @@ -1094,4 +1094,3 @@ def _shorthand_to_pred_curie(shorthand: str) -> Union[PRED_CURIE, List[PRED_CURI return [IS_A, RDF_TYPE, EQUIVALENT_CLASS, DISJOINT_WITH, RDFS_DOMAIN, RDFS_RANGE] else: return shorthand - diff --git a/src/oaklib/utilities/associations/association_queries.py b/src/oaklib/utilities/associations/association_queries.py index cec2e84f3..14a720bfd 100644 --- a/src/oaklib/utilities/associations/association_queries.py +++ b/src/oaklib/utilities/associations/association_queries.py @@ -1,19 +1,22 @@ import itertools import logging -from typing import List, Optional, Iterator +from typing import Iterator, List, Optional from oaklib.datamodels.association import Association -from oaklib.interfaces.association_provider_interface import AssociationProviderInterface, SubjectOrObjectRole +from oaklib.interfaces.association_provider_interface import ( + AssociationProviderInterface, + SubjectOrObjectRole, +) from oaklib.types import CURIE, PRED_CURIE def get_association_iterator( - impl: AssociationProviderInterface, - curies: List[CURIE], - terms_role: Optional[str] = None, - association_predicates: Optional[List[PRED_CURIE]] = None, - ontology_predicates: Optional[List[PRED_CURIE]] = None, - **kwargs, + impl: AssociationProviderInterface, + curies: List[CURIE], + terms_role: Optional[str] = None, + association_predicates: Optional[List[PRED_CURIE]] = None, + ontology_predicates: Optional[List[PRED_CURIE]] = None, + **kwargs, ) -> Iterator[Association]: """ Query associations for a list of curies. diff --git a/src/oaklib/utilities/obograph_utils.py b/src/oaklib/utilities/obograph_utils.py index c6ae8cddf..ba5a79eaa 100644 --- a/src/oaklib/utilities/obograph_utils.py +++ b/src/oaklib/utilities/obograph_utils.py @@ -24,7 +24,6 @@ import yaml from curies import Converter from linkml_runtime.dumpers import json_dumper -from linkml_runtime.loaders import json_loader from pydantic import BaseModel # https://stackoverflow.com/questions/6028000/how-to-read-a-static-file-from-inside-a-python-package @@ -67,6 +66,7 @@ def remove_unlabeled_nodes(g: Union[GraphDocument, Graph], rescue_connected_node else: g.nodes = [n for n in g.nodes if n.lbl is not None] + def load_obograph_document(path: Union[str, Path]) -> GraphDocument: """ Load an OBOGraph document from a file. From feba8d7937f28e98db4fc8438830890e494944e5 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 10 Feb 2025 18:02:25 -0800 Subject: [PATCH 3/3] format --- src/oaklib/implementations/uniprot/uniprot_implementation.py | 2 -- src/oaklib/utilities/obograph_utils.py | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/src/oaklib/implementations/uniprot/uniprot_implementation.py b/src/oaklib/implementations/uniprot/uniprot_implementation.py index fb5f9387f..d5616a606 100644 --- a/src/oaklib/implementations/uniprot/uniprot_implementation.py +++ b/src/oaklib/implementations/uniprot/uniprot_implementation.py @@ -158,9 +158,7 @@ def relationships( :param include_entailed: TODO :return: """ - from bioservices import UniProt - u = UniProt() exclude_predicates = [ "up:mappedCitation", "up:mappedAnnotation", diff --git a/src/oaklib/utilities/obograph_utils.py b/src/oaklib/utilities/obograph_utils.py index ba5a79eaa..62dfec27a 100644 --- a/src/oaklib/utilities/obograph_utils.py +++ b/src/oaklib/utilities/obograph_utils.py @@ -58,7 +58,7 @@ def graph_node_ids_from_subject_and_objects(g: Graph) -> List[CURIE]: def remove_unlabeled_nodes(g: Union[GraphDocument, Graph], rescue_connected_nodes=True) -> None: if isinstance(g, GraphDocument): for graph in g.graphs: - remove_unlabeled(graph, rescue_connected_nodes=rescue_connected_nodes) + remove_unlabeled_nodes(graph, rescue_connected_nodes=rescue_connected_nodes) else: if rescue_connected_nodes: rescued = graph_node_ids_from_subject_and_objects(g)