From 5dc1893384592aa3888ced58d5cee593095a2d57 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 11 Jul 2023 17:50:01 -0500 Subject: [PATCH 01/39] Using semsimian v0.1.17-rc2 that writes output directly rather than using oaklib --- src/oaklib/cli.py | 46 +++++++++++++------ .../semsimian/semsimian_implementation.py | 27 +++++++++++ 2 files changed, 58 insertions(+), 15 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 4bd7d14f6..109c64ffa 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2654,6 +2654,12 @@ def similarity_pair(terms, predicates, autolabel: bool, output: TextIO, output_t show_default=True, help="Score used for summarization", ) +@click.option( + "--quick/--no-quick", + default=False, + show_default=True, + help="If set, results will be generated by Rust.", +) @autolabel_option @output_type_option @click.argument("terms", nargs=-1) @@ -2663,6 +2669,7 @@ def similarity( set1_file, set2_file, autolabel: bool, + quick: bool, min_jaccard_similarity: Optional[float], min_ancestor_information_content: Optional[float], main_score_field, @@ -2752,21 +2759,30 @@ def similarity( else: set2it = query_terms_iterator(terms, impl) actual_predicates = _process_predicates_arg(predicates) - for sim in impl.all_by_all_pairwise_similarity( - set1it, - set2it, - predicates=actual_predicates, - min_jaccard_similarity=min_jaccard_similarity, - min_ancestor_information_content=min_ancestor_information_content, - ): - if autolabel: - # TODO: this can be made more efficient - sim.subject_label = impl.label(sim.subject_id) - sim.object_label = impl.label(sim.object_id) - sim.ancestor_label = impl.label(sim.ancestor_id) - writer.emit(sim) - writer.finish() - writer.file.close() + if quick: + impl.all_by_all_pairwise_similarity_quick( + set1it, + set2it, + predicates=actual_predicates, + min_jaccard_similarity=min_jaccard_similarity, + min_ancestor_information_content=min_ancestor_information_content, + ) + else: + for sim in impl.all_by_all_pairwise_similarity( + set1it, + set2it, + predicates=actual_predicates, + min_jaccard_similarity=min_jaccard_similarity, + min_ancestor_information_content=min_ancestor_information_content, + ): + if autolabel: + # TODO: this can be made more efficient + sim.subject_label = impl.label(sim.subject_id) + sim.object_label = impl.label(sim.object_id) + sim.ancestor_label = impl.label(sim.ancestor_id) + writer.emit(sim) + writer.finish() + writer.file.close() else: raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 93d7cf181..9b2231e39 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -165,3 +165,30 @@ def all_by_all_pairwise_similarity( sim.jaccard_similarity = 0 sim.ancestor_information_content = 0 yield sim + + def all_by_all_pairwise_similarity_quick( + self, + subjects: Iterable[CURIE], + objects: Iterable[CURIE], + predicates: List[PRED_CURIE] = None, + min_jaccard_similarity: Optional[float] = None, + min_ancestor_information_content: Optional[float] = None, + ) -> None: + """ + Compute similarity for all combinations of terms in subsets vs all terms in objects + + :param subjects: + :param objects: + :param predicates: + :return: + """ + objects = list(objects) + logging.info(f"Calculating all-by-all pairwise similarity for {len(objects)} objects") + self.semsimian.all_by_all_pairwise_similarity_quick( + subject_terms=set(subjects), + object_terms=set(objects), + minimum_jaccard_threshold=min_jaccard_similarity, + minimum_resnik_threshold=min_ancestor_information_content, + predicates=set(predicates) if predicates else None, + outfile="rust_output.tsv", + ) From f62e096a186baeaf7785baab26b5375cf873c709 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 12 Jul 2023 10:33:43 -0500 Subject: [PATCH 02/39] ~quick~ => --low-memory --- src/oaklib/cli.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 109c64ffa..fe9a68c37 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2655,7 +2655,7 @@ def similarity_pair(terms, predicates, autolabel: bool, output: TextIO, output_t help="Score used for summarization", ) @click.option( - "--quick/--no-quick", + "--low-memory/--no-low-memory", default=False, show_default=True, help="If set, results will be generated by Rust.", @@ -2669,7 +2669,7 @@ def similarity( set1_file, set2_file, autolabel: bool, - quick: bool, + low_memory: bool, min_jaccard_similarity: Optional[float], min_ancestor_information_content: Optional[float], main_score_field, @@ -2759,7 +2759,7 @@ def similarity( else: set2it = query_terms_iterator(terms, impl) actual_predicates = _process_predicates_arg(predicates) - if quick: + if low_memory: impl.all_by_all_pairwise_similarity_quick( set1it, set2it, From 514a44b2b5fbe6deff7a34a2868418d5b0a2cc77 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 12 Jul 2023 17:31:02 -0500 Subject: [PATCH 03/39] TODO added as comment --- src/oaklib/cli.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index fe9a68c37..5efd37bf7 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2767,6 +2767,7 @@ def similarity( min_jaccard_similarity=min_jaccard_similarity, min_ancestor_information_content=min_ancestor_information_content, ) + # TODO: Grab the outfile, add columns needed and run `fill-table`. else: for sim in impl.all_by_all_pairwise_similarity( set1it, From 15fbce3363f3f30234ee58ccab26a311ccc9f467 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 13 Jul 2023 17:36:51 -0500 Subject: [PATCH 04/39] passing outfile --- .../implementations/semsimian/semsimian_implementation.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 9b2231e39..f9ab0cfe7 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -173,6 +173,7 @@ def all_by_all_pairwise_similarity_quick( predicates: List[PRED_CURIE] = None, min_jaccard_similarity: Optional[float] = None, min_ancestor_information_content: Optional[float] = None, + outfile: str = None, ) -> None: """ Compute similarity for all combinations of terms in subsets vs all terms in objects @@ -190,5 +191,5 @@ def all_by_all_pairwise_similarity_quick( minimum_jaccard_threshold=min_jaccard_similarity, minimum_resnik_threshold=min_ancestor_information_content, predicates=set(predicates) if predicates else None, - outfile="rust_output.tsv", + outfile=outfile, ) From 32eba2e2219e6c7c99043efcde6d931d3724ae39 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 13 Jul 2023 17:37:24 -0500 Subject: [PATCH 05/39] get colun names from TermPairwiseSimilarity --- src/oaklib/cli.py | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 5efd37bf7..cbc809c4f 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -44,6 +44,7 @@ from linkml_runtime.utils.introspection import package_schemaview from prefixmaps.io.parser import load_multi_context from sssom.parsers import parse_sssom_table, to_mapping_set_document +from oaklib.datamodels.similarity import TermPairwiseSimilarity import oaklib.datamodels.taxon_constraints as tcdm from oaklib import datamodels @@ -2760,14 +2761,36 @@ def similarity( set2it = query_terms_iterator(terms, impl) actual_predicates = _process_predicates_arg(predicates) if low_memory: + term_pairwise_similarity_attributes = [attr for attr in vars(TermPairwiseSimilarity) if not attr.startswith("class_")] impl.all_by_all_pairwise_similarity_quick( set1it, set2it, predicates=actual_predicates, min_jaccard_similarity=min_jaccard_similarity, min_ancestor_information_content=min_ancestor_information_content, + outfile=output ) - # TODO: Grab the outfile, add columns needed and run `fill-table`. + + # Read the output file line by line and store the contents in a list + with open(output, "r") as f: + lines = f.readlines() + + # Add the column names to the first line of the list + columns_already_present = lines[0].split("\t") + columns_missing = [col for col in term_pairwise_similarity_attributes if col not in columns_already_present] + columns_missing_as_str = "\t".join(columns_missing) + "\n" + header = lines[0].strip() + columns_missing_as_str + lines[0] = header + + # Write the updated contents back to the output file + with open(output, "w") as file: + file.writelines(lines) + + if autolabel: + pass + # TODO: Run `fill-table`. + # fill_table() + else: for sim in impl.all_by_all_pairwise_similarity( set1it, From 25c588d35e8f81d71414b4589f3899a05e99d5c3 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 13 Jul 2023 17:37:58 -0500 Subject: [PATCH 06/39] formatted --- src/oaklib/cli.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index cbc809c4f..a04a10784 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -44,7 +44,6 @@ from linkml_runtime.utils.introspection import package_schemaview from prefixmaps.io.parser import load_multi_context from sssom.parsers import parse_sssom_table, to_mapping_set_document -from oaklib.datamodels.similarity import TermPairwiseSimilarity import oaklib.datamodels.taxon_constraints as tcdm from oaklib import datamodels @@ -62,6 +61,7 @@ ) from oaklib.datamodels.search import create_search_configuration from oaklib.datamodels.settings import Settings +from oaklib.datamodels.similarity import TermPairwiseSimilarity from oaklib.datamodels.summary_statistics_datamodel import ( GroupedStatistics, UngroupedStatistics, @@ -2761,23 +2761,29 @@ def similarity( set2it = query_terms_iterator(terms, impl) actual_predicates = _process_predicates_arg(predicates) if low_memory: - term_pairwise_similarity_attributes = [attr for attr in vars(TermPairwiseSimilarity) if not attr.startswith("class_")] + term_pairwise_similarity_attributes = [ + attr for attr in vars(TermPairwiseSimilarity) if not attr.startswith("class_") + ] impl.all_by_all_pairwise_similarity_quick( set1it, set2it, predicates=actual_predicates, min_jaccard_similarity=min_jaccard_similarity, min_ancestor_information_content=min_ancestor_information_content, - outfile=output + outfile=output, ) - + # Read the output file line by line and store the contents in a list with open(output, "r") as f: lines = f.readlines() # Add the column names to the first line of the list columns_already_present = lines[0].split("\t") - columns_missing = [col for col in term_pairwise_similarity_attributes if col not in columns_already_present] + columns_missing = [ + col + for col in term_pairwise_similarity_attributes + if col not in columns_already_present + ] columns_missing_as_str = "\t".join(columns_missing) + "\n" header = lines[0].strip() + columns_missing_as_str lines[0] = header From 4608fc224dc909c19eba35cdef3e5700c694bef5 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 13 Jul 2023 23:28:52 -0500 Subject: [PATCH 07/39] bug fix: all values must be a str to run `match` --- src/oaklib/utilities/table_filler.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/utilities/table_filler.py b/src/oaklib/utilities/table_filler.py index 175821fa4..070abe4aa 100644 --- a/src/oaklib/utilities/table_filler.py +++ b/src/oaklib/utilities/table_filler.py @@ -123,7 +123,7 @@ def parse_table(input_file: IO, delimiter="\t") -> List[ROW]: v = row[col] if v == "": row[col] = None - m = LIST_PATTERN.match(v) + m = LIST_PATTERN.match(str(v)) if m: row[col] = m.group(1).split("|") return rows From 288fcd51bb4eb578bb0977d17268287b293cac6a Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 13 Jul 2023 23:29:22 -0500 Subject: [PATCH 08/39] improved column generation from class attr --- src/oaklib/cli.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index a04a10784..f49978c9e 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2762,7 +2762,9 @@ def similarity( actual_predicates = _process_predicates_arg(predicates) if low_memory: term_pairwise_similarity_attributes = [ - attr for attr in vars(TermPairwiseSimilarity) if not attr.startswith("class_") + attr + for attr in vars(TermPairwiseSimilarity) + if not any(attr.startswith(s) for s in ["class_", "__"]) ] impl.all_by_all_pairwise_similarity_quick( set1it, @@ -2778,14 +2780,14 @@ def similarity( lines = f.readlines() # Add the column names to the first line of the list - columns_already_present = lines[0].split("\t") + columns_already_present = lines[0].strip().split("\t") columns_missing = [ col for col in term_pairwise_similarity_attributes if col not in columns_already_present ] columns_missing_as_str = "\t".join(columns_missing) + "\n" - header = lines[0].strip() + columns_missing_as_str + header = lines[0].strip() + "\t" + columns_missing_as_str lines[0] = header # Write the updated contents back to the output file @@ -2794,8 +2796,6 @@ def similarity( if autolabel: pass - # TODO: Run `fill-table`. - # fill_table() else: for sim in impl.all_by_all_pairwise_similarity( From 64fea01fffbbea079029c2c57eaf309a90eaa7ff Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 14 Jul 2023 09:25:41 -0500 Subject: [PATCH 09/39] fill-table used via subversion --- src/oaklib/cli.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index f49978c9e..b81d6ce6b 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -12,6 +12,7 @@ import os import re import secrets +import subprocess import sys from collections import defaultdict from enum import Enum, unique @@ -2795,7 +2796,13 @@ def similarity( file.writelines(lines) if autolabel: - pass + new_output = output.replace(".tsv", "_filled.tsv") + command = f"runoak -i {impl.resource.slug} fill-table {output} -o {new_output} --allow-missing" + try: + subprocess.run(command, shell=True, check=True) + print(f"{output} filled successfully by oaklib and results are in {new_output}.") + except subprocess.CalledProcessError as e: + print(f"Command execution failed with error code {e.returncode}.") else: for sim in impl.all_by_all_pairwise_similarity( From 13660174c88edb4d90aca50624f1740114bc64ac Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 14 Jul 2023 09:34:04 -0500 Subject: [PATCH 10/39] formatted --- src/oaklib/cli.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index b81d6ce6b..cace6e1cb 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2799,11 +2799,12 @@ def similarity( new_output = output.replace(".tsv", "_filled.tsv") command = f"runoak -i {impl.resource.slug} fill-table {output} -o {new_output} --allow-missing" try: - subprocess.run(command, shell=True, check=True) - print(f"{output} filled successfully by oaklib and results are in {new_output}.") + subprocess.run(command, shell=True, check=True) # noqa + print( + f"{output} filled successfully by oaklib and results are in {new_output}." + ) except subprocess.CalledProcessError as e: print(f"Command execution failed with error code {e.returncode}.") - else: for sim in impl.all_by_all_pairwise_similarity( set1it, From 724b91efc52d56dd89edb634a7917677df25b783 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 14 Jul 2023 10:37:58 -0500 Subject: [PATCH 11/39] added gilda dependency to tox --- tox.ini | 1 + 1 file changed, 1 insertion(+) diff --git a/tox.ini b/tox.ini index 21fb554b1..0af606fe0 100644 --- a/tox.ini +++ b/tox.ini @@ -25,6 +25,7 @@ deps = pytest coverage semsimian + gilda [testenv:lint] deps = From 29b9cd8a51f32681d5082227a44616470a5511ed Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 14 Jul 2023 10:41:23 -0500 Subject: [PATCH 12/39] poetry update uses latest semsimian rc3 version --- poetry.lock | 1108 ++++++++++++++++++++++++++---------------------- pyproject.toml | 2 +- 2 files changed, 605 insertions(+), 505 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8e72ce16b..e17e8cb6f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -72,13 +72,13 @@ files = [ [[package]] name = "anyio" -version = "3.7.0" +version = "3.7.1" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.7" files = [ - {file = "anyio-3.7.0-py3-none-any.whl", hash = "sha256:eddca883c4175f14df8aedce21054bfca3adb70ffe76a9f607aef9d7fa2ea7f0"}, - {file = "anyio-3.7.0.tar.gz", hash = "sha256:275d9973793619a5374e1c89a4f4ad3f4b0a5510a2b5b939444bee8f4c4d37ce"}, + {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"}, + {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"}, ] [package.dependencies] @@ -87,7 +87,7 @@ idna = ">=2.8" sniffio = ">=1.1" [package.extras] -doc = ["Sphinx (>=6.1.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme", "sphinxcontrib-jquery"] +doc = ["Sphinx", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery"] test = ["anyio[trio]", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] trio = ["trio (<0.22)"] @@ -271,20 +271,20 @@ lxml = ["lxml"] [[package]] name = "bioregistry" -version = "0.9.61" +version = "0.9.75" description = "Integrated registry of biological databases and nomenclatures" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "bioregistry-0.9.61-py3-none-any.whl", hash = "sha256:311042e7ab17b02b2e0789de25d0a9d254a9748442d6b66232a1bb23e6bd4d4b"}, - {file = "bioregistry-0.9.61.tar.gz", hash = "sha256:736c4ebbc72c38cda90bd5fbbce369befc4809364375a3ac2cbdaac82456c184"}, + {file = "bioregistry-0.9.75-py3-none-any.whl", hash = "sha256:cf74e21c9c11dc19fa65b59da70d60bdcea259dc37a785f834eaa4f3c4eb4b1f"}, + {file = "bioregistry-0.9.75.tar.gz", hash = "sha256:46ac79e9683d36c66f3114692d903c3e24a1105f4a18b764faf6af2f2ed71d88"}, ] [package.dependencies] click = "*" -curies = ">=0.5.1" +curies = ">=0.5.6" more-click = ">=0.1.2" -pydantic = "*" +pydantic = "<2.0" pystow = ">=0.1.13" requests = "*" tqdm = "*" @@ -319,17 +319,17 @@ css = ["tinycss2 (>=1.1.0,<1.2)"] [[package]] name = "boto3" -version = "1.26.165" +version = "1.28.3" description = "The AWS SDK for Python" optional = true python-versions = ">= 3.7" files = [ - {file = "boto3-1.26.165-py3-none-any.whl", hash = "sha256:fa85b67147c8dc99b6e7c699fc086103f958f9677db934f70659e6e6a72a818c"}, - 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"sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"}, + {file = "zipp-3.16.1-py3-none-any.whl", hash = "sha256:0b37c326d826d5ca35f2b9685cd750292740774ef16190008b00a0227c256fe0"}, + {file = "zipp-3.16.1.tar.gz", hash = "sha256:857b158da2cbf427b376da1c24fd11faecbac5a4ac7523c3607f8a01f94c2ec0"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [extras] docs = [] @@ -5451,4 +5551,4 @@ seaborn = [] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0.0" -content-hash = "1b7e1e6e0784460b21cf46cddd1ee4906e1ee9b63f413a3a5ff75888b9b8b66e" +content-hash = "be7b29fa9fa7c64d9f3e033b4e3b534a85542f7f1f222208652c8e34210b6b28" diff --git a/pyproject.toml b/pyproject.toml index fb3a53ef0..3c80064d7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,7 +37,7 @@ pysolr = "^3.9.0" eutils = ">=0.6.0" requests-cache = "^1.0.1" click = "*" -semsimian = "^0.1.16" +semsimian = "0.1.17rc3" urllib3 = {version = "< 2", optional = true} [tool.poetry.dev-dependencies] From 6a4ca3ccfec61b939f41a86185e40332aa759748 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 14 Jul 2023 19:43:37 -0500 Subject: [PATCH 13/39] added cosine score to similarity model --- src/oaklib/datamodels/similarity.owl.ttl | 121 +++++++++++------------ src/oaklib/datamodels/similarity.py | 12 ++- src/oaklib/datamodels/similarity.yaml | 4 + 3 files changed, 74 insertions(+), 63 deletions(-) diff --git a/src/oaklib/datamodels/similarity.owl.ttl b/src/oaklib/datamodels/similarity.owl.ttl index 1684247f7..387a6353c 100644 --- a/src/oaklib/datamodels/similarity.owl.ttl +++ b/src/oaklib/datamodels/similarity.owl.ttl @@ -1,5 +1,4 @@ @prefix IAO: . -@prefix dcterms: . @prefix linkml: . @prefix owl: . @prefix rdfs: . @@ -8,48 +7,41 @@ @prefix sssom: . @prefix xsd: . -linkml:similarity.owl.ttl a owl:Ontology ; - rdfs:label "similarity" ; - IAO:0000700 sim:BestMatch, - sim:PairwiseSimilarity, - sim:TermInfo ; - dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - dcterms:title "Semantic Similarity" ; - linkml:generation_date "2022-12-18T15:11:17" ; - linkml:metamodel_version "1.7.0" ; - linkml:source_file "similarity.yaml" ; - linkml:source_file_date "2022-10-26T21:40:09" ; - linkml:source_file_size 5512 . - sim:TermSetPairwiseSimilarity a owl:Class ; rdfs:label "TermSetPairwiseSimilarity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onDataRange xsd:float ; - owl:onProperty sim:average_score ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:anyURI ; + owl:onProperty sim:metric ], [ a owl:Restriction ; owl:allValuesFrom sim:BestMatch ; owl:onProperty sim:object_best_matches ], - [ a owl:Restriction ; - owl:onDataRange xsd:float ; - owl:onProperty sim:best_score ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom sim:TermInfo ; - owl:onProperty sim:object_termset ], + owl:onProperty sim:subject_termset ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:anyURI ; - owl:onProperty sim:metric ], + owl:onDataRange xsd:float ; + owl:onProperty sim:average_score ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:float ; + owl:onProperty sim:best_score ], [ a owl:Restriction ; owl:allValuesFrom sim:TermInfo ; - owl:onProperty sim:subject_termset ], + owl:onProperty sim:object_termset ], [ a owl:Restriction ; owl:allValuesFrom sim:BestMatch ; owl:onProperty sim:subject_best_matches ], sim:PairwiseSimilarity ; skos:definition "A simple pairwise similarity between two sets of concepts/terms" . +sim:cosine_similarity a owl:DatatypeProperty ; + rdfs:label "cosine_similarity" ; + rdfs:range xsd:float ; + rdfs:subPropertyOf sim:score ; + skos:definition "the dot product of two node embeddings divided by the product of their lengths" . + sim:intersection_count a owl:DatatypeProperty ; rdfs:label "intersection_count" ; rdfs:range xsd:integer ; @@ -75,6 +67,14 @@ sim:union_count a owl:DatatypeProperty ; rdfs:range xsd:integer ; rdfs:subPropertyOf sim:score . + a owl:Ontology ; + rdfs:label "similarity" ; + IAO:0000700 sim:BestMatch, + sim:PairwiseSimilarity, + sim:TermInfo ; + linkml:id "https://w3id.org/oak/similarity" ; + linkml:imports "linkml:types" . + sim:ancestor_id a owl:DatatypeProperty ; rdfs:label "ancestor_id" ; rdfs:range xsd:anyURI ; @@ -120,8 +120,7 @@ sim:jaccard_similarity a owl:DatatypeProperty ; sim:match_source a owl:DatatypeProperty ; rdfs:label "match_source" ; - rdfs:range xsd:string ; - skos:note "note that the match_source is either the subject or the object" . + rdfs:range xsd:string . sim:match_source_label a owl:DatatypeProperty ; rdfs:label "match_source_label" ; @@ -232,11 +231,11 @@ sim:TermPairwiseSimilarity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; - owl:onProperty sssom:subject_source ], + owl:onProperty sssom:subject_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:float ; - owl:onProperty sim:dice_similarity ], + owl:onDataRange xsd:string ; + owl:onProperty sssom:object_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; @@ -244,39 +243,27 @@ sim:TermPairwiseSimilarity a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; - owl:onProperty sssom:subject_label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:float ; - owl:onProperty sim:phenodigm_score ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:float ; - owl:onProperty sim:jaccard_similarity ], + owl:onProperty sim:ancestor_source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:float ; - owl:onProperty sim:object_information_content ], + owl:onDataRange xsd:string ; + owl:onProperty sim:ancestor_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:float ; - owl:onProperty sim:ancestor_information_content ], + owl:onDataRange xsd:string ; + owl:onProperty sssom:subject_source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:anyURI ; owl:onProperty sim:ancestor_id ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:string ; - owl:onProperty sim:ancestor_source ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:string ; - owl:onProperty sim:ancestor_label ], + owl:onDataRange xsd:float ; + owl:onProperty sim:jaccard_similarity ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:string ; - owl:onProperty sssom:object_label ], + owl:onDataRange xsd:float ; + owl:onProperty sim:dice_similarity ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:anyURI ; @@ -285,10 +272,22 @@ sim:TermPairwiseSimilarity a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:float ; owl:onProperty sim:subject_information_content ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:float ; + owl:onProperty sim:ancestor_information_content ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:float ; + owl:onProperty sim:object_information_content ], [ a owl:Restriction ; owl:onDataRange xsd:anyURI ; owl:onProperty sssom:subject_id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:float ; + owl:onProperty sim:phenodigm_score ], sim:PairwiseSimilarity ; skos:definition "A simple pairwise similarity between two atomic concepts/terms" . @@ -306,13 +305,17 @@ sim:information_content a owl:DatatypeProperty ; sim:BestMatch a owl:Class ; rdfs:label "BestMatch" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:string ; + owl:onProperty sim:match_source_label ], + [ a owl:Restriction ; owl:onDataRange xsd:string ; owl:onProperty sim:match_source ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; - owl:onProperty sim:match_source_label ], + owl:onProperty sim:match_target_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; @@ -321,22 +324,18 @@ sim:BestMatch a owl:Class ; owl:onDataRange xsd:float ; owl:onProperty sim:score ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass sim:TermPairwiseSimilarity ; - owl:onProperty sim:similarity ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; owl:onProperty sim:match_target ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:string ; - owl:onProperty sim:match_target_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:anyURI ; - owl:onProperty sim:match_subsumer ] . + owl:onProperty sim:match_subsumer ], + [ a owl:Restriction ; + owl:onClass sim:TermPairwiseSimilarity ; + owl:onProperty sim:similarity ; + owl:qualifiedCardinality 1 ] . sim:TermInfo a owl:Class ; rdfs:label "TermInfo" ; diff --git a/src/oaklib/datamodels/similarity.py b/src/oaklib/datamodels/similarity.py index 1ec039278..a8273142d 100644 --- a/src/oaklib/datamodels/similarity.py +++ b/src/oaklib/datamodels/similarity.py @@ -1,5 +1,5 @@ # Auto generated from similarity.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-04-10T09:38:53 +# Generation date: 2023-07-14T19:42:43 # Schema: similarity # # id: https://w3id.org/oak/similarity @@ -8,7 +8,6 @@ import dataclasses import re -import sys from dataclasses import dataclass from typing import Any, ClassVar, Dict, List, Optional, Union @@ -505,6 +504,15 @@ class slots: range=Optional[Union[float, NonNegativeFloat]], ) +slots.cosine_similarity = Slot( + uri=SIM.cosine_similarity, + name="cosine_similarity", + curie=SIM.curie("cosine_similarity"), + model_uri=SIM.cosine_similarity, + domain=None, + range=Optional[float], +) + slots.overlap_coefficient = Slot( uri=SIM.overlap_coefficient, name="overlap_coefficient", diff --git a/src/oaklib/datamodels/similarity.yaml b/src/oaklib/datamodels/similarity.yaml index 005c61ea2..a0c820786 100644 --- a/src/oaklib/datamodels/similarity.yaml +++ b/src/oaklib/datamodels/similarity.yaml @@ -181,6 +181,10 @@ slots: range: NonNegativeFloat description: the geometric mean of the jaccard similarity and the information content equals_expression: sqrt({jaccard_similarity} * {information_content}) + cosine_similarity: + is_a: score + range: float + description: the dot product of two node embeddings divided by the product of their lengths overlap_coefficient: is_a: score range: ZeroToOne From e27ad72b941281f353a2f2679ebef9d1d8c68321 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 14 Jul 2023 19:45:21 -0500 Subject: [PATCH 14/39] added cosine score to similarity model --- src/oaklib/datamodels/similarity.owl.ttl | 102 ++++++++++++----------- src/oaklib/datamodels/similarity.py | 6 +- src/oaklib/datamodels/similarity.yaml | 1 + 3 files changed, 59 insertions(+), 50 deletions(-) diff --git a/src/oaklib/datamodels/similarity.owl.ttl b/src/oaklib/datamodels/similarity.owl.ttl index 387a6353c..8a959f446 100644 --- a/src/oaklib/datamodels/similarity.owl.ttl +++ b/src/oaklib/datamodels/similarity.owl.ttl @@ -10,6 +10,16 @@ sim:TermSetPairwiseSimilarity a owl:Class ; rdfs:label "TermSetPairwiseSimilarity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom sim:TermInfo ; + owl:onProperty sim:object_termset ], + [ a owl:Restriction ; + owl:allValuesFrom sim:BestMatch ; + owl:onProperty sim:subject_best_matches ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:float ; + owl:onProperty sim:average_score ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:anyURI ; owl:onProperty sim:metric ], @@ -19,29 +29,13 @@ sim:TermSetPairwiseSimilarity a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom sim:TermInfo ; owl:onProperty sim:subject_termset ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:float ; - owl:onProperty sim:average_score ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:float ; owl:onProperty sim:best_score ], - [ a owl:Restriction ; - owl:allValuesFrom sim:TermInfo ; - owl:onProperty sim:object_termset ], - [ a owl:Restriction ; - owl:allValuesFrom sim:BestMatch ; - owl:onProperty sim:subject_best_matches ], sim:PairwiseSimilarity ; skos:definition "A simple pairwise similarity between two sets of concepts/terms" . -sim:cosine_similarity a owl:DatatypeProperty ; - rdfs:label "cosine_similarity" ; - rdfs:range xsd:float ; - rdfs:subPropertyOf sim:score ; - skos:definition "the dot product of two node embeddings divided by the product of their lengths" . - sim:intersection_count a owl:DatatypeProperty ; rdfs:label "intersection_count" ; rdfs:range xsd:integer ; @@ -103,6 +97,12 @@ sim:best_score a owl:DatatypeProperty ; rdfs:label "best_score" ; rdfs:range xsd:float . +sim:cosine_similarity a owl:DatatypeProperty ; + rdfs:label "cosine_similarity" ; + rdfs:range xsd:float ; + rdfs:subPropertyOf sim:score ; + skos:definition "the dot product of two node embeddings divided by the product of their lengths" . + sim:dice_similarity a owl:DatatypeProperty ; rdfs:label "dice_similarity" ; rdfs:range xsd:float ; @@ -230,12 +230,8 @@ sim:TermPairwiseSimilarity a owl:Class ; rdfs:label "TermPairwiseSimilarity" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:string ; - owl:onProperty sssom:subject_label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:string ; - owl:onProperty sssom:object_label ], + owl:onDataRange xsd:float ; + owl:onProperty sim:ancestor_information_content ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; @@ -244,6 +240,18 @@ sim:TermPairwiseSimilarity a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; owl:onProperty sim:ancestor_source ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:float ; + owl:onProperty sim:phenodigm_score ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:float ; + owl:onProperty sim:subject_information_content ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:anyURI ; + owl:onProperty sim:ancestor_id ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; @@ -255,39 +263,35 @@ sim:TermPairwiseSimilarity a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:anyURI ; - owl:onProperty sim:ancestor_id ], + owl:onProperty sssom:object_id ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:float ; - owl:onProperty sim:jaccard_similarity ], + owl:onProperty sim:object_information_content ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:float ; - owl:onProperty sim:dice_similarity ], + owl:onProperty sim:cosine_similarity ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:anyURI ; - owl:onProperty sssom:object_id ], + owl:onDataRange xsd:string ; + owl:onProperty sssom:object_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:float ; - owl:onProperty sim:subject_information_content ], + owl:onProperty sim:dice_similarity ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:float ; - owl:onProperty sim:ancestor_information_content ], + owl:onProperty sim:jaccard_similarity ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:float ; - owl:onProperty sim:object_information_content ], + owl:onDataRange xsd:string ; + owl:onProperty sssom:subject_label ], [ a owl:Restriction ; owl:onDataRange xsd:anyURI ; owl:onProperty sssom:subject_id ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:float ; - owl:onProperty sim:phenodigm_score ], sim:PairwiseSimilarity ; skos:definition "A simple pairwise similarity between two atomic concepts/terms" . @@ -305,21 +309,17 @@ sim:information_content a owl:DatatypeProperty ; sim:BestMatch a owl:Class ; rdfs:label "BestMatch" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onDataRange xsd:string ; - owl:onProperty sim:match_source_label ], - [ a owl:Restriction ; - owl:onDataRange xsd:string ; - owl:onProperty sim:match_source ; + owl:onClass sim:TermPairwiseSimilarity ; + owl:onProperty sim:similarity ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; - owl:onProperty sim:match_target_label ], + owl:onProperty sim:match_subsumer_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; - owl:onProperty sim:match_subsumer_label ], + owl:onProperty sim:match_target_label ], [ a owl:Restriction ; owl:onDataRange xsd:float ; owl:onProperty sim:score ; @@ -333,20 +333,24 @@ sim:BestMatch a owl:Class ; owl:onDataRange xsd:anyURI ; owl:onProperty sim:match_subsumer ], [ a owl:Restriction ; - owl:onClass sim:TermPairwiseSimilarity ; - owl:onProperty sim:similarity ; + owl:maxQualifiedCardinality 1 ; + owl:onDataRange xsd:string ; + owl:onProperty sim:match_source_label ], + [ a owl:Restriction ; + owl:onDataRange xsd:string ; + owl:onProperty sim:match_source ; owl:qualifiedCardinality 1 ] . sim:TermInfo a owl:Class ; rdfs:label "TermInfo" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; - owl:onProperty sim:id ; - owl:qualifiedCardinality 1 ], + owl:onProperty rdfs:label ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onDataRange xsd:string ; - owl:onProperty rdfs:label ] . + owl:onProperty sim:id ; + owl:qualifiedCardinality 1 ] . sim:score a owl:DatatypeProperty . diff --git a/src/oaklib/datamodels/similarity.py b/src/oaklib/datamodels/similarity.py index a8273142d..d54d414be 100644 --- a/src/oaklib/datamodels/similarity.py +++ b/src/oaklib/datamodels/similarity.py @@ -1,5 +1,5 @@ # Auto generated from similarity.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-07-14T19:42:43 +# Generation date: 2023-07-14T19:44:47 # Schema: similarity # # id: https://w3id.org/oak/similarity @@ -133,6 +133,7 @@ class TermPairwiseSimilarity(PairwiseSimilarity): subject_information_content: Optional[Union[float, NegativeLogValue]] = None ancestor_information_content: Optional[Union[float, NegativeLogValue]] = None jaccard_similarity: Optional[Union[float, ZeroToOne]] = None + cosine_similarity: Optional[float] = None dice_similarity: Optional[Union[float, ZeroToOne]] = None phenodigm_score: Optional[Union[float, NonNegativeFloat]] = None @@ -186,6 +187,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): ): self.jaccard_similarity = ZeroToOne(self.jaccard_similarity) + if self.cosine_similarity is not None and not isinstance(self.cosine_similarity, float): + self.cosine_similarity = float(self.cosine_similarity) + if self.dice_similarity is not None and not isinstance(self.dice_similarity, ZeroToOne): self.dice_similarity = ZeroToOne(self.dice_similarity) diff --git a/src/oaklib/datamodels/similarity.yaml b/src/oaklib/datamodels/similarity.yaml index a0c820786..1cddeb190 100644 --- a/src/oaklib/datamodels/similarity.yaml +++ b/src/oaklib/datamodels/similarity.yaml @@ -60,6 +60,7 @@ classes: - subject_information_content - ancestor_information_content - jaccard_similarity + - cosine_similarity - dice_similarity - phenodigm_score From d97b3b747a4f589842075aa6425e4c1ad5a115fe Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 14 Jul 2023 20:05:52 -0500 Subject: [PATCH 15/39] bumped semsimian version --- poetry.lock | 107 +++++++++++++++++++++++++++++-------------------- pyproject.toml | 2 +- 2 files changed, 64 insertions(+), 45 deletions(-) diff --git a/poetry.lock b/poetry.lock index e17e8cb6f..b485174f0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2230,13 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oaklib.datamodels.text_annotator import TextAnnotationConfiguration from oaklib.datamodels.validation_datamodel import ValidationConfiguration from oaklib.datamodels.vocabulary import ( + DEFAULT_SIMILARITY_MAP_FILE_BY_SEMSIMIAN, DEVELOPS_FROM, EQUIVALENT_CLASS, HAS_OBO_NAMESPACE, @@ -2649,6 +2650,11 @@ def similarity_pair(terms, predicates, autolabel: bool, output: TextIO, output_t type=float, help="Minimum value for information content", ) +@click.option( + "--embeddings-file", + type=click.File(mode="r"), + help="file containing embeddings of all necessary nodes.", +) @click.option("-o", "--output", help="path to output") @click.option( "--main-score-field", @@ -2674,6 +2680,7 @@ def similarity( low_memory: bool, min_jaccard_similarity: Optional[float], min_ancestor_information_content: Optional[float], + embeddings_file: TextIO, main_score_field, output_type, output, @@ -2773,10 +2780,13 @@ def similarity( predicates=actual_predicates, min_jaccard_similarity=min_jaccard_similarity, min_ancestor_information_content=min_ancestor_information_content, + embeddings_file=embeddings_file, outfile=output, ) # Read the output file line by line and store the contents in a list + if output is None: + output = DEFAULT_SIMILARITY_MAP_FILE_BY_SEMSIMIAN with open(output, "r") as f: lines = f.readlines() diff --git a/src/oaklib/datamodels/vocabulary.py b/src/oaklib/datamodels/vocabulary.py index e21148a0c..4bdae7f6d 100644 --- a/src/oaklib/datamodels/vocabulary.py +++ b/src/oaklib/datamodels/vocabulary.py @@ -161,6 +161,8 @@ OWL_VERSION_INFO = "owl:versionInfo" OWL_VERSION_IRI = "owl:versionIRI" +DEFAULT_SIMILARITY_MAP_FILE_BY_SEMSIMIAN = "similarity_map.tsv" + class SEMAPV(Enum): """SEMAPV Enum containing different mapping_justification.""" diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index f9ab0cfe7..965f8ff11 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -173,6 +173,7 @@ def all_by_all_pairwise_similarity_quick( predicates: List[PRED_CURIE] = None, min_jaccard_similarity: Optional[float] = None, min_ancestor_information_content: Optional[float] = None, + embeddings_file: str = None, outfile: str = None, ) -> None: """ @@ -185,11 +186,13 @@ def all_by_all_pairwise_similarity_quick( """ objects = list(objects) logging.info(f"Calculating all-by-all pairwise similarity for {len(objects)} objects") + self.semsimian.all_by_all_pairwise_similarity_quick( subject_terms=set(subjects), object_terms=set(objects), minimum_jaccard_threshold=min_jaccard_similarity, minimum_resnik_threshold=min_ancestor_information_content, predicates=set(predicates) if predicates else None, + embeddings_file=embeddings_file.name, outfile=outfile, ) From f66f27b1b903b81ff0e060ac86542b9ba7d9c3ca Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 18 Jul 2023 14:25:00 -0500 Subject: [PATCH 17/39] Semsimian ojct creation required term_pairwise_similarity_attributes --- .../implementations/semsimian/semsimian_implementation.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 965f8ff11..2fe654a19 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -56,8 +56,13 @@ def __post_init__(self): mn = m if isinstance(m, str) else m.__name__ setattr(SemSimianImplementation, mn, methods[mn]) + term_pairwise_similarity_attributes = [ + attr + for attr in vars(TermPairwiseSimilarity) + if not any(attr.startswith(s) for s in ["class_", "__"]) + ] spo = [r for r in self.wrapped_adapter.relationships(include_entailed=True)] - self.semsimian = Semsimian(spo) + self.semsimian = Semsimian(spo, term_pairwise_similarity_attributes) def pairwise_similarity( self, From f3e5bd55cb96bf5fab6f1fa58ae7d39b664b868f Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 21 Jul 2023 13:10:55 -0500 Subject: [PATCH 18/39] Addresses #619 --- .../semsimian/semsimian_implementation.py | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 2fe654a19..62f59a37f 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -56,13 +56,15 @@ def __post_init__(self): mn = m if isinstance(m, str) else m.__name__ setattr(SemSimianImplementation, mn, methods[mn]) - term_pairwise_similarity_attributes = [ + self.term_pairwise_similarity_attributes = [ attr for attr in vars(TermPairwiseSimilarity) - if not any(attr.startswith(s) for s in ["class_", "__"]) + if not any(attr.startswith(s) for s in ["class_", "_"]) ] - spo = [r for r in self.wrapped_adapter.relationships(include_entailed=True)] - self.semsimian = Semsimian(spo, term_pairwise_similarity_attributes) + + def create_semsimian_object(self, predicates: List[PRED_CURIE] = None): + spo = [r for r in self.wrapped_adapter.relationships(include_entailed=True, predicates=predicates)] + self.semsimian = Semsimian(spo, self.term_pairwise_similarity_attributes) def pairwise_similarity( self, @@ -88,6 +90,7 @@ def pairwise_similarity( """ logging.debug(f"Calculating pairwise similarity for {subject} x {object} over {predicates}") + self.create_semsimian_object(predicates=predicates) jaccard_val = self.semsimian.jaccard_similarity(subject, object, set(predicates)) if math.isnan(jaccard_val): @@ -139,6 +142,7 @@ def all_by_all_pairwise_similarity( :param predicates: :return: """ + self.create_semsimian_object(predicates=predicates) objects = list(objects) logging.info(f"Calculating all-by-all pairwise similarity for {len(objects)} objects") all_results = self.semsimian.all_by_all_pairwise_similarity( @@ -189,6 +193,7 @@ def all_by_all_pairwise_similarity_quick( :param predicates: :return: """ + self.create_semsimian_object(predicates=predicates) objects = list(objects) logging.info(f"Calculating all-by-all pairwise similarity for {len(objects)} objects") @@ -198,6 +203,6 @@ def all_by_all_pairwise_similarity_quick( minimum_jaccard_threshold=min_jaccard_similarity, minimum_resnik_threshold=min_ancestor_information_content, predicates=set(predicates) if predicates else None, - embeddings_file=embeddings_file.name, + embeddings_file=embeddings_file.name if embeddings_file else None, outfile=outfile, ) From fa7f3fa37130c84dcb5e282ccec695f7161c428e Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 21 Jul 2023 14:57:23 -0500 Subject: [PATCH 19/39] poetry updated to latest version of semsimian --- poetry.lock | 777 ++++++++++++++++++++++++++----------------------- pyproject.toml | 2 +- 2 files changed, 417 insertions(+), 362 deletions(-) diff --git a/poetry.lock b/poetry.lock index b485174f0..add041096 100644 --- a/poetry.lock +++ b/poetry.lock @@ -200,6 +200,20 @@ six = "*" [package.extras] test = ["astroid", "pytest"] +[[package]] +name = "async-lru" +version = "2.0.3" +description = "Simple LRU cache for asyncio" +optional = false +python-versions = ">=3.8" +files = [ + {file = "async-lru-2.0.3.tar.gz", hash = "sha256:b714c9d1415fca4e264da72a9e2abc66880ce7430e03a973341f88ea4c0d4869"}, + {file = "async_lru-2.0.3-py3-none-any.whl", hash = "sha256:00c0a8899c20b9c88663a47732689ff98189c9fa08ad9f734d7722f934d250b1"}, +] + +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} + [[package]] name = "attrs" version = "23.1.0" @@ -271,13 +285,13 @@ lxml = ["lxml"] [[package]] name = "bioregistry" -version = "0.9.75" +version = "0.9.81" description = 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only. + + :param predicates: List of desired predicates, defaults to None. + """ + spo = [ + r + for r in self.wrapped_adapter.relationships( + include_entailed=True, predicates=predicates + ) + ] self.semsimian = Semsimian(spo, self.term_pairwise_similarity_attributes) def pairwise_similarity( From 65f0dbfc4a7172d84d86b23a55e3f1fe16022b8f Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 24 Jul 2023 22:16:36 -0500 Subject: [PATCH 21/39] poetry update --- poetry.lock | 352 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 177 insertions(+), 177 deletions(-) diff --git a/poetry.lock b/poetry.lock index add041096..04ed987ed 100644 --- a/poetry.lock +++ b/poetry.lock @@ -285,13 +285,13 @@ lxml = ["lxml"] [[package]] name = "bioregistry" -version = "0.9.81" +version = "0.9.84" description = "Integrated registry of biological databases and nomenclatures" optional = false python-versions = ">=3.8" files = [ - {file = 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Jul 2023 11:05:35 -0500 Subject: [PATCH 22/39] removed subprocess for autolabel --- src/oaklib/cli.py | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 832d1db40..670bf3676 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -12,7 +12,6 @@ import os import re import secrets -import subprocess import sys from collections import defaultdict from enum import Enum, unique @@ -2806,15 +2805,19 @@ def similarity( file.writelines(lines) if autolabel: - new_output = output.replace(".tsv", "_filled.tsv") - command = f"runoak -i {impl.resource.slug} fill-table {output} -o {new_output} --allow-missing" - try: - subprocess.run(command, shell=True, check=True) # noqa - print( - f"{output} filled successfully by oaklib and results are in {new_output}." - ) - except subprocess.CalledProcessError as e: - print(f"Command execution failed with error code {e.returncode}.") + logging.warning( + "SemsimianImplementation does not support labelling yet.\ + Please use oak's `fill-table` command on the output file." + ) + # new_output = output.replace(".tsv", "_filled.tsv") + # command = f"runoak -i {impl.resource.slug} fill-table {output} -o {new_output} --allow-missing" + # try: + # subprocess.run(command, shell=True, check=True) # noqa + # print( + # f"{output} filled successfully by oaklib and results are in {new_output}." + # ) + # except subprocess.CalledProcessError as e: + # print(f"Command execution failed with error code {e.returncode}.") else: for sim in impl.all_by_all_pairwise_similarity( set1it, From 5f711d95cddd342ea7c375d67e78f8a34899eaee Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 28 Jul 2023 11:28:00 -0500 Subject: [PATCH 23/39] switched --embeddings-file to more generic --term-vectors --- src/oaklib/cli.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 670bf3676..85e6ded08 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2650,9 +2650,9 @@ def similarity_pair(terms, predicates, autolabel: bool, output: TextIO, output_t help="Minimum value for information content", ) @click.option( - "--embeddings-file", + "--term-vectors", type=click.File(mode="r"), - help="file containing embeddings of all necessary nodes.", + help="file (tsv or parquet) containing embeddings (or other vectors) of all necessary nodes.", ) @click.option("-o", "--output", help="path to output") @click.option( @@ -2679,7 +2679,7 @@ def similarity( low_memory: bool, min_jaccard_similarity: Optional[float], min_ancestor_information_content: Optional[float], - embeddings_file: TextIO, + term_vectors: TextIO, main_score_field, output_type, output, @@ -2779,7 +2779,7 @@ def similarity( predicates=actual_predicates, min_jaccard_similarity=min_jaccard_similarity, min_ancestor_information_content=min_ancestor_information_content, - embeddings_file=embeddings_file, + embeddings_file=term_vectors, outfile=output, ) From c23d28a22b213fc8a1e7b954599b2a500ce9d937 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 28 Jul 2023 11:36:09 -0500 Subject: [PATCH 24/39] Added docs from --term-vectors --- src/oaklib/cli.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 85e6ded08..01ef4fb14 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2729,6 +2729,15 @@ def similarity( runoak -i hp.db similarity -p i .desc//p=i HP:0000118 @ .desc//p=i HP:0000118 + Term vectors: + Term vector files (or embedding files) can be provided via the --term-vectors parameter. + Example: + + runoak -i semsimian:sqlite:obo:bfo similarity -p i .all @ .all --low-memory --term-vectors bfo.tsv + + where `bfo.tsv` is an embeddings file with the first column being CURIEs of all terms + and n columns consisting of unsigned float values representing a n-dimensional matrix. + Python API: https://incatools.github.io/ontology-access-kit/interfaces/semantic-similarity From 54e7cfaa1b3f0ccc12cce9dcec665d93b395d2af Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 28 Jul 2023 11:59:26 -0500 Subject: [PATCH 25/39] Added config file and renamed create object function --- semsimian_config.yaml | 1 + src/oaklib/cli.py | 31 +++++++++++-------- src/oaklib/datamodels/vocabulary.py | 1 + .../semsimian/semsimian_implementation.py | 8 ++--- 4 files changed, 24 insertions(+), 17 deletions(-) create mode 100644 semsimian_config.yaml diff --git a/semsimian_config.yaml b/semsimian_config.yaml new file mode 100644 index 000000000..987a037d4 --- /dev/null +++ b/semsimian_config.yaml @@ -0,0 +1 @@ +low_memory: true \ No newline at end of file diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 01ef4fb14..1433a7bce 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -75,6 +75,7 @@ HAS_OBO_NAMESPACE, IS_A, IS_DEFINED_BY, + LOW_MEMORY_FLAG, OBSOLETION_RELATIONSHIP_PREDICATES, OWL_CLASS, OWL_OBJECT_PROPERTY, @@ -438,6 +439,13 @@ def clear_cli_settings(): help="shortcut for --group-by-property sh:prefix. Groups by the prefix of the CURIE", ) +config_file_option = click.option( + "-c", + "--config-file", + # type=click.File(mode="r"), + help="""Config file for additional params. Presently used by `fhirjson` and `similarity`.""", +) + def _process_predicates_arg( predicates_str: str, @@ -2366,11 +2374,7 @@ def descendants( @click.argument("terms", nargs=-1) @click.option("-o", "--output", help="Path to output file") @output_type_option -@click.option( - "-c", - "--config-file", - help="""Config file for additional params. Presently used by `fhirjson` only.""", -) +@config_file_option @click.option( "--enforce-canonical-ordering/--no-enforce-canonical-ordering", default=False, @@ -2661,12 +2665,7 @@ def similarity_pair(terms, predicates, autolabel: bool, output: TextIO, output_t show_default=True, help="Score used for summarization", ) -@click.option( - "--low-memory/--no-low-memory", - default=False, - show_default=True, - help="If set, results will be generated by Rust.", -) +@config_file_option @autolabel_option @output_type_option @click.argument("terms", nargs=-1) @@ -2676,13 +2675,13 @@ def similarity( set1_file, set2_file, autolabel: bool, - low_memory: bool, min_jaccard_similarity: Optional[float], min_ancestor_information_content: Optional[float], term_vectors: TextIO, main_score_field, output_type, output, + config_file: str = None, ): """ All by all similarity. @@ -2734,7 +2733,7 @@ def similarity( Example: runoak -i semsimian:sqlite:obo:bfo similarity -p i .all @ .all --low-memory --term-vectors bfo.tsv - + where `bfo.tsv` is an embeddings file with the first column being CURIEs of all terms and n columns consisting of unsigned float values representing a n-dimensional matrix. @@ -2756,6 +2755,12 @@ def similarity( if isinstance(impl, SemanticSimilarityInterface): set1it = None set2it = None + low_memory = True + if config_file: + with open(config_file) as file: + config_options = yaml.safe_load(file) + low_memory = config_options.get(LOW_MEMORY_FLAG, True) + if not (set1_file or set2_file): terms = list(terms) ix = terms.index("@") diff --git a/src/oaklib/datamodels/vocabulary.py b/src/oaklib/datamodels/vocabulary.py index 4bdae7f6d..c49335033 100644 --- a/src/oaklib/datamodels/vocabulary.py +++ b/src/oaklib/datamodels/vocabulary.py @@ -162,6 +162,7 @@ OWL_VERSION_IRI = "owl:versionIRI" DEFAULT_SIMILARITY_MAP_FILE_BY_SEMSIMIAN = "similarity_map.tsv" +LOW_MEMORY_FLAG = "low_memory" class SEMAPV(Enum): diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 99acf59b5..4bd5ab66d 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -62,7 +62,7 @@ def __post_init__(self): if not any(attr.startswith(s) for s in ["class_", "_"]) ] - def create_semsimian_object(self, predicates: List[PRED_CURIE] = None): + def create_term_pairwise_similarity_output_object(self, predicates: List[PRED_CURIE] = None): """Create a new Semsimian object (rust) with desired predicates only. :param predicates: List of desired predicates, defaults to None. @@ -99,7 +99,7 @@ def pairwise_similarity( """ logging.debug(f"Calculating pairwise similarity for {subject} x {object} over {predicates}") - self.create_semsimian_object(predicates=predicates) + self.create_term_pairwise_similarity_output_object(predicates=predicates) jaccard_val = self.semsimian.jaccard_similarity(subject, object, set(predicates)) if math.isnan(jaccard_val): @@ -151,7 +151,7 @@ def all_by_all_pairwise_similarity( :param predicates: :return: """ - self.create_semsimian_object(predicates=predicates) + self.create_term_pairwise_similarity_output_object(predicates=predicates) objects = list(objects) logging.info(f"Calculating all-by-all pairwise similarity for {len(objects)} objects") all_results = self.semsimian.all_by_all_pairwise_similarity( @@ -202,7 +202,7 @@ def all_by_all_pairwise_similarity_quick( :param predicates: :return: """ - self.create_semsimian_object(predicates=predicates) + self.create_term_pairwise_similarity_output_object(predicates=predicates) objects = list(objects) logging.info(f"Calculating all-by-all pairwise similarity for {len(objects)} objects") From bd2325e854584c4b79140d35830c3adcc6436a32 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 28 Jul 2023 12:01:45 -0500 Subject: [PATCH 26/39] Added docs --- .../implementations/semsimian/semsimian_implementation.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 4bd5ab66d..f33c2367c 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -63,7 +63,10 @@ def __post_init__(self): ] def create_term_pairwise_similarity_output_object(self, predicates: List[PRED_CURIE] = None): - """Create a new Semsimian object (rust) with desired predicates only. + """Create a new Semsimian object (in rust) with desired predicates only. + + This basically creates an object with attributes from TermPairwiseSimilarity class. + These are used as columns for the output file generated via `similarity`. :param predicates: List of desired predicates, defaults to None. """ From 7cc87ac098a084473e39958df6365e23724d84f6 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 28 Jul 2023 12:04:24 -0500 Subject: [PATCH 27/39] Added documentation --- src/oaklib/cli.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 1433a7bce..f72e0c87c 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2736,6 +2736,7 @@ def similarity( where `bfo.tsv` is an embeddings file with the first column being CURIEs of all terms and n columns consisting of unsigned float values representing a n-dimensional matrix. + This helps calculate the `cosine_similarity` column in the output. Python API: From 4219e5a38a253ea664d03bd59e74ac84756a942a Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 28 Jul 2023 14:19:15 -0500 Subject: [PATCH 28/39] formatted warning --- src/oaklib/cli.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index f72e0c87c..e7db01761 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2821,8 +2821,7 @@ def similarity( if autolabel: logging.warning( - "SemsimianImplementation does not support labelling yet.\ - Please use oak's `fill-table` command on the output file." + "SemsimianImplementation does not support labelling yet. Please use oak's `fill-table` command on the output file." # noqa ) # new_output = output.replace(".tsv", "_filled.tsv") # command = f"runoak -i {impl.resource.slug} fill-table {output} -o {new_output} --allow-missing" From 041e948fced141280ce7f70835c0960e6fb678d9 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 28 Jul 2023 14:43:40 -0500 Subject: [PATCH 29/39] --low-memory should be Flase by default. --- src/oaklib/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index e7db01761..6694a2995 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2756,7 +2756,7 @@ def similarity( if isinstance(impl, SemanticSimilarityInterface): set1it = None set2it = None - low_memory = True + low_memory = False if config_file: with open(config_file) as file: config_options = yaml.safe_load(file) From b2ec561d31f140d9473acd750244f479a18ec4ce Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 3 Aug 2023 16:08:16 -0500 Subject: [PATCH 30/39] typo fix --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 7e3b6ad85..21c5611c9 100644 --- a/Makefile +++ b/Makefile @@ -110,7 +110,7 @@ phenio-benchmarks: $(RUNOAK) -i sqlite:obo:hp descendants -p i HP:0000118 > $(HP_TERMS) $(RUNOAK) -i sqlite:obo:mp descendants -p i MP:0000001 > $(MP_TERMS) time python -m cProfile -o $(SEMSIMIAN_PHENIO_PROFILE) -s tottime $(RUNOAK) -i semsimian:sqlite:obo:phenio similarity -p i --set1-file $(HP_TERMS) --set2-file $(MP_TERMS) -O csv -o HP_vs_MP_semsimian.tsv - time python -m cProfile -o $(NON_SEMSIMIAN_PHENIO_PROFILE) -s tottime $(RUNOAK) -i sqlite:obo:phenio similarity -p i --set1-file $(HP_TERMS) --set2-file $(MP_TERMS) -O csv -o HP_vs_MP_semsimian.tsv + time python -m cProfile -o $(NON_SEMSIMIAN_PHENIO_PROFILE) -s tottime $(RUNOAK) -i sqlite:obo:phenio similarity -p i --set1-file $(HP_TERMS) --set2-file $(MP_TERMS) -O csv -o HP_vs_MP_oak.tsv phenio-profiles: python $(PROFILER_SCRIPT) $(SEMSIMIAN_PHENIO_PROFILE) From bca6c57b1e5a307383f0790af1a53ce9d48c78fd Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 3 Aug 2023 22:17:25 -0500 Subject: [PATCH 31/39] pass resource path to rust --- .../semsimian/semsimian_implementation.py | 32 ++++++++++++------- 1 file changed, 21 insertions(+), 11 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index f33c2367c..fad09bf99 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -9,6 +9,7 @@ from oaklib.datamodels.similarity import TermPairwiseSimilarity from oaklib.datamodels.vocabulary import OWL_THING +from oaklib.implementations.sqldb.sql_implementation import SqlImplementation from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface from oaklib.interfaces.obograph_interface import OboGraphInterface from oaklib.interfaces.search_interface import SearchInterface @@ -62,6 +63,11 @@ def __post_init__(self): if not any(attr.startswith(s) for s in ["class_", "_"]) ] + if isinstance(self.wrapped_adapter, SqlImplementation): + self.resource_path = str(self.wrapped_adapter.engine.url).lstrip("sqlite:") + else: + self.resource_path = str(self.wrapped_adapter.engine.url) + def create_term_pairwise_similarity_output_object(self, predicates: List[PRED_CURIE] = None): """Create a new Semsimian object (in rust) with desired predicates only. @@ -70,13 +76,19 @@ def create_term_pairwise_similarity_output_object(self, predicates: List[PRED_CU :param predicates: List of desired predicates, defaults to None. """ - spo = [ - r - for r in self.wrapped_adapter.relationships( - include_entailed=True, predicates=predicates - ) - ] - self.semsimian = Semsimian(spo, self.term_pairwise_similarity_attributes) + # spo = [ + # r + # for r in self.wrapped_adapter.relationships( + # include_entailed=True, predicates=predicates + # ) + # ] + # self.semsimian = Semsimian(spo, self.term_pairwise_similarity_attributes) + + self.semsimian: Semsimian = Semsimian( + resource_path=self.resource_path, + predicates=predicates, + term_pairwise_similarity_attributes=self.term_pairwise_similarity_attributes, + ) def pairwise_similarity( self, @@ -103,7 +115,7 @@ def pairwise_similarity( logging.debug(f"Calculating pairwise similarity for {subject} x {object} over {predicates}") self.create_term_pairwise_similarity_output_object(predicates=predicates) - jaccard_val = self.semsimian.jaccard_similarity(subject, object, set(predicates)) + jaccard_val = self.semsimian.jaccard_similarity(subject, object) if math.isnan(jaccard_val): return None @@ -112,7 +124,7 @@ def pairwise_similarity( return None _, ancestor_information_content_val = self.semsimian.resnik_similarity( - subject, object, set(predicates) + subject, object ) if math.isnan(ancestor_information_content_val): @@ -162,7 +174,6 @@ def all_by_all_pairwise_similarity( object_terms=set(objects), minimum_jaccard_threshold=min_jaccard_similarity, minimum_resnik_threshold=min_ancestor_information_content, - predicates=set(predicates) if predicates else None, ) logging.info("Post-processing results from semsimian") for term1_key, values in all_results.items(): @@ -214,7 +225,6 @@ def all_by_all_pairwise_similarity_quick( object_terms=set(objects), minimum_jaccard_threshold=min_jaccard_similarity, minimum_resnik_threshold=min_ancestor_information_content, - predicates=set(predicates) if predicates else None, embeddings_file=embeddings_file.name if embeddings_file else None, outfile=outfile, ) From 3c9a2497a00378556d22691e0fdeb1379ce65e28 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 3 Aug 2023 22:17:49 -0500 Subject: [PATCH 32/39] move semsimian config file --- semsimian_config.yaml => src/oaklib/conf/semsimian_config.yaml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename semsimian_config.yaml => src/oaklib/conf/semsimian_config.yaml (100%) diff --git a/semsimian_config.yaml b/src/oaklib/conf/semsimian_config.yaml similarity index 100% rename from semsimian_config.yaml rename to src/oaklib/conf/semsimian_config.yaml From 05b43da6ae4245ffc1577e2360fdd77a2a12db11 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 3 Aug 2023 22:21:29 -0500 Subject: [PATCH 33/39] Updated docstring --- src/oaklib/cli.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 6694a2995..d5f00df7b 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2732,12 +2732,17 @@ def similarity( Term vector files (or embedding files) can be provided via the --term-vectors parameter. Example: - runoak -i semsimian:sqlite:obo:bfo similarity -p i .all @ .all --low-memory --term-vectors bfo.tsv + runoak -i semsimian:sqlite:obo:bfo similarity -p i .all @ .all --term-vectors bfo.tsv where `bfo.tsv` is an embeddings file with the first column being CURIEs of all terms and n columns consisting of unsigned float values representing a n-dimensional matrix. This helps calculate the `cosine_similarity` column in the output. + Semsimian Config file: + If the `semsimian` implementation is used, a YAML file can be passed via --config. + For now the only param used is `low_memory:true` and an example YAML file is located + at conf/semsimian_config.yaml. + Python API: https://incatools.github.io/ontology-access-kit/interfaces/semantic-similarity From d0992fdd8e502ca2cab2a5588f2157fca3be3fff Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 3 Aug 2023 22:24:39 -0500 Subject: [PATCH 34/39] formatted --- .../implementations/semsimian/semsimian_implementation.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index fad09bf99..b9ba30567 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -123,9 +123,7 @@ def pairwise_similarity( if min_jaccard_similarity is not None and jaccard_val < min_jaccard_similarity: return None - _, ancestor_information_content_val = self.semsimian.resnik_similarity( - subject, object - ) + _, ancestor_information_content_val = self.semsimian.resnik_similarity(subject, object) if math.isnan(ancestor_information_content_val): return None From b31ae1dce2206677eee0bd75d4405431f7dbfba3 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 4 Aug 2023 11:11:44 -0500 Subject: [PATCH 35/39] updated poetry --- poetry.lock | 372 +++++++++++++++++++++++++++------------------------- 1 file changed, 194 insertions(+), 178 deletions(-) diff --git a/poetry.lock b/poetry.lock index 04ed987ed..6d46d3f7e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -202,13 +202,13 @@ test = ["astroid", "pytest"] [[package]] name = "async-lru" -version = "2.0.3" +version = "2.0.4" description = "Simple LRU cache for asyncio" optional = false python-versions = ">=3.8" files = [ - 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if col not in columns_already_present - ] - columns_missing_as_str = "\t".join(columns_missing) + "\n" - header = lines[0].strip() + "\t" + columns_missing_as_str - lines[0] = header - - # Write the updated contents back to the output file - with open(output, "w") as file: - file.writelines(lines) + # TODO: Check if this block is needed ################################# + # # Read the output file line by line and store the contents in a list + # if output is None: + # output = DEFAULT_SIMILARITY_MAP_FILE_BY_SEMSIMIAN + # with open(output, "r") as f: + # lines = f.readlines() + + # # Add the column names to the first line of the list + # columns_already_present = lines[0].strip().split("\t") + # columns_missing = [ + # col + # for col in term_pairwise_similarity_attributes + # if col not in columns_already_present + # ] + # columns_missing_as_str = "\t".join(columns_missing) + "\n" + # header = lines[0].strip() + "\t" + columns_missing_as_str + # lines[0] = header + + # # Write the updated contents back to the output file + # with open(output, "w") as file: + # file.writelines(lines) + # TODO: ########################################################################## if autolabel: logging.warning( From e9ca0729681fb8e2be6f39f37b2d624da75cf15a Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 4 Aug 2023 11:12:57 -0500 Subject: [PATCH 37/39] deleted commented codeblock --- src/oaklib/cli.py | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 2454b2bf3..c5a32545c 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2803,29 +2803,6 @@ def similarity( outfile=output, ) - # TODO: Check if this block is needed ################################# - # # Read the output file line by line and store the contents in a list - # if output is None: - # output = DEFAULT_SIMILARITY_MAP_FILE_BY_SEMSIMIAN - # with open(output, "r") as f: - # lines = f.readlines() - - # # Add the column names to the first line of the list - # columns_already_present = lines[0].strip().split("\t") - # columns_missing = [ - # col - # for col in term_pairwise_similarity_attributes - # if col not in columns_already_present - # ] - # columns_missing_as_str = "\t".join(columns_missing) + "\n" - # header = lines[0].strip() + "\t" + columns_missing_as_str - # lines[0] = header - - # # Write the updated contents back to the output file - # with open(output, "w") as file: - # file.writelines(lines) - # TODO: ########################################################################## - if autolabel: logging.warning( "SemsimianImplementation does not support labelling yet. Please use oak's `fill-table` command on the output file." # noqa From de0377bb5eea5772618b6942397e1ac701b734e7 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 4 Aug 2023 11:14:00 -0500 Subject: [PATCH 38/39] not needed since done by semsimianImplementation --- src/oaklib/cli.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index c5a32545c..7c49777fe 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2788,11 +2788,6 @@ def similarity( set2it = query_terms_iterator(terms, impl) actual_predicates = _process_predicates_arg(predicates) if low_memory: - term_pairwise_similarity_attributes = [ - attr - for attr in vars(TermPairwiseSimilarity) - if not any(attr.startswith(s) for s in ["class_", "__"]) - ] impl.all_by_all_pairwise_similarity_quick( set1it, set2it, From 8af2b7199c2b7cb5bc3198e0572e5dfe8cda5db7 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 7 Aug 2023 10:22:12 -0500 Subject: [PATCH 39/39] added code to support semsimian's termset similarity --- .../semsimian/semsimian_implementation.py | 59 ++++++++++++++++--- 1 file changed, 52 insertions(+), 7 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index b9ba30567..6ee785d1d 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -3,11 +3,14 @@ import logging import math from dataclasses import dataclass -from typing import ClassVar, Iterable, Iterator, List, Optional +from typing import ClassVar, Iterable, Iterator, List, Optional, TextIO from semsimian import Semsimian -from oaklib.datamodels.similarity import TermPairwiseSimilarity +from oaklib.datamodels.similarity import ( + TermPairwiseSimilarity, + TermSetPairwiseSimilarity, +) from oaklib.datamodels.vocabulary import OWL_THING from oaklib.implementations.sqldb.sql_implementation import SqlImplementation from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface @@ -63,12 +66,20 @@ def __post_init__(self): if not any(attr.startswith(s) for s in ["class_", "_"]) ] + self.termset_pairwise_similarity_attributes = [ + attr + for attr in vars(TermSetPairwiseSimilarity) + if not any(attr.startswith(s) for s in ["class_", "_"]) + ] + if isinstance(self.wrapped_adapter, SqlImplementation): self.resource_path = str(self.wrapped_adapter.engine.url).lstrip("sqlite:") else: self.resource_path = str(self.wrapped_adapter.engine.url) - def create_term_pairwise_similarity_output_object(self, predicates: List[PRED_CURIE] = None): + def create_pairwise_similarity_output_object( + self, predicates: List[PRED_CURIE] = None, attributes: List[str] = None + ): """Create a new Semsimian object (in rust) with desired predicates only. This basically creates an object with attributes from TermPairwiseSimilarity class. @@ -87,7 +98,7 @@ def create_term_pairwise_similarity_output_object(self, predicates: List[PRED_CU self.semsimian: Semsimian = Semsimian( resource_path=self.resource_path, predicates=predicates, - term_pairwise_similarity_attributes=self.term_pairwise_similarity_attributes, + pairwise_similarity_attributes=attributes, ) def pairwise_similarity( @@ -114,7 +125,7 @@ def pairwise_similarity( """ logging.debug(f"Calculating pairwise similarity for {subject} x {object} over {predicates}") - self.create_term_pairwise_similarity_output_object(predicates=predicates) + self.create_pairwise_similarity_output_object(predicates=predicates) jaccard_val = self.semsimian.jaccard_similarity(subject, object) if math.isnan(jaccard_val): @@ -164,7 +175,9 @@ def all_by_all_pairwise_similarity( :param predicates: :return: """ - self.create_term_pairwise_similarity_output_object(predicates=predicates) + self.create_pairwise_similarity_output_object( + predicates=predicates, attributes=self.term_pairwise_similarity_attributes + ) objects = list(objects) logging.info(f"Calculating all-by-all pairwise similarity for {len(objects)} objects") all_results = self.semsimian.all_by_all_pairwise_similarity( @@ -214,7 +227,9 @@ def all_by_all_pairwise_similarity_quick( :param predicates: :return: """ - self.create_term_pairwise_similarity_output_object(predicates=predicates) + self.create_pairwise_similarity_output_object( + predicates=predicates, attributes=self.term_pairwise_similarity_attributes + ) objects = list(objects) logging.info(f"Calculating all-by-all pairwise similarity for {len(objects)} objects") @@ -226,3 +241,33 @@ def all_by_all_pairwise_similarity_quick( embeddings_file=embeddings_file.name if embeddings_file else None, outfile=outfile, ) + + def termset_pairwise_similarity( + self, + subjects: List[CURIE], + objects: List[CURIE], + outfile: TextIO, + predicates: List[PRED_CURIE] = None, + labels=False, + ) -> TermSetPairwiseSimilarity: + self.create_pairwise_similarity_output_object( + predicates=predicates, attributes=self.termset_pairwise_similarity_attributes + ) + objects = list(objects) + logging.info(f"Calculating termset pairwise similarity for {len(objects)} objects") + semsimian_termset_pairwise_similarity_dict = self.semsimian.termset_pairwise_similarity( + subject_terms=subjects, object_terms=objects, outfile=outfile + ) + return TermSetPairwiseSimilarity( + subject_termset=semsimian_termset_pairwise_similarity_dict.get("subject_termset"), + object_termset=semsimian_termset_pairwise_similarity_dict.get("object_termset"), + subject_best_matches=semsimian_termset_pairwise_similarity_dict.get( + "subject_best_matches" + ), + object_best_matches=semsimian_termset_pairwise_similarity_dict.get( + "object_best_matches" + ), + average_score=semsimian_termset_pairwise_similarity_dict.get("average_score"), + best_score=semsimian_termset_pairwise_similarity_dict.get("best_score"), + metric=semsimian_termset_pairwise_similarity_dict.get("metric"), + )