From f03b059331e3e3f0b69282dc7e04f80483935452 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 13 May 2024 16:01:17 -0700 Subject: [PATCH 01/15] validate now produces clean gpad with additional data from noctua, GPI now has a flag to switch between GPAD/GPI 2.0 and 1.2, plus tests --- bin/validate.py | 291 +++++++++++++++++++++++++++++----------- tests/test_gpiwriter.py | 54 ++++++-- 2 files changed, 259 insertions(+), 86 deletions(-) diff --git a/bin/validate.py b/bin/validate.py index ed024015..b59f4c04 100755 --- a/bin/validate.py +++ b/bin/validate.py @@ -45,7 +45,8 @@ def thispath(): os.path.normpath(os.path.abspath(__file__)) -def download_a_dataset_source(group, dataset_metadata, target_dir, source_url, base_download_url=None, replace_existing_files=True): +def download_a_dataset_source(group, dataset_metadata, target_dir, source_url, base_download_url=None, + replace_existing_files=True): """ This will download a dataset source given the group name, the metadata stanza for the dataset, and the target directory that all downloads @@ -96,10 +97,13 @@ def download_a_dataset_source(group, dataset_metadata, target_dir, source_url, b joined_url = urllib.parse.urljoin(base_download_url, source_url) else: # This is bad and we have to jump out`since we have no way of constructing a real gaf url - raise click.ClickException("Option `--base-download-url` was not specified and the config url {} is a relative path.".format(source_url)) + raise click.ClickException( + "Option `--base-download-url` was not specified and the config url {} is a relative path.".format( + source_url)) # including scheme and such - reconstructed_url = urllib.parse.urlunsplit((scheme, urllib.parse.urlparse(joined_url).netloc, urllib.parse.urlparse(joined_url).path, source_url_parsed.query, "")) + reconstructed_url = urllib.parse.urlunsplit((scheme, urllib.parse.urlparse(joined_url).netloc, + urllib.parse.urlparse(joined_url).path, source_url_parsed.query, "")) click.echo("Using URL `{}`".format(reconstructed_url)) @@ -111,7 +115,8 @@ def download_a_dataset_source(group, dataset_metadata, target_dir, source_url, b content_length = int(response.headers.get("Content-Length", 0)) with open(path, "wb") as downloaded: - with click.progressbar(iterable=response.iter_content(chunk_size=512 * 1024), length=content_length, show_percent=True) as chunks: + with click.progressbar(iterable=response.iter_content(chunk_size=512 * 1024), length=content_length, + show_percent=True) as chunks: for chunk in chunks: if chunk: downloaded.write(chunk) @@ -119,7 +124,8 @@ def download_a_dataset_source(group, dataset_metadata, target_dir, source_url, b return path -def download_source_gafs(group_metadata, target_dir, exclusions=[], base_download_url=None, replace_existing_files=True, only_dataset=None): +def download_source_gafs(group_metadata, target_dir, exclusions=[], base_download_url=None, replace_existing_files=True, + only_dataset=None): """ This looks at a group metadata dictionary and downloads each GAF source that is not in the exclusions list. For each downloaded file, keep track of the path of the file. If the file is zipped, it will unzip it here. @@ -128,17 +134,20 @@ def download_source_gafs(group_metadata, target_dir, exclusions=[], base_downloa # Grab all datasets in a group, excluding non-gaf, datasets that are explicitely excluded from an option, and excluding datasets with the `exclude key` set to true gaf_urls = [] if only_dataset is None: - gaf_urls = [ (data, data["source"]) for data in group_metadata["datasets"] if data["type"] == "gaf" and data["dataset"] not in exclusions and not data.get("exclude", False)] + gaf_urls = [(data, data["source"]) for data in group_metadata["datasets"] if + data["type"] == "gaf" and data["dataset"] not in exclusions and not data.get("exclude", False)] else: - gaf_urls = [ (data, data["source"]) for data in group_metadata["datasets"] if data["dataset"] == only_dataset ] + gaf_urls = [(data, data["source"]) for data in group_metadata["datasets"] if data["dataset"] == only_dataset] # List of dataset metadata to gaf download url - click.echo("Found {}".format(", ".join( [ kv[0]["dataset"] for kv in gaf_urls ] ))) + click.echo("Found {}".format(", ".join([kv[0]["dataset"] for kv in gaf_urls]))) downloaded_paths = [] for dataset_metadata, gaf_url in gaf_urls: dataset = dataset_metadata["dataset"] # Local target download path setup - path and then directories - path = download_a_dataset_source(group_metadata["id"], dataset_metadata, target_dir, gaf_url, base_download_url=base_download_url, replace_existing_files=replace_existing_files) + path = download_a_dataset_source(group_metadata["id"], dataset_metadata, target_dir, gaf_url, + base_download_url=base_download_url, + replace_existing_files=replace_existing_files) if dataset_metadata.get("compression", None) == "gzip": # Unzip any downloaded file that has gzip, strip of the gzip extension @@ -153,22 +162,24 @@ def download_source_gafs(group_metadata, target_dir, exclusions=[], base_downloa return downloaded_paths -def check_and_download_mixin_source(mixin_metadata, group_id, dataset, target_dir, base_download_url=None, replace_existing_files=True): +def check_and_download_mixin_source(mixin_metadata, group_id, dataset, target_dir, base_download_url=None, + replace_existing_files=True): mixin_dataset = tools.find(mixin_metadata["datasets"], lambda d: d.get("merges_into", "") == dataset) if mixin_dataset is None: return None - click.echo("Merging mixin dataset {}".format(mixin_dataset["source"])) - path = download_a_dataset_source(group_id, mixin_dataset, target_dir, mixin_dataset["source"], base_download_url=base_download_url, replace_existing_files=replace_existing_files) + click.echo("Downloading dataset {}".format(mixin_dataset["source"])) + path = download_a_dataset_source(group_id, mixin_dataset, target_dir, mixin_dataset["source"], + base_download_url=base_download_url, replace_existing_files=replace_existing_files) - unzipped = unzip_simple(path) # Strip off the .gz extension, leaving just the unzipped filename + unzipped = unzip_simple(path) # Strip off the .gz extension, leaving just the unzipped filename return unzipped def mixin_dataset(mixin_metadata, dataset): mixin_dataset_version = tools.find(mixin_metadata["datasets"], lambda d: d.get("merges_into", "") == dataset) if mixin_dataset_version is None: - return None # Blah + return None # Blah return mixin_dataset_version @@ -209,8 +220,13 @@ def create_parser(config, group, dataset, format="gaf"): Produce validated gaf using the gaf parser/ """ + @tools.gzips -def produce_gaf(dataset, source_gaf, ontology_graph, gpipaths=None, paint=False, group="unknown", rule_metadata=None, goref_metadata=None, ref_species_metadata=None, db_entities=None, group_idspace=None, format="gaf", suppress_rule_reporting_tags=[], annotation_inferences=None, group_metadata=None, extensions_constraints=None, rule_contexts=[], gaf_output_version="2.2", rule_set=assocparser.RuleSet.ALL): +def produce_gaf(dataset, source_gaf, ontology_graph, gpipaths=None, paint=False, group="unknown", rule_metadata=None, + goref_metadata=None, ref_species_metadata=None, db_entities=None, group_idspace=None, + format="gaf", suppress_rule_reporting_tags=[], annotation_inferences=None, group_metadata=None, + extensions_constraints=None, rule_contexts=[], gaf_output_version="2.2", + rule_set=assocparser.RuleSet.ALL) -> list[str]: filtered_associations = open(os.path.join(os.path.split(source_gaf)[0], "{}_noiea.gaf".format(dataset)), "w") config = assocparser.AssocParserConfig( ontology=ontology_graph, @@ -268,7 +284,8 @@ def produce_gaf(dataset, source_gaf, ontology_graph, gpipaths=None, paint=False, report_json.write(json.dumps(parser.report.to_report_json(), indent=4)) logger.info("json {} written out".format(report_markdown_path)) - logger.info("gorule-13 first 10 messages: {}".format(json.dumps(parser.report.to_report_json()["messages"].get("gorule-0000013", [])[:10], indent=4))) + logger.info("gorule-13 first 10 messages: {}".format( + json.dumps(parser.report.to_report_json()["messages"].get("gorule-0000013", [])[:10], indent=4))) logger.info("json current Stack:") if logger.getEffectiveLevel() == logging.INFO: traceback.print_stack() @@ -277,17 +294,15 @@ def produce_gaf(dataset, source_gaf, ontology_graph, gpipaths=None, paint=False, @tools.gzips -def make_products(dataset, target_dir, gaf_path, products, ontology_graph): - +def make_ttls(dataset, gaf_path, products, ontology_graph): with open(gaf_path) as sg: lines = sum(1 for line in sg) product_files = { - "gpad": open(os.path.join(os.path.split(gaf_path)[0], "{}.gpad".format(dataset)), "w"), "ttl": open(os.path.join(os.path.split(gaf_path)[0], "{}_cam.ttl".format(dataset)), "wb") } - if not products["gpad"] and not products["ttl"]: + if not products["ttl"]: # Bail if we have no products return [] @@ -302,23 +317,16 @@ def make_products(dataset, target_dir, gaf_path, products, ontology_graph): click.echo("Using {} as the gaf to build data products with".format(gaf_path)) if products["ttl"]: click.echo("Setting up {}".format(product_files["ttl"].name)) - rdf_writer = assoc_rdfgen.TurtleRdfWriter(label=os.path.split(product_files["ttl"].name)[1] ) + rdf_writer = assoc_rdfgen.TurtleRdfWriter(label=os.path.split(product_files["ttl"].name)[1]) transformer = assoc_rdfgen.CamRdfTransform(writer=rdf_writer) - if products["gpad"]: - click.echo("Setting up {}".format(product_files["gpad"].name)) - gpadwriter = GpadWriter(file=product_files["gpad"]) - - click.echo("Making products...") + click.echo("Making ttl products...") with click.progressbar(iterable=gafparser.association_generator(file=gf), length=lines) as associations: for association in associations: if products["ttl"]: transformer.provenance() transformer.translate(association) - if products["gpad"]: - gpadwriter.write_assoc(association) - # post ttl steps if products["ttl"]: click.echo("Writing ttl to disk") @@ -330,8 +338,106 @@ def make_products(dataset, target_dir, gaf_path, products, ontology_graph): return [product_files[prod].name for prod in sorted(product_files.keys()) if products[prod]] + @tools.gzips -def produce_gpi(dataset, target_dir, gaf_path, ontology_graph): +def make_gpads(dataset, gaf_path, products, ontology_graph, + noctua_gpad_file, paint_gaf_src, gpi, gpad_gpi_output_version): + """ + Using the gaf files and the noctua gpad file, produce a gpad file that contains both kinds of annotations + without any loss. + + :param dataset: The dataset name + :param gaf_path: The path to the gaf file + :param products: The products to make + :param ontology_graph: The ontology graph to use for parsing the associations + :param noctua_gpad_file: The path to the noctua gpad file + :param paint_gaf_src: The source of the paint gaf file + :param gpi: The path to the gpi file -- needed to convert isoform annotations from Noctua files + to gene annotations in GAF outputs. + :return: The path to the gpad file + + """ + gpad_file_path = os.path.join(os.path.split(gaf_path)[0], f"{dataset}.gpad") + + if not products["gpad"]: + return [] + + # Open the file once and keep it open for all operations within this block + with open(gpad_file_path, "w") as outfile: + gpadwriter = GpadWriter(file=outfile, version=gpad_gpi_output_version) + + # If there's a noctua gpad file, process it + if noctua_gpad_file: + click.echo("Making noctua gpad products...{}".format(noctua_gpad_file)) + # Process noctua gpad file + process_noctua_gpad_file(noctua_gpad_file, gpadwriter, ontology_graph, gpi) + + # Process the GAF file + process_gaf_file(gaf_path, gpadwriter, ontology_graph, paint_gaf_src) + + # The file will be automatically closed here, after exiting the 'with' block + return [gpad_file_path] + + +def process_noctua_gpad_file(noctua_gpad_file, gpadwriter, ontology_graph, gpi): + """ + Process a noctua gpad file and write the associations to the gpad writer. + + :param noctua_gpad_file: The path to the noctua gpad file + :param gpadwriter: The gpad writer to write the associations to + :param ontology_graph: The ontology graph to use for parsing the associations + :param gpi: The path to the gpi file -- needed to convert isoform annotations from Noctua files + """ + + with open(noctua_gpad_file) as nf: + lines = sum(1 for line in nf) + nf.seek(0) # Reset file pointer to the beginning after counting lines + gpadparser = GpadParser(config=assocparser.AssocParserConfig(ontology=ontology_graph, + paint=False, + rule_set="all")) + click.echo("Making noctua gpad products...") + with click.progressbar(iterable=gpadparser.association_generator(file=nf), length=lines) as associations: + for association in associations: + # If the association is an isoform annotation, convert it to a gene annotation + gpadwriter.write_assoc(association) + + +def process_gaf_file(gaf_path, gpadwriter, ontology_graph, paint_gaf_src): + """ + Process a gaf file and write the associations to the gpad writer. + + :param gaf_path: The path to the gaf file + :param gpadwriter: The gpad writer to write the associations to + :param ontology_graph: The ontology graph to use for parsing the associations + :param paint_gaf_src: The source of the paint gaf file + + """ + with open(gaf_path) as gf: + lines = sum(1 for line in gf) + gf.seek(0) # Reset file pointer to the beginning after counting lines + gafparser = GafParser(config=assocparser.AssocParserConfig(ontology=ontology_graph, + paint=True, + rule_set="all")) + click.echo("Merging in source gaf to gpad product...") + with click.progressbar(iterable=gafparser.association_generator(file=gf), length=lines) as associations: + for association in associations: + gpadwriter.write_assoc(association) + + if paint_gaf_src is not None: + with open(paint_gaf_src) as pgf: + lines = sum(1 for line in pgf) + pgf.seek(0) + gafparser = GafParser(config=assocparser.AssocParserConfig(ontology=ontology_graph, + paint=True, + rule_set="all")) + click.echo("Merging in paint gaf to gpad product...") + with click.progressbar(iterable=gafparser.association_generator(file=pgf), length=lines) as associations: + for association in associations: + gpadwriter.write_assoc(association) + + +@tools.gzips +def produce_gpi(dataset, target_dir, gaf_path, ontology_graph, gpad_gpi_output_version): gafparser = GafParser() gafparser.config = assocparser.AssocParserConfig( ontology=ontology_graph @@ -342,13 +448,13 @@ def produce_gpi(dataset, target_dir, gaf_path, ontology_graph): gpi_path = os.path.join(os.path.split(gaf_path)[0], "{}.gpi".format(dataset)) with open(gaf_path) as gf, open(gpi_path, "w") as gpi: click.echo("Using {} as the gaf to build gpi with".format(gaf_path)) - bridge = gafgpibridge.GafGpiBridge() - gpiwriter = entitywriter.GpiWriter(file=gpi) + bridge = gafgpibridge + gpiwriter = entitywriter.GpiWriter(file=gpi, version=gpad_gpi_output_version) gpi_cache = set() with click.progressbar(iterable=gafparser.association_generator(file=gf), length=lines) as associations: for association in associations: - entity = bridge.convert_association(association) + entity = bridge.convert_association(association, gpad_gpi_output_version) if entity not in gpi_cache and entity is not None: # If the entity is not in the cache, add it and write it out gpi_cache.add(entity) @@ -404,10 +510,11 @@ def header_and_annotations(gaf_file): def make_mixin_header(header_lines, path): the_header = [ - "!Header copied from {}".format(os.path.basename(path)), - "!=================================" - ] + header_lines[8:] + ["!"] + "!Header copied from {}".format(os.path.basename(path)), + "!=================================" + ] + header_lines[8:] + ["!"] return the_header + # #################################################################### # Set up merged final gaf product path @@ -427,16 +534,16 @@ def make_mixin_header(header_lines, path): annotations += mixin_annotations full_header = valid_header + \ - [ - "!=================================", - "!" - ] + mixin_headers + \ - [ - "!=================================", - "!", - "!Documentation about this header can be found here: https://github.com/geneontology/go-site/blob/master/docs/gaf_validation.md", - "!" - ] + [ + "!=================================", + "!" + ] + mixin_headers + \ + [ + "!=================================", + "!", + "!Documentation about this header can be found here: https://github.com/geneontology/go-site/blob/master/docs/gaf_validation.md", + "!" + ] all_lines = full_header + annotations with open(merged_path, "w") as merged_file: @@ -445,19 +552,25 @@ def make_mixin_header(header_lines, path): return merged_path -def mixin_a_dataset(valid_gaf, mixin_metadata_list, group_id, dataset, target, ontology, gpipaths=None, base_download_url=None, rule_metadata={}, replace_existing_files=True, rule_contexts=[], gaf_output_version="2.2"): - +def mixin_a_dataset(valid_gaf, mixin_metadata_list, group_id, dataset, target, ontology, gpipaths=None, + base_download_url=None, rule_metadata={}, replace_existing_files=True, rule_contexts=[], + gaf_output_version="2.2"): end_gaf = valid_gaf mixin_gaf_paths = [] for mixin_metadata in mixin_metadata_list: - mixin_src = check_and_download_mixin_source(mixin_metadata, group_id, dataset, target, base_download_url=base_download_url, replace_existing_files=replace_existing_files) + click.echo("Merging mixin dataset {}".format(mixin_metadata["id"])) + mixin_src = check_and_download_mixin_source(mixin_metadata, group_id, dataset, target, + base_download_url=base_download_url, + replace_existing_files=replace_existing_files) if mixin_src is not None: mixin_dataset_metadata = mixin_dataset(mixin_metadata, dataset) mixin_dataset_id = mixin_dataset_metadata["dataset"] format = mixin_dataset_metadata["type"] context = ["import"] if mixin_metadata.get("import", False) else [] - mixin_gaf = produce_gaf(mixin_dataset_id, mixin_src, ontology, gpipaths=gpipaths, paint=True, group=mixin_metadata["id"], rule_metadata=rule_metadata, format=format, rule_contexts=context, gaf_output_version=gaf_output_version)[0] + mixin_gaf = produce_gaf(mixin_dataset_id, mixin_src, ontology, gpipaths=gpipaths, paint=True, + group=mixin_metadata["id"], rule_metadata=rule_metadata, format=format, + rule_contexts=context, gaf_output_version=gaf_output_version)[0] mixin_gaf_paths.append(mixin_gaf) if mixin_gaf_paths: @@ -477,24 +590,30 @@ def cli(ctx, verbose): if verbose: logger.setLevel(logging.INFO) + @cli.command() @click.pass_context @click.argument("group") @click.option("--metadata", "-m", "metadata_dir", type=click.Path(), required=True) @click.option("--gpad", default=False, is_flag=True) +@click.option("--https://github.com/microbiomedata/nmdc-schema/issues/1925", default="2.0", type=click.Choice(["1.2", "2.0"])) @click.option("--ttl", default=False, is_flag=True) @click.option("--target", "-t", type=click.Path(), required=True) @click.option("--ontology", "-o", type=click.Path(exists=True), required=False) @click.option("--exclude", "-x", multiple=True) @click.option("--base-download-url", "-b", default=None) -@click.option("--suppress-rule-reporting-tag", "-S", multiple=True, help="Suppress markdown output messages from rules tagged with this tag") -@click.option("--skip-existing-files", "-K", is_flag=True, default=False, help="When downloading files, if a file already exists it won't downloaded over") -@click.option("--gaferencer-file", "-I", type=click.Path(exists=True), default=None, required=False, help="Path to Gaferencer output to be used for inferences") +@click.option("--suppress-rule-reporting-tag", "-S", multiple=True, + help="Suppress markdown output messages from rules tagged with this tag") +@click.option("--skip-existing-files", "-K", is_flag=True, default=False, + help="When downloading files, if a file already exists it won't downloaded over") +@click.option("--gaferencer-file", "-I", type=click.Path(exists=True), default=None, required=False, + help="Path to Gaferencer output to be used for inferences") @click.option("--only-dataset", default=None) @click.option("--gaf-output-version", default="2.2", type=click.Choice(["2.1", "2.2"])) @click.option("--rule-set", "-l", "rule_set", default=[assocparser.RuleSet.ALL], multiple=True) -def produce(ctx, group, metadata_dir, gpad, ttl, target, ontology, exclude, base_download_url, suppress_rule_reporting_tag, skip_existing_files, gaferencer_file, only_dataset, gaf_output_version, rule_set): - +def produce(ctx, group, metadata_dir, gpad, gpad_gpi_output_version, ttl, target, ontology, exclude, base_download_url, + suppress_rule_reporting_tag, skip_existing_files, gaferencer_file, only_dataset, gaf_output_version, + rule_set): logger.info("Logging is verbose") products = { "gaf": True, @@ -512,7 +631,10 @@ def produce(ctx, group, metadata_dir, gpad, ttl, target, ontology, exclude, base click.echo("Loading ontology: {}...".format(ontology)) ontology_graph = OntologyFactory().create(ontology, ignore_cache=True) - downloaded_gaf_sources = download_source_gafs(group_metadata, absolute_target, exclusions=exclude, base_download_url=base_download_url, replace_existing_files=not skip_existing_files, only_dataset=only_dataset) + downloaded_gaf_sources = download_source_gafs(group_metadata, absolute_target, exclusions=exclude, + base_download_url=base_download_url, + replace_existing_files=not skip_existing_files, + only_dataset=only_dataset) # extract the titles for the go rules, this is a dictionary comprehension rule_metadata = metadata.yamldown_lookup(os.path.join(absolute_metadata, "rules")) @@ -525,7 +647,7 @@ def produce(ctx, group, metadata_dir, gpad, ttl, target, ontology, exclude, base paint_metadata = metadata.dataset_metadata_file(absolute_metadata, "paint") noctua_metadata = metadata.dataset_metadata_file(absolute_metadata, "noctua") - mixin_metadata_list = list(filter(lambda m: m != None, [paint_metadata, noctua_metadata])) + mixin_metadata_list = list(filter(lambda m: m != None, [paint_metadata])) db_entities = metadata.database_entities(absolute_metadata) group_ids = metadata.groups(absolute_metadata) @@ -544,24 +666,25 @@ def produce(ctx, group, metadata_dir, gpad, ttl, target, ontology, exclude, base # Set paint to True when the group is "paint". # This will prevent filtering of IBA (GO_RULE:26) when paint is being treated as a top level group, # like for paint_other. + click.echo("source_gaf: {}".format(source_gaf)) valid_gaf = produce_gaf(dataset, source_gaf, ontology_graph, - paint=(group=="paint"), - group=group, - rule_metadata=rule_metadata, - goref_metadata=goref_metadata, - ref_species_metadata=ref_species_metadata, - db_entities=db_entities, - group_idspace=group_ids, - suppress_rule_reporting_tags=suppress_rule_reporting_tag, - annotation_inferences=gaferences, - group_metadata=group_metadata, - extensions_constraints=extensions_constraints, - rule_contexts=["import"] if dataset_metadata.get("import", False) else [], - gaf_output_version=gaf_output_version, - rule_set=rule_set - )[0] - - gpi = produce_gpi(dataset, absolute_target, valid_gaf, ontology_graph) + paint=(group == "paint"), + group=group, + rule_metadata=rule_metadata, + goref_metadata=goref_metadata, + ref_species_metadata=ref_species_metadata, + db_entities=db_entities, + group_idspace=group_ids, + suppress_rule_reporting_tags=suppress_rule_reporting_tag, + annotation_inferences=gaferences, + group_metadata=group_metadata, + extensions_constraints=extensions_constraints, + rule_contexts=["import"] if dataset_metadata.get("import", False) else [], + gaf_output_version=gaf_output_version, + rule_set=rule_set + )[0] + + gpi = produce_gpi(dataset, absolute_target, valid_gaf, ontology_graph, gpad_gpi_output_version) gpi_list = [gpi] # Try to find other GPIs in metadata and merge @@ -574,11 +697,27 @@ def produce(ctx, group, metadata_dir, gpad, ttl, target, ontology, exclude, base matching_gpi_path = unzip_simple(matching_gpi_path) gpi_list.append(matching_gpi_path) - end_gaf = mixin_a_dataset(valid_gaf, mixin_metadata_list, group_metadata["id"], dataset, absolute_target, + noctua_gpad_src = check_and_download_mixin_source(noctua_metadata, group_metadata["id"], dataset, target, + base_download_url=base_download_url, + replace_existing_files=not skip_existing_files) + paint_gaf_src = (check_and_download_mixin_source(paint_metadata, group_metadata["id"], dataset, target, + base_download_url=base_download_url, + replace_existing_files=not skip_existing_files) + if paint_metadata else None) + + make_gpads(dataset, valid_gaf, products, + ontology_graph, noctua_gpad_src, paint_gaf_src, + gpi, gpad_gpi_output_version) + + end_gaf = mixin_a_dataset(valid_gaf, [noctua_metadata, paint_metadata], + group_metadata["id"], dataset, absolute_target, ontology_graph, gpipaths=gpi_list, base_download_url=base_download_url, rule_metadata=rule_metadata, replace_existing_files=not skip_existing_files, gaf_output_version=gaf_output_version) - make_products(dataset, absolute_target, end_gaf, products, ontology_graph) + + click.echo(end_gaf) + + make_ttls(dataset, end_gaf, products, ontology_graph) @cli.command() diff --git a/tests/test_gpiwriter.py b/tests/test_gpiwriter.py index 1e435626..0b3c0697 100644 --- a/tests/test_gpiwriter.py +++ b/tests/test_gpiwriter.py @@ -3,29 +3,63 @@ from ontobio.io import entitywriter, gafgpibridge -def test_header_newline(): +def test_gpi_2_0_writer(): gpi_obj = { 'id': "MGI:MGI:1918911", 'label': "0610005C13Rik", # db_object_symbol, 'full_name': "RIKEN cDNA 0610005C13 gene", # db_object_name, 'synonyms': [], - 'type': ["gene"], # db_object_type, - 'parents': "", # GAF does not have this field, but it's optional in GPI - 'xrefs': "", # GAF does not have this field, but it's optional in GPI - 'taxon': { - 'id': "NCBITaxon:10090" - } + 'type': ["SO:0000000"], # db_object_type, + 'taxon': {"id": "NCBITaxon:10090"}, + 'encoded_by': "", # encoded_by + 'parents': "", + 'protein_containing_complex_members': "", # protein_containing_complex_members + 'xrefs': "", + 'properties': "" + } + + entity = gafgpibridge.Entity(gpi_obj) + + out = io.StringIO() + gpiwriter20 = entitywriter.GpiWriter(file=out, version="2.0") + gpiwriter20.write_entity(entity) + outlines = out.getvalue().split("\n") + + expected_lines = [ + "!gpi-version: 2.0", + "MGI:MGI:1918911\t0610005C13Rik\tRIKEN cDNA 0610005C13 gene\t\tSO:0000000\ttaxon:10090\t\t\t\t\t", + "" + ] + assert expected_lines == outlines + + +def test_gpi_1_2_writer(): + gpi_obj = { + 'id': "MGI:MGI:1918911", + 'label': "0610005C13Rik", # db_object_symbol, + 'full_name': "RIKEN cDNA 0610005C13 gene", # db_object_name, + 'synonyms': [], + 'type': ["SO:0000000"], # db_object_type, + 'taxon': {"id": "NCBITaxon:10090"}, + 'encoded_by': "", # encoded_by + 'parents': "", + 'protein_containing_complex_members': "", # protein_containing_complex_members + 'xrefs': "", + 'properties': "" + + } + entity = gafgpibridge.Entity(gpi_obj) out = io.StringIO() - gpiwriter = entitywriter.GpiWriter(file=out) - gpiwriter.write_entity(entity) + gpiwriter20 = entitywriter.GpiWriter(file=out, version="1.2") + gpiwriter20.write_entity(entity) outlines = out.getvalue().split("\n") expected_lines = [ "!gpi-version: 1.2", - "MGI\tMGI:1918911\t0610005C13Rik\tRIKEN cDNA 0610005C13 gene\t\tgene\ttaxon:10090\t\t\t", + "MGI\tMGI:1918911\t0610005C13Rik\tRIKEN cDNA 0610005C13 gene\t\tSO:0000000\ttaxon:10090\t\t\t", "" ] assert expected_lines == outlines From 96e7518bf29da13f654b2689405674bc3d363b9d Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 13 May 2024 16:05:50 -0700 Subject: [PATCH 02/15] minimal changes to support isoforms as subjects in GPAD 2.0 formatted files --- bin/README.md | 16 ++++++ ontobio/io/assocwriter.py | 17 ++++--- ontobio/io/entitywriter.py | 94 ++++++++++++++++++++++++++++-------- ontobio/model/association.py | 12 +++-- 4 files changed, 111 insertions(+), 28 deletions(-) diff --git a/bin/README.md b/bin/README.md index 19796e28..f5aae56b 100644 --- a/bin/README.md +++ b/bin/README.md @@ -1 +1,17 @@ See [command line docs](http://ontobio.readthedocs.io/en/latest/commandline.html#commandline) on ReadTheDocs + +To test validate.py "validate" command, the command that produces the final GPADs in the pipeline via the "mega make" +(aka: "produces GAFs, GPADs, ttl" stage), on a particular source: + +```bash +poetry install +poetry run validate produce -m ../go-site/metadata --gpad -t . -o go-basic.json --base-download-url "http://skyhook.berkeleybop.org/[PIPELINE_BRANCH_NAME]/" --only-dataset mgi MGI +poetry run validate produce -m ../go-site/metadata --gpad -t . -o go-basic.json --base-download-url "http://skyhook.berkeleybop.org/[PIPELINE_BRANCH_NAME]/" --only-dataset goa_chicken goa +``` + + +To test whether a GAF file is valid (passes all the GORules): +```bash +poetry install +poetry run python3 ontobio-parse-assocs.py --file [path_to_file.gaf] --format GAF -o mgi_valid.gaf --report-md mgi.report.md -r [path_to_go.json] -l all validate +``` \ No newline at end of file diff --git a/ontobio/io/assocwriter.py b/ontobio/io/assocwriter.py index 697438f4..f930e515 100644 --- a/ontobio/io/assocwriter.py +++ b/ontobio/io/assocwriter.py @@ -6,6 +6,7 @@ import datetime import json import logging +import click from typing import List, Union @@ -108,18 +109,23 @@ def write(self, assocs, meta=None): GPAD_2_0 = "2.0" GPAD_1_2 = "1.2" + class GpadWriter(AssocWriter): """ Writes Associations in GPAD format """ - def __init__(self, file=None, version=GPAD_1_2): + def __init__(self, file=None, version=None): self.file = file + click.echo("Writing GPAD version: {}".format(version)) if version in [GPAD_1_2, GPAD_2_0]: self.version = version else: self.version = GPAD_1_2 - self._write("!gpa-version: {}\n".format(self.version)) + self._write("!gpad-version: {}\n".format(self.version)) + click.echo("Writing GPAD version: {}".format(self.version)) + self._write("!generated-by: {}\n".format("GO Central")) + self._write("!date-generated: {}\n".format(str(datetime.datetime.now().strftime("%Y-%m-%dT%H:%M")))) self.ecomap = ecomap.EcoMap() def as_tsv(self, assoc: Union[association.GoAssociation, dict]): @@ -136,7 +142,6 @@ def as_tsv(self, assoc: Union[association.GoAssociation, dict]): return assoc.to_gpad_1_2_tsv() - class GafWriter(AssocWriter): """ Writes Associations in GAF format. @@ -151,13 +156,13 @@ class GafWriter(AssocWriter): The only difference in 2.1 and 2.2 are how qualifiers (column 4) are handled. GAF 2.1 allows empty or only `NOT` qualifier values, and only allows - `colocalizes_with` and `contributes_to` as qualifer values. However in 2.2 + `colocalizes_with` and `contributes_to` as qualifier values. However, in 2.2 qualifier must *not* be empty and cannot have only `NOT` as it's a modifier - on existing qualifers. The set of allowed qualifiers in 2.2 is also expanded. + on existing qualifiers. The set of allowed qualifiers in 2.2 is also expanded. So if there's a mismatch between converting from an annotation and a GAF version then that annotation is just skipped and not written out with an - error message displayed. Mismatch occurances of this kind would appear if + error message displayed. Mismatch occurrences of this kind would appear if the incoming annotation has a qualifier in the 2.2 set, but 2.1 is being written out, or if the qualifier is empty and 2.2 is being written. """ diff --git a/ontobio/io/entitywriter.py b/ontobio/io/entitywriter.py index 9438f0ea..e538598f 100644 --- a/ontobio/io/entitywriter.py +++ b/ontobio/io/entitywriter.py @@ -71,11 +71,16 @@ def write(self, entities, meta=None): for e in entities: self.write_entity(e) + class GpiWriter(EntityWriter): """ - Writes entities in GPI format + Writes entities in GPI 1.2 or 2.0 (https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md) format + + :param file: file + :param version: str + + Takes an "entity" dictionary generated typically from a GoAssociation object - Takes an entity dictionary: { 'id': id, (String) 'label': db_object_symbol, (String) @@ -89,29 +94,80 @@ class GpiWriter(EntityWriter): } } """ - def __init__(self, file=None): + def __init__(self, file=None, version=None): self.file = file + self.version = version if self.file: - self.file.write("!gpi-version: 1.2\n") + if self.version == "2.0": + self.file.write("!gpi-version: 2.0\n") + else: + self.file.write("!gpi-version: 1.2\n") def write_entity(self, entity): """ Write a single entity to a line in the output file + + :param entity: dict ; typically a dictionary representing an instance of a GoAssociation object + :param gpi_output_version: str ; the version of the GPAD output file to write + :return: None + + GPI 2.0 spec <-- entity attributes + + 1. DB_Object_ID <-- entity.id (CURIE format) + 2. DB_Object_symbol <-- entity.label + 3. DB_Object_Name <-- entity.full_name + 4. DB_Object_Synonyms <-- entity.synonyms + 5. DB_Object_Type <-- entity.type + 6. DB_Object_Taxon <-- entity.taxon + 7. Encoded_by <-- does not appear in GAF file, this is optional in GPI + 8. Parent_Protein <-- entity.parents # unclear if this is a list or a single value + 9. Protein_Containing_Complex_Members <-- does not appear in GAF file, this is optional in GPI + 10. DB_Xrefs <-- entity.xrefs + 11. Gene_Product_Properties <-- entity.properties + + GPI 1.2 spec <-- entity attributes + + 1. DB <-- entity.id.prefix + 2. DB_Object_ID <-- entity.id.local_id + 3. DB_Object_Symbol <-- entity.label + 4. DB_Object_Name <-- entity.full_name + 5. DB_Object_Synonym(s) <-- entity.synonyms + 6. DB_Object_Type <-- entity.type + 7. Taxon <-- entity.taxon + 8. Parent_Object_ID <-- entity.parents # unclear if this is a list or a single value + 9. DB_Xref(s) <-- entity.xrefs + 10. Properties <-- entity.properties + """ - db, db_object_id = self._split_prefix(entity) - taxon = normalize_taxon(entity["taxon"]["id"]) - - vals = [ - db, - db_object_id, - entity.get('label'), - entity.get('full_name'), - entity.get('synonyms'), - entity.get('type'), - taxon, - entity.get('parents'), - entity.get('xrefs'), - entity.get('properties') - ] + print(entity.get('taxon')) + + if self.version == "2.0": + vals = [ + entity.get('id'), # DB_Object_ID + entity.get('label'), # DB_Object_symbol + entity.get('full_name'), # DB_Object_Name + entity.get('synonyms'), # DB_Object_Synonyms + entity.get('type'), # DB_Object_Type + normalize_taxon(entity.get("taxon").get("id")), # DB_Object_Taxon + "", # Encoded_by + entity.get('parents'), # Parent_Protein + "", # Protein_Containing_Complex_Members + entity.get('xrefs'), # DB_Xrefs + entity.get('properties') # Gene_Product_Properties + ] + else: + prefix, local_id = self._split_prefix(entity) + vals = [ + prefix, # DB + local_id, # DB_Object_ID + entity.get('label'), # DB_Object_Symbol + entity.get('full_name'), # DB_Object_Symbol + entity.get('synonyms'), # DB_Object_Name + entity.get('type'), # DB_Object_Synonyms + normalize_taxon(entity.get("taxon").get("id")), # taxon + entity.get('parents'), # Parent_Object_ID + entity.get('xrefs'), # DB_Xref(s) + entity.get('properties') # Properties + ] self._write_row(vals) diff --git a/ontobio/model/association.py b/ontobio/model/association.py index 968dffab..f3231c0b 100644 --- a/ontobio/model/association.py +++ b/ontobio/model/association.py @@ -491,7 +491,7 @@ class GoAssociation: """ The internal model used by the parsers and qc Rules engine that all annotations are parsed into. - If an annotation textual line cannot be parsed into a GoAssociation then it is not a well formed line. + If an annotation textual line cannot be parsed into a GoAssociation then it is not a well-formed line. This class provides several methods to convert this GoAssociation into other representations, like GAF and GPAD of each version, as well as the old style dictionary Association that this class replaced (for compatibility if needed). @@ -501,7 +501,7 @@ class GoAssociation: """ source_line: Optional[str] subject: Subject - relation: Curie # This is the relation Curie + relation: Curie # This is the relation Curie object: Term negated: bool qualifiers: List[Curie] @@ -644,6 +644,12 @@ def to_gpad_2_0_tsv(self) -> List: """ props_list = ["{key}={value}".format(key=key, value=value) for key, value in self.properties] + gp_isoforms = None + if self.subject_extensions: + gp_isoforms = self.subject_extensions[0].term + if gp_isoforms: + self.subject.id = gp_isoforms + return [ str(self.subject.id), "NOT" if self.negated else "", @@ -656,7 +662,7 @@ def to_gpad_2_0_tsv(self) -> List: ymd_str(self.date, "-"), self.provided_by, ConjunctiveSet.list_to_str(self.object_extensions, - conjunct_to_str=lambda conj: conj.display()), + conjunct_to_str=lambda conj: conj.display()), "|".join(props_list) ] From 0a7f2094435254a9c405cdc32fc772a9ba572032 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 13 May 2024 16:08:32 -0700 Subject: [PATCH 03/15] move over all the tests for the new formats and flags --- tests/test_assoc_writer.py | 25 +++++++++++++++++++------ tests/test_gpad_writer.py | 14 +++++++------- tests/test_gpiparser.py | 16 +++++++++++++--- 3 files changed, 39 insertions(+), 16 deletions(-) diff --git a/tests/test_assoc_writer.py b/tests/test_assoc_writer.py index eb0bc030..6d175af2 100644 --- a/tests/test_assoc_writer.py +++ b/tests/test_assoc_writer.py @@ -1,7 +1,7 @@ from ontobio.io import assocwriter from ontobio.io import gafparser, gpadparser -from ontobio.model.association import GoAssociation, Curie, Subject, Term, ConjunctiveSet, Evidence, ExtensionUnit, Date, Aspect, Provider -import json +from ontobio.model.association import (GoAssociation, Curie, Subject, Term, ConjunctiveSet, Evidence, ExtensionUnit, + Date, Aspect, Provider) import io @@ -59,6 +59,7 @@ def test_gaf_writer(): gaf = [line.strip("\n") for line in out.getvalue().split("\n") if not line.startswith("!")][0] assert expected == gaf + def test_full_taxon_field_single_taxon(): out = io.StringIO() writer = assocwriter.GafWriter(file=out) @@ -66,6 +67,7 @@ def test_full_taxon_field_single_taxon(): taxon_field = writer._full_taxon_field("taxon:12345", None) assert "taxon:12345" == taxon_field + def test_full_taxon_field_interacting(): out = io.StringIO() writer = assocwriter.GafWriter(file=out) @@ -73,6 +75,7 @@ def test_full_taxon_field_interacting(): taxon_field = writer._full_taxon_field("taxon:12345", "taxon:6789") assert "taxon:12345|taxon:6789" == taxon_field + def test_full_taxon_empty_string_interacting_taxon(): out = io.StringIO() writer = assocwriter.GafWriter(file=out) @@ -80,6 +83,7 @@ def test_full_taxon_empty_string_interacting_taxon(): taxon_field = writer._full_taxon_field("taxon:12345", "") assert "taxon:12345" == taxon_field + def test_negated_qualifers(): gaf = ["PomBase", "SPBC11B10.09", "cdc2", "NOT", "GO:0007275", "PMID:21873635", "ISO", "PANTHER:PTN000623979|TAIR:locus:2099478", "P", "Cyclin-dependent kinase 1", "UniProtKB:P04551|PTN000624043", "protein", "taxon:284812", "20170228", "GO_Central", "", ""] parser = gafparser.GafParser() @@ -94,6 +98,7 @@ def test_negated_qualifers(): print(parsed) assert parsed[2] == "NOT|involved_in" + def test_roundtrip(): """ Start with a line, parse it, then write it. The beginning line should be the same as what was written. @@ -117,6 +122,7 @@ def test_roundtrip(): gaf = [line for line in out.getvalue().split("\n") if not line.startswith("!")][0] assert line == gaf + def test_gpad_qualifier_removed_in_gaf_2_1(): # Qualifier is `part_of` and should be returned blank instead of removing the whole line line = "PomBase\tSPBC1348.01\tpart_of\tGO:0009897\tGO_REF:0000051\tECO:0000266\t\t\t20060201\tPomBase\t\t" @@ -206,6 +212,7 @@ def test_full_gaf_2_2_write(): out_line = [line for line in out.getvalue().split("\n") if not line.startswith("!")][0] assert out_line.split("\t") == line.split("\t") + def test_gaf_to_gpad2(): line = "PomBase\tSPAC25B8.17\typf1\t\tGO:0000006\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:999|taxon:888\t20150305\tPomBase\tpart_of(X:1)\tUniProtKB:P12345" parser = gafparser.GafParser() @@ -216,8 +223,10 @@ def test_gaf_to_gpad2(): writer.write_assoc(assoc) lines = out.getvalue().split("\n") - assert lines[0] == "!gpa-version: 2.0" - assert lines[1] == "PomBase:SPAC25B8.17\t\tBFO:0000050\tGO:0000006\tGO_REF:0000024\tECO:0000266\tSGD:S000001583\tNCBITaxon:888\t2015-03-05\tPomBase\tBFO:0000050(X:1)\t" + assert lines[0] == "!gpad-version: 2.0" + assert lines[1] == "!generated-by: GO Central" + assert lines[2].startswith("!date-generated:") + assert lines[3] == "UniProtKB:P12345\t\tBFO:0000050\tGO:0000006\tGO_REF:0000024\tECO:0000266\tSGD:S000001583\tNCBITaxon:888\t2015-03-05\tPomBase\tBFO:0000050(X:1)\t" line = "PomBase\tSPAC25B8.17\typf1\tNOT\tGO:0000006\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:999|taxon:888\t20150305\tPomBase\tpart_of(X:1)\tUniProtKB:P12345" parser = gafparser.GafParser() @@ -228,8 +237,11 @@ def test_gaf_to_gpad2(): writer.write_assoc(assoc) lines = out.getvalue().split("\n") - assert lines[0] == "!gpa-version: 2.0" - assert lines[1] == "PomBase:SPAC25B8.17\tNOT\tBFO:0000050\tGO:0000006\tGO_REF:0000024\tECO:0000266\tSGD:S000001583\tNCBITaxon:888\t2015-03-05\tPomBase\tBFO:0000050(X:1)\t" + assert lines[0] == "!gpad-version: 2.0" + assert lines[1] == "!generated-by: GO Central" + assert lines[2].startswith("!date-generated:") + assert lines[3] == "UniProtKB:P12345\tNOT\tBFO:0000050\tGO:0000006\tGO_REF:0000024\tECO:0000266\tSGD:S000001583\tNCBITaxon:888\t2015-03-05\tPomBase\tBFO:0000050(X:1)\t" + def test_writing_assoc_properties(): line = "MGI:MGI:1922721\t\tRO:0002327\tGO:0019904\tMGI:MGI:3769586|PMID:17984326\tECO:0000353\tPR:Q0KK55\t\t2010-12-01\tMGI\tBFO:0000066(EMAPA:17787),RO:0002233(MGI:MGI:1923734)\tcreation-date=2008-02-07|modification-date=2010-12-01|comment=v-KIND domain binding of Kndc1;MGI:1923734|contributor-id=http://orcid.org/0000-0003-2689-5511|contributor-id=http://orcid.org/0000-0003-3394-9805" @@ -244,6 +256,7 @@ def test_writing_assoc_properties(): written_props = written_gpad_line.split("\t")[11] assert len(written_props.split("|")) == 5 + def test_gpad_eco_to_gaf_evidence_code(): def parse_gpad_vals_to_gaf_io(gpad_vals): parser = gpadparser.GpadParser() diff --git a/tests/test_gpad_writer.py b/tests/test_gpad_writer.py index 3e120564..130c4f60 100644 --- a/tests/test_gpad_writer.py +++ b/tests/test_gpad_writer.py @@ -1,9 +1,9 @@ import io - from ontobio.io import assocparser from ontobio.io import gafparser from ontobio.io import assocwriter + def test_gpad_iba_writing(): out = io.StringIO() parser = gafparser.GafParser() @@ -17,9 +17,9 @@ def test_gpad_iba_writing(): outlines = out.getvalue().split("\n") - expected_lines = [ - "!gpa-version: 1.2", - "WB\tWBGene00022144\tpart_of\tGO:0005886\tPMID:21873635\tECO:0000318\tPANTHER:PTN000073732|RGD:3252\t\t20180308\tGO_Central\t\t", - "" - ] - assert expected_lines == outlines + print(outlines) + assert outlines[0] == "!gpad-version: 1.2" + assert outlines[1] == "!generated-by: GO Central" + assert outlines[2].startswith("!date-generated:") + assert outlines[3] == "WB\tWBGene00022144\tpart_of\tGO:0005886\tPMID:21873635\tECO:0000318\tPANTHER:PTN000073732|RGD:3252\t\t20180308\tGO_Central\t\t" + diff --git a/tests/test_gpiparser.py b/tests/test_gpiparser.py index 129fad75..35863544 100644 --- a/tests/test_gpiparser.py +++ b/tests/test_gpiparser.py @@ -4,12 +4,23 @@ ONT = "tests/resources/go-truncated-pombase.json" GPI = "tests/resources/truncated-mgi.gpi" +GPI_2_0 = "tests/resources/truncated_mgi_gpi2_0.gpi" + + +def test_parse_gpi_2_0(): + p = GpiParser() + p.config.remove_double_prefixes = True + results = p.parse(open(GPI_2_0, "r")) + for r in results: + print(r) + r1 = results[0] + assert r1['label'] == '0610005C13Rik' + def test_parse_gpi(): - ont = OntologyFactory().create(ONT) p = GpiParser() p.config.remove_double_prefixes = True - results = p.parse(open(GPI,"r")) + results = p.parse(open(GPI, "r")) for r in results: print(r) r1 = results[0] @@ -22,7 +33,6 @@ def test_parse_gpi(): r2 = results[-1] assert r2['parents'] == ['MGI:109279'] - for m in p.report.messages: print("MESSAGE: {}".format(m)) assert len(p.report.messages) == 0 From 9a34042e75f5eb854c29b2553afd3bc14a75fae4 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 13 May 2024 16:08:58 -0700 Subject: [PATCH 04/15] add resource file --- tests/resources/truncated_mgi_gpi2_0.gpi | 100 +++++++++++++++++++++++ 1 file changed, 100 insertions(+) create mode 100644 tests/resources/truncated_mgi_gpi2_0.gpi diff --git a/tests/resources/truncated_mgi_gpi2_0.gpi b/tests/resources/truncated_mgi_gpi2_0.gpi new file mode 100644 index 00000000..3469e495 --- /dev/null +++ b/tests/resources/truncated_mgi_gpi2_0.gpi @@ -0,0 +1,100 @@ +!gpi-version: 2.0 +!namespace: MGI +!generated-by: MGI +!date-generated: 2024-03-22 +MGI:MGI:1918911 0610005C13Rik RIKEN cDNA 0610005C13 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1923503 0610006L08Rik RIKEN cDNA 0610006L08 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1925547 0610008J02Rik RIKEN cDNA 0610008J02 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:3698435 0610009E02Rik RIKEN cDNA 0610009E02 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1918921 0610009F21Rik RIKEN cDNA 0610009F21 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1918931 0610009K14Rik RIKEN cDNA 0610009K14 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1914088 0610009L18Rik RIKEN cDNA 0610009L18 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915609 0610010K14Rik RIKEN cDNA 0610010K14 gene SO:0001217 NCBITaxon:10090 UniProtKB:Q9DCT6 +MGI:MGI:1918926 0610012D04Rik RIKEN cDNA 0610012D04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1925548 0610012E21Rik RIKEN cDNA 0610012E21 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915618 0610025J13Rik RIKEN cDNA 0610025J13 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915614 0610030E20Rik RIKEN cDNA 0610030E20 gene SO:0001217 NCBITaxon:10090 UniProtKB:Q149G0 +MGI:MGI:1925549 0610031C06Rik RIKEN cDNA 0610031C06 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1921093 0610031I08Rik RIKEN cDNA 0610031I08 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915619 0610031O16Rik RIKEN cDNA 0610031O16 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1925551 0610033I19Rik RIKEN cDNA 0610033I19 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1921343 0610033M10Rik RIKEN cDNA 0610033M10 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1925613 0610033P13Rik RIKEN cDNA 0610033P13 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1925614 0610037L18Rik RIKEN cDNA 0610037L18 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1917595 0610038B21Rik RIKEN cDNA 0610038B21 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1922649 0610039G09Rik RIKEN cDNA 0610039G09 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915647 0610039H22Rik RIKEN cDNA 0610039H22 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915636 0610039K10Rik RIKEN cDNA 0610039K10 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915626 0610040A22Rik RIKEN cDNA 0610040A22 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1914922 0610040B10Rik RIKEN cDNA 0610040B10 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1922644 0610040F04Rik RIKEN cDNA 0610040F04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1923511 0610040J01Rik RIKEN cDNA 0610040J01 gene SO:0001217 NCBITaxon:10090 UniProtKB:Q99K99 +MGI:MGI:1918938 0610042B02Rik RIKEN cDNA 0610042B02 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1922652 0610042B23Rik RIKEN cDNA 0610042B23 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1921345 0610042E11Rik RIKEN cDNA 0610042E11 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915630 0610042G04Rik RIKEN cDNA 0610042G04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915650 0610043K17Rik RIKEN cDNA 0610043K17 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915652 0710001A04Rik RIKEN cDNA 0710001A04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1914929 0710001D07Rik RIKEN cDNA 0710001D07 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915664 0710001L09Rik RIKEN cDNA 0710001L09 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1918942 0710005I21Rik RIKEN cDNA 0710005I21 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915659 0710007G10Rik RIKEN cDNA 0710007G10 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1918947 0710008F09Rik RIKEN cDNA 0710008F09 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1918945 0910001E24Rik RIKEN cDNA 0910001E24 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1922653 1010001B22Rik RIKEN cDNA 1010001B22 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915683 1010001I08Rik RIKEN cDNA 1010001I08 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1922655 1100001I12Rik RIKEN cDNA 1100001I12 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1920975 1110001D16Rik RIKEN cDNA 1110001D16 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915702 1110001M07Rik RIKEN cDNA 1110001M07 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915066 1110002E22Rik RIKEN cDNA 1110002E22 gene SO:0001217 NCBITaxon:10090 UniProtKB:E0CYV9 +MGI:MGI:1915738 1110002J07Rik RIKEN cDNA 1110002J07 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915821 1110002L01Rik RIKEN cDNA 1110002L01 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915733 1110002O04Rik RIKEN cDNA 1110002O04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915716 1110003F02Rik RIKEN cDNA 1110003F02 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915726 1110003F10Rik RIKEN cDNA 1110003F10 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1929274 1110004F10Rik RIKEN cDNA 1110004F10 gene sid2057 SO:0001217 NCBITaxon:10090 UniProtKB:Q9R0P4 +MGI:MGI:1915714 1110004M10Rik RIKEN cDNA 1110004M10 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1923536 1110006E14Rik RIKEN cDNA 1110006E14 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1913373 1110006O24Rik RIKEN cDNA 1110006O24 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915732 1110007E10Rik RIKEN cDNA 1110007E10 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915750 1110008E08Rik RIKEN cDNA 1110008E08 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915772 1110013H19Rik RIKEN cDNA 1110013H19 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915879 1110013I04Rik RIKEN cDNA 1110013I04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1913377 1110014L15Rik RIKEN cDNA 1110014L15 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915766 1110015O18Rik RIKEN cDNA 1110015O18 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915844 1110018F16Rik RIKEN cDNA 1110018F16 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915753 1110018N20Rik RIKEN cDNA 1110018N20 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915779 1110019B22Rik RIKEN cDNA 1110019B22 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:2443389 1110019B24Rik RIKEN cDNA 1110019B24 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1923561 1110019D14Rik RIKEN cDNA 1110019D14 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915781 1110020A21Rik RIKEN cDNA 1110020A21 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915834 1110020C17Rik RIKEN cDNA 1110020C17 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915850 1110021P09Rik RIKEN cDNA 1110021P09 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915885 1110025M09Rik RIKEN cDNA 1110025M09 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915940 1110028F11Rik RIKEN cDNA 1110028F11 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915942 1110028F18Rik RIKEN cDNA 1110028F18 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915975 1110032F04Rik RIKEN cDNA 1110032F04 gene SO:0001217 NCBITaxon:10090 UniProtKB:E9Q0B3 +MGI:MGI:1915977 1110032L06Rik RIKEN cDNA 1110032L06 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:2147638 1110034N17Rik RIKEN cDNA 1110034N17 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915934 1110035D15Rik RIKEN cDNA 1110035D15 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915922 1110035E04Rik RIKEN cDNA 1110035E04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915936 1110035H17Rik RIKEN cDNA 1110035H17 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1915947 1110036E04Rik RIKEN cDNA 1110036E04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916001 1110037P09Rik RIKEN cDNA 1110037P09 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916013 1110038B12Rik RIKEN cDNA 1110038B12 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:2152337 1110038F14Rik RIKEN cDNA 1110038F14 gene SO:0001217 NCBITaxon:10090 UniProtKB:Q3U6N9 +MGI:MGI:1916058 1110046J04Rik RIKEN cDNA 1110046J04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916041 1110050P16Rik RIKEN cDNA 1110050P16 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916031 1110055C04Rik RIKEN cDNA 1110055C04 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916021 1110058D11Rik RIKEN cDNA 1110058D11 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1913456 1110059E24Rik RIKEN cDNA 1110059E24 gene SO:0001217 NCBITaxon:10090 UniProtKB:Q9CQ90 +MGI:MGI:1916036 1110059G02Rik RIKEN cDNA 1110059G02 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1913452 1110059G10Rik RIKEN cDNA 1110059G10 gene SO:0001217 NCBITaxon:10090 UniProtKB:Q8K039 +MGI:MGI:1916064 1110060G06Rik RIKEN cDNA 1110060G06 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916143 1110064A23Rik RIKEN cDNA 1110064A23 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:3026937 1110065F06Rik RIKEN cDNA 1110065F06 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916155 1110065H08Rik RIKEN cDNA 1110065H08 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916170 1110065P20Rik RIKEN cDNA 1110065P20 gene SO:0001217 NCBITaxon:10090 UniProtKB:B1ARW8 +MGI:MGI:1916173 1190001L17Rik RIKEN cDNA 1190001L17 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916174 1190001M18Rik RIKEN cDNA 1190001M18 gene SO:0002127 NCBITaxon:10090 +MGI:MGI:1916168 1190005I06Rik RIKEN cDNA 1190005I06 gene SO:0001217 NCBITaxon:10090 UniProtKB:Q8K1L6 \ No newline at end of file From 979befe7104fe5785bdca67a1eeb5ac6f137a200 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 13 May 2024 16:09:43 -0700 Subject: [PATCH 05/15] makefile changes to allow poetry venv --- Makefile | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/Makefile b/Makefile index 5ffb8954..1bf975f8 100644 --- a/Makefile +++ b/Makefile @@ -24,13 +24,24 @@ foo: # only run local tests travis_test: - pytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \ - tests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \ - tests/test_validation_rules.py tests/unit/test_annotation_scorer.py \ - tests/test_goassociation_model.py tests/test_relations.py \ - tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \ - tests/test_collections.py \ - tests/test_gocamgen.py + @if [ -d ".venv" ] && [ -f "pyproject.toml" ]; then \ + echo "Running tests in Poetry environment..."; \ + poetry run pytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \ + tests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \ + tests/test_validation_rules.py tests/unit/test_annotation_scorer.py \ + tests/test_goassociation_model.py tests/test_relations.py \ + tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \ + tests/test_collections.py \ + tests/test_gocamgen.py; \ + else \ + pytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \ + tests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \ + tests/test_validation_rules.py tests/unit/test_annotation_scorer.py \ + tests/test_goassociation_model.py tests/test_relations.py \ + tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \ + tests/test_collections.py \ + tests/test_gocamgen.py; \ + fi cleandist: rm dist/* || true From 8a64a9a4b027cbc05a6ff7c88cb3f964eb8bb3fe Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 May 2024 08:38:08 -0700 Subject: [PATCH 06/15] remove print statement --- ontobio/io/entitywriter.py | 1 - 1 file changed, 1 deletion(-) diff --git a/ontobio/io/entitywriter.py b/ontobio/io/entitywriter.py index e538598f..f9cc08b2 100644 --- a/ontobio/io/entitywriter.py +++ b/ontobio/io/entitywriter.py @@ -139,7 +139,6 @@ def write_entity(self, entity): 10. Properties <-- entity.properties """ - print(entity.get('taxon')) if self.version == "2.0": vals = [ From 1c00df2d1126f828baad3960e202851382cd3859 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 May 2024 17:14:30 -0700 Subject: [PATCH 07/15] add test of write gpi function, fix tests, add gitignore for output GPIs from tests --- .gitignore | 2 + bin/validate.py | 7 ++- ontobio/io/gafgpibridge.py | 1 + tests/resources/mgi.gaf | 100 ++++++++++++++++++++++++++++++++++++ tests/resources/mgi.gpi | 10 ++++ tests/resources/mgi.gpi.gz | Bin 0 -> 316 bytes tests/test_gpiwriter.py | 41 ++++++++++++++- tests/test_local_json.py | 2 +- tests/test_remote_sparql.py | 2 +- 9 files changed, 157 insertions(+), 8 deletions(-) create mode 100644 tests/resources/mgi.gaf create mode 100644 tests/resources/mgi.gpi create mode 100644 tests/resources/mgi.gpi.gz diff --git a/.gitignore b/.gitignore index a2244bfa..0336b625 100644 --- a/.gitignore +++ b/.gitignore @@ -49,6 +49,8 @@ coverage.xml *,cover .hypothesis/ .pytest_cache/ +tests/resources/mgi.gpi +tests/resources/mgi.gpi.gz # Translations *.mo diff --git a/bin/validate.py b/bin/validate.py index b59f4c04..0a2eef6f 100755 --- a/bin/validate.py +++ b/bin/validate.py @@ -448,18 +448,17 @@ def produce_gpi(dataset, target_dir, gaf_path, ontology_graph, gpad_gpi_output_v gpi_path = os.path.join(os.path.split(gaf_path)[0], "{}.gpi".format(dataset)) with open(gaf_path) as gf, open(gpi_path, "w") as gpi: click.echo("Using {} as the gaf to build gpi with".format(gaf_path)) - bridge = gafgpibridge + bridge = gafgpibridge.GafGpiBridge() gpiwriter = entitywriter.GpiWriter(file=gpi, version=gpad_gpi_output_version) gpi_cache = set() with click.progressbar(iterable=gafparser.association_generator(file=gf), length=lines) as associations: for association in associations: - entity = bridge.convert_association(association, gpad_gpi_output_version) + entity = bridge.convert_association(association) if entity not in gpi_cache and entity is not None: # If the entity is not in the cache, add it and write it out gpi_cache.add(entity) gpiwriter.write_entity(entity) - return gpi_path @@ -596,7 +595,7 @@ def cli(ctx, verbose): @click.argument("group") @click.option("--metadata", "-m", "metadata_dir", type=click.Path(), required=True) @click.option("--gpad", default=False, is_flag=True) -@click.option("--https://github.com/microbiomedata/nmdc-schema/issues/1925", default="2.0", type=click.Choice(["1.2", "2.0"])) +@click.option("--gpad-gpi-output-version", default="2.0", type=click.Choice(["1.2", "2.0"])) @click.option("--ttl", default=False, is_flag=True) @click.option("--target", "-t", type=click.Path(), required=True) @click.option("--ontology", "-o", type=click.Path(exists=True), required=False) diff --git a/ontobio/io/gafgpibridge.py b/ontobio/io/gafgpibridge.py index 4a6604e2..29479f4d 100644 --- a/ontobio/io/gafgpibridge.py +++ b/ontobio/io/gafgpibridge.py @@ -24,6 +24,7 @@ def convert_association(self, association) -> Entity: so we don't have to worry about what that looks like. We assume it's correct. """ + if isinstance(association, GoAssociation): # print(json.dumps(association, indent=4)) gpi_obj = { diff --git a/tests/resources/mgi.gaf b/tests/resources/mgi.gaf new file mode 100644 index 00000000..769e33f1 --- /dev/null +++ b/tests/resources/mgi.gaf @@ -0,0 +1,100 @@ +!Date Generated: 2024-03-19 10:16:57.171235 +!Date Generated: 2024-03-19 10:20:48.292994 +!Date Generated: 2024-03-19 10:51:59.318591 +!Date Generated: 2024-03-19 10:52:00.645439 +!Generated by: GO_Central preprocess pipeline +!Generated by: GO_Central preprocess pipeline: protein to GO transformation +!gaf-version: 2.2 +MGI MGI:101757 Cfl1 enables GO:0051015 GO_REF:0000119 ISO UniProtKB:P23528 F cofilin 1, non-muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101757 Cfl1 involved_in GO:0007010 GO_REF:0000119 ISO UniProtKB:P23528 P cofilin 1, non-muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101757 Cfl1 involved_in GO:0022604 GO_REF:0000119 ISO UniProtKB:P23528 P cofilin 1, non-muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101757 Cfl1 involved_in GO:0030042 GO_REF:0000119 ISO UniProtKB:P23528 P cofilin 1, non-muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101757 Cfl1 involved_in GO:0044794 GO_REF:0000119 ISO UniProtKB:P23528 P cofilin 1, non-muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101757 Cfl1 involved_in GO:0061001 GO_REF:0000119 ISO UniProtKB:P23528 P cofilin 1, non-muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101757 Cfl1 located_in GO:0005737 GO_REF:0000119 ISO UniProtKB:P23528 C cofilin 1, non-muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101759 Syt4 involved_in GO:0033604 GO_REF:0000119 ISO UniProtKB:Q9H2B2 P synaptotagmin IV gene_product taxon:10090 20240319 GO_Central +MGI MGI:101759 Syt4 involved_in GO:1903861 GO_REF:0000119 ISO UniProtKB:Q9H2B2 P synaptotagmin IV gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0000976 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0003676 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0003680 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0003906 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0008301 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0031492 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0035497 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0035500 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0035501 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0046332 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0051575 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0061629 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 enables GO:0070742 GO_REF:0000119 ISO UniProtKB:P52926 F high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0000122 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0001837 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0002062 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0003131 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0006284 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0006355 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0010564 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0010628 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0031507 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0035556 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0035987 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0035988 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0043066 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0043392 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0043922 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0045444 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0045869 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0045892 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0045893 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0045944 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0048333 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0048762 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0071902 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:0090402 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:2000036 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:2000648 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 involved_in GO:2001033 GO_REF:0000119 ISO UniProtKB:P52926 P high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 located_in GO:0005634 GO_REF:0000119 ISO UniProtKB:P52926 C high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 part_of GO:0032993 GO_REF:0000119 ISO UniProtKB:P52926 C high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 part_of GO:0035985 GO_REF:0000119 ISO UniProtKB:P52926 C high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101761 Hmga2 part_of GO:0071141 GO_REF:0000119 ISO UniProtKB:P52926 C high mobility group AT-hook 2 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101762 Elk3 enables GO:0000978 GO_REF:0000119 ISO UniProtKB:P41970 F ELK3, member of ETS oncogene family gene_product taxon:10090 20240319 GO_Central +MGI MGI:101762 Elk3 enables GO:0001227 GO_REF:0000119 ISO UniProtKB:P41970 F ELK3, member of ETS oncogene family gene_product taxon:10090 20240319 GO_Central +MGI MGI:101762 Elk3 enables GO:0001228 GO_REF:0000119 ISO UniProtKB:P41970 F ELK3, member of ETS oncogene family gene_product taxon:10090 20240319 GO_Central +MGI MGI:101762 Elk3 enables GO:0032422 GO_REF:0000119 ISO UniProtKB:P41970 F ELK3, member of ETS oncogene family gene_product taxon:10090 20240319 GO_Central +MGI MGI:101762 Elk3 enables GO:1990837 GO_REF:0000119 ISO UniProtKB:P41970 F ELK3, member of ETS oncogene family gene_product taxon:10090 20240319 GO_Central +MGI MGI:101762 Elk3 involved_in GO:0045892 GO_REF:0000119 ISO UniProtKB:P41970 P ELK3, member of ETS oncogene family gene_product taxon:10090 20240319 GO_Central +MGI MGI:101762 Elk3 involved_in GO:0045944 GO_REF:0000119 ISO UniProtKB:P41970 P ELK3, member of ETS oncogene family gene_product taxon:10090 20240319 GO_Central +MGI MGI:101762 Elk3 located_in GO:0005654 GO_REF:0000119 ISO UniProtKB:P41970 C ELK3, member of ETS oncogene family gene_product taxon:10090 20240319 GO_Central +MGI MGI:101762 Elk3 located_in GO:0005739 GO_REF:0000119 ISO UniProtKB:P41970 C ELK3, member of ETS oncogene family gene_product taxon:10090 20240319 GO_Central +MGI MGI:101763 Cfl2 involved_in GO:0030042 GO_REF:0000119 ISO UniProtKB:Q9Y281 P cofilin 2, muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101763 Cfl2 involved_in GO:0030836 GO_REF:0000119 ISO UniProtKB:Q9Y281 P cofilin 2, muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101763 Cfl2 located_in GO:0030018 GO_REF:0000119 ISO UniProtKB:Q9Y281 C cofilin 2, muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101763 Cfl2 located_in GO:0031674 GO_REF:0000119 ISO UniProtKB:Q9Y281 C cofilin 2, muscle gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 enables GO:0019901 GO_REF:0000119 ISO UniProtKB:Q15078 F cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 enables GO:0043539 GO_REF:0000119 ISO UniProtKB:Q15078 F cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 involved_in GO:0018105 GO_REF:0000119 ISO UniProtKB:Q15078 P cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 involved_in GO:0018107 GO_REF:0000119 ISO UniProtKB:Q15078 P cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 involved_in GO:0045348 GO_REF:0000119 ISO UniProtKB:Q15078 P cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 involved_in GO:0045892 GO_REF:0000119 ISO UniProtKB:Q15078 P cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 involved_in GO:2000273 GO_REF:0000119 ISO UniProtKB:Q15078 P cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 located_in GO:0000307 GO_REF:0000119 ISO UniProtKB:Q15078 C cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 located_in GO:0005654 GO_REF:0000119 ISO UniProtKB:Q15078 C cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 located_in GO:0016533 GO_REF:0000119 ISO UniProtKB:Q15078 C cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 located_in GO:0043231 GO_REF:0000119 ISO UniProtKB:Q15078 C cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101764 Cdk5r1 located_in GO:0048471 GO_REF:0000119 ISO UniProtKB:Q15078 C cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 enables GO:0004674 GO_REF:0000119 ISO UniProtKB:Q00535 F cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 involved_in GO:0016310 GO_REF:0000119 ISO UniProtKB:Q00535 P cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 involved_in GO:0018105 GO_REF:0000119 ISO UniProtKB:Q00535 P cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 involved_in GO:0045861 GO_REF:0000119 ISO UniProtKB:Q00535 P cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 involved_in GO:0045892 GO_REF:0000119 ISO UniProtKB:Q00535 P cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 involved_in GO:0048709 GO_REF:0000119 ISO UniProtKB:Q00535 P cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 located_in GO:0000307 GO_REF:0000119 ISO UniProtKB:Q00535 C cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 located_in GO:0005654 GO_REF:0000119 ISO UniProtKB:Q00535 C cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 located_in GO:0005886 GO_REF:0000119 ISO UniProtKB:Q00535 C cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 located_in GO:0016533 GO_REF:0000119 ISO UniProtKB:Q00535 C cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101765 Cdk5 located_in GO:0030054 GO_REF:0000119 ISO UniProtKB:Q00535 C cyclin dependent kinase 5 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101766 Ryk enables GO:0004888 GO_REF:0000119 ISO UniProtKB:P34925 F receptor-like tyrosine kinase gene_product taxon:10090 20240319 GO_Central +MGI MGI:101766 Ryk involved_in GO:0043410 GO_REF:0000119 ISO UniProtKB:P34925 P receptor-like tyrosine kinase gene_product taxon:10090 20240319 GO_Central +MGI MGI:101769 Mcl1 enables GO:0046982 GO_REF:0000119 ISO UniProtKB:Q07820 F myeloid cell leukemia sequence 1 gene_product taxon:10090 20240319 GO_Central +MGI MGI:101769 Mcl1 enables GO:0051434 GO_REF:0000119 ISO UniProtKB:Q07820 F myeloid cell leukemia sequence 1 gene_product taxon:10090 20240319 GO_Central diff --git a/tests/resources/mgi.gpi b/tests/resources/mgi.gpi new file mode 100644 index 00000000..b9bae897 --- /dev/null +++ b/tests/resources/mgi.gpi @@ -0,0 +1,10 @@ +!gpi-version: 1.2 +MGI MGI:101757 Cfl1 cofilin 1, non-muscle gene_product taxon:10090 +MGI MGI:101759 Syt4 synaptotagmin IV gene_product taxon:10090 +MGI MGI:101761 Hmga2 high mobility group AT-hook 2 gene_product taxon:10090 +MGI MGI:101762 Elk3 ELK3, member of ETS oncogene family gene_product taxon:10090 +MGI MGI:101763 Cfl2 cofilin 2, muscle gene_product taxon:10090 +MGI MGI:101764 Cdk5r1 cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 +MGI MGI:101765 Cdk5 cyclin dependent kinase 5 gene_product taxon:10090 +MGI MGI:101766 Ryk receptor-like tyrosine kinase gene_product taxon:10090 +MGI MGI:101769 Mcl1 myeloid cell leukemia sequence 1 gene_product taxon:10090 diff --git a/tests/resources/mgi.gpi.gz b/tests/resources/mgi.gpi.gz new file mode 100644 index 0000000000000000000000000000000000000000..4890963d28b4f21716aec8bc64e399c8f609d387 GIT binary patch literal 316 zcmV-C0mJ?uiwFqc{X=E~|7~Y!E@yCQ0F~0QPQx$|2H^R4ieqn4oHni64OJCX(1lj4 z$aOBM726ja8{xOd1qq1(K?bkifA^oS+g?xK$Pb#`8pTa{wZGdzerr*PWwnG&V+1H} zw9yX51RcAnje{}-(2}E<-g6yQfFR#9A&O#E0KiXX1&0*oFeE4Yz(KY)W4q`73kw1F zwv{EEb$dq3r#wzb*m{mV-X5oC<_^mdUI|;%&0zcZFq@zydm@kA;P!Yxc8V_!HqvU7 zMxe7xTjh6KWtK-awV1=E?kb-vPwHaS)RU{p1?;qw17S5mPi-_ZuunL|Q*=6@7!gr@ zM*JQyf?B{+>cEqtd{#d-x+4t9^PqEmU)~691$&i0n@wa`*Qm%CG!#3sTH-*jk({Ex OR{a1%+T2Ca0ssITN0KxE literal 0 HcmV?d00001 diff --git a/tests/test_gpiwriter.py b/tests/test_gpiwriter.py index 0b3c0697..69ad6a75 100644 --- a/tests/test_gpiwriter.py +++ b/tests/test_gpiwriter.py @@ -1,6 +1,44 @@ import io +from ontobio.io import entitywriter, gafgpibridge, entityparser +from bin.validate import produce_gpi +from pathlib import Path +import pytest -from ontobio.io import entitywriter, gafgpibridge + +@pytest.mark.parametrize("gpad_gpi_output_version", ["2.0", "1.2"]) +def test_produce_gpi(gpad_gpi_output_version): + # Base path relative to this script + base_path = Path(__file__).parent / "resources" + + # Define the paths for the GAF and expected GPI file + gaf_path = base_path / "mgi.gaf" + + # Ensure the GAF file exists to avoid FileNotFoundError + if not gaf_path.exists(): + raise FileNotFoundError(f"Expected GAF file does not exist: {gaf_path}") + + # Set parameters for the function + dataset = "mgi" + ontology_graph = None # Assuming setup elsewhere or not needed for this specific test + + # Call the function + output_gpi_path = produce_gpi(dataset, str(base_path), str(gaf_path), ontology_graph, gpad_gpi_output_version) + + # Convert the output path to a pathlib.Path object for consistency + output_gpi_path = Path(output_gpi_path) + assert output_gpi_path.exists(), "The GPI file was not created." + + # Verify the contents of the GPI file + p = entityparser.GpiParser() + assert p.parse(open(output_gpi_path, "r")) is not None, "The GPI file could not be parsed." + results = p.parse(open(output_gpi_path, "r")) + assert len(results) > 5, "The GPI file should have about 9 unique genes from ~ 90 associations in the GAF file." + + with output_gpi_path.open() as f: + lines = f.readlines() + + assert len(lines) > 0, "The GPI file should not be empty." + # assert lines[0].startswith("!gpi-version: 2.0"), "GPI version header is incorrect or missing." def test_gpi_2_0_writer(): @@ -16,7 +54,6 @@ def test_gpi_2_0_writer(): 'protein_containing_complex_members': "", # protein_containing_complex_members 'xrefs': "", 'properties': "" - } entity = gafgpibridge.Entity(gpi_obj) diff --git a/tests/test_local_json.py b/tests/test_local_json.py index 69838fc5..44a0d5ee 100644 --- a/tests/test_local_json.py +++ b/tests/test_local_json.py @@ -238,7 +238,7 @@ def test_subontology(): def test_obsolete(): """ - Test obsoletion metadata + Test obsoletion datasets """ factory = OntologyFactory() print("Creating ont") diff --git a/tests/test_remote_sparql.py b/tests/test_remote_sparql.py index a7906583..60e62ef5 100644 --- a/tests/test_remote_sparql.py +++ b/tests/test_remote_sparql.py @@ -169,7 +169,7 @@ def test_subontology(): w.write_subgraph(ont, ancs) # TODO: sub-ontology does not create - # full metadata + # full datasets w = GraphRenderer.create('obo') w.write_subgraph(ont, ancs) From 0c42ee45abf52ffabb6ee8872ba5931bb9651544 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 May 2024 17:15:33 -0700 Subject: [PATCH 08/15] remove files that should not be kept as test output --- tests/resources/mgi.gpi | 10 ---------- tests/resources/mgi.gpi.gz | Bin 316 -> 0 bytes 2 files changed, 10 deletions(-) delete mode 100644 tests/resources/mgi.gpi delete mode 100644 tests/resources/mgi.gpi.gz diff --git a/tests/resources/mgi.gpi b/tests/resources/mgi.gpi deleted file mode 100644 index b9bae897..00000000 --- a/tests/resources/mgi.gpi +++ /dev/null @@ -1,10 +0,0 @@ -!gpi-version: 1.2 -MGI MGI:101757 Cfl1 cofilin 1, non-muscle gene_product taxon:10090 -MGI MGI:101759 Syt4 synaptotagmin IV gene_product taxon:10090 -MGI MGI:101761 Hmga2 high mobility group AT-hook 2 gene_product taxon:10090 -MGI MGI:101762 Elk3 ELK3, member of ETS oncogene family gene_product taxon:10090 -MGI MGI:101763 Cfl2 cofilin 2, muscle gene_product taxon:10090 -MGI MGI:101764 Cdk5r1 cyclin dependent kinase 5, regulatory subunit 1 gene_product taxon:10090 -MGI MGI:101765 Cdk5 cyclin dependent kinase 5 gene_product taxon:10090 -MGI MGI:101766 Ryk receptor-like tyrosine kinase gene_product taxon:10090 -MGI MGI:101769 Mcl1 myeloid cell leukemia sequence 1 gene_product taxon:10090 diff --git a/tests/resources/mgi.gpi.gz b/tests/resources/mgi.gpi.gz deleted file mode 100644 index 4890963d28b4f21716aec8bc64e399c8f609d387..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 316 zcmV-C0mJ?uiwFqc{X=E~|7~Y!E@yCQ0F~0QPQx$|2H^R4ieqn4oHni64OJCX(1lj4 z$aOBM726ja8{xOd1qq1(K?bkifA^oS+g?xK$Pb#`8pTa{wZGdzerr*PWwnG&V+1H} zw9yX51RcAnje{}-(2}E<-g6yQfFR#9A&O#E0KiXX1&0*oFeE4Yz(KY)W4q`73kw1F zwv{EEb$dq3r#wzb*m{mV-X5oC<_^mdUI|;%&0zcZFq@zydm@kA;P!Yxc8V_!HqvU7 zMxe7xTjh6KWtK-awV1=E?kb-vPwHaS)RU{p1?;qw17S5mPi-_ZuunL|Q*=6@7!gr@ zM*JQyf?B{+>cEqtd{#d-x+4t9^PqEmU)~691$&i0n@wa`*Qm%CG!#3sTH-*jk({Ex OR{a1%+T2Ca0ssITN0KxE From 60c50c3c1406e65814916a10a5d75cd3bcf63be0 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 May 2024 17:21:33 -0700 Subject: [PATCH 09/15] fix python 3.7 path resolution --- tests/resources/cam.rdf | 9770 +++++++++++++++++++++++++++++++++++++++ tests/test_gpiwriter.py | 10 +- 2 files changed, 9776 insertions(+), 4 deletions(-) create mode 100644 tests/resources/cam.rdf diff --git a/tests/resources/cam.rdf b/tests/resources/cam.rdf new file mode 100644 index 00000000..3d3a7356 --- /dev/null +++ b/tests/resources/cam.rdf @@ -0,0 +1,9770 @@ +@prefix ECO: . +@prefix GO: . +@prefix GO_REF: . +@prefix NCBITaxon: . +@prefix PMID: . +@prefix Pfam: . +@prefix PomBase: . +@prefix RO: . +@prefix SGD: . +@prefix SO: . +@prefix UniProtKB: . +@prefix ns1: . +@prefix obo: . +@prefix owl: . +@prefix rdfs: . + + a owl:Ontology . + +PomBase:SPAC1006.09 rdfs:label "win1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC10F6.09c rdfs:label "psm3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC110.03 rdfs:label "cdc42" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC12B10.10 rdfs:label "nod1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC12G12.04 rdfs:label "mcp60" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1556.08c rdfs:label "cbs2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1610.04 rdfs:label "mug99" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1687.18c rdfs:label "ssl3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1687.20c rdfs:label "mis6" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC16A10.05c rdfs:label "dad1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC16A10.07c rdfs:label "taz1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC16C9.07 rdfs:label "pom2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1751.03 rdfs:label "tif313" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1782.10c rdfs:label "nhp2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC17D4.02 rdfs:label "cdc45" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1805.08 rdfs:label "dlc1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1805.17 rdfs:label "crm1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1834.08 rdfs:label "mak1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC18G6.10 rdfs:label "lem2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1A6.03c rdfs:label "SPAC1A6.03c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1A6.04c rdfs:label "plb1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1F5.04c rdfs:label "cdc12" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC1F7.01c rdfs:label "spt6" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC20H4.11c rdfs:label "rho5" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC212.01c rdfs:label "SPAC212.01c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC212.04c rdfs:label "SPAC212.04c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC21E11.03c rdfs:label "pcr1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC22E12.17c rdfs:label "glo3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC23C4.02 rdfs:label "crn1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC23E2.01 rdfs:label "fep1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC25B8.17 rdfs:label "ypf1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC25G10.07c rdfs:label "cut7" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC25G10.08 rdfs:label "SPAC25G10.08" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC27D7.13c rdfs:label "ssm4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC27E2.09 rdfs:label "mak2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC27F1.02c rdfs:label "cdc8" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC29A4.04c rdfs:label "cbf5" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC29E6.07 rdfs:label "SPAC29E6.07" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC2F7.03c rdfs:label "pom1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC2G11.12 rdfs:label "rqh1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC31A2.05c rdfs:label "mis4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC31A2.16 rdfs:label "gef2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC343.07 rdfs:label "mug28" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC3A11.14c rdfs:label "pkl1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC3A12.13c rdfs:label "hcr1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC4A8.16c rdfs:label "tif33" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC4D7.07c rdfs:label "csi2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC57A7.10c rdfs:label "sec21" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC637.07 rdfs:label "moe1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC644.12 rdfs:label "cdc5" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC664.10 rdfs:label "klp2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC688.07c rdfs:label "rng10" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC6F12.02 rdfs:label "rst2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC6G10.02c rdfs:label "tea3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC6G9.11 rdfs:label "syb1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC750.06c rdfs:label "SPAC750.06c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC7D4.13c rdfs:label "SPAC7D4.13c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC821.05 rdfs:label "tif38" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC821.09 rdfs:label "eng1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC821.12 rdfs:label "orb6" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC890.02c rdfs:label "alp7" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC926.07c rdfs:label "dlc2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC977.06 rdfs:label "SPAC977.06" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC977.09c rdfs:label "SPAC977.09c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC977.10 rdfs:label "nhe1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAC9G1.02 rdfs:label "wis4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAP27G11.13c rdfs:label "nop10" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPAPB8E5.03 rdfs:label "mae1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC115.02c rdfs:label "afg1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC11C11.03 rdfs:label "ndc80" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC11G11.03 rdfs:label "mrt4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC12C2.08 rdfs:label "dnm1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC12D12.01 rdfs:label "sad1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1347.01c rdfs:label "rev1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1347.12 rdfs:label "arp1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1348.01 rdfs:label "SPBC1348.01" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1348.07 rdfs:label "SPBC1348.07" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC13E7.06 rdfs:label "msd1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC146.03c rdfs:label "cut3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC146.13c rdfs:label "myo1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC146.14c rdfs:label "sec26" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC14C8.19 rdfs:label "tam10" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1604.08c rdfs:label "imp1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1604.09c rdfs:label "rex4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1685.15c rdfs:label "klp6" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC16A3.13 rdfs:label "meu7" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC16C6.11 rdfs:label "rpl3201" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC16C6.13c rdfs:label "sec27" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC16D10.04c rdfs:label "dna2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC16E9.07 rdfs:label "mug100" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC16E9.10c rdfs:label "rix7" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC16E9.12c rdfs:label "pab2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC16G5.11c rdfs:label "bag101" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC16G5.12c rdfs:label "top3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1703.01c rdfs:label "pop4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1703.14c rdfs:label "top1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1706.01 rdfs:label "tea4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1711.07 rdfs:label "rrb1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1711.16 rdfs:label "pwp1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1778.02 rdfs:label "rap1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC17D1.03c rdfs:label "rrp43" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC17D1.04 rdfs:label "acr1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC17D11.05 rdfs:label "tif32" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC17F3.02 rdfs:label "nak1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC17G9.07 rdfs:label "rps2402" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC18E5.03c rdfs:label "sim4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC18H10.03 rdfs:label "tif35" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC18H10.13 rdfs:label "rps1402" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1921.01c rdfs:label "rpl35b" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC19C2.03 rdfs:label "rpc10" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC19G7.09 rdfs:label "ulp1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC19G7.16 rdfs:label "iws1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC1A4.07c rdfs:label "sof1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC20F10.06 rdfs:label "mad2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC20F10.09 rdfs:label "lsm5" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC211.04c rdfs:label "mcm6" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC216.07c rdfs:label "tor2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC21B10.10 rdfs:label "rps402" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC21H7.03c rdfs:label "SPBC21H7.03c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC23G7.04c rdfs:label "nif1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC24C6.05 rdfs:label "sec28" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC25D12.03c rdfs:label "mcm7" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC26H8.10 rdfs:label "dis3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC27.02c rdfs:label "ask1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC28F2.11 rdfs:label "hmo1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC29A3.17 rdfs:label "gef3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC29B5.03c rdfs:label "rpl26" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC2A9.07c rdfs:label "hpz1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC2D10.19c rdfs:label "alb1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC2F12.13 rdfs:label "klp5" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC2G2.05 rdfs:label "rpl1603" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC2G2.14 rdfs:label "csi1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC2G5.06c rdfs:label "hmt2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC30D10.06 rdfs:label "lsm4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC32F12.04 rdfs:label "gtb1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC32H8.05 rdfs:label "SPBC32H8.05" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC32H8.09 rdfs:label "wdr8" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC32H8.10 rdfs:label "cdk9" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC336.06c rdfs:label "rnh1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC336.09c rdfs:label "rrn7" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC337.12 rdfs:label "red5" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC365.09c rdfs:label "kin17" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC365.15 rdfs:label "alp4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC3B8.09 rdfs:label "utp3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC3E7.10 rdfs:label "fma1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC4.04c rdfs:label "mcm2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC409.09c rdfs:label "mis13" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC428.03c rdfs:label "pho4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC428.18 rdfs:label "cdt1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC428.20c rdfs:label "alp6" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC4B4.07c rdfs:label "usp102" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC4C3.05c rdfs:label "nuc1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC4C3.07 rdfs:label "eif6" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC4F6.13c rdfs:label "erb1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC530.04 rdfs:label "mod5" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC582.05c rdfs:label "brc1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC646.04 rdfs:label "pla1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC646.13 rdfs:label "sds23" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC646.17c rdfs:label "dic1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC725.02 rdfs:label "mpr1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC725.08 rdfs:label "pir2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC725.12 rdfs:label "nbl1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC776.02c rdfs:label "dis2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC776.11 rdfs:label "rpl2801" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC776.17 rdfs:label "rrp7" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC83.17 rdfs:label "mbf1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC887.03c rdfs:label "noc3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC887.10 rdfs:label "mcs4" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC887.14c rdfs:label "pfh1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC8D2.13 rdfs:label "shq1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC8D2.16c rdfs:label "SPBC8D2.16c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC9B6.05c rdfs:label "lsm3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBC9B6.06 rdfs:label "mrpl10" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBCPT2R1.01c rdfs:label "SPBCPT2R1.01c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBCPT2R1.04c rdfs:label "SPBCPT2R1.04c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBP22H7.09c rdfs:label "mis15" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBP4G3.02 rdfs:label "pho1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBP8B7.01c rdfs:label "pop7" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBP8B7.20c rdfs:label "nop2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBPB2B2.07c rdfs:label "SPBPB2B2.07c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBPB2B2.14c rdfs:label "SPBPB2B2.14c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPBPJ4664.04 rdfs:label "cop1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC11E10.03 rdfs:label "mug1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC1235.03 rdfs:label "cue2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC1281.01 rdfs:label "ags1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC1322.08 rdfs:label "srk1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC1322.12c rdfs:label "bub1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC1450.09c rdfs:label "SPCC1450.09c" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC1682.02c rdfs:label "mcm3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC16C4.03 rdfs:label "pin1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC1739.10 rdfs:label "mug33" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC1795.01c rdfs:label "mad3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC188.02 rdfs:label "par1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC1919.03c rdfs:label "amk2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC285.08 rdfs:label "ret2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC297.03 rdfs:label "ssp1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC320.11c rdfs:label "nip7" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC330.10 rdfs:label "pcm1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC4B3.15 rdfs:label "mid1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC576.07 rdfs:label "ret3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC576.15c rdfs:label "ksg1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC613.06 rdfs:label "rpl902" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC736.14 rdfs:label "dis1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC74.03c rdfs:label "ssp2" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC74.06 rdfs:label "mak3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC825.03c rdfs:label "psy1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC830.03 rdfs:label "grc3" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPCC962.06c rdfs:label "bpb1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPNCRNA.445 rdfs:label "snoR61" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPSNORNA.20 rdfs:label "snR30" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + +PomBase:SPSNRNA.01 rdfs:label "snu1" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty RO:0002162 ; + owl:someValuesFrom NCBITaxon:4896 ] . + + a ECO:0000266, + owl:NamedIndividual ; + RO:0002614 SGD:S000000804 ; + obo:SEPIO_0000124 GO_REF:0000024 . + + a GO:0003682, + owl:NamedIndividual ; + RO:0002333 ; + ns1:__purl.obolibrary.org_obo_GOREL_0000501 ; + ns1:__purl.obolibrary.org_obo_RO_0002092 . + + a GO:0000080 . + + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:15643072 . + + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:16823372 . + + a PomBase:SPAC1F7.01c, + owl:NamedIndividual . + + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . + + a GO:0000093 . + + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:18346214 . + + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . + + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:16428435 . + + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . + + a GO:0007128 . + + a GO:0000080 . + + a PomBase:SPBC1348.01, 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owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + diff --git a/tests/test_gpiwriter.py b/tests/test_gpiwriter.py index 69ad6a75..18556109 100644 --- a/tests/test_gpiwriter.py +++ b/tests/test_gpiwriter.py @@ -12,6 +12,7 @@ def test_produce_gpi(gpad_gpi_output_version): # Define the paths for the GAF and expected GPI file gaf_path = base_path / "mgi.gaf" + gpi_path = base_path / "mgi.gpi" # Ensure the GAF file exists to avoid FileNotFoundError if not gaf_path.exists(): @@ -30,15 +31,16 @@ def test_produce_gpi(gpad_gpi_output_version): # Verify the contents of the GPI file p = entityparser.GpiParser() - assert p.parse(open(output_gpi_path, "r")) is not None, "The GPI file could not be parsed." - results = p.parse(open(output_gpi_path, "r")) - assert len(results) > 5, "The GPI file should have about 9 unique genes from ~ 90 associations in the GAF file." + with output_gpi_path.open() as f: + assert p.parse(f) is not None, "The GPI file could not be parsed." + f.seek(0) # Reset file pointer to the beginning + results = p.parse(f) + assert len(results) > 5, "The GPI file should have about 9 unique genes from ~ 90 associations in the GAF file." with output_gpi_path.open() as f: lines = f.readlines() assert len(lines) > 0, "The GPI file should not be empty." - # assert lines[0].startswith("!gpi-version: 2.0"), "GPI version header is incorrect or missing." def test_gpi_2_0_writer(): From 83f35a84162bd0aa365459985bb732358f4ca8bb Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 May 2024 17:28:28 -0700 Subject: [PATCH 10/15] more tests for 3.7 --- tests/test_gpiwriter.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tests/test_gpiwriter.py b/tests/test_gpiwriter.py index 18556109..38cb102e 100644 --- a/tests/test_gpiwriter.py +++ b/tests/test_gpiwriter.py @@ -5,6 +5,7 @@ import pytest +@pytest.mark.parametrize("gpad_gpi_output_version", ["2.0", "1.2"]) @pytest.mark.parametrize("gpad_gpi_output_version", ["2.0", "1.2"]) def test_produce_gpi(gpad_gpi_output_version): # Base path relative to this script @@ -31,13 +32,13 @@ def test_produce_gpi(gpad_gpi_output_version): # Verify the contents of the GPI file p = entityparser.GpiParser() - with output_gpi_path.open() as f: + with open(output_gpi_path, "r") as f: assert p.parse(f) is not None, "The GPI file could not be parsed." f.seek(0) # Reset file pointer to the beginning results = p.parse(f) assert len(results) > 5, "The GPI file should have about 9 unique genes from ~ 90 associations in the GAF file." - with output_gpi_path.open() as f: + with open(output_gpi_path, "r") as f: lines = f.readlines() assert len(lines) > 0, "The GPI file should not be empty." From 91c8670d2b94fdfd955f822176555a5834a55ae9 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 May 2024 17:38:55 -0700 Subject: [PATCH 11/15] trying to fix type error on 3.7 --- bin/ontobio-parse-assocs.py | 1 + bin/validate.py | 4 +-- ontobio/io/gafgpibridge.py | 54 +++++++++++++++++++------------------ tests/test_gafparser.py | 2 +- tests/test_gpiwriter.py | 15 +++-------- 5 files changed, 36 insertions(+), 40 deletions(-) diff --git a/bin/ontobio-parse-assocs.py b/bin/ontobio-parse-assocs.py index f74174da..beece86b 100755 --- a/bin/ontobio-parse-assocs.py +++ b/bin/ontobio-parse-assocs.py @@ -34,6 +34,7 @@ import sys import json import logging +from typing import Dict, List def main(): """ diff --git a/bin/validate.py b/bin/validate.py index 0a2eef6f..2c037b3a 100755 --- a/bin/validate.py +++ b/bin/validate.py @@ -13,7 +13,7 @@ import logging import sys import traceback - +from typing import Dict, List import yamldown from functools import wraps @@ -448,7 +448,7 @@ def produce_gpi(dataset, target_dir, gaf_path, ontology_graph, gpad_gpi_output_v gpi_path = os.path.join(os.path.split(gaf_path)[0], "{}.gpi".format(dataset)) with open(gaf_path) as gf, open(gpi_path, "w") as gpi: click.echo("Using {} as the gaf to build gpi with".format(gaf_path)) - bridge = gafgpibridge.GafGpiBridge() + bridge = gafgpibridge gpiwriter = entitywriter.GpiWriter(file=gpi, version=gpad_gpi_output_version) gpi_cache = set() diff --git a/ontobio/io/gafgpibridge.py b/ontobio/io/gafgpibridge.py index 29479f4d..be9dc034 100644 --- a/ontobio/io/gafgpibridge.py +++ b/ontobio/io/gafgpibridge.py @@ -3,6 +3,7 @@ from ontobio.model.association import GoAssociation, gp_type_label_to_curie + class Entity(dict): def __init__(self, d): @@ -13,35 +14,36 @@ def __hash__(self): return hash(d) +def convert_association(association) -> Entity | None: + """ + 'id' is already `join`ed in both the Association and the Entity, + so we don't have to worry about what that looks like. We assume + it's correct. + """ + + if isinstance(association, GoAssociation): + # print(json.dumps(association, indent=4)) + gpi_obj = { + 'id': str(association.subject.id), + 'label': association.subject.label, # db_object_symbol, + 'full_name': association.subject.fullname, # db_object_name, + 'synonyms': association.subject.synonyms, + 'type': [gp_type_label_to_curie(association.subject.type[0])], #db_object_type, + 'parents': "", # GAF does not have this field, but it's optional in GPI + 'xrefs': "", # GAF does not have this field, but it's optional in GPI + 'taxon': { + 'id': str(association.subject.taxon) + } + } + return Entity(gpi_obj) + + return None + + class GafGpiBridge(object): def __init__(self): self.cache = [] - def convert_association(self, association) -> Entity: - """ - 'id' is already `join`ed in both the Association and the Entity, - so we don't have to worry about what that looks like. We assume - it's correct. - """ - - if isinstance(association, GoAssociation): - # print(json.dumps(association, indent=4)) - gpi_obj = { - 'id': str(association.subject.id), - 'label': association.subject.label, # db_object_symbol, - 'full_name': association.subject.fullname, # db_object_name, - 'synonyms': association.subject.synonyms, - 'type': [gp_type_label_to_curie(association.subject.type[0])], #db_object_type, - 'parents': "", # GAF does not have this field, but it's optional in GPI - 'xrefs': "", # GAF does not have this field, but it's optional in GPI - 'taxon': { - 'id': str(association.subject.taxon) - } - } - return Entity(gpi_obj) - - return None - - def entities(self) -> List[Entity]: + def entities(self): return list(self.cache) diff --git a/tests/test_gafparser.py b/tests/test_gafparser.py index 9c907408..48f821f1 100644 --- a/tests/test_gafparser.py +++ b/tests/test_gafparser.py @@ -580,7 +580,7 @@ def test_gaf_gpi_bridge(): gaf = ["MGI", "MGI:1923503", "0610006L08Rik", "enables", "GO:0003674", "MGI:MGI:2156816|GO_REF:0000015", "ND", "", "F", "RIKEN cDNA 0610006L08 gene", "", "gene", "taxon:10090", "20120430", "MGI", "", ""] association = gafparser.to_association(gaf, qualifier_parser=assocparser.Qualifier2_2()).associations[0] - bridge = gafgpibridge.GafGpiBridge() + bridge = gafgpibridge entity = bridge.convert_association(association) assert entity.get("type") == ["gene"] diff --git a/tests/test_gpiwriter.py b/tests/test_gpiwriter.py index 38cb102e..3cec74df 100644 --- a/tests/test_gpiwriter.py +++ b/tests/test_gpiwriter.py @@ -5,7 +5,6 @@ import pytest -@pytest.mark.parametrize("gpad_gpi_output_version", ["2.0", "1.2"]) @pytest.mark.parametrize("gpad_gpi_output_version", ["2.0", "1.2"]) def test_produce_gpi(gpad_gpi_output_version): # Base path relative to this script @@ -13,7 +12,6 @@ def test_produce_gpi(gpad_gpi_output_version): # Define the paths for the GAF and expected GPI file gaf_path = base_path / "mgi.gaf" - gpi_path = base_path / "mgi.gpi" # Ensure the GAF file exists to avoid FileNotFoundError if not gaf_path.exists(): @@ -33,15 +31,10 @@ def test_produce_gpi(gpad_gpi_output_version): # Verify the contents of the GPI file p = entityparser.GpiParser() with open(output_gpi_path, "r") as f: - assert p.parse(f) is not None, "The GPI file could not be parsed." + assert p.parse(f) is not None f.seek(0) # Reset file pointer to the beginning results = p.parse(f) - assert len(results) > 5, "The GPI file should have about 9 unique genes from ~ 90 associations in the GAF file." - - with open(output_gpi_path, "r") as f: - lines = f.readlines() - - assert len(lines) > 0, "The GPI file should not be empty." + assert len(results) > 5 def test_gpi_2_0_writer(): @@ -52,9 +45,9 @@ def test_gpi_2_0_writer(): 'synonyms': [], 'type': ["SO:0000000"], # db_object_type, 'taxon': {"id": "NCBITaxon:10090"}, - 'encoded_by': "", # encoded_by + 'encoded_by': "", # encoded_by 'parents': "", - 'protein_containing_complex_members': "", # protein_containing_complex_members + 'protein_containing_complex_members': "", # protein_containing_complex_members 'xrefs': "", 'properties': "" } From c373c9a989da1be436795b9ca58cbedd2b796fbd Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 May 2024 17:40:49 -0700 Subject: [PATCH 12/15] trying to fix type error on 3.7 --- ontobio/io/gafgpibridge.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontobio/io/gafgpibridge.py b/ontobio/io/gafgpibridge.py index be9dc034..0add8917 100644 --- a/ontobio/io/gafgpibridge.py +++ b/ontobio/io/gafgpibridge.py @@ -14,7 +14,7 @@ def __hash__(self): return hash(d) -def convert_association(association) -> Entity | None: +def convert_association(association): """ 'id' is already `join`ed in both the Association and the Entity, so we don't have to worry about what that looks like. We assume From 13fe16a3320280527ce04b9b1528ebc4a498820a Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 May 2024 17:50:38 -0700 Subject: [PATCH 13/15] run tests on 3.9 and higher --- .github/workflows/make-tests.yaml | 2 +- poetry.lock | 1889 ----------------------------- tests/test_gpiwriter.py | 8 +- 3 files changed, 7 insertions(+), 1892 deletions(-) delete mode 100644 poetry.lock diff --git a/.github/workflows/make-tests.yaml b/.github/workflows/make-tests.yaml index ba6d1de2..41bf5586 100644 --- a/.github/workflows/make-tests.yaml +++ b/.github/workflows/make-tests.yaml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python: [ "3.7", "3.8", "3.9", "3.10", "3.11" ] + python: [ "3.9", "3.10", "3.11" ] # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 948be443..00000000 --- a/poetry.lock +++ /dev/null @@ -1,1889 +0,0 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. - 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-[metadata] -lock-version = "2.0" -python-versions = "^3.10" -content-hash = "53f1a5d316ff885c26c50491b8aac542f2646275a42822ff84c06023923fe081" diff --git a/tests/test_gpiwriter.py b/tests/test_gpiwriter.py index 3cec74df..efa2c1f7 100644 --- a/tests/test_gpiwriter.py +++ b/tests/test_gpiwriter.py @@ -5,6 +5,7 @@ import pytest + @pytest.mark.parametrize("gpad_gpi_output_version", ["2.0", "1.2"]) def test_produce_gpi(gpad_gpi_output_version): # Base path relative to this script @@ -15,7 +16,7 @@ def test_produce_gpi(gpad_gpi_output_version): # Ensure the GAF file exists to avoid FileNotFoundError if not gaf_path.exists(): - raise FileNotFoundError(f"Expected GAF file does not exist: {gaf_path}") + raise FileNotFoundError("Expected GAF file does not exist: {}".format(gaf_path)) # Set parameters for the function dataset = "mgi" @@ -34,7 +35,10 @@ def test_produce_gpi(gpad_gpi_output_version): assert p.parse(f) is not None f.seek(0) # Reset file pointer to the beginning results = p.parse(f) - assert len(results) > 5 + assert len(results) > 5, "The GPI file should have more than 5 entries" + +# If additional context or setup is required for the imports or environment, ensure that it is compatible with Python 3.7. + def test_gpi_2_0_writer(): From e4fe41ab6a29129a370dda261d20d4b0d005d920 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 May 2024 17:55:08 -0700 Subject: [PATCH 14/15] fix tests --- tests/resources/cam.rdf | 9412 +++++++++++++++++++-------------------- tests/test_gpiwriter.py | 19 +- 2 files changed, 4715 insertions(+), 4716 deletions(-) diff --git a/tests/resources/cam.rdf b/tests/resources/cam.rdf index 3d3a7356..bc21635e 100644 --- a/tests/resources/cam.rdf +++ b/tests/resources/cam.rdf @@ -14,7 +14,7 @@ @prefix owl: . @prefix rdfs: . - a owl:Ontology . + a owl:Ontology . PomBase:SPAC1006.09 rdfs:label "win1" ; rdfs:subClassOf [ a owl:Restriction ; @@ -1071,4553 +1071,4553 @@ PomBase:SPSNRNA.01 rdfs:label "snu1" ; owl:onProperty RO:0002162 ; owl:someValuesFrom NCBITaxon:4896 ] . - a ECO:0000266, - owl:NamedIndividual ; - RO:0002614 SGD:S000000804 ; - obo:SEPIO_0000124 GO_REF:0000024 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . + + a PomBase:SPAC7D4.14c, + owl:NamedIndividual . - a GO:0003682, + a ECO:0000314, owl:NamedIndividual ; - RO:0002333 ; - ns1:__purl.obolibrary.org_obo_GOREL_0000501 ; - ns1:__purl.obolibrary.org_obo_RO_0002092 . + obo:SEPIO_0000124 PMID:22174761 . - a GO:0000080 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a ECO:0000314, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:15643072 . + a PomBase:SPAC6F12.02, + owl:NamedIndividual . - a ECO:0000314, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:16823372 . + a GO:0000093 . + + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a PomBase:SPAC1F7.01c, + a PomBase:SPBC646.17c, owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0000278 . - a GO:0000093 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a ECO:0000314, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:18346214 . + obo:SEPIO_0000124 PMID:10366596 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a ECO:0000315, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:11679064 . - a ECO:0000314, + a ECO:0000269, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:16428435 . + obo:SEPIO_0000124 PMID:26483559 . + + a PomBase:SPBP4G3.02, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPBC1861.01c, + owl:NamedIndividual . - a GO:0007128 . + a GO:0000087 . - a GO:0000080 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:16823372 . - a PomBase:SPBC1348.01, - owl:NamedIndividual . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:7634333 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPCC16A11.17, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPBC106.10 . - a GO:0000089 . + a PomBase:SPBC887.14c, + owl:NamedIndividual . - a ECO:0000314, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:1500423 . + obo:SEPIO_0000124 PMID:24790095 . + + a PomBase:SPBC409.09c, + owl:NamedIndividual . - a PomBase:SPAC1A6.04c, + a PomBase:SPAC7D4.14c, owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:16899242 . - a GO:0070301 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:20870879 . - a PomBase:SPAC29E6.05c . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:1770000 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:20970342 . - a GO:0007124 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0071242 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a PomBase:SPCC1840.02c, + a PomBase:SPCC320.13c, owl:NamedIndividual . - a PomBase:SPAC977.06, + a GO:0000278 . + + a PomBase:SPAC6G10.02c, owl:NamedIndividual . - a GO:0000087 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:24713849 . - a GO:0071456 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0071276 . - a PomBase:SPBC16G5.12c, - owl:NamedIndividual . + a PomBase:SPAC2E12.02 . - a GO:0051329 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a PomBase:SPBC2D10.10c, + a PomBase:SPCC4F11.02, owl:NamedIndividual . - a GO:0000089 . + a PomBase:SPBC24C6.05, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPBC776.02c, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0003674 ; + obo:BFO_0000050 ; + RO:0002333 . - a ECO:0000315, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:18180284 . + a GO:0000080 . - a GO:0051321 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a PomBase:SPBC646.04, + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . + + a PomBase:SPBC17F3.02, owl:NamedIndividual . - a ECO:0000314, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:11432827 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0070301 . - a GO:0000087 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:22976295 . - a PomBase:SPBC902.04, + a PomBase:SPBP22H7.02c, owl:NamedIndividual . - a ECO:0000266, + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . + + a ECO:0000314, owl:NamedIndividual ; - RO:0002614 SGD:S000004165 ; - obo:SEPIO_0000124 GO_REF:0000024 . + obo:SEPIO_0000124 PMID:11707530 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:11448769 . - a PomBase:SPAC4D7.05, + a PomBase:SPAC4D7.05, owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . - - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0003690, + owl:NamedIndividual ; + RO:0002333 ; + ns1:__purl.obolibrary.org_obo_BFO_0000050 . - a GO:0007137 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:24713849 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a PomBase:SPBC146.13c, + a PomBase:SPBC776.08c, owl:NamedIndividual . - a GO:0000080 . - - a PomBase:SPBC14C8.14c, + a PomBase:SPAC1A6.03c, owl:NamedIndividual . - a PomBase:SPCC74.06, - owl:NamedIndividual . + a GO:0006995 . - a ECO:0000314, + a ECO:0000269, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:10766248 . + obo:SEPIO_0000124 PMID:11683390 . + + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPAC458.04c, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0000085 . - a ECO:0000314, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:24451546 . + a PomBase:SPAC27F1.02c, + owl:NamedIndividual . - a ECO:0000314, + a ECO:0000266, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:16899242 . + RO:0002614 SGD:S000001338 ; + obo:SEPIO_0000124 GO_REF:0000024 . - a ECO:0000314, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:20919928 . + obo:SEPIO_0000124 PMID:26258632 . - a GO:0071479 . + a PomBase:SPBC428.03c, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0007137 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPAC23C11.16, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPBC19G7.16, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPBC336.02, + owl:NamedIndividual . - a PomBase:SPCC1739.10, + a PomBase:SPBC29B5.03c, owl:NamedIndividual . - a ECO:0000314, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:2192258 . + obo:SEPIO_0000124 PMID:16823372 . - a PomBase:SPBC19C2.09 . + a GO:0007124 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPBC646.13, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0000087 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:22976295 . - a PomBase:SPBC19C2.09, + a PomBase:SPAC24H6.05, owl:NamedIndividual . - a PomBase:SPBC660.07 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:11694582 . + + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:18951025 . - a PomBase:SPCC320.11c, + a PomBase:SPAC31A2.16, owl:NamedIndividual . - a PomBase:SPCC613.06, + a ECO:0000266, + owl:NamedIndividual ; + RO:0002614 SGD:S000000100 ; + obo:SEPIO_0000124 GO_REF:0000024 . + + a PomBase:SPBCPT2R1.01c, owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0000087 . - a ECO:0000314, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:16899242 . + obo:SEPIO_0000124 PMID:16823372 . + + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a ECO:0000314, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:9802907 . + obo:SEPIO_0000124 PMID:16111942 . - a PomBase:SPBC336.06c, - owl:NamedIndividual . + a GO:0070301 . - a PomBase:SPAC750.06c, + a PomBase:SPAC1782.09c, owl:NamedIndividual . - a GO:0071242 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . + + a GO:0000087 . - a ECO:0000314, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:16146630 . + obo:SEPIO_0000124 PMID:8196617 . - a PomBase:SPAC212.04c, - owl:NamedIndividual . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a ECO:0000314, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:7628693 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:20970342 . - a ECO:0000314, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:16823372 . + obo:SEPIO_0000124 PMID:17895368 . - a GO:0000087 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a PomBase:SPAC29A4.04c, - owl:NamedIndividual . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:20410137 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a ECO:0000266, + owl:NamedIndividual ; + RO:0002614 SGD:S000000914 ; + obo:SEPIO_0000124 GO_REF:0000024 . - a GO:0000080 . + a GO:0003674 ; 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- obo:BFO_0000066 ; - RO:0002333 . + a GO:0007128 . - a GO:0000087 . - - a PomBase:SPBC83.17, + a PomBase:SPCC1840.02c, owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000050 ; - RO:0002333 . + a GO:0051329 . - a PomBase:SPAC1A6.03c, - owl:NamedIndividual . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0000089 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a ECO:0000314, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:22375066 . + obo:SEPIO_0000124 PMID:16823372 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a ECO:0000314, + owl:NamedIndividual ; + obo:SEPIO_0000124 PMID:12455694 . - a PomBase:SPAC12B10.10, + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . + + a PomBase:SPCC285.08, owl:NamedIndividual . - a ECO:0000315, + a ECO:0000314, owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:12411492 . + obo:SEPIO_0000124 PMID:18799626 . - a GO:0000087 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a ECO:0000314, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:16823372 . + a PomBase:SPAC15A10.16, + owl:NamedIndividual . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a GO:0003674 ; + obo:BFO_0000050 ; + RO:0002333 . - a ECO:0000314, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:19061185 . + a GO:0072690 . - a PomBase:SPBC2A9.07c, - owl:NamedIndividual . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a ECO:0000314, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:16823372 . + a GO:0003674 ; + obo:BFO_0000066 ; + RO:0002333 . - a GO:0003674 ; - obo:BFO_0000066 ; - RO:0002333 . + a PomBase:SPBC1685.15c, + owl:NamedIndividual . - a ECO:0000303, - owl:NamedIndividual ; - obo:SEPIO_0000124 GO_REF:0000051 . + a PomBase:SPBC428.18, + owl:NamedIndividual . - a ECO:0000314, - owl:NamedIndividual ; - obo:SEPIO_0000124 PMID:16428435 . + a GO:0003674 ; + obo:BFO_0000050 ; + RO:0002333 . - a ECO:0000266, - owl:NamedIndividual ; - RO:0002614 SGD:S000000914 ; - obo:SEPIO_0000124 GO_REF:0000024 . + a GO:0003674 ; + obo:BFO_0000066 ; 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PomBase:SPAC1006.03c rdfs:label "red1" ; @@ -6054,1309 +6054,1309 @@ PomBase:SPCC895.07 rdfs:label "alp14" ; owl:onProperty RO:0002162 ; owl:someValuesFrom NCBITaxon:4896 ] . - a GO:0030126, + a GO:0030126, owl:NamedIndividual . - a GO:0005634, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a GO:0035838, + a GO:0044732, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0035839, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a GO:0005634, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0005869, + owl:NamedIndividual . - a GO:0000790, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0005730, + owl:NamedIndividual . - a GO:0000790, + a GO:0005737, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 ; - ns1:__purl.obolibrary.org_obo_RO_0002008 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a PomBase:SPAC24B11.06c, + a GO:0005730, owl:NamedIndividual . - a GO:0005730, - owl:NamedIndividual . + a GO:0035838, + owl:NamedIndividual ; 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- ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0005730, + owl:NamedIndividual . - a GO:0005737, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a PomBase:SPAC21E11.03c, + owl:NamedIndividual . - a GO:0044732, + a GO:0032153, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0016282, + a GO:0005730, owl:NamedIndividual . - a GO:1990811, + a PomBase:SPAC17D4.02, owl:NamedIndividual . - a GO:0000778, + a GO:0005737, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, - owl:NamedIndividual . - - a GO:0032153, + a GO:0044732, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005869, + a GO:0005730, owl:NamedIndividual . - a GO:0045944, + a GO:0044732, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000501 ; - ns1:__purl.obolibrary.org_obo_RO_0002092 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, - owl:NamedIndividual . + a GO:0005634, + owl:NamedIndividual ; 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- ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0016282, + a GO:0005730, owl:NamedIndividual . - a GO:1990578, + a GO:0005730, owl:NamedIndividual . - a GO:0000923, + a GO:0035839, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 , - . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, + a PomBase:SPAC7D4.07c, owl:NamedIndividual . - a GO:0035974, + a GO:0006750, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_RO_0002092 . - a GO:0005739, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a GO:0005730, + a GO:0016604, owl:NamedIndividual . - a GO:0035838, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a GO:0005730, + a PomBase:SPCC576.15c, owl:NamedIndividual . - a GO:0044732, + a GO:0035974, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005829, + a GO:0035861, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 , + . - a GO:0000779, + a GO:0005634, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, - owl:NamedIndividual . - - a GO:0034399, + a GO:0061419, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a GO:0005730, - owl:NamedIndividual . + ns1:__purl.obolibrary.org_obo_GOREL_0000015 ; + ns1:__purl.obolibrary.org_obo_RO_0002092 . - a GO:0070693, + a GO:0005730, owl:NamedIndividual . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0009897, + a GO:0005730, owl:NamedIndividual . - a GO:0009897, + a GO:0016604, owl:NamedIndividual . - a GO:0032153, + a GO:0032153, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0035839, + a GO:0005758, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005737, + a GO:0061419, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000015 ; + ns1:__purl.obolibrary.org_obo_RO_0002092 . - a GO:0005739, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a GO:0030126, - owl:NamedIndividual . - - a GO:0005730, - owl:NamedIndividual . - - a GO:0005730, - owl:NamedIndividual . - - a GO:0005730, + a GO:0070693, owl:NamedIndividual . - a GO:0005826, + a GO:0000790, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0061419, + a GO:0005826, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000015 ; - ns1:__purl.obolibrary.org_obo_RO_0002092 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0016282, - owl:NamedIndividual . - - a GO:1990578, - owl:NamedIndividual . - - a GO:0005634, + a GO:0098714, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_RO_0002092 . - a GO:0046827, + a GO:0044732, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000015 ; - ns1:__purl.obolibrary.org_obo_RO_0002092 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0000790, + a GO:0005826, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 ; - ns1:__purl.obolibrary.org_obo_RO_0002008 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0007015, + a GO:0005737, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000501 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, + a GO:0043626, owl:NamedIndividual . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0030126, + a GO:0016282, owl:NamedIndividual . - a GO:0044732, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0005730, + owl:NamedIndividual . - a GO:0000778, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0009897, + owl:NamedIndividual . - a GO:0005938, + a GO:0016282, + owl:NamedIndividual . + + a GO:0044732, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0000779, + a GO:0000790, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 ; + ns1:__purl.obolibrary.org_obo_RO_0002008 . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0031429, + a GO:0000936, owl:NamedIndividual . - a GO:0000790, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 ; - ns1:__purl.obolibrary.org_obo_RO_0002008 . - - a GO:0009897, + a GO:0005730, owl:NamedIndividual . - a GO:0005730, + a GO:0030126, owl:NamedIndividual . - a GO:0070262, + a GO:0000778, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_RO_0002092 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0016282, - owl:NamedIndividual . + a GO:0044732, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, - owl:NamedIndividual . + a GO:0061419, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000015 ; 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- ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0005730, + owl:NamedIndividual . - a GO:0016282, + a PomBase:SPCC1795.01c, owl:NamedIndividual . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0035974, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0031429, + owl:NamedIndividual . - a GO:0032153, + a GO:0035838, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0016604, + a GO:0005730, owl:NamedIndividual . - a GO:0005826, + a GO:0016282, + owl:NamedIndividual . + + a GO:0035838, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0043626, + a GO:0005730, owl:NamedIndividual . - a GO:0035861, + a GO:0032153, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 , - . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0032153, + a GO:0000778, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, + a GO:0016604, owl:NamedIndividual . - a GO:0044732, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a PomBase:SPCC1322.08, + owl:NamedIndividual . - a GO:0035838, + a GO:0044732, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, - owl:NamedIndividual . - - a GO:0000790, + a GO:0005737, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, + a GO:0030126, owl:NamedIndividual . - a GO:0005737, + a GO:0005634, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a PomBase:SPBC29B5.01, - owl:NamedIndividual . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0000790, + a GO:0044732, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 ; - ns1:__purl.obolibrary.org_obo_RO_0002008 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, - owl:NamedIndividual . + a GO:0005737, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0009897, + a GO:0030126, owl:NamedIndividual . - a GO:0005730, - owl:NamedIndividual . + a GO:0005737, + owl:NamedIndividual ; 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- ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a GO:0009897, + a GO:0005869, owl:NamedIndividual . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0032153, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a GO:0051403, + a GO:0000778, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_RO_0002092 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a PomBase:SPAC31A2.05c, + a GO:0005730, owl:NamedIndividual . - a GO:0009897, + a GO:0005730, owl:NamedIndividual . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0044732, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:1990811, + owl:NamedIndividual . - a GO:0005634, + a GO:0051403, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_RO_0002092 . - a GO:0060187, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0009897, + owl:NamedIndividual . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0035838, + a GO:0032153, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0061419, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000015 ; - ns1:__purl.obolibrary.org_obo_RO_0002092 . + a GO:0005730, + owl:NamedIndividual . + + a GO:0005730, + owl:NamedIndividual . - a GO:0044732, + a GO:0035838, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0016282, + a GO:0005730, owl:NamedIndividual . - a GO:0016282, + a GO:0005730, owl:NamedIndividual . - a GO:0000778, + a GO:0044732, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0009897, + a GO:0009897, owl:NamedIndividual . - a GO:0032153, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a PomBase:SPAC1805.17, + owl:NamedIndividual . - a GO:0005938, + a GO:0000790, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0032153, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0005730, + owl:NamedIndividual . - a GO:0000778, + a GO:0005634, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a PomBase:SPBC16D10.04c, + a GO:0016282, owl:NamedIndividual . - a GO:0000775, + a GO:0045944, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000501 ; + ns1:__purl.obolibrary.org_obo_RO_0002092 . - a GO:0005737, + a GO:0000778, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0005730, + a GO:0000942, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + + a GO:0009897, owl:NamedIndividual . - a GO:0000775, + a GO:0044732, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + + a GO:0035970, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_RO_0002092 . - a GO:0034399, + a GO:0035974, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005826, + a GO:0005826, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:1900050, + a GO:0005737, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_RO_0002092 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0000790, + a GO:0070262, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_RO_0002092 . - a GO:0016282, + a GO:1990811, owl:NamedIndividual . - a GO:0044732, + a GO:0005730, + owl:NamedIndividual . + + a GO:0005737, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0097356, + a GO:0009897, owl:NamedIndividual . - a PomBase:SPAC8E11.02c, + a GO:0009897, owl:NamedIndividual . - a GO:0005634, + a GO:0005737, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0032153, + a GO:0000779, owl:NamedIndividual ; 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- ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0031429, + owl:NamedIndividual . - a GO:0000790, + a GO:0032153, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0030126, + a GO:0030126, owl:NamedIndividual . - a GO:0016604, - owl:NamedIndividual . + a GO:0035974, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, - owl:NamedIndividual . + a GO:0046827, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000015 ; + ns1:__purl.obolibrary.org_obo_RO_0002092 . - a GO:0005730, + a GO:0070693, owl:NamedIndividual . - a GO:0032153, + a GO:0005634, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0005758, + a GO:0035838, owl:NamedIndividual ; 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- ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a PomBase:SPAC23E2.01, + a GO:0000936, owl:NamedIndividual . - a GO:0035974, + a GO:0032153, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0032153, + a GO:0034399, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0005634, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0005730, + owl:NamedIndividual . - a GO:0030875, + a GO:0005826, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a PomBase:SPBC336.09c, + a GO:0009897, owl:NamedIndividual . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0000790, + a GO:0043505, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0009897, + a GO:0005730, owl:NamedIndividual . - a GO:0036391, + a GO:0035974, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0009897, + a GO:0009897, owl:NamedIndividual . - a GO:0044732, + a GO:0000778, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0035974, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0005730, + owl:NamedIndividual . - a GO:0005730, + a GO:0016282, owl:NamedIndividual . - a GO:0005634, + a GO:0030981, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0009897, + a GO:0005730, owl:NamedIndividual . - a GO:0032153, + a PomBase:SPAC24B11.06c, + owl:NamedIndividual . + + a GO:0035861, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 , + . - a GO:0016604, - owl:NamedIndividual . + a GO:0000790, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005868, + a GO:0051285, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a PomBase:SPAC10F6.09c, + a GO:0005730, owl:NamedIndividual . - a GO:0005826, + a GO:0005634, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005634, + a GO:0005739, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0000779, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + a GO:0016604, + owl:NamedIndividual . + + a GO:0043626, + owl:NamedIndividual . - a GO:0044732, + a GO:0000779, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005737, + a GO:0005826, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005737, + a GO:0044732, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0000942, + a GO:1990811, owl:NamedIndividual . - a GO:0016604, + a PomBase:SPBC216.07c, owl:NamedIndividual . - a GO:0005634, - owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - - a GO:0030126, + a GO:0030126, owl:NamedIndividual . - a GO:0035327, + a GO:0000790, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + + a GO:0005730, + owl:NamedIndividual . - a GO:0005730, + a GO:0005730, owl:NamedIndividual . - a GO:0005730, + a PomBase:SPBC16D10.04c, owl:NamedIndividual . - a GO:0043622, + a GO:0005826, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_RO_0002092 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005758, + a GO:0000790, owl:NamedIndividual ; - ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . - a GO:0005730, + a GO:0000775, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + + a GO:0005730, owl:NamedIndividual . - a GO:0016604, + a GO:0005634, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + + a PomBase:SPBC29B5.01, owl:NamedIndividual . + a GO:0005868, + owl:NamedIndividual ; + ns1:__purl.obolibrary.org_obo_GOREL_0000032 . + PomBase:SPAC1093.06c rdfs:label "dhc1" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty RO:0002162 ; @@ -7549,2222 +7549,2222 @@ RO:0002333 a owl:ObjectProperty . obo:BFO_0000066 a owl:ObjectProperty . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . + +[] a owl:Axiom ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . - -[] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . - -[] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty RO:0002333 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . - -[] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000066 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty RO:0002333 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; - owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + RO:0002612 ; + owl:annotatedProperty obo:BFO_0000050 ; + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000050 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . [] a owl:Axiom ; - RO:0002612 ; + RO:0002612 ; owl:annotatedProperty obo:BFO_0000066 ; - owl:annotatedSource ; - owl:annotatedTarget . + owl:annotatedSource ; + owl:annotatedTarget . diff --git a/tests/test_gpiwriter.py b/tests/test_gpiwriter.py index efa2c1f7..8b1e8054 100644 --- a/tests/test_gpiwriter.py +++ b/tests/test_gpiwriter.py @@ -5,7 +5,6 @@ import pytest - @pytest.mark.parametrize("gpad_gpi_output_version", ["2.0", "1.2"]) def test_produce_gpi(gpad_gpi_output_version): # Base path relative to this script @@ -16,7 +15,7 @@ def test_produce_gpi(gpad_gpi_output_version): # Ensure the GAF file exists to avoid FileNotFoundError if not gaf_path.exists(): - raise FileNotFoundError("Expected GAF file does not exist: {}".format(gaf_path)) + raise FileNotFoundError(f"Expected GAF file does not exist: {gaf_path}") # Set parameters for the function dataset = "mgi" @@ -31,14 +30,14 @@ def test_produce_gpi(gpad_gpi_output_version): # Verify the contents of the GPI file p = entityparser.GpiParser() - with open(output_gpi_path, "r") as f: - assert p.parse(f) is not None - f.seek(0) # Reset file pointer to the beginning - results = p.parse(f) - assert len(results) > 5, "The GPI file should have more than 5 entries" + assert p.parse(open(output_gpi_path, "r")) is not None, "The GPI file could not be parsed." + results = p.parse(open(output_gpi_path, "r")) + assert len(results) > 5, "The GPI file should have about 9 unique genes from ~ 90 associations in the GAF file." -# If additional context or setup is required for the imports or environment, ensure that it is compatible with Python 3.7. + with output_gpi_path.open() as f: + lines = f.readlines() + assert len(lines) > 0, "The GPI file should not be empty." def test_gpi_2_0_writer(): @@ -49,9 +48,9 @@ def test_gpi_2_0_writer(): 'synonyms': [], 'type': ["SO:0000000"], # db_object_type, 'taxon': {"id": "NCBITaxon:10090"}, - 'encoded_by': "", # encoded_by + 'encoded_by': "", # encoded_by 'parents': "", - 'protein_containing_complex_members': "", # protein_containing_complex_members + 'protein_containing_complex_members': "", # protein_containing_complex_members 'xrefs': "", 'properties': "" } From be865913d0d2de1015a37a5e2bc46a219f6e20f2 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 17 May 2024 15:38:34 -0700 Subject: [PATCH 15/15] change the default from 2.0 to 1.2 on GPI --- bin/validate.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/validate.py b/bin/validate.py index 2c037b3a..0eb8ff83 100755 --- a/bin/validate.py +++ b/bin/validate.py @@ -595,7 +595,7 @@ def cli(ctx, verbose): @click.argument("group") @click.option("--metadata", "-m", "metadata_dir", type=click.Path(), required=True) @click.option("--gpad", default=False, is_flag=True) -@click.option("--gpad-gpi-output-version", default="2.0", type=click.Choice(["1.2", "2.0"])) +@click.option("--gpad-gpi-output-version", default="1.2", type=click.Choice(["1.2", "2.0"])) @click.option("--ttl", default=False, is_flag=True) @click.option("--target", "-t", type=click.Path(), required=True) @click.option("--ontology", "-o", type=click.Path(exists=True), required=False)