diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 03cb4ce..5d3f055 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -10,7 +10,7 @@ jobs: - uses: actions/setup-python@v2 name: setup python with: - python-version: 3.8 + python-version: "3.10" - name: Install Dependencies run: | python -m pip install --upgrade pip @@ -18,14 +18,3 @@ jobs: pip install .[test] pip install types-PyYAML pip install types-requests - - name: run pytest - run: | - coverage erase - pytest --cov=kg_bioportal --cov-report xml:coverage.xml - coverage combine --append || true - coverage report - coverage xml - - name: run mypy - run: mypy --strict-optional kg_bioportal - - name: run yamllint - run: yamllint -d relaxed merge.yaml download.yaml diff --git a/README.md b/README.md index bf77c92..d0c5cf1 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,15 @@ # KG-Bioportal -[Bioportal](https://bioportal.bioontology.org/), as a Knowledge Graph. +[Bioportal](https://bioportal.bioontology.org/), as a set of knowledge graphs. ## Data Sources -In this graph pipeline, source data is primarily derived from [Bioportal-to-KGX](https://github.com/ncbo/BioPortal-to-KGX), starting from a 4store dump of the BioPortal ontologies. +Source data is derived from the Bioportal API (). ## Components -### Download - -The [download.yaml](download.yaml) contains all the URLs for source data. In this KG project, sources are pre-processed and this component is used for data transfer only. - -### Transform - -The [transform_utils](kg_bioportal/transform_utils) serve as a passthrough, allowing paths for sources to be stored. - -### Merge - -Implementation of the 'cat-merge' function from [cat-merge](https://github.com/monarch-initiative/cat-merge). +TBA ## Example -`python run.py catmerge --merge_all` +TBA diff --git a/download.yaml b/download.yaml deleted file mode 100644 index 7898969..0000000 --- a/download.yaml +++ /dev/null @@ -1,20 +0,0 @@ -# This file is a list of things to be downloaded using the command: -# run.py download ---- - -# **** Transformed BioPortal Ontologies **** -# Note: this file is not publicly accessible, -# so this link is just a reminder, not what -# is passed to the download function. -- - url: https://kg-hub.berkeleybop.io/frozen_incoming_data/bioportal_transformed/bioportal_transformed.tar.gz - local_name: bioportal_transformed.tar.gz - -# **** ROBOT **** - -- - url: https://github.com/ontodev/robot/releases/download/v1.8.3/robot.jar - local_name: robot.jar -- - url: https://raw.githubusercontent.com/ontodev/robot/master/bin/robot - local_name: robot diff --git a/kg_bioportal/__init__.py b/kg_bioportal/__init__.py deleted file mode 100644 index 2279f3f..0000000 --- a/kg_bioportal/__init__.py +++ /dev/null @@ -1,6 +0,0 @@ -from .download import download -from .transform import transform - -__all__ = [ - "download", "transform" -] \ No newline at end of file diff --git a/kg_bioportal/__version__.py b/kg_bioportal/__version__.py deleted file mode 100644 index 7ec6ad0..0000000 --- a/kg_bioportal/__version__.py +++ /dev/null @@ -1,2 +0,0 @@ -"""Current version of package kg_bioportal""" -__version__ = "1.0.0" diff --git a/kg_bioportal/download.py b/kg_bioportal/download.py deleted file mode 100644 index 652ac0a..0000000 --- a/kg_bioportal/download.py +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - - -from kghub_downloader.download_utils import download_from_yaml # type: ignore - - -def download(yaml_file: str, output_dir: str, snippet_only: bool, ignore_cache: bool = False) -> None: - """Downloads data files from list of URLs (default: download.yaml) into data directory (default: data/). - - Args: - yaml_file: A string pointing to the yaml file utilized to facilitate the downloading of data. - output_dir: A string pointing to the location to download data to. - snippet_only: Downloads only the first 5 kB of the source, for testing and file checks. - ignore_cache: Ignore cache and download files even if they exist [false] - - Returns: - None. - """ - - download_from_yaml(yaml_file=yaml_file, output_dir=output_dir, - snippet_only=snippet_only, - ignore_cache=ignore_cache) - - return None diff --git a/kg_bioportal/merge_utils/merge_kg.py b/kg_bioportal/merge_utils/merge_kg.py deleted file mode 100644 index 5ab4713..0000000 --- a/kg_bioportal/merge_utils/merge_kg.py +++ /dev/null @@ -1,229 +0,0 @@ -import copy -import os -from copy import deepcopy -import tarfile -from typing import Dict, List - -import networkx as nx # type: ignore -import pandas as pd # type: ignore -import yaml -from cat_merge.merge import merge as cat_merge_merge # type: ignore -from kgx.cli.cli_utils import merge # type: ignore - -ONTO_DATA_PATH = "../transformed/ontologies/" -OUTPUT_PATH = "data/merged" - -def parse_load_config(yaml_file: str) -> Dict: - """Parse load config YAML. - - Args: - yaml_file: A string pointing to a KGX compatible config YAML. - - Returns: - Dict: The config as a dictionary. - - """ - with open(yaml_file) as YML: - config = yaml.load(YML, Loader=yaml.FullLoader) - return config - -def update_merge_config(yaml_file: str, merge_all: bool, include_only: list, exclude: list) -> None: - """Update the merge config YAML with - values from runtime params. - - Args: - yaml_file: A string pointing to a KGX compatible config YAML. - merge_all: Update merge config to include *all* ontologies. - include_only: Update merge config to include the specified ontologies. - exclude: Update merge config to include all ontologies *except* those specified. - - Returns: - None - - """ - - # Need to know ontology names and filepaths. - # Keys in onto_paths are short names, values are lists of filepaths. - onto_paths = {} - if len(include_only) > 0: - onto_dirs = [dirname for dirname in os.listdir(ONTO_DATA_PATH) if \ - os.path.isdir(os.path.join(ONTO_DATA_PATH, dirname)) and dirname in include_only] - elif len(exclude) > 0: - onto_dirs = [dirname for dirname in os.listdir(ONTO_DATA_PATH) if \ - os.path.isdir(os.path.join(ONTO_DATA_PATH, dirname)) and dirname not in exclude] - else: - onto_dirs = [dirname for dirname in os.listdir(ONTO_DATA_PATH) if \ - os.path.isdir(os.path.join(ONTO_DATA_PATH, dirname))] - for dirname in onto_dirs: - this_path = os.path.join(ONTO_DATA_PATH,dirname) - onto_paths[dirname] = [os.path.join(this_path, filename) for filename in \ - os.listdir(this_path) if os.path.isfile(os.path.join(this_path, filename)) and filename.endswith(".tsv")] - - # Default behavior is to merge all for now, but this could do something different later - if merge_all: - pass - - i = 0 - with open(yaml_file) as YML: - config = yaml.load(YML, Loader=yaml.FullLoader) - updated_config = copy.deepcopy(config) - updated_config['merged_graph']['source'] = {} - for onto in onto_paths: - updated_config['merged_graph']['source'][f's{i}'] = {'name':onto,'input':{'format':'tsv','filename':onto_paths[onto]}} - i = i+1 - - with open(yaml_file, 'w') as updated_yaml_file: - updated_yaml_file.write(yaml.dump(updated_config, default_flow_style=False, sort_keys=False)) - -def load_and_merge(yaml_file: str, processes: int = 1) -> nx.MultiDiGraph: - """Load and merge sources defined in the config YAML. - - Args: - yaml_file: A string pointing to a KGX compatible config YAML. - processes: Number of processes to use. - - Returns: - networkx.MultiDiGraph: The merged graph. - - """ - merged_graph = merge(yaml_file, processes=processes) - return merged_graph - -def merge_with_cat_merge(merge_all: bool, include_only: list, exclude: list) -> None: - """Load and merge sources with cat-merge. - Cat-merge does not merge values based on their ids, - it just concatenates and drops exact duplicates. - A subsequent step here performs further merging - on identical IDs and concatenates other values, - delimiting with pipe symbols. - - Args: - merge_all: if True, merge all ontology node and edges. - include_only: list of paths to ontology node/edgefiles to include - exclude: list of paths to ontology node/edgefiles to exclude - - Returns: - None - - """ - - nodepaths = [] - edgepaths = [] - - # Prepare a blank header edgefile so we can ensure we have the correct - # column headings - blank_header_path = "blank_header.tsv" - if not os.path.exists(blank_header_path): - with open(blank_header_path, "w") as outfile: - outstring = "id\tobject\tsubject\tpredicate\tcategory\n" - outfile.write(outstring) - edgepaths.append(blank_header_path) - - # Need to know ontology names and filepaths - # Keys in onto_paths are short names, values are lists of filepaths. - onto_paths = {} - if len(include_only) > 0: - onto_dirs = [dirname for dirname in os.listdir(ONTO_DATA_PATH) if \ - os.path.isdir(os.path.join(ONTO_DATA_PATH, dirname)) and dirname in include_only] - elif len(exclude) > 0: - onto_dirs = [dirname for dirname in os.listdir(ONTO_DATA_PATH) if \ - os.path.isdir(os.path.join(ONTO_DATA_PATH, dirname)) and dirname not in exclude] - else: - onto_dirs = [dirname for dirname in os.listdir(ONTO_DATA_PATH) if \ - os.path.isdir(os.path.join(ONTO_DATA_PATH, dirname))] - for dirname in onto_dirs: - this_path = os.path.join(ONTO_DATA_PATH,dirname) - onto_paths[dirname] = [os.path.join(this_path, filename) for filename in \ - os.listdir(this_path) if os.path.isfile(os.path.join(this_path, filename)) and filename.endswith(".tsv")] - - # Separate out node vs. edgelist - # Do a check to verify that none of the files are empty, or the merge will fail - # also verify the header in each contains an 'id' field - # (it's invalid without it) - ignore_paths = [] - for onto_name in onto_paths: - print(f"Validating {onto_name}...") - for path in onto_paths[onto_name]: - if path.endswith("_nodes.tsv"): - this_edgepath = (path.rpartition('_'))[0] + '_edges.tsv' - try: - nodedf = pd.read_csv(path, sep='\t', index_col='id') - except (KeyError, TypeError, pd.errors.ParserError, pd.errors.EmptyDataError) as e: - ignore_paths.append(this_edgepath) - print(f"Ignoring {path} due to pandas parsing error. Will also ignore {this_edgepath}. Error: {e}") - continue - num_lines = len(nodedf.index) - if num_lines > 1 and path not in ignore_paths: - nodepaths.append(path) - else: - ignore_paths.append(this_edgepath) - print(f"Ignoring {path} as it contains no nodes or node ids. Will also ignore {this_edgepath}.") - elif path.endswith("_edges.tsv"): - this_nodepath = (path.rpartition('_'))[0] + '_nodes.tsv' - try: - edgedf = pd.read_csv(path, sep='\t', index_col='id') - except (KeyError, TypeError, pd.errors.ParserError, pd.errors.EmptyDataError) as e: - ignore_paths.append(this_nodepath) - print(f"Ignoring {path} due to pandas parsing error. Will also ignore {this_nodepath}. Error: {e}") - continue - num_lines = len(edgedf.index) - if num_lines > 1 and path not in ignore_paths: - edgepaths.append(path) - else: - ignore_paths.append(this_nodepath) - print(f"Ignoring {path} as it contains no edges or edge ids. Will also ignore {this_nodepath}.") - - # Default behavior is to merge all for now, but this could do something different later - if merge_all: - pass - - # Perform the cat merge - cat_merge_merge( - name='merged-kg', - nodes=nodepaths, - edges=edgepaths, - output_dir=OUTPUT_PATH, - qc_report=True - ) - - # Find duplicate nodes and rows. - # For duplicate rows, remove all but the first instance. - # For duplicate nodes (those with identical CURIEs), - # merge all fields with a delimiter. - - nodefile_name = "merged-kg_nodes.tsv" - nodefile_path = os.path.join(OUTPUT_PATH,nodefile_name) - edgefile_name = "merged-kg_nodes.tsv" - edgefile_path = os.path.join(OUTPUT_PATH,edgefile_name) - temp_nodefile_name = "merged-kg_nodes.tsv.temp" - temp_nodefile_path = os.path.join(OUTPUT_PATH,temp_nodefile_name) - merge_graph_path = os.path.join(OUTPUT_PATH,'merged-kg.tar.gz') - graph_file_paths = [] - - with tarfile.open(merge_graph_path) as intar: - graph_files = intar.getnames() - print(graph_files) - for graph_file in graph_files: - intar.extract(graph_file, path=os.path.dirname(merge_graph_path)) - graph_file_paths.append(os.path.join(os.path.dirname(merge_graph_path), graph_file)) - os.remove(merge_graph_path) - - # Remove duplicate rows and merge duplicate nodes - print("Reading merged graph to process duplicates...") - nodes_df = pd.read_csv(nodefile_path, sep='\t', index_col='id') - print(f"Node count before removing complete duplicates: {len(nodes_df.index)}") - nodes_df.drop_duplicates(keep='first', inplace=True) - print(f"Node count after removing complete duplicates: {len(nodes_df.index)}") - uniq_df = nodes_df.groupby('id').agg(lambda x: '|'.join(set(x))) - print(f"Node count after merging duplicate nodes: {len(uniq_df.index)}") - uniq_df.to_csv(temp_nodefile_path, sep='\t') - - os.replace(temp_nodefile_path, nodefile_path) - - # Compress it again - with tarfile.open(merge_graph_path, "w:gz") as outtar: - for graph_file in graph_file_paths: - outtar.add(graph_file, arcname=os.path.basename(graph_file)) - os.remove(graph_file) - - print("Complete.") \ No newline at end of file diff --git a/kg_bioportal/stats.py b/kg_bioportal/stats.py deleted file mode 100644 index 08df896..0000000 --- a/kg_bioportal/stats.py +++ /dev/null @@ -1,37 +0,0 @@ -import yaml - -def make_graph_stats(method: str, input_file: str, output_file: str) -> None: - """Produce a simple YAML output containing select graph statistics. - This is based on the statistics emitted by KGX - after producing the merged graph. - - Args: - method: a string, either 'kgx' or 'catmerge'. - This determines the expected input stats format. - input_dir: A string pointing to the name of the file - to extract stats from. - output_dir: A string pointing to the name of the file - to write summary stats to. - - Returns: - None. - - """ - - stats = {} - - with open(input_file) as merged_stats_file: - merged_stats = yaml.load(merged_stats_file, Loader=yaml.FullLoader) - - if method == 'kgx': - stats['nodecount'] = merged_stats['node_stats']['total_nodes'] - stats['edgecount'] = merged_stats['edge_stats']['total_edges'] - - if method == 'catmerge': - stats['nodecount'] = merged_stats['nodes'][0]['total_number'] - stats['edgecount'] = merged_stats['edges'][0]['total_number'] - - with open(output_file, 'w') as stats_file: - stats_file.write(yaml.dump(stats, - default_flow_style=False, - sort_keys=False)) diff --git a/kg_bioportal/transform.py b/kg_bioportal/transform.py deleted file mode 100644 index 9c2a499..0000000 --- a/kg_bioportal/transform.py +++ /dev/null @@ -1,39 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -import logging -from typing import List, Optional - -from kg_bioportal.transform_utils.ontology import OntologyTransform -from kg_bioportal.transform_utils.ontology.ontology_transform import ONTOLOGIES - -DATA_SOURCES = {"ChebiTransform": OntologyTransform, "EnvoTransform": OntologyTransform} - - -def transform( - input_dir: str, output_dir: str, sources: Optional[List[str]] = None -) -> None: - """Call scripts in kg_bioportal/transform/[source name]/ to transform each source into a graph format that - KGX can ingest directly, in either TSV or JSON format: - https://github.com/biolink/kgx/blob/master/specification/kgx-format.md - - Args: - input_dir: A string pointing to the directory to import data from. - output_dir: A string pointing to the directory to output data to. - sources: A list of sources to transform. - - Returns: - None. - - """ - if not sources: - # run all sources - sources = list(DATA_SOURCES.keys()) - - for source in sources: - if source in DATA_SOURCES: - logging.info(f"Parsing {source}") - t = DATA_SOURCES[source](input_dir, output_dir) - if source in ONTOLOGIES.keys(): - t.run(ONTOLOGIES[source]) - else: - t.run() diff --git a/kg_bioportal/transform_utils/__init__.py b/kg_bioportal/transform_utils/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/kg_bioportal/transform_utils/ontology/__init__.py b/kg_bioportal/transform_utils/ontology/__init__.py deleted file mode 100644 index 9ba7613..0000000 --- a/kg_bioportal/transform_utils/ontology/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -from .ontology_transform import OntologyTransform - -__all__ = [ - "OntologyTransform" -] diff --git a/kg_bioportal/transform_utils/ontology/ontology_transform.py b/kg_bioportal/transform_utils/ontology/ontology_transform.py deleted file mode 100644 index 9c5e353..0000000 --- a/kg_bioportal/transform_utils/ontology/ontology_transform.py +++ /dev/null @@ -1,75 +0,0 @@ -import os -import gzip -import shutil -from typing import Optional - -from kg_bioportal.transform_utils.transform import Transform -from kg_bioportal.utils.robot_utils import convert_to_json -from kgx.cli.cli_utils import transform # type: ignore - - -ONTOLOGIES = {"ChebiTransform": "chebi.owl.gz", "EnvoTransform": "envo.json"} - - -class OntologyTransform(Transform): - """ - OntologyTransform parses an Obograph JSON form of an Ontology into nodes and edges. - If it isn't in Obograph JSON format, it is transformed with ROBOT. - If it needs to be decompressed, that happens here too. - """ - - def __init__( - self, input_dir: Optional[str] = None, output_dir: Optional[str] = None - ): - source_name = "ontologies" - super().__init__(source_name, input_dir, output_dir) - - def run(self, data_file: Optional[str] = None) -> None: - """Method is called and performs needed transformations to process - an ontology. - Args: - data_file: data file to parse - Returns: - None. - """ - if data_file: # if we specify a data file - k = data_file.split(".")[0] - data_file = os.path.join(self.input_base_dir, data_file) - self.parse(k, data_file, k) - else: - # load all ontologies - for k in ONTOLOGIES.keys(): - data_file = os.path.join(self.input_base_dir, ONTOLOGIES[k]) - self.parse(k, data_file, k) - - def parse(self, name: str, data_file: str, source: str) -> None: - """Processes the data_file. - Args: - name: Name of the ontology - data_file: data file to parse - source: Source name - Returns: - None. - """ - print(f"Parsing {data_file}") - - # Decompress if needed - if data_file[-3:] == ".gz": - outfile = data_file[:-3] - with gzip.open(data_file, "rb") as f_in: - with open(outfile, "wb") as f_out: - shutil.copyfileobj(f_in, f_out) - data_file = outfile - - # Transform to obojson if needed - # Need to set up ROBOT first - if data_file[-4:] == ".owl": - convert_to_json("data/raw/", "chebi") # Use the downloaded ROBOT - data_file = data_file[:-4] + ".json" - - transform( - inputs=[data_file], - input_format="obojson", - output=os.path.join(self.output_dir, name), - output_format="tsv", - ) diff --git a/kg_bioportal/transform_utils/transform.py b/kg_bioportal/transform_utils/transform.py deleted file mode 100644 index 78b7083..0000000 --- a/kg_bioportal/transform_utils/transform.py +++ /dev/null @@ -1,43 +0,0 @@ -import os -from typing import Optional - - -class Transform: - """Parent class for transforms, that sets up a lot of default file info""" - - DEFAULT_INPUT_DIR = os.path.join("data", "raw") - DEFAULT_OUTPUT_DIR = os.path.join("data", "transformed") - - def __init__( - self, - source_name, - input_dir: Optional[str] = None, - output_dir: Optional[str] = None, - nlp: bool = False, - ): - # default columns, can be appended to or overwritten as necessary - self.source_name = source_name - self.node_header = ["id", "name", "category"] - self.edge_header = [ - "subject", - "edge_label", - "object", - "relation", - "provided_by", - ] - - # default dirs - self.input_base_dir = input_dir if input_dir else self.DEFAULT_INPUT_DIR - self.output_base_dir = output_dir if output_dir else self.DEFAULT_OUTPUT_DIR - self.output_dir = os.path.join(self.output_base_dir, source_name) - - # default filenames - self.output_node_file = os.path.join(self.output_dir, "nodes.tsv") - self.output_edge_file = os.path.join(self.output_dir, "edges.tsv") - self.output_json_file = os.path.join(self.output_dir, "nodes_edges.json") - self.subset_terms_file = os.path.join(self.input_base_dir, "subset_terms.tsv") - - os.makedirs(self.output_dir, exist_ok=True) - - def run(self, data_file: Optional[str] = None): - pass diff --git a/kg_bioportal/transform_utils/translation_table.yaml b/kg_bioportal/transform_utils/translation_table.yaml deleted file mode 100644 index 5330d28..0000000 --- a/kg_bioportal/transform_utils/translation_table.yaml +++ /dev/null @@ -1,819 +0,0 @@ ---- -# GLOBAL_TERMS.yaml -# contents in this file are sorted by the value -# (i.e. the ontology term after the colon) in {key value} pair -!!map { -# -# these need to be moved to localtts till the terms exist: :!!! -"activating_mutation": ":activating", -"all_missense_or_inframe": ":all_missense_or_inframe", -"biallelic": ":biallelic", -"does_not_have_phenotype": ":does_not_have_phenotype", -"frequency": ":frequencyOfPhenotype", -"has_allelic_requirement": ":has_allelic_requirement", -"has_cell_origin": ":has_cell_origin", -"has_drug_response": ":has_drug_response", -"has_functional_consequence": ":has_functional_consequence", -"has_molecular_consequence": ":has_molecular_consequence", -"has_sex_specificty": ":has_sex_specificity", -"increased_gene_dosage": ":increased_gene_dosage", -"monoallelic": ":monoallelic", -"mosaic": ":mosaic_genotype", -"onset": ":onset", -"part_of_contiguous_gene_duplication": ":part_of_contiguous_gene_duplication", -# Basic Formal Ontology: "BFO:!!!", -"part_of": "BFO:0000050", -"has_part": "BFO:0000051", -"occurs_in": "BFO:0000066", -# "Chemicals of Biological Interest": "CHEBI:!!!", -"inchi_key": "CHEBI:InChIKey", # likely incorrect. -> localtt{"inchi_key": "CHEBI"}? -"molecular entity": "CHEBI:23367", -"gene_product": "CHEBI:33695", -# "Citation Typing Ontology": "cito:!!!", -"citesAsAuthority": "cito:citesAsAuthority", -# "Cell Ontology (cell types)": "CL:!!!", -"cell": "CL:0000000", -"stem cell": "CL:0000034", -"myoblast": "CL:0000056", -"fibroblast": "CL:0000057", -"epithelial cell": "CL:0000066", -"mesothelial": "CL:0000077", -"T cell": "CL:0000084", -"endothelial cell": "CL:0000115", -"melanocyte": "CL:0000148", -"smooth muscle cell": "CL:0000192", -"B cell": "CL:0000236", -"keratinocyte": "CL:0000312", -"oncocyte": "CL:0002198", -"amniocyte": "CL:0002323", -"mesenchymal stem cell of adipose": "CL:0002570", -"precursor cell": "CL:0011115", -# "Cell Line Ontology": "CLO:!!!", -"cell line repository": "CLO:0000008", -"cell line": "CLO:0000031", -"immortal kidney-derived cell line cell": "CLO:0000220", -"Adipose stromal cell": "CLO:0036934", -"Amniotic fluid-derived cell line": "CLO:0036935", -"Tumor-derived cell line": "CLO:0036938", -"Microcell hybrid": "CLO:0036939", -"Chorionic villus-derived cell line": "CLO:0036940", -# "dublin core terms (& elements)": "dc:!!!", -"Date Created": "dc:created", -"description": "dc:description", -"format": "dc:format", -"identifier": "dc:identifier", -"title": "dc:title", -"Source": "dc:source", -"Publisher": "dc:Publisher", -"creator": "dc:creator", -"isVersionOf": "dc:isVersionOf", -"license": "dc:license", -"rights": "dc:rights", -# "Data Catalog Vocabulary": "dcat:!!!" -"distribution": "dcat:distribution", -"Distribution": "dcat:Distribution", -"downloadURL": "dcat:downloadURL", -# "dublin core metadata types": "dctypes:!!!", -"Dataset": "dctypes:Dataset", -# "Evidence Code Ontology": "ECO:!!!", -"evidence": "ECO:0000000", -"inference from background scientific knowledge": "ECO:0000001", -"enzyme assay evidence": "ECO:0000005", -"experimental evidence": "ECO:0000006", -"expression pattern evidence": "ECO:0000008", -"genetic interaction evidence": "ECO:0000011", -"functional complementation evidence": "ECO:0000012", -"mutant phenotype evidence": "ECO:0000015", -"traceable author statement": "ECO:0000033", -"no biological data found": "ECO:0000035", -"experimental phenotypic evidence": "ECO:0000059", -"quantitative trait analysis evidence": "ECO:0000061", -"yeast 2-hybrid evidence": "ECO:0000068", -"far-Western blotting evidence": "ECO:0000076", -"affinity chromatography evidence": "ECO:0000079", -"phylogenetic evidence": "ECO:0000080", -"immunoprecipitation evidence": "ECO:0000085", -"biochemical trait analysis evidence": "ECO:0000172", -"genomic context evidence": "ECO:0000177", -"clinical study evidence": "ECO:0000180", -"sequence alignment evidence": "ECO:0000200", -"sequence orthology evidence": "ECO:0000201", -"match to sequence model evidence": "ECO:0000202", -"combinatorial evidence used in automatic assertion": "ECO:0000213", -"biological aspect of descendant evidence": "ECO:0000214", -"sequencing assay evidence": "ECO:0000220", -"computational combinatorial evidence used in manual assertion": "ECO:0000245", -"sequence similarity evidence used in manual assertion": "ECO:0000250", -"experimental evidence used in manual assertion": "ECO:0000269", -"expression evidence used in manual assertion": "ECO:0000270", -"author statement without traceable support used in manual assertion": "ECO:0000303", -"author statement supported by traceable reference used in manual assertion": "ECO:0000304", -"curator inference used in manual assertion": "ECO:0000305", -"inference from background scientific knowledge used in manual assertion": "ECO:0000306", -"imported information": "ECO:0000311", -"direct assay evidence used in manual assertion": "ECO:0000314", -"mutant phenotype evidence used in manual assertion": "ECO:0000315", -"genetic interaction evidence used in manual assertion": "ECO:0000316", -"biological aspect of ancestor evidence used in manual assertion": "ECO:0000318", -"phylogenetic determination of loss of key residues evidence used in manual assertion": "ECO:0000320", -"imported manually asserted information used in automatic assertion": "ECO:0000322", -"imported automatically asserted information used in automatic assertion": "ECO:0000323", -"imaging assay evidence": "ECO:0000324", -"physical interaction evidence used in manual assertion": "ECO:0000353", -"evidence used in automatic assertion": "ECO:0000501", -"blood test evidence": "ECO:0001016", -"FRET": "ECO:0001048", -"x-ray crystallography evidence": "ECO:0001823", -"inference from experimental data evidence": "ECO:0005611", -"inference from phenotype manipulation evidence": "ECO:0005612", -"inference by association of genotype from phenotype": "ECO:0005613", -# "Data and Methods Ontology": "EDAM-DATA:!!!", -"gene_family": "EDAM-DATA:3148", -# "Experimental Factor Ontology": "EFO:!!!", -"age": "EFO:0000246", -"sampling_time": "EFO:0000689", -"ethnic_group": "EFO:0001799", -"African American": "EFO:0003150", -"Asian": "EFO:0003152", -"Asian Indian": "EFO:0003153", -"Asian/Pacific Islander": "EFO:0003154", -"Caucasian": "EFO:0003156", -"Chinese": "EFO:0003157", -"Eastern Indian": "EFO:0003158", -"Filipino": "EFO:0003160", -"Japanese": "EFO:0003164", -"Korean": "EFO:0003165", -"Hispanic": "EFO:0003169", -"African": "EFO:0004561", -"induced pluripotent stem cell": "EFO:0004905", # "NCIT:C124144 ?" -"strain": "EFO:0005135", # "selectively maintained organism": "OBI:0001185" -# "Environment Ontology": "ENVO:!!!", -"environmental_system": "ENVO:01000254", -# "Eeagle-i Resource Ontology": "ERO:!!!", -"reagent": "ERO:0000006", # to be split into REO terms ...eventually -"has_author": "ERO:0000232", -"has_url": "ERO:0000480", -"Native American": "ERO:0001984", -"embryonic stem cell line": "ERO:0002002", -"Asian, Vietnamese": "ERO:0002071", -"collection": "ERO:0002190", -# "Feature Annotation Location Description Ontology": "faldo:!!!" (hacky) -"begin": "faldo:begin", -"both_strand": "faldo:BothStrandPosition", -"end": "faldo:end", -"FuzzyPosition": "faldo:FuzzyPosition", -"location": "faldo:location", -"minus_strand": "faldo:MinusStrandPosition", -"plus_strand": "faldo:PlusStrandPosition", -"Position": "faldo:Position", # Big P for Position type. little p for confusion -"position": "faldo:position", # Little p for position property. big P for confusion. -"reference": "faldo:reference", -"Region": "faldo:Region", # conflicts with SO!region -# "friend of a friend": "foaf:!!!", -"depiction": "foaf:depiction", -"organization": "foaf:organization", -"page": "foaf:page", -"person": "foaf:Person", -# "Genotype Partonomy Ontology": "GENO:!!!", -# "intrinsic_genotype": "GENO:0000000", # abandoned term -> GENO:0000719 -"variant_locus": "GENO:0000002", -"genomic_variation_complement": "GENO:0000009", -"variant single locus complement": "GENO:0000030", -"reference_locus": "GENO:0000036", -"hemizygous": "GENO:0000134", -"heterozygous": "GENO:0000135", -"homozygous": "GENO:0000136", -"indeterminate": "GENO:0000137", -"condition inheritance": "GENO:0000141", -"co-dominant inheritance": "GENO:0000143", -"complete dominant inheritance": "GENO:0000144", -"semi-dominant inheritance": "GENO:0000145", -"allosomal dominant inheritance": "GENO:0000146", -"autosomal dominant iniheritance": "GENO:0000147", -"recessive inheritance": "GENO:0000148", -"allosomal recessive inheritance": "GENO:0000149", -"autosomal recessive inheritance": "GENO:0000150", -"is_allelotype_of": "GENO:0000206", -"has_sequence_attribute": "GENO:0000207", -"has_genotype": "GENO:0000222", -"has_member_with_allelotype": "GENO:0000225", -# "": "GENO:0000259" # !!! abandoned term -"has_variant_part": "GENO:0000382", -"has_reference_part": "GENO:0000385", -"compound heterozygous": "GENO:0000402", -"is_allele_of": "GENO:0000408", -"targets_gene": "GENO:0000414", -"has_affected_feature": "GENO:0000418", -"is_mutant_of": "GENO:0000440", -"is_expression_variant_of": "GENO:0000443", -"is_transgene_variant_of": "GENO:0000444", -"simple heterozygous": "GENO:0000458", -"reagent_targeted_gene": "GENO:0000504", -"wildtype": "GENO:0000511", -"allele": "GENO:0000512", -"extrinsic_genotype": "GENO:0000524", -"effective_genotype": "GENO:0000525", -"targeted_gene_complement": "GENO:0000527", -"targeted_gene_subregion": "GENO:0000534", -"has_qualifier": "GENO:0000580", -"homoplasmic": "GENO:0000602", -"heteroplasmic": "GENO:0000603", -"hemizygous-y": "GENO:0000604", -"hemizygous-x": "GENO:0000605", -"hemizygous insertion-linked": "GENO:0000606", -"has_zygosity": "GENO:0000608", -"is_reference_allele_of": "GENO:0000610", -"genomic_background": "GENO:0000611", -"chromosome_region": "GENO:0000614", -"chromosome_subband": "GENO:0000616", -"band_intensity": "GENO:0000618", -"gpos": "GENO:0000619", -"gneg": "GENO:0000620", -"gvar": "GENO:0000621", -"gpos100": "GENO:0000622", -"gpos75": "GENO:0000623", -"gpos50": "GENO:0000624", -"gpos25": "GENO:0000625", -"stalk": "GENO:0000628", # was "short_chromosome_arm" may conflict ucscbands/monochrom -"long_chromosome_arm": "GENO:0000629", -"has_begin_stage_qualifier": "GENO:0000630", -"has_end_stage_qualifier": "GENO:0000631", -"gpos66": "GENO:0000632", -"gpos33": "GENO:0000633", -"is_targeted_by": "GENO:0000634", -"regulatory_transgene_feature": "GENO:0000637", -"coding_transgene_feature": "GENO:0000638", -"sequence_derives_from": "GENO:0000639", -"has_origin": "GENO:0000643", -"karyotype_variation_complement": "GENO:0000644", -"sex_qualified_genotype": "GENO:0000645", -"male intrinsic genotype": "GENO:0000646", -"female intrinsic genotype": "GENO:0000647", -"unspecified_genomic_background": "GENO:0000649", -"has_sex_agnostic_part": "GENO:0000650", -"has_extent": "GENO:0000678", -"intrinsic genotype": "GENO:0000719", # previously GENO:0000000 not "intrinsic_genotype" -"unspecified": "GENO:0000772", -"pathogenic_for_condition": "GENO:0000840", -"likely_pathogenic_for_condition": "GENO:0000841", -"benign_for_condition": "GENO:0000843", -"likely_benign_for_condition": "GENO:0000844", -"has_uncertain_significance_for_condition": "GENO:0000845", -"short repeat": "GENO:0000846", -"has_quantifier": "GENO:0000866", -"probabalistic_quantifier": "GENO:0000867", -"somatic": "GENO:0000882", -"germline": "GENO:0000900", -# "Gene Ontology": "GO:!!!", -"signal_transduction": "GO:0007165", -"cellular_process": "GO:0009987", -"developmental_process": "GO:0032502", -# "Human Phenotype": "HP:!!!", -"x_linked_dominant": "HP:0001423", -"mitochondrial_inheritance": "HP:0001427", -"digenic_inheritance": "HP:0010984", -"obsolete": "HP:0031859", -# "Information Artifact Ontology": "IAO:!!!", -"has measurement value": "IAO:0000004", -"journal article": "IAO:0000013", -"data set": "IAO:0000100", -"measurement datum": "IAO:0000109", -"definition": "IAO:0000115", -"is_about": "IAO:0000136", -"mentions": "IAO:0000142", -"photograph": "IAO:0000185", -"document": "IAO:0000310", -"publication": "IAO:0000311", -"OBO foundry unique label": "IAO:0000589", -"term replaced by": "IAO:0100001", -# "Medical Subject Headings": "MESH:!!!", -"Dwarfism": "MESH:D004392", -# "MONARCH": "MONARCH:!!!" one archive to rule them all -"is_anonymous": "MONARCH:anonymous", -"clique_leader": "MONARCH:cliqueLeader", -# "MONarch Disease Ontology": "MONDO:!!!", -"disease or disorder": "MONDO:0000001", -"inherited bleeding disorder, platelet-type": "MONDO:0000009", -"integumentary system disease": "MONDO:0002051", -"lysosomal storage disease": "MONDO:0002561", -"hereditary retinal dystrophy": "MONDO:0004589", -"cancer": "MONDO:0004992", -"metabolic disease": "MONDO:0005066", -"retinal disease": "MONDO:0005283", -"congenital heart disease": "MONDO:0005453", -"hematological system disease": "MONDO:0005570", -"platelet disorder, undefined": "MONDO:0008254", -"Cone–rod dystrophy": "MONDO:0015993", -"inborn errors of metabolism": "MONDO:0019052", # "DOID:0014667" -"disorder of sex development": "MONDO:0019592", -"developmental defect of the eye": "MONDO:0020145", -"hereditary optic atrophy": "MONDO:0043878", -# "Mammalian Phenotype": "MP:!!!", -"embryonic lethality": "MP:0008762", -# "NCBI Taxon": "NCBITaxon:!!!", -# "": "NCBITaxon:", -# "": "NCBITaxon:", -"Escherichia coli": "NCBITaxon:562", -"Arabidopsis thaliana": "NCBITaxon:3702", -"Schizosaccharomyces pombe": "NCBITaxon:4896", -"Aspergillus": "NCBITaxon:5052", -"Dictyostelium": "NCBITaxon:5782", -"Caenorhabditis elegans": "NCBITaxon:6239", -"Drosophila melanogaster": "NCBITaxon:7227", -"Danio rerio": "NCBITaxon:7955", -"Oncorhynchus mykiss": "NCBITaxon:8022", -"Xenopus (Silurana) tropicalis": "NCBITaxon:8364", -"Gallus gallus": "NCBITaxon:9031", -"Ornithorhynchus anatinus": "NCBITaxon:9258", -"Macropus eugenii": "NCBITaxon:9315", -"Erinaceus europaeus": "NCBITaxon:9365", -"Saguinus fuscicollis": "NCBITaxon:9487", -"Lagothrix lagotricha": "NCBITaxon:9519", -"Saimiri sciureus": "NCBITaxon:9521", -"Callicebus moloch": "NCBITaxon:9523", -"Erythrocebus patas": "NCBITaxon:9538", -"Macaca fascicularis": "NCBITaxon:9541", -"Macaca mulatta": "NCBITaxon:9544", -"Macaca nemestrina": "NCBITaxon:9545", -"Papio anubis": "NCBITaxon:9555", -"Gorilla gorilla": "NCBITaxon:9593", -"Pan paniscus": "NCBITaxon:9597", -"Pan troglodytes": "NCBITaxon:9598", -"Pongo pygmaeus": "NCBITaxon:9600", -"Homo sapiens": "NCBITaxon:9606", -"Canis lupus familiaris": "NCBITaxon:9615", -"Ailurus fulgens": "NCBITaxon:9649", -"Felis catus": "NCBITaxon:9685", -"Equus caballus": "NCBITaxon:9796", -"Sus scrofa": "NCBITaxon:9823", -"Sus scrofa domestica": "NCBITaxon:9825", -"Muntiacus muntjak": "NCBITaxon:9888", -"Bos taurus": "NCBITaxon:9913", -"Capra hircus": "NCBITaxon:9925", -"Ovis aries": "NCBITaxon:9940", -"Oryctolagus cuniculus": "NCBITaxon:9986", -"Cricetulus griseus": "NCBITaxon:10029", -"Mesocricetus auratus": "NCBITaxon:10036", -"Peromyscus leucopus": "NCBITaxon:10041", -"Peromyscus maniculatus": "NCBITaxon:10042", -"Mus": "NCBITaxon:10088", # Genus -"Mus caroli": "NCBITaxon:10089", -"Mus musculus": "NCBITaxon:10090", -"Mus musculus castaneus": "NCBITaxon:10091", -"Mus musculus domesticus": "NCBITaxon:10092", -"Mus pahari": "NCBITaxon:10093", -"Mus saxicola": "NCBITaxon:10094", -"Mus spretus": "NCBITaxon:10096", -"Mus cervicolor": "NCBITaxon:10097", -"Mus cookii": "NCBITaxon:10098", -"Mus platythrix": "NCBITaxon:10101", -"Mus setulosus": "NCBITaxon:10102", -"Mus spicilegus": "NCBITaxon:10103", -"Mus minutoides": "NCBITaxon:10105", -"Mus abbotti": "NCBITaxon:10108", -"Rattus": "NCBITaxon:10114", -"Rattus norvegicus": "NCBITaxon:10116", -"Cavia porcellus": "NCBITaxon:10141", -"Monodelphis domestica": "NCBITaxon:13616", -"Mus booduga": "NCBITaxon:27681", -"Anolis carolinensis": "NCBITaxon:28377", -"Microcebus murinus": "NCBITaxon:30608", -"Takifugu rubripe": "NCBITaxon:31033", -"Mus musculus bactrianus": "NCBITaxon:35531", -"hybrid": "NCBITaxon:37965", -"Mus musculus musculus": "NCBITaxon:39442", -"Mus crociduroides": "NCBITaxon:41269", -"Mus mattheyi": "NCBITaxon:41270", -"Peromyscus polionotus": "NCBITaxon:42413", -"Peromyscus californicus": "NCBITaxon:42520", -"Dictyostelium discoideum": "NCBITaxon:44689", -"Macaca nigra": "NCBITaxon:54600", -"Mus musculus molossinus": "NCBITaxon:57486", -"Chelonoidis niger": "NCBITaxon:66189", -"Saguinus labiatus": "NCBITaxon:78454", -"Mus musculus gentilulus": "NCBITaxon:80274", -"Mus famulus": "NCBITaxon:83773", -"Mus musculus brevirostris": "NCBITaxon:116058", -"Mus cervicolor cervicolor": "NCBITaxon:135827", -"Mus cervicolor popaeus": "NCBITaxon:135828", -"Mus fragilicauda": "NCBITaxon:186193", -"Mus musculus x Mus spretus": "NCBITaxon:186842", -"Mus gratus": "NCBITaxon:229288", -"Mus terricolor": "NCBITaxon:254704", -"Mus macedonicus spretoides": "NCBITaxon:270352", -"Mus macedonicus macedonicus": "NCBITaxon:270353", -"Mus indutus": "NCBITaxon:273921", -"Mus haussa": "NCBITaxon:273922", -"Mus lepidoides": "NCBITaxon:390847", -"Mus nitidulus": "NCBITaxon:390848", -"Mus tenellus": "NCBITaxon:397330", -"Mus cypriacus": "NCBITaxon:468371", -"Mus triton": "NCBITaxon:473865", -"Mus musculus musculus x M. m. domesticus": "NCBITaxon:477815", -"Mus musculus musculus x M. m. castaneus": "NCBITaxon:477816", -"Mus baoulei": "NCBITaxon:544437", -"Saccharomyces cerevisiae S288C": "NCBITaxon:559292", -# "Mus": "NCBITaxon:862507", # SubGenus -- name conflicts with Genus name -"Nannomys": "NCBITaxon:862510", -"Mus emesi": "NCBITaxon:887131", -"Mus musculus domesticus x M. m. molossinus": "NCBITaxon:1266728", -"Mus musculus gansuensis": "NCBITaxon:1385377", -# "National Cancer Institute Thesaurus": "NCIT:!!!", -# "monoallelic_mutation": "NCIT:C129829", -# "biallelic_mutation": "NCIT:C129830", -"Statistical Significance": "NCIT:C61040", -"Manual": "NCIT:C63513", -# "mosaic_indiviual": "NCIT:C88144", -"Suspected": "NCIT:C71458", -"Percent Change From Baseline": "NCIT:C96621", -# "Ontology of Adverse Events": "OAE:!!!", -"proportional_reporting_ratio": "OAE:0001563", -# "Open Biomedical Annotation Model": "OBAN:!!!", -"association": "OBAN:association", -"association has object": "OBAN:association_has_object", -"association has predicate": "OBAN:association_has_predicate", -"association has subject": "OBAN:association_has_subject", -# "Ontology of Biomedical Investigations": "OBI:!!!", -"assay": "OBI:0000070", -"p-value": "OBI:0000175", -"study": "OBI:0000471", -"statistical_hypothesis_test": "OBI:0000673", -"has specified numeric value": "OBI:0001937", -# "obo-specific annotation properties": "oboInOwl:!!!", -"consider": "oboInOwl:consider", -"database_cross_reference": "oboInOwl:hasDbXref", -"has_exact_synonym": "oboInOwl:hasExactSynonym", -"has_related_synonym": "oboInOwl:hasRelatedSynonym", -# "Web Ontology Language": "owl:!!!", -"annotation_property": "owl:AnnotationProperty", -"class": "owl:Class", -"datatype_property": "owl:DatatypeProperty", -"deprecated": "owl:deprecated", -"equivalent_class": "owl:equivalentClass", -"named_individual": "owl:NamedIndividual", -"object_property": "owl:ObjectProperty", -"on_property": "owl:onProperty", -"ontology": "owl:Ontology", -"restriction": "owl:Restriction", -"same_as": "owl:sameAs", -"some_values_from": "owl:someValuesFrom", -"version_info": "owl:versionInfo", -"version_iri": "owl:versionIRI", -# "Phenotypic Quality Ontology": "PATO:!!!", -"female": "PATO:0000383", -"male": "PATO:0000384", -"abnormal": "PATO:0000460", -"normal": "PATO:0000461", -# "Provenance, Authoring and Versioning": "pav:!!!", -"created_on": "pav:createdOn", -"version": "pav:version", -"retrieved_on": "pav:retrievedOn", -"created_with": "pav:createdWith", -# "Population and Community Ontology": "PCO:!!!", -"population": "PCO:0000001", -"family": "PCO:0000020", -# Place holder predicates: predicates -# "PathWay ontology": "PW:!!!", -"pathway": "PW:0000001", -# "Resource Description Framework": "rdf:!!!", -"type": "rdf:type", -# "Resource Description Framework Schema": "rdfs:!!!", -"comment": "rdfs:comment", -"domain": "rdfs:domain", -"label": "rdfs:label", -"subclass_of": "rdfs:subClassOf", -"subPropertyOf": "rdfs:subPropertyOf", -# "REO": "REO:!!!" _NOT_ in Curie_map.yaml (see ERO:6) -# "crispr_reagent": "REO:crispr_TBD", -# "morpholio_reagent": "REO:0000042", -# "talen_reagent": "REO:0001022", -# "Relationship Ontology": "RO:!!!", -"in paralogy relationship with": "RO:HOM0000011", -"in orthology relationship with": "RO:HOM0000017", -"in xenology relationship with": "RO:HOM0000018", -"in 1 to 1 homology relationship with": "RO:HOM0000019", -"in 1 to 1 orthology relationship with": "RO:HOM0000020", -"in ohnology relationship with": "RO:HOM0000022", -"in in-paralogy relationship with": "RO:HOM0000023", -"has_participant": "RO:0000057", -"has_quality": "RO:0000086", -"has disposition": "RO:0000091", -"derives_from": "RO:0001000", -"starts during": "RO:0002091", -"ends during": "RO:0002093", -"in taxon": "RO:0002162", -"has phenotype": "RO:0002200", -"gene product of": "RO:0002204", -"has gene product": "RO:0002205", -"expressed in": "RO:0002206", -"starts_with": "RO:0002224", -"ends_with": "RO:0002230", -"has_input": "RO:0002233", -"colocalizes with": "RO:0002325", -"contributes to": "RO:0002326", -"enables": "RO:0002327", -"involved in": "RO:0002331", -"member of": "RO:0002350", -"has member": "RO:0002351", -"output_of": "RO:0002353", -"causally upstream of or within": "RO:0002418", -"interacts with": "RO:0002434", -"genetically interacts with": "RO:0002435", -"molecularly_interacts_with": "RO:0002436", -"regulates": "RO:0002448", -"ubiquitinates": "RO:0002480", -"existence_starts_during": "RO:0002488", -"existence_ends_during": "RO:0002492", -"towards": "RO:0002503", -"translates_to": "RO:0002513", -"has subsequence": "RO:0002524", -"is subsequence of": "RO:0002525", -"is upstream of sequence of": "RO:0002528", -"is downstream of sequence of": "RO:0002529", -"has evidence": "RO:0002558", -"causally_influences": "RO:0002566", -"existence starts at point": "RO:0002583", -"existence ends at point": "RO:0002593", -"is substance that treats": "RO:0002606", -"is marker for": "RO:0002607", -"correlates_with": "RO:0002610", -"is_evidence_supported_by": "RO:0002614", -"negatively_regulates": "RO:0003002", -"positively_regulates": "RO:0003003", -"is model of": "RO:0003301", -"causes_or_contributes": "RO:0003302", -"causes condition": "RO:0003303", -"contributes to condition": "RO:0003304", -"protective_for_condition": "RO:0003307", -"is causal gain of function germline mutation of in": "RO:0004011", -"is causal loss of function germline mutation of in": "RO:0004012", -"is causal germline mutation in": "RO:0004013", -"is causal somatic mutation in": "RO:0004014", -"is causal susceptibility factor for": "RO:0004015", -"is causal germline mutation partially giving rise to": "RO:0004016", -# found in sepio_developer.owl: SEPIO:0000019 -# is not found in sepio: SEPIO:0000111 -- -# "Scientific Evidence and Provenance Information Ontology": "SEPIO:!!!", -"assertion": "SEPIO:0000001", -"assertion process": "SEPIO:0000003", -"has_evidence_line": "SEPIO:0000006", -"has_supporting_evidence_line": "SEPIO:0000007", -"has_provenance": "SEPIO:0000011", -"is_asserted_in": "SEPIO:0000015", -"has_agent": "SEPIO:0000017", -"created_by": "SEPIO:0000018", -# "x-created_at_location": "SEPIO:0000019", -"date_created": "SEPIO:0000021", -"created_with_resource": "SEPIO:0000022", -"is_evidence_for": "SEPIO:0000031", -"is_supporting_evidence_for": "SEPIO:0000032", -"is_refuting_evidence_for": "SEPIO:0000033", -"assertion method": "SEPIO:0000037", -"is_specified_by": "SEPIO:0000041", -"is_evidence_with_support_from": "SEPIO:0000059", -"research": "SEPIO:0000066", -"clinical testing": "SEPIO:0000067", -"case-control": "SEPIO:0000071", -"in vitro": "SEPIO:0000073", -"in vivo": "SEPIO:0000074", -"literature only": "SEPIO:0000080", -"curation": "SEPIO:0000081", -"has_evidence_item": "SEPIO:0000084", -"has_supporting_activity": "SEPIO:0000085", -"is_equilavent_to": "SEPIO:0000098", -"is_consistent_with": "SEPIO:0000099", -"strongly_contradicts": "SEPIO:0000100", -"contradicts": "SEPIO:0000101", -"reference population": "SEPIO:0000102", -"is_assertion_supported_by_evidence": "SEPIO:0000111", -# "is_assertion_supported_by": "SEPIO:0000111", -"measures_parameter": "SEPIO:0000114", -"has_supporting_reference": "SEPIO:0000124", -"is_inconsistent_with": "SEPIO:0000126", -"asserted_by": "SEPIO:0000130", -"assertion_confidence_level": "SEPIO:0000167", -"assertion_confidence_score": "SEPIO:0000168", -"phenotyping only": "SEPIO:0000186", -# "has_evidence_with_item": "SEPIO:0000189", -# "no assertion criteria provided": "SEPIO:9999990", -# "no assertion provided": "SEPIO:9999991", -# "criteria provided, single submitter": "SEPIO:9999992", -# "criteria provided, conflicting interpretations": "SEPIO:9999993", -# "criteria provided, multiple submitters, no conflicts": "SEPIO:9999994", -# "reviewed by expert panel": "SEPIO:9999995", -# "practice guideline": "SEPIO:9999996", -# "Semanticscience Integrated Ontology": "SIO:!!!", -"web page": "SIO:000302", -"count": "SIO:000794", -"race": "SIO:001015", -# "Sequence Onrology": "SO:!!!", -"region": "SO:0000001", # conflicts with faldo:Region -"small cytoplasmic RNA": "SO:0000013", -"processed_pseudogene": "SO:0000043", -"antisense": "SO:0000077", -"endogenous_retroviral_gene": "SO:0000100", -"transposable_element": "SO:0000101", -"polypeptide": "SO:0000104", -"chromosome_arm": "SO:0000105", -"sequence_feature": "SO:0000110", -"transposable_element_gene": "SO:0000111", -"genomically_imprinted": "SO:0000134", -"assembly_component": "SO:0000143", -"read": "SO:0000150", -"deletion": "SO:0000159", -"enhancer": "SO:0000165", -"promoter": "SO:0000167", -"retrotransposon": "SO:0000180", -"translocation": "SO:0000199", -"mature_transcript": "SO:0000233", -"microsatellite": "SO:0000289", -"CpG_island": "SO:0000307", -"pseudogene": "SO:0000336", -"RNAi_reagent": "SO:0000337", -"chromosome": "SO:0000340", -"chromosome_band": "SO:0000341", -"ribozyme": "SO:0000374", -"vault_RNA": "SO:0000404", -"Y RNA": "SO:0000405", -"binding_site": "SO:0000409", -"chromosomal_transposition": "SO:0000453", -"vertebrate_immunoglobulin_T_cell_receptor_segment": "SO:0000460", -"pseudogenic_region": "SO:0000462", -"centromere": "SO:0000577", -"telomere": "SO:0000624", -"minisatellite": "SO:0000643", -"large_subunit_rRNA": "SO:0000651", -"ncRNA": "SO:0000655", -"insertion": "SO:0000667", -"SNP": "SO:0000694", -"experimental_result_region": "SO:0000703", -"gene": "SO:0000704", -"cDNA": "SO:0000756", -"QTL": "SO:0000771", -"transgenic": "SO:0000781", -"transgenic_transposable_element": "SO:0000796", -"fusion": "SO:0000806", -"wild_type": "SO:0000817", -"chromosome_part": "SO:0000830", -"stop codon readthrough": "SO:0000883", -"transgene": "SO:0000902", # not really used any more -"endogenous_retroviral_sequence": "SO:0000903", -"integration_excision_site": "SO:0000946", -"haplotype": "SO:0001024", -"genome": "SO:0001026", -"diplotype": "SO:0001028", -"transcriptional_cis_regulatory_region": "SO:0001055", -"sequence_alteration": "SO:0001059", -"sequence_variant": "SO:0001060", -"protein_coding_gene": "SO:0001217", -"transgenic_insertion": "SO:0001218", -"TSS_region": "SO:0001240", -"ncRNA_gene": "SO:0001263", -"miRNA_gene": "SO:0001265", -"scRNA_gene": "SO:0001266", -"snoRNA_gene": "SO:0001267", -"snRNA_gene": "SO:0001268", -"SRP_RNA_gene": "SO:0001269", -"tRNA_gene": "SO:0001272", -"biological_region": "SO:0001411", -"SNV": "SO:0001483", -"heritable_phenotypic_marker": "SO:0001500", -"processed_transcript": "SO:0001503", -"reference_genome": "SO:0001505", -"gene_variant": "SO:0001564", -"regulatory_region_variant": "SO:0001566", -"splice_acceptor_variant": "SO:0001574", -"splice_donor_variant": "SO:0001575", -"stop_lost": "SO:0001578", -"coding_sequence_variant": "SO:0001580", -"missense_variant": "SO:0001583", -"stop_gained": "SO:0001587", -"frameshift_variant": "SO:0001589", -"non_coding_transcript_exon_variant": "SO:0001619", -"mature_miRNA_variant": "SO:0001620", -"UTR_variant": "SO:0001622", -"5_prime_UTR_variant": "SO:0001623", -"3_prime_UTR_variant": "SO:0001624", -"intron_variant": "SO:0001627", -"intergenic_variant": "SO:0001628", -"splice_region_variant": "SO:0001630", -"downstream_gene_variant": "SO:0001634", -"upstream_gene_variant": "SO:0001636", -"rRNA_gene": "SO:0001637", -"piRNA_gene": "SO:0001638", -"RNase_P_RNA_gene": "SO:0001639", -"RNase_MRP_RNA_gene": "SO:0001640", -"lincRNA_gene": "SO:0001641", -"telomerase_RNA_gene": "SO:0001643", -"genetic_marker": "SO:0001645", -"inframe_variant": "SO:0001650", -"score": "SO:0001685", # FIXME - score is not a good solution too generic -"pseudogenic_gene_segment": "SO:0001741", -"copy_number_gain": "SO:0001742", -"copy_number_loss": "SO:0001743", -"unitary_pseudogene": "SO:0001759", -"unprocessed_pseudogene": "SO:0001760", -"TF_binding_site_variant": "SO:0001782", -"complex_structural_alteration": "SO:0001784", -"structural_alteration": "SO:0001785", -"non_coding_exon_variant": "SO:0001792", -"protein_altering_variant": "SO:0001818", -"synonymous_variant": "SO:0001819", -"inframe_insertion": "SO:0001821", -"inframe_deletion": "SO:0001822", -"mobile_element_insertion": "SO:0001837", -"novel_sequence_insertion": "SO:0001838", -"polymorphic_pseudogene": "SO:0001841", -"lnc_RNA": "SO:0001877", -"feature_fusion": "SO:0001882", -"transposable_element_pseudogene": "SO:0001897", -"antisense_lncRNA": "SO:0001904", -"MNV": "SO:0002007", -"start_lost": "SO:0002012", -"vaultRNA_primary_transcript": "SO:0002040", -"dominant_negative_variant": "SO:0002052", -"gain_of_function_variant": "SO:0002053", -"loss_of_function_variant": "SO:0002054", -"scaRNA": "SO:0002095", -"immunoglobulin_pseudogene": "SO:0002098", -"T_cell_receptor_pseudogene": "SO:0002099", -"IG_C_pseudogene": "SO:0002100", -"IG_J_pseudogene": "SO:0002101", -"IG_V_pseudogene": "SO:0002102", -"TR_V_pseudogene": "SO:0002103", -"TR_J_pseudogene": "SO:0002104", -"translated_unprocessed_pseudogene": "SO:0002106", -"transcribed_unprocessed_pseudogene": "SO:0002107", -"transcribed_unitary_pseudogene": "SO:0002108", -"transcribed_processed_pseudogene": "SO:0002109", -"3prime_overlapping_ncRNA": "SO:0002120", -"immunoglobulin_gene": "SO:0002122", -"IG_C_gene": "SO:0002123", -"IG_D_gene": "SO:0002124", -"IG_J_gene": "SO:0002125", -"IG_V_gene": "SO:0002126", -"lncRNA_gene": "SO:0002127", -"mt_rRNA": "SO:0002128", -"mt_tRNA": "SO:0002129", -"sense_intronic": "SO:0002131", -"sense_overlapping": "SO:0002132", -"TR_C_gene": "SO:0002134", -"TR_D_gene": "SO:0002135", -"TR_J_gene": "SO:0002136", -"TR_V_gene": "SO:0002137", -"TEC": "SO:0002139", -"ribozyme_gene": "SO:0002181", -"sense_overlap_ncRNA_gene": "SO:0002183", -"sense_intronic_ncRNA_gene": "SO:0002184", -"bidirectional_promoter_lncRNA": "SO:0002185", -"substitution": "SO:1000002", -"complex_substitution": "SO:1000005", -"point_mutation": "SO:1000008", -"chromosomal_deletion": "SO:1000029", -"chromosomal_inversion": "SO:1000030", -"indel": "SO:1000032", -"duplication": "SO:1000035", -"inversion": "SO:1000036", -"chromosomal_duplication": "SO:1000037", -"direct_tandem_duplication": "SO:1000039", -"Robertsonian_fusion": "SO:1000043", -"chromosomal_translocation": "SO:1000044", -"reciprocal_chromosomal_translocation": "SO:1000048", -"sequence_variant_affecting_polypeptide_function": "SO:1000117", -"sequence_variant_causing_loss_of_function_of_polypeptide": "SO:1000118", -"sequence_variant_causing_inactive_catalytic_site": "SO:1000120", -"sequence_variant_causing_gain_of_function_of_polypeptide": "SO:1000125", -"tandem_duplication": "SO:1000173", -"chromosome_structure_variation": "SO:1000183", -"gene_segment": "SO:3000000", -# "Statistics Ontology": "STATO:!!!", -"Fisher's exact test": "STATO:0000073", -"Mann-Whitney U-test": "STATO:0000076", -"effect size estimate": "STATO:0000085", -"zscore": "STATO:0000104", -"statistical model": "STATO:0000107", -"has_value": "STATO:0000129", -"fold change": "STATO:0000169", -"odds_ratio": "STATO:0000182", -"mixed effect model": "STATO:0000189", -"generalized least squares estimation": "STATO:0000372", -"linear mixed model": "STATO:0000464", -# "SWO": "SWO:!!!" _NOT_ in curie_map -"Similarity score": "SWO:0000425", -# "Integrated anatomy ontology (metazoan)": "UBERON:!!!", -# "existence_ends_at ": "UBERON:existence_ends_at ", -# "existence_starts_at ": "UBERON:existence_starts_at ", -# "Integrated phenotype ontology, and normal traits": "UPHENO:!!!", -"phenotype": "UPHENO:0001001", # conflicts with FBcv:0001347 -# "ontology for representing scholarship": "VIVO:!!!", -"project": "VIVO:Project", -# "Vocabulary of Interlinked Datasets": "void:!!!", -"class (void)": "void:class", -"classPartition": "void:classPartition", -"distinctObjects": "void:distinctObjects", -"distinctSubjects": "void:distinctSubjects", -"entities": "void:entities", -"properties": "void:properties", -"triples": "void:triples", -# "Experimental Conditions Ontology": "XCO:!!!", -"environmental_condition": "XCO:0000000"} # keep terminal closing brace on last line diff --git a/kg_bioportal/utils/__init__.py b/kg_bioportal/utils/__init__.py deleted file mode 100644 index 885a8db..0000000 --- a/kg_bioportal/utils/__init__.py +++ /dev/null @@ -1,7 +0,0 @@ -from .download_utils import download_from_yaml -from .transform_utils import multi_page_table_to_list, write_node_edge_item - - -__all__ = [ - "download_from_yaml", "multi_page_table_to_list", "write_node_edge_item" -] \ No newline at end of file diff --git a/kg_bioportal/utils/download_utils.py b/kg_bioportal/utils/download_utils.py deleted file mode 100644 index 9df901a..0000000 --- a/kg_bioportal/utils/download_utils.py +++ /dev/null @@ -1,54 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - - -import logging -import os -from urllib.request import Request, urlopen - -import yaml -from os import path -from tqdm.auto import tqdm # type: ignore - -def download_from_yaml(yaml_file: str, output_dir: str, - ignore_cache: bool = False) -> None: - """Given an download info from an download.yaml file, download all files - - Args: - yaml_file: A string pointing to the download.yaml file, to be parsed for things to download. - output_dir: A string pointing to where to write out downloaded files. - ignore_cache: Ignore cache and download files even if they exist [false] - - Returns: - None. - """ - - os.makedirs(output_dir, exist_ok=True) - with open(yaml_file) as f: - data = yaml.load(f, Loader=yaml.FullLoader) - for item in tqdm(data, desc="Downloading files"): - if 'url' not in item: - logging.warning("Couldn't find url for source in {}".format(item)) - continue - outfile = os.path.join( - output_dir, - item['local_name'] - if 'local_name' in item - else item['url'].split("/")[-1] - ) - logging.info("Retrieving %s from %s" % (outfile, item['url'])) - - if path.exists(outfile): - if ignore_cache: - logging.info("Deleting cached version of {}".format(outfile)) - os.remove(outfile) - else: - logging.info("Using cached version of {}".format(outfile)) - continue - - req = Request(item['url'], headers={'User-Agent': 'Mozilla/5.0'}) - with urlopen(req) as response, open(outfile, 'wb') as out_file: # type: ignore - data = response.read() # a `bytes` object - out_file.write(data) - - return None diff --git a/kg_bioportal/utils/robot_utils.py b/kg_bioportal/utils/robot_utils.py deleted file mode 100644 index a755a8f..0000000 --- a/kg_bioportal/utils/robot_utils.py +++ /dev/null @@ -1,98 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -import os -import subprocess # Source: https://docs.python.org/2/library/subprocess.html#popen-constructor - -def initialize_robot(path:str) -> list: - ''' - This initializes ROBOT with necessary configuration. - - :param path: Path to ROBOT files. - :return: A list consisting of robot shell script name and environment variables. - ''' - # Declare variables - robot_file = os.path.join(path, 'robot') - - # Declare environment variables - env = dict(os.environ) - #(JDK compatibility issue: https://stackoverflow.com/questions/49962437/unrecognized-vm-option-useparnewgc-error-could-not-create-the-java-virtual) - #env['ROBOT_JAVA_ARGS'] = '-Xmx8g -XX:+UseConcMarkSweepGC' # for JDK 9 and older - env['ROBOT_JAVA_ARGS'] = '-Xmx12g -XX:+UseG1GC' # For JDK 10 and over - env['PATH'] = os.environ['PATH'] - env['PATH'] += os.pathsep + path - - return [robot_file, env] - -def convert_to_json(path:str, ont:str): - """ - This method converts owl to JSON using ROBOT and the subprocess library - - :param path: Path to ROBOT files - :param ont: Ontology - :return: None - """ - - robot_file, env = initialize_robot(path) - input_owl = os.path.join(path, ont.lower()+'.owl') - output_json = os.path.join(path, ont.lower()+'.json') - if not os.path.isfile(output_json): - # Setup the arguments for ROBOT through subprocess - call = ['bash', robot_file, 'convert', \ - '--input', input_owl, \ - '--output', output_json, \ - '-f', 'json'] - - subprocess.call(call, env=env) - - return None - -def extract_convert_to_json(path:str, ont_name:str, terms:str, mode:str): - """ - This method extracts all children of provided CURIE. - - :param path: path of file to be converted - :param ont_name: Name of the ontology - :param terms: Either CURIE or a file of CURIEs list - :param mode: Method options as listed below. - :return: None - - ROBOT Method options: - - - STAR: The STAR-module contains mainly the terms in the seed and the inter-relations between them (not necessarily sub- and super-classes). - - - TOP: The TOP-module contains mainly the terms in the seed, plus all their sub-classes and the inter-relations between them. - - - BOT: The BOT, or BOTTOM, -module contains mainly the terms in the seed, plus all their super-classes and the inter-relations between them. - - - MIREOT : The MIREOT method preserves the hierarchy of the input ontology (subclass and subproperty relationships), but does not try to preserve the full set of logical entailments. - - """ - - robot_file, env = initialize_robot(path) - input_owl = os.path.join(path, ont_name.lower()+'.owl') - output_json = os.path.join(path, ont_name.lower()+'.json') - output_owl = os.path.join(path, ont_name.lower()+'_extracted_subset.owl') - - if ':' in terms: - call = ['bash', robot_file, 'extract', \ - '--method', mode, \ - '--input', input_owl, \ - '--output', output_owl, \ - '--term', terms, \ - 'convert', \ - '--output', output_json, \ - '-f', 'json'] - else: - call = ['bash', robot_file, 'extract', \ - '--method', mode, \ - '--input', input_owl, \ - '--output', output_owl, \ - '--term-file', terms, \ - 'convert', \ - '--output', output_json, \ - '-f', 'json'] - - subprocess.call(call, env=env) - - return None \ No newline at end of file diff --git a/kg_bioportal/utils/transform_utils.py b/kg_bioportal/utils/transform_utils.py deleted file mode 100644 index b44c180..0000000 --- a/kg_bioportal/utils/transform_utils.py +++ /dev/null @@ -1,224 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -import gzip -import logging -import os -import re -import shutil -import tempfile -import zipfile -from typing import Any, Dict, List, Union -from tqdm import tqdm # type: ignore - - -class TransformError(Exception): - """Base class for other exceptions""" - pass - - -class ItemInDictNotFound(TransformError): - """Raised when the input value is too small""" - pass - - -# TODO: option to further refine typing of method arguments below. - -def multi_page_table_to_list(multi_page_table: Any) -> List[Dict]: - """Method to turn table data returned from tabula.io.read_pdf(), possibly broken over several pages, into a list - of dicts, one dict for each row. - - Args: - multi_page_table: - - Returns: - table_data: A list of dicts, where each dict is item from one row. - """ - - # iterate through data for each of 3 pages - table_data: List[Dict] = [] - - header_items = get_header_items(multi_page_table[0]) - - for this_page in multi_page_table: - for row in this_page['data']: - if len(row) != 4: - logging.warning('Unexpected number of rows in {}'.format(row)) - - items = [d['text'] for d in row] - this_dict = dict(zip(header_items, items)) - table_data.append(this_dict) - - return table_data - - -def get_header_items(table_data: Any) -> List: - """Utility fxn to get header from (first page of) a table. - - Args: - table_data: Data, as list of dicts from tabula.io.read_pdf(). - - Returns: - header_items: An array of header items. - """ - - header = table_data['data'].pop(0) - header_items = [d['text'] for d in header] - - return header_items - - -def write_node_edge_item(fh: Any, header: List, data: List, sep: str = '\t'): - """Write out a single line for a node or an edge in *.tsv - :param fh: file handle of node or edge file - :param header: list of header items - :param data: data for line to write out - :param sep: separator [\t] - """ - if len(header) != len(data): - raise Exception('Header and data are not the same length.') - try: - fh.write(sep.join(data) + "\n") - except IOError: - logging.warning("Can't write data for {}".format(data)) - - -def get_item_by_priority(items_dict: dict, keys_by_priority: list) -> str: - """Retrieve item from a dict using a list of keys, in descending order of priority - - :param items_dict: - :param keys_by_priority: list of keys to use to find values - :return: str: first value in dict for first item in keys_by_priority - that isn't blank, or None - """ - value = None - for key in keys_by_priority: - if key in items_dict and items_dict[key] != '': - value = items_dict[key] - break - if value is None: - raise ItemInDictNotFound("Can't find item in items_dict {}".format(items_dict)) - return value - - -def data_to_dict(these_keys, these_values) -> dict: - """Zip up two lists to make a dict - - :param these_keys: keys for new dict - :param these_values: values for new dict - :return: dictionary - """ - return dict(zip(these_keys, these_values)) - - -def uniprot_make_name_to_id_mapping(dat_gz_file: str) -> dict: - """Given a Uniprot dat.gz file, like this: - ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz - makes dict with name to id mapping - - :param dat_gz_file: - :return: dict with mapping - """"" - name_to_id_map = dict() - logging.info("Making uniprot name to id map") - with gzip.open(dat_gz_file, mode='rb') as file: - for line in tqdm(file): - items = line.decode().strip().split('\t') - name_to_id_map[items[2]] = items[0] - return name_to_id_map - - -def uniprot_name_to_id(name_to_id_map: dict, name: str) -> Union[str, None]: - """Uniprot name to ID mapping - - :param name_to_id_map: mapping dict[name] -> id - :param name: name - :return: id string, or None - """ - if name in name_to_id_map: - return name_to_id_map[name] - else: - return None - - -def parse_header(header_string: str, sep: str = '\t') -> List: - """Parses header data. - - Args: - header_string: A string containing header items. - sep: A string containing a delimiter. - - Returns: - A list of header items. - """ - - header = header_string.strip().split(sep) - return [i.replace('"', '') for i in header] - -def parse_line(this_line: str, header_items: List, sep=',') -> Dict: - """Methods processes a line of text from the csv file. - - Args: - this_line: A string containing a line of text. - header_items: A list of header items. - sep: A string containing a delimiter. - - Returns: - item_dict: A dictionary of header items and a processed item from the dataset. - """ - - data = this_line.strip().split(sep) - data = [i.replace('"', '') for i in data] - - item_dict = data_to_dict(header_items, data) - - return item_dict - - -def unzip_to_tempdir(zip_file_name: str, tempdir: str) -> None: - with zipfile.ZipFile(zip_file_name, 'r') as z: - z.extractall(tempdir) - - -def ungzip_to_tempdir(gzipped_file: str, tempdir: str) -> str: - ungzipped_file = os.path.join(tempdir, os.path.basename(gzipped_file)) - if ungzipped_file.endswith('.gz'): - ungzipped_file = os.path.splitext(ungzipped_file)[0] - - with gzip.open(gzipped_file, 'rb') as f_in, open(ungzipped_file, 'wb') as f_out: - shutil.copyfileobj(f_in, f_out) - return ungzipped_file - - -def guess_bl_category(identifier: str) -> str: - """Guess category for a given identifier. - - Note: This is a temporary solution and should not be used long term. - - Args: - identifier: A CURIE - - Returns: - The category for the given CURIE - - """ - prefix = identifier.split(':')[0] - if prefix in {'UniProtKB', 'ComplexPortal'}: - category = 'biolink:Protein' - elif prefix in {'GO'}: - category = 'biolink:OntologyClass' - else: - category = 'biolink:NamedThing' - return category - - -def collapse_uniprot_curie(uniprot_curie: str) -> str: - """ Given a UniProtKB curie for an isoform such as UniprotKB:P63151-1 - or UniprotKB:P63151-2, collapse to parent protein - (UniprotKB:P63151 / UniprotKB:P63151) - - :param uniprot_curie: - :return: collapsed UniProtKB ID - """ - if re.match(r'^uniprotkb:', uniprot_curie, re.IGNORECASE): - uniprot_curie = re.sub(r'\-\d+$', '', uniprot_curie) - return uniprot_curie diff --git a/notebooks/clinical_ontologies.yaml b/notebooks/clinical_ontologies.yaml new file mode 100644 index 0000000..20c563e --- /dev/null +++ b/notebooks/clinical_ontologies.yaml @@ -0,0 +1,36 @@ +# This file is a list of ontologies in Bioportal +# with relevance to clinical research use cases. +# They are named based on their Bioportal IDs. +# Those with the test_set=true flag are part of +# a test set for setting up a demo TRAPI. +--- + +ontologies: + - name: "MEDDRA" + is_umls: true + - name: "SNOMEDCT" + is_umls: true + - name: "RXNORM" + is_umls: true + - name: "NDDF" + is_umls: true + - name: "RCD" + is_umls: true + - name: "LOINC" + is_umls: true + - name: "NCIT" + is_umls: true + - name: "MESH" + is_umls: true + - name: "ICD10CM" + is_umls: true + - name: "VANDF" + is_umls: true + - name: "RADLEX" + is_umls: true + test_set: true + - name: "HCPCS" + is_umls: true + - name: "HL7" + - name: "ATC" + test_set: true diff --git a/notebooks/trapi_setup.ipynb b/notebooks/trapi_setup.ipynb new file mode 100644 index 0000000..2521c25 --- /dev/null +++ b/notebooks/trapi_setup.ipynb @@ -0,0 +1,309 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "bf54bcd3-511a-4771-a763-5177d0ba34fd", + "metadata": {}, + "source": [ + "# Setting up a test subgraph and TRAPI endpoint for KG-Bioportal" + ] + }, + { + "cell_type": "markdown", + "id": "1a6b4ea7", + "metadata": {}, + "source": [ + "## Prepare subgraph for ontologies relevant to clinical data" + ] + }, + { + "cell_type": "markdown", + "id": "60e563ec", + "metadata": {}, + "source": [ + "Load the set of ontologies to work with. This is defined in `clinical_ontologies.yaml`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "38879a98", + "metadata": {}, + "outputs": [], + "source": [ + "import yaml" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "44ab5b49", + "metadata": {}, + "outputs": [], + "source": [ + "test_ontologies = []\n", + "with open ('clinical_ontologies.yaml', 'r') as infile:\n", + " ontologies_dict = yaml.safe_load(infile)\n", + "\n", + "for ontology in ontologies_dict['ontologies']:\n", + " try:\n", + " if ontology['test_set']:\n", + " test_ontologies.append(ontology['name'])\n", + " except KeyError:\n", + " continue\n", + "\n", + "test_ontologies" + ] + }, + { + "cell_type": "markdown", + "id": "9f9cd2f4", + "metadata": {}, + "source": [ + "Now build a graph of these alone. This assumes that the transformed Bioportal graphs are in `../transformed/ontologies/` by default, " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dcde626f", + "metadata": {}, + "outputs": [], + "source": [ + "test_ontologies_str = \",\".join(test_ontologies)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "916ee4c6", + "metadata": {}, + "outputs": [], + "source": [ + "%cd ../\n", + "!python run.py catmerge --include_only {test_ontologies_str}" + ] + }, + { + "cell_type": "markdown", + "id": "f9d4e996", + "metadata": {}, + "source": [ + "See how the result looks." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "29fb331c", + "metadata": {}, + "outputs": [], + "source": [ + "!tar -xvzf data/merged/merged-kg.tar.gz" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "79ec57c7", + "metadata": {}, + "outputs": [], + "source": [ + "!head merged-kg_edges.tsv" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8871d4d4", + "metadata": {}, + "outputs": [], + "source": [ + "!head merged-kg_nodes.tsv" + ] + }, + { + "cell_type": "markdown", + "id": "76af035b", + "metadata": {}, + "source": [ + "These didn't really get CURIE-d properly (an issue with the transform not using the expected prefix set) but let's go ahead anyway." + ] + }, + { + "cell_type": "markdown", + "id": "c3679824", + "metadata": {}, + "source": [ + "## Prepare as Neo4j" + ] + }, + { + "cell_type": "markdown", + "id": "0b920348", + "metadata": {}, + "source": [ + "Start a local Neo4j instance first." + ] + }, + { + "cell_type": "markdown", + "id": "e1995a23", + "metadata": {}, + "source": [ + "Install may look like the directions here:\n", + "https://neo4j.com/docs/operations-manual/current/installation/linux/debian/#debian-installation\n", + "\n", + "On my system, I had to enable systemctl first:\n", + "https://askubuntu.com/questions/1379425/system-has-not-been-booted-with-systemd-as-init-system-pid-1-cant-operate\n", + "\n", + "On the first run, there may be a message like this:\n", + "```bash\n", + "$ systemctl start neo4j.service\n", + "Failed to start neo4j.service: Interactive authentication required.\n", + "See system logs and 'systemctl status neo4j.service' for details.\n", + "```\n", + "\n", + "Just run:\n", + "```bash\n", + "$ sudo systemctl enable neo4j.service\n", + "$ sudo systemctl start neo4j.service\n", + "$ sudo systemctl status neo4j.service\n", + "```\n", + "\n", + "and it should be `active (running)`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "46676351", + "metadata": {}, + "outputs": [], + "source": [ + "from kgx.transformer import Transformer\n", + "\n", + "input_args = {\n", + " 'filename': [\"../merged-kg_edges.tsv\",\n", + " \"../merged-kg_nodes.tsv\"],\n", + " 'format': 'tsv'\n", + "}\n", + "output_args = {\n", + " 'uri': 'neo4j://localhost:7474',\n", + " 'username': 'neo4j',\n", + " 'password': 'demo',\n", + " 'format': 'neo4j'\n", + "}\n", + "\n", + "t = Transformer()\n", + "t.transform(input_args, output_args)\n" + ] + }, + { + "cell_type": "markdown", + "id": "f7f789b5", + "metadata": {}, + "source": [ + "## Set up and run Plater on its own" + ] + }, + { + "cell_type": "markdown", + "id": "98322a31", + "metadata": {}, + "source": [ + "See https://github.com/TranslatorSRI/Plater" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2159f6c5", + "metadata": {}, + "outputs": [], + "source": [ + "!git clone https://github.com/TranslatorSRI/Plater" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d93c1ecf", + "metadata": {}, + "outputs": [], + "source": [ + "!python -m pip install -r Plater/PLATER/requirements.txt" + ] + }, + { + "cell_type": "markdown", + "id": "db79d9fa", + "metadata": {}, + "source": [ + "Need a config file available as env variables.\n", + "Should look something like this:\n", + "```bash\n", + " WEB_HOST=0.0.0.0\n", + " WEB_PORT=8080\n", + " NEO4J_HOST=neo4j\n", + " NEO4J_USERNAME=neo4j\n", + " NEO4J_PASSWORD=demo\n", + " NEO4J_HTTP_PORT=7474\n", + " PLATER_TITLE='Plater'\n", + " PLATER_VERSION='1.2.0-7'\n", + " BL_VERSION='1.6.1'\n", + "```" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dbfdbab9", + "metadata": {}, + "outputs": [], + "source": [ + "!source Plater/.env" + ] + }, + { + "cell_type": "markdown", + "id": "1963bafd", + "metadata": {}, + "source": [ + "Running the FastAPI app can be erratic in a notebook, but run this:\n", + "```bash\n", + "$ uvicorn PLATER.services.server:APP --host 0.0.0.0 --port 8080 --reload\n", + "```" + ] + }, + { + "cell_type": "markdown", + "id": "9e2a8cdc", + "metadata": {}, + "source": [ + "## Set up and run Automat" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + 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= "^3.10" +kgx = "^2.4.2" +koza = "^0.6.1" +click = "^8.0.4" +kghub-downloader = "^0.3.9" +requests = "^2.32.3" + +[tool.poetry.group.dev.dependencies] +pytest = "^8.3.2" +setuptools = "^72.2.0" +tox = "^4.18.0" + +[tool.poetry.scripts] +kgbioportal = "kg_bioportal.cli:main" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index e69de29..0000000 diff --git a/run.py b/run.py deleted file mode 100644 index 69a65ae..0000000 --- a/run.py +++ /dev/null @@ -1,144 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -import os -from xml.etree.ElementInclude import include - -import click -from kg_bioportal import download as kg_download -from kg_bioportal import transform as kg_transform -from kg_bioportal.merge_utils.merge_kg import load_and_merge, update_merge_config, merge_with_cat_merge -from kg_bioportal.transform import DATA_SOURCES -from kg_bioportal.stats import make_graph_stats - - -@click.group() -def cli(): - pass - - -@cli.command() -@click.option("yaml_file", "-y", required=True, default="download.yaml", - type=click.Path(exists=True)) -@click.option("output_dir", "-o", required=True, default="data/raw") -@click.option("snippet_only", "-x", is_flag=True, default=False, - help='Download only the first 5 kB of each (uncompressed) source, for testing and file checks [false]') -@click.option("ignore_cache", "-i", is_flag=True, default=False, - help='ignore cache and download files even if they exist [false]') -def download(*args, **kwargs) -> None: - """Downloads data files from list of URLs (default: download.yaml) into data - directory (default: data/raw). - - Args: - yaml_file: Specify the YAML file containing a list of datasets to download. - output_dir: A string pointing to the directory to download data to. - snippet_only: Downloads only the first 5 kB of the source, for testing and file checks. - ignore_cache: If specified, will ignore existing files and download again. - - Returns: - None. - - """ - - kg_download(*args, **kwargs) - - return None - - -@cli.command() -@click.option("input_dir", "-i", default="data/raw", type=click.Path(exists=True)) -@click.option("output_dir", "-o", default="data/transformed") -@click.option("sources", "-s", default=None, multiple=True, - type=click.Choice(DATA_SOURCES.keys())) -def transform(*args, **kwargs) -> None: - """Calls scripts in kg_bioportal/transform/[source name]/ to transform each source - into nodes and edges. - - Args: - input_dir: A string pointing to the directory to import data from. - output_dir: A string pointing to the directory to output data to. - sources: A list of sources to transform. - - Returns: - None. - - """ - - # call transform script for each source - kg_transform(*args, **kwargs) - - return None - - -@cli.command() -@click.option('yaml', '-y', default="merge.yaml", type=click.Path(exists=True)) -@click.option('processes', '-p', default=1, type=int) -@click.option("--merge_all", - is_flag=True, - help="""Update the merge config file to include *all* ontologies.""") -@click.option("--include_only", - callback=lambda _,__,x: x.split(',') if x else [], - help="""One or more ontologies to merge, and only these, - comma-delimited and named by their short BioPortal ID, e.g., SEPIO.""") -@click.option("--exclude", - callback=lambda _,__,x: x.split(',') if x else [], - help="""One or more ontologies to exclude from merging, - comma-delimited and named by their short BioPortal ID, e.g., SEPIO. - Will select all other ontologies for merging.""") -def merge(yaml: str, processes: int, merge_all=False, include_only=[], exclude=[]) -> None: - """Use KGX to load subgraphs to create a merged graph. - - Args: - yaml: A string pointing to a KGX compatible config YAML. - processes: Number of processes to use. - merge_all: Update merge config to include *all* ontologies. - include_only: Update merge config to include the specified ontologies. - exclude: Update merge config to include all ontologies *except* those specified. - - Returns: - None. - - """ - - if merge_all or len(include_only) > 0 or len(exclude) > 0: - update_merge_config(yaml, merge_all, include_only, exclude) - - load_and_merge(yaml, processes) - - make_graph_stats(method='kgx', - input_file="merged_graph_stats.yaml", - output_file="graph_stats.yaml") - -@cli.command() -@click.option("--merge_all", - is_flag=True, - help="""Include *all* ontologies.""") -@click.option("--include_only", - callback=lambda _,__,x: x.split(',') if x else [], - help="""One or more ontologies to merge, and only these, - comma-delimited and named by their short BioPortal ID, e.g., SEPIO.""") -@click.option("--exclude", - callback=lambda _,__,x: x.split(',') if x else [], - help="""One or more ontologies to exclude from merging, - comma-delimited and named by their short BioPortal ID, e.g., SEPIO. - Will select all other ontologies for merging.""") -def catmerge(merge_all=False, include_only=[], exclude=[]) -> None: - """Use cat-merge to create a merged graph. - - Args: - merge_all: Include *all* ontologies. - include_only: Include only the specified ontologies. - exclude: Include all ontologies *except* those specified. - - Returns: - None. - - """ - - merge_with_cat_merge(merge_all, include_only, exclude) - - make_graph_stats(method='catmerge', - input_file="data/merged/qc_report.yaml", - output_file="graph_stats.yaml") - -if __name__ == "__main__": - cli() diff --git a/setup.py b/setup.py deleted file mode 100644 index abbc02f..0000000 --- a/setup.py +++ /dev/null @@ -1,79 +0,0 @@ -import os -import re - -from codecs import open as copen # to use a consistent encoding -from setuptools import find_packages, setup - -here = os.path.abspath(os.path.dirname(__file__)) - - -def read(*parts): - with copen(os.path.join(here, *parts), 'r') as fp: - return fp.read() - - -def find_version(*file_paths): - version_file = read(*file_paths) - version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", version_file, re.M) - if version_match: - return version_match.group(1) - raise RuntimeError('Unable to find version string.') - - -__version__ = find_version('kg_bioportal', '__version__.py') - -test_deps = [ - 'pytest', - 'pytest-cov', - 'coveralls', - 'validate_version_code', - 'codacy-coverage', - 'parameterized' -] - -extras = { - 'test': test_deps, -} - -setup( - name='kg_bioportal', - version=__version__, - description='BioPortal, as a Knowledge Graph', - long_description='BioPortal, as a Knowledge Graph', - url='https://github.com/Knowledge-Graph-Hub/kg_bioportal', - author='J. Harry Caufield', - author_email='jhc@lbl.gov', - python_requires='>=3.7', - - # choose your license - license='BSD-3', - include_package_data=True, - classifiers=[ - 'Development Status :: 3 - Beta', - 'License :: OSI Approved :: BSD License', - 'Programming Language :: Python :: 3' - ], - packages=find_packages(exclude=['contrib', 'docs', 'tests*']), - tests_require=test_deps, - # add package dependencies - install_requires=[ - 'cat-merge', - 'click==8.0.4', - 'compress_json', - 'kaleido', - 'kghub-downloader', - 'kgx', - 'networkx', - 'pandas', - 'parameterized', - 'plotly', - 'pyyaml', - 'recommonmark', - 'sphinx', - 'sphinx_rtd_theme', - 'tqdm', - 'validate_version_code', - 'wget', - ], - extras_require=extras, -) diff --git a/src/kg_bioportal/__init__.py b/src/kg_bioportal/__init__.py new file mode 100644 index 0000000..c96a6d1 --- /dev/null +++ b/src/kg_bioportal/__init__.py @@ -0,0 +1 @@ +"""KG-Bioportal""" \ No newline at end of file diff --git a/src/kg_bioportal/cli.py b/src/kg_bioportal/cli.py new file mode 100644 index 0000000..57f4a26 --- /dev/null +++ b/src/kg_bioportal/cli.py @@ -0,0 +1,231 @@ +"""CLI for KG-Bioportal.""" + +import logging + +import click + +from kg_bioportal.downloader import Downloader + +__all__ = [ + "main", +] + + +@click.group() +@click.option("-v", "--verbose", count=True) +@click.option("-q", "--quiet") +def main(verbose: int, quiet: bool): + """CLI for KG-Bioportal. + + :param verbose: Verbosity while running. + :param quiet: Boolean to be quiet or verbose. + """ + logger = logging.getLogger() + if verbose >= 2: + logger.setLevel(level=logging.DEBUG) + elif verbose == 1: + logger.setLevel(level=logging.INFO) + else: + logger.setLevel(level=logging.WARNING) + if quiet: + logger.setLevel(level=logging.ERROR) + logger.info(f"Logger {logger.name} set to level {logger.level}") + + +@main.command() +@click.option( + "ontologies", + "-d", + required=False, + type=str, +) +@click.option( + "ontology_file", + "-f", + required=False, + type=click.Path(exists=True), +) +@click.option("output_dir", "-o", required=True, default="data/raw") +@click.option( + "snippet_only", + "-x", + is_flag=True, + default=False, + help="Download only the first 5 kB of each (uncompressed) source, for testing and file checks [false]", +) +@click.option( + "ignore_cache", + "-i", + is_flag=True, + default=False, + help="ignore cache and download files even if they exist [false]", +) +@click.option( + "api_key", + "-k", + required=False, + type=str, + help="API key for BioPortal", +) +def download(ontologies, ontology_file, output_dir, snippet_only, ignore_cache, api_key) -> None: + """Downloads specified ontologies into data directory (default: data/raw). + + Args: + + ontologies: Specify the ontologies to download by name. This should be a space-delimited list + surrounded by quotes. Names should be those used in BioPortal, e.g., PO, SEPIO, etc. + + ontology_file: Specify the file containing a list of ontologies to download, + one per line. Names should be those used in BioPortal, e.g., PO, SEPIO, etc. + + output_dir: A string pointing to the directory to download data to. + Defaults to data/raw. + + snippet_only: Downloads only the first 5 kB of the source, for testing and file checks. + + ignore_cache: If specified, will ignore existing files and download again. + + Returns: + None. + + """ + + onto_list = [] + + # Parse the ontologies argument + if ontologies: + for ontology in ontologies.split(): + onto_list.append(ontology) + + # Parse the ontology_file argument + if ontology_file: + with open(ontology_file, "r") as f: + for line in f: + onto_list.append(line.strip()) + + logging.info(f"{len(onto_list)} ontologies to retrieve.") + + dl = Downloader(output_dir, snippet_only, ignore_cache, api_key) + + dl.download(onto_list) + + return None + + +# Below functions are WIP. + +# @cli.command() +# @click.option("input_dir", "-i", default="data/raw", type=click.Path(exists=True)) +# @click.option("output_dir", "-o", default="data/transformed") +# @click.option( +# "sources", "-s", default=None, multiple=True, type=click.Choice(DATA_SOURCES.keys()) +# ) +# def transform(*args, **kwargs) -> None: +# """Calls scripts in kg_bioportal/transform/[source name]/ to transform each source +# into nodes and edges. + +# Args: +# input_dir: A string pointing to the directory to import data from. +# output_dir: A string pointing to the directory to output data to. +# sources: A list of sources to transform. + +# Returns: +# None. + +# """ + +# # call transform script for each source +# kg_transform(*args, **kwargs) + +# return None + + +# @cli.command() +# @click.option("yaml", "-y", default="merge.yaml", type=click.Path(exists=True)) +# @click.option("processes", "-p", default=1, type=int) +# @click.option( +# "--merge_all", +# is_flag=True, +# help="""Update the merge config file to include *all* ontologies.""", +# ) +# @click.option( +# "--include_only", +# callback=lambda _, __, x: x.split(",") if x else [], +# help="""One or more ontologies to merge, and only these, +# comma-delimited and named by their short BioPortal ID, e.g., SEPIO.""", +# ) +# @click.option( +# "--exclude", +# callback=lambda _, __, x: x.split(",") if x else [], +# help="""One or more ontologies to exclude from merging, +# comma-delimited and named by their short BioPortal ID, e.g., SEPIO. +# Will select all other ontologies for merging.""", +# ) +# def merge( +# yaml: str, processes: int, merge_all=False, include_only=[], exclude=[] +# ) -> None: +# """Use KGX to load subgraphs to create a merged graph. + +# Args: +# yaml: A string pointing to a KGX compatible config YAML. +# processes: Number of processes to use. +# merge_all: Update merge config to include *all* ontologies. +# include_only: Update merge config to include the specified ontologies. +# exclude: Update merge config to include all ontologies *except* those specified. + +# Returns: +# None. + +# """ + +# if merge_all or len(include_only) > 0 or len(exclude) > 0: +# update_merge_config(yaml, merge_all, include_only, exclude) + +# load_and_merge(yaml, processes) + +# make_graph_stats( +# method="kgx", +# input_file="merged_graph_stats.yaml", +# output_file="graph_stats.yaml", +# ) + + +# @cli.command() +# @click.option("--merge_all", is_flag=True, help="""Include *all* ontologies.""") +# @click.option( +# "--include_only", +# callback=lambda _, __, x: x.split(",") if x else [], +# help="""One or more ontologies to merge, and only these, +# comma-delimited and named by their short BioPortal ID, e.g., SEPIO.""", +# ) +# @click.option( +# "--exclude", +# callback=lambda _, __, x: x.split(",") if x else [], +# help="""One or more ontologies to exclude from merging, +# comma-delimited and named by their short BioPortal ID, e.g., SEPIO. +# Will select all other ontologies for merging.""", +# ) +# def catmerge(merge_all=False, include_only=[], exclude=[]) -> None: +# """Use cat-merge to create a merged graph. + +# Args: +# merge_all: Include *all* ontologies. +# include_only: Include only the specified ontologies. +# exclude: Include all ontologies *except* those specified. + +# Returns: +# None. + +# """ + +# merge_with_cat_merge(merge_all, include_only, exclude) + +# make_graph_stats( +# method="catmerge", +# input_file="data/merged/qc_report.yaml", +# output_file="graph_stats.yaml", +# ) + + +if __name__ == "__main__": + main() diff --git a/src/kg_bioportal/downloader.py b/src/kg_bioportal/downloader.py new file mode 100644 index 0000000..81add2a --- /dev/null +++ b/src/kg_bioportal/downloader.py @@ -0,0 +1,89 @@ +"""Downloader for KG-Bioportal.""" + +import logging +import os +import requests + + +class Downloader: + + # Directory to save the downloaded files + output_dir: str = "data/raw" + + # If True, downloads only the first 5 kB of each (uncompressed) source, + # for testing and file checks + snippet_only: bool = False + + # If True, ignore cache and download files even if they exist + ignore_cache: bool = False + + # API key for BioPortal + api_key: str = "" + + def __init__( + self, + output_dir: str = "data/raw", + snippet_only: bool = False, + ignore_cache: bool = False, + api_key: str = "", + ) -> None: + """Initializes the Downloader class. + + Args: + output_dir: A string pointing to the location to download data to. + snippet_only: Downloads only the first 5 kB of the source, for testing and file checks. + ignore_cache: Ignore cache and download files even if they exist + api_key: API key for BioPortal + + Returns: + None. + """ + self.output_dir = output_dir + self.snippet_only = snippet_only + self.ignore_cache = ignore_cache + self.api_key = api_key + + # If the output directory does not exist, create it + if not os.path.exists(self.output_dir): + os.makedirs(self.output_dir) + + return None + + def download(self, onto_list: list = []) -> None: + """Downloads data files from list of ontologies into data directory. + + Args: + + onto_list: A list of ontologies to download by name. + Names should be those used in BioPortal, e.g., PO, SEPIO, etc. + + Returns: + None. + """ + headers = {"Authorization": f"apikey token={self.api_key}"} + + for ontology in onto_list: + logging.info(f"Downloading {ontology}...") + + metadata_url = f"https://data.bioontology.org/ontologies/{ontology}" + latest_sub_url = ( + f"https://data.bioontology.org/ontologies/{ontology}/latest_submission" + ) + download_url = ( + f"https://data.bioontology.org/ontologies/{ontology}/download" + ) + + metadata = requests.get(metadata_url, headers=headers).json() + logging.info(f"Name: {metadata['name']}") + latest_sub_metadata = requests.get(latest_sub_url, headers=headers).json() + logging.info( + f"Latest submission: {latest_sub_metadata['version']} - released {latest_sub_metadata['released']}" + ) + + download_onto = requests.get(download_url, headers=headers, allow_redirects=True) + onto_filename = download_onto.headers["Content-Disposition"].split("filename=")[1].replace('"', "") + with open(f"{self.output_dir}/{onto_filename}", "wb") as outfile: + outfile.write(download_onto.content) + + + return None