From 5bcd67ec4d17f9c5a66b5594bdf9f7c31739d484 Mon Sep 17 00:00:00 2001 From: Babaiha Date: Wed, 30 Aug 2023 14:44:54 +0200 Subject: [PATCH 1/9] update --- ebel/manager/neo4j/bel.py | 2 + ebel/manager/neo4j/n4j_structure.py | 1 + gpt3.5-prompt2-set1-trial1_cleaned.bel.json | 84791 ++++++++++++++++++ neo4j-import.py | 18 + 4 files changed, 84812 insertions(+) create mode 100644 gpt3.5-prompt2-set1-trial1_cleaned.bel.json create mode 100644 neo4j-import.py diff --git a/ebel/manager/neo4j/bel.py b/ebel/manager/neo4j/bel.py index 0923f4f..895494f 100644 --- a/ebel/manager/neo4j/bel.py +++ b/ebel/manager/neo4j/bel.py @@ -76,8 +76,10 @@ def import_json( else: # It is a list files_to_import = [Path(fp) for fp in input_path] + print(files_to_import) for path in files_to_import: if path.is_file(): + print("import: " + path.name) logger.info(f"Begin import: {path.name}") try: diff --git a/ebel/manager/neo4j/n4j_structure.py b/ebel/manager/neo4j/n4j_structure.py index 33627ac..933769d 100644 --- a/ebel/manager/neo4j/n4j_structure.py +++ b/ebel/manager/neo4j/n4j_structure.py @@ -52,6 +52,7 @@ "has_components": "HAS_COMPONENTS", "has_member": "HAS_MEMBER", "has_members": "HAS_MEMBERS", + "has_modification": "HAS_MODIFICATION", "increases": "INCREASES", "is_a": "IS_A", "negative_correlation": "NEGATIVE_CORRELATION", diff --git a/gpt3.5-prompt2-set1-trial1_cleaned.bel.json b/gpt3.5-prompt2-set1-trial1_cleaned.bel.json new file mode 100644 index 0000000..dcca013 --- /dev/null +++ b/gpt3.5-prompt2-set1-trial1_cleaned.bel.json @@ -0,0 +1,84791 @@ +[ + { + "document": { + "authors": "xxx", + "contact_info": "xxx@scai.fraunhofer.de", + "copyright": "Copyright \u00a9 2023 Fraunhofer Institute SCAI, All rights reserved.", + "description": "ChatGPT generated BEL statements Tau KG.", + "licences": "MIT License", + "name": "chatGPT-BEL", + "version": "1.0.0" + } + }, + { + "definitions": [ + { + "namespace": { + "keyword": "CHEBI", + "type": "URL", + "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/chebi/chebi-20220531.belns", + "value_list": [] + } + }, + { + "namespace": { + "keyword": "DO", + "type": "URL", + "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/disease-ontology/disease-ontology-20200407.belns", + "value_list": [] + } + }, + { + "namespace": { + "keyword": "MESHD", + "type": "URL", + "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-diseases/mesh-diseases-20190128.belns", + "value_list": [] + } + }, + { + "namespace": { + "keyword": "MESH", + "type": "URL", + "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh/mesh-names-20181007.belns", + "value_list": [] + } + }, + { + "namespace": { + "keyword": "HGNC", + "type": "URL", + "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hgnc/hgnc-20200529.belns", + "value_list": [] + } + }, + { + "namespace": { + "keyword": "MGI", + "type": "URL", + "value": 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+ ] + }, + { + "sets": [ + { + "citation": { + "type": "PubMed", + "title": "", + "ref": "9099822.0", + "pub_date": "", + "author_list": "", + "comment": "" + } + }, + { + "set": { + "DataSource": [ + "chatGPT" + ] + } + }, + { + "evidence": "Because the elevation of transglutaminase in the Alzheimer's disease samples occurred in the prefrontal cortex, where neurofibrillary pathology is usually abundant." + } + ] + }, + { + "statement": [ + { + "subject": [ + { + "function": { + "type": "abundance", + "name": "protein" + } + }, + [ + { + "namespace": "HGNC", + "name": "TGM2" + } + ] + ] + }, + { + "relation": "increases" + }, + { + "object": [ + { + "function": { + "type": "process", + "name": "pathology" + } + }, + [ + { + "namespace": "MESH", + "name": "prefrontal cortex" + } + ] + ] + } + ] + }, + { + "sets": [ + { + "citation": { + "type": "PubMed", + "title": "", + "ref": "9099822.0", + "pub_date": "", + "author_list": "", + "comment": "" + } + }, + { + "set": { + "DataSource": [ + "chatGPT" + ] + } + }, + { + "evidence": "There were no significant differences in transglutaminase activity or levels in the cerebellum between control and Alzheimer's disease cases." + } + ] + }, + { + "statement": [ + { + "subject": [ + { + "function": { + "type": "abundance", + "name": "protein" + } + }, + [ + { + "namespace": "HGNC", + "name": "TGM2" + } + ] + ] + }, + { + "relation": "increases" + }, + { + "object": [ + { + "function": { + "type": "process", + "name": "pathology" + } + }, + [ + { + "namespace": "MESH", + "name": "cerebellum" + } + ] + ] + } + ] + } + ] + } +] \ No newline at end of file diff --git a/neo4j-import.py b/neo4j-import.py new file mode 100644 index 0000000..b415c70 --- /dev/null +++ b/neo4j-import.py @@ -0,0 +1,18 @@ + +from pathlib import Path + +from ebel.manager.neo4j.n4j_meta import Neo4jClient +from ebel.manager.neo4j.bel import Neo4jBel + +sherpa_json = "C:\\Users\\nbabaiha\\Documents\\GitHub\\chatgpt-paper\\bel-files\\Sherpa\\total_sherpa_results_cleaned.bel.json" +gpt3_5_json = "C:\\Users\\nbabaiha\\Documents\\GitHub\\chatgpt-paper\\bel-files\\gpt3.5-turbo\\gpt3.5-prompt2-set1-trial1_cleaned.bel.json" + + +neo = Neo4jClient(uri="bolt://localhost:7687", database="neo4j", user="neo4j", password="12345678") +# print(neo.session.run("MATCH (n) RETURN n").data()) + +n4jbel = Neo4jBel(client=neo) + + +n4jbel.import_json([sherpa_json, gpt3_5_json]) +print("Done") \ No newline at end of file From 0c78df073f4e371dd833df84ae536a78eb678bb9 Mon Sep 17 00:00:00 2001 From: Babaiha Date: Wed, 30 Aug 2023 20:15:19 +0200 Subject: [PATCH 2/9] update --- ebel/manager/neo4j/n4j_importer.py | 32 ++++++++++++++++-------------- neo4j-import.py | 3 ++- 2 files changed, 19 insertions(+), 16 deletions(-) diff --git a/ebel/manager/neo4j/n4j_importer.py b/ebel/manager/neo4j/n4j_importer.py index 2fecf57..8936877 100644 --- a/ebel/manager/neo4j/n4j_importer.py +++ b/ebel/manager/neo4j/n4j_importer.py @@ -77,7 +77,7 @@ def insert_statements_and_sets(self, statements_and_sets: dict) -> int: new_edges = 0 for e in tqdm(statements_and_sets, desc="Insert BEL Statements"): - + #print(e) dtype, data = tuple(e.items())[0] if dtype == "sets": @@ -109,20 +109,22 @@ def insert_statements_and_sets(self, statements_and_sets: dict) -> int: annotation.pop(anno_keyword, None) elif dtype == "statement" and len(data) >= 1: - - _, subj_class, subject_id = self.get_node_id(data[0]['subject']) - - if len(data) > 1 and 'object' in data[2]: - # TODO: nested statements are missing - - _, obj_class, object_id = self.get_node_id(data[2]['object']) - - relation = data[1]['relation'] - neo4j_relation_class = edge_map[relation] - - new_edges += self.insert_bel_edge(annotation, citation, evidence, pmid, neo4j_relation_class, - subject_id, object_id) - + #print(data[0]["subject"]) + try: + _, subj_class, subject_id = self.get_node_id(data[0]['subject']) + + if len(data) > 1 and 'object' in data[2]: + # TODO: nested statements are missing + + _, obj_class, object_id = self.get_node_id(data[2]['object']) + + relation = data[1]['relation'] + neo4j_relation_class = edge_map[relation] + + new_edges += self.insert_bel_edge(annotation, citation, evidence, pmid, neo4j_relation_class, + subject_id, object_id) + except Exception as e: + print("error", e) return new_edges @staticmethod diff --git a/neo4j-import.py b/neo4j-import.py index b415c70..61ce9cb 100644 --- a/neo4j-import.py +++ b/neo4j-import.py @@ -14,5 +14,6 @@ n4jbel = Neo4jBel(client=neo) -n4jbel.import_json([sherpa_json, gpt3_5_json]) +n4jbel.import_json([gpt3_5_json]) +#n4jbel.import_json([sherpa_json, gpt3_5_json]) print("Done") \ No newline at end of file From 2d2efcca0f8351341e56b9de7624f8adbe8ab42a Mon Sep 17 00:00:00 2001 From: Babaiha Date: Wed, 30 Aug 2023 20:39:18 +0200 Subject: [PATCH 3/9] update --- gpt3.5-prompt2-set1-trial1_cleaned.bel.json | 84791 ------------------ neo4j-import.py | 4 +- 2 files changed, 2 insertions(+), 84793 deletions(-) delete mode 100644 gpt3.5-prompt2-set1-trial1_cleaned.bel.json diff --git a/gpt3.5-prompt2-set1-trial1_cleaned.bel.json b/gpt3.5-prompt2-set1-trial1_cleaned.bel.json deleted file mode 100644 index dcca013..0000000 --- a/gpt3.5-prompt2-set1-trial1_cleaned.bel.json +++ /dev/null @@ -1,84791 +0,0 @@ -[ - { - "document": { - "authors": "xxx", - "contact_info": "xxx@scai.fraunhofer.de", - "copyright": "Copyright \u00a9 2023 Fraunhofer Institute SCAI, All rights reserved.", - "description": "ChatGPT generated BEL statements Tau KG.", - "licences": "MIT License", - "name": "chatGPT-BEL", - "version": "1.0.0" - } - }, - { - "definitions": [ - { - "namespace": { - "keyword": "CHEBI", - "type": "URL", - "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/chebi/chebi-20220531.belns", - "value_list": [] - } - }, - { - "namespace": { - "keyword": "DO", - "type": "URL", - "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/disease-ontology/disease-ontology-20200407.belns", - "value_list": [] - } - }, - { - "namespace": { - "keyword": "MESHD", - "type": "URL", - "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-diseases/mesh-diseases-20190128.belns", - "value_list": [] - } - }, - { - "namespace": { - "keyword": "MESH", - "type": "URL", - "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh/mesh-names-20181007.belns", - "value_list": [] - } - }, - { - "namespace": { - "keyword": "HGNC", - "type": "URL", - "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hgnc/hgnc-20200529.belns", - "value_list": [] - } - }, - { - "namespace": { - "keyword": "MGI", - "type": "URL", - "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mgi-mouse-genes/mgi-mouse-genes-20190128.belns", - "value_list": [] - } - }, - { - "namespace": { - "keyword": "GO", - "type": "URL", - "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/go/go-20180109.belns", - "value_list": [] - } - }, - { - "namespace": { - "keyword": "GOBP", - "type": "URL", - "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/go-biological-process/go-biological-process-20190128.belns", - "value_list": [] - } - }, - { - "namespace": { - "keyword": "MESHPP", - "type": "URL", - "value": "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-processes/mesh-processes-20190128.belns", - "value_list": [] - } - }, - { - "annotation": { - "keyword": "Score", - "type": "PATTERN", - "value": "0.\\d+", - "value_list": [] - } - }, - { - "annotation": { - "keyword": "DataSource", - "type": "LIST", - "value": null, - "value_list": [ - "chatGPT", - "gpt4-prompt2-set1-trial1" - ] - } - } - ] - }, - { - "statements_and_sets": [ - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "10391244.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - 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"statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "phosphorylation" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "10391244.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Phosphorylation on a serine or threonine that precedes proline (pS/T-P) alters the rate of prolyl isomerization." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "phosphorylation" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { 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Disruption of these normal interactions could contribute significantly to development of tauopathies such as Alzheimer's disease." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "tauopathies" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer's disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "10998059.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "These two enzymes are responsible for most of the hyperphosphorylation of the microtubule-binding protein tau, a feature observed in the brains of patients with Alzheimer's disease and other neurodegenerative 'taupathies'." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "GSK3B" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "tau" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11013232.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The bis-indole indirubin is an active ingredient of Danggui Longhui Wan, a traditional Chinese medicine recipe used in the treatment of chronic diseases such as leukemias." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "treatment of chronic diseases" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "leukemias" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11013232.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "GSK-3 beta, along with CDK5, is responsible for most of the abnormal hyperphosphorylation of the microtubule-binding protein tau observed in Alzheimer's disease." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "GSK-3 beta's abnormal hyperphosphorylation of the microtubule-binding protein tau" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer's disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11089576.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The mechanisms leading to the abnormal self-polymerization of tau into straight and paired helical filaments (PHFs) and neurofibrillary tangles (NFT) in Alzheimer disease (AD) and progressive supranuclear palsy (PSP) are not known." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "abnormal self-polymerization of tau into straight and paired helical filaments (PHFs) and neurofibrillary tangles (NFT)" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "neurofibrillary tangle formation" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11089576.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Tissue homogenates from PSP and normal age-matched controls were used to immunoaffinity-purify proteins containing transglutaminase-induced epsilon-(gamma-glutamyl) lysine cross-links. 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} - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "epsilon-(gamma-glutamyl) lysine cross-linking of PHF-tau" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "PHF-tau" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11089576.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Double-label immunofluorescence demonstrated the colocalization of the cross-link and PHF-tau in NFT in pons of PSP." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "cross-linking of PHF-tau protein" - 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"title": "", - "ref": "11606569.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "yet it is able to polymerize into the ordered paired helical filaments (PHF) of Alzheimer's disease." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "polymerization" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11606569.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "In the splice isoforms lacking exon 10, this process is facilitated by the formation of beta-structure around the hexapeptide motif PHF6 ((306)VQIVYK(311)) encoded by exon 11." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "facilitation" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "polymerization" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11606569.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "We have investigated the structural requirements for PHF polymerization in the context of adult tau isoforms containing four repeats (including exon 10)." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "formation" - } - ] - 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"type": "PubMed", - "title": "", - "ref": "11606569.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "there is a cross-talk between the two hexapeptide motifs during PHF aggregation." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "cross-talk" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "aggregation" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11606569.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "We also show that two of the tau mutations found in hereditary frontotemporal dementias, DeltaK280 and P301L, have a much stronger tendency for PHF aggregation which correlates with their high propensity for beta-structure around the hexapeptide motifs." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "aggregation" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "polymerization" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11738469.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Transglutaminase-catalyzed epsilon(gamma-glutamyl)lysine cross-links exist in Alzheimer's disease (AD) paired helical filament (PHF) tau protein but not normal soluble tau." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer's disease" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "paired helical filament tau protein" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "11738469.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "To test the hypothesis that these cross-links could play a role in the formation of neurofibrillary tangles (NFT), we used single- and double-label immunofluorescence confocal microscopy and immunoaffinity purification and immunoblotting to examine epsilon(gamma-glutamyl)lysine cross-links in AD and control brains." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "cross-links" - } - ] - ] - 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"type": "PubMed", - "title": "", - "ref": "12578227.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Our previous studies demonstrated that transglutaminase-induced cross-linking of tau proteins occurs in Alzheimer disease." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "protein cross-linking" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "12578227.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Our previous studies demonstrated that transglutaminase-induced cross-linking of tau proteins occurs in progressive supranuclear palsy (PSP)." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "protein cross-linking" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "progressive supranuclear palsy" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "12578227.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Protein and mRNA levels of transglutaminase 1 were increased in globus pallidus of PSP as compared to controls." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "transglutaminase 1" - } - ] - ] - }, - { - "relation": "increases" - 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} - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "synaptic loss" - } - ] - ] - }, - { - "relation": "positive_correlation" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "cognitive decline" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "21843595.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Here we investigated global changes in protein SUMOylation and ubiquitination in vivo in a model of AD." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "protein SUMOylation" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer Disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "21843595.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "A significant increase in the global level of ubiquitinated proteins was observed in the hippocampus of Tg2576 mice." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "ubiquitinated proteins" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer Disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "21843595.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Significant or close to significant changes in individual bands of SUMO-1 or SUMO-2/3 conjugation were apparent in all brain regions investigated." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "SUMO-1 conjugation" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer Disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "21843595.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Significant or close to significant changes in individual bands of SUMO-1 or SUMO-2/3 conjugation were apparent in all brain regions investigated." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "SUMO-2/3 conjugation" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer Disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "21843595.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Levels of SUMO-specific conjugating and deconjugating enzymes, UBC9 and SENP-1 were also unaltered in any of the brain regions analysed." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "UBC9" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer Disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "21843595.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Levels of SUMO-specific conjugating and deconjugating enzymes, UBC9 and SENP-1 were also unaltered in any of the brain regions analysed." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "SENP-1" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer Disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "21843595.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "These results suggest that alterations in SUMO substrate conjugation may occur and that global posttranslational modifications by ubiquitin may play an important role in the mechanisms underlying AD." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "posttranslational modifications by ubiquitin" - } - ] - ] - }, - { - "relation": "regulates" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer Disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "21910444.0", - "pub_date": "", - "author_list": "", - "comment": "" - 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} - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "transient folding of tau" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "21910444.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Together with previous studies on the Parkinson-related protein \u03b1-synuclein, our data indicate that networks of transient long-range interactions are common properties of intrinsically disordered proteins and that their modulation is important for aggregation." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - 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] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "22057784.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "In this report, we examined whether tau nitration at these sites also occurs in corticobasal degeneration (CBD), progressive supranuclear palsy (PSP) and Pick's disease (PiD), three neurodegenerative tauopathies that contain abundant tau deposits within glial and neuronal cell types but lack amyloid deposition." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "CBD" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau nitrated at tyrosine 197" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "22057784.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "In this report, we examined whether tau nitration at these sites also occurs in corticobasal degeneration (CBD), progressive supranuclear palsy (PSP) and Pick's disease (PiD), three neurodegenerative tauopathies that contain abundant tau deposits within glial and neuronal cell types but lack amyloid deposition." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "PSP" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau nitrated at tyrosine 197" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "22057784.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "In this report, we examined whether tau nitration at these sites also occurs in corticobasal degeneration (CBD), progressive supranuclear palsy (PSP) and Pick's disease (PiD), three neurodegenerative tauopathies that contain abundant tau deposits within glial and neuronal cell types but lack amyloid deposition." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "PiD" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau nitrated at tyrosine 197" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "22057784.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The reactivity of these antibodies was also compared to two previously characterized antibodies Tau-nY18 and Tau-nY29, specific for tau nitrated at tyrosine 18 and tyrosine 29, respectively. In the present experiments, Tau-nY18 did not label the classical pathological lesions of CBD or PSP but did label the neuronal lesions associated with PiD to a limited extent." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "PiD" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau nitrated at tyrosine 18" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "22057784.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The reactivity of these antibodies was also compared to two previously characterized antibodies Tau-nY18 and Tau-nY29, specific for tau nitrated at tyrosine 18 and tyrosine 29, respectively. In contrast, Tau-nY29 revealed some, but not all classes of tau inclusions associated with both CBD and PSP but did label numerous Pick body inclusions in PiD." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "CBD" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau nitrated at tyrosine 29" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "22057784.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The reactivity of these antibodies was also compared to two previously characterized antibodies Tau-nY18 and Tau-nY29, specific for tau nitrated at tyrosine 18 and tyrosine 29, respectively. In contrast, Tau-nY29 revealed some, but not all classes of tau inclusions associated with both CBD and PSP but did label numerous Pick body inclusions in PiD." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "PSP" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau nitrated at tyrosine 29" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "22057784.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Tau-nY197 was restricted to the neuropil threads in both CBD and PSP; however, similar to Tau-nY29, extensive Pick body pathology was clearly labeled." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "PiD" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau nitrated at tyrosine 197" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "22057784.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Tau-nY394 did not detect any of the lesions associated with these disorders." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "PiD" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau nitrated at tyrosine 394" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "22057784.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Based on our Western and IHC experiments, it appears that nitration of tau at tyrosine 29 is a pathological modification that might be associated with neurodegeneration." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "neurodegenerative tauopathies" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau tyrosine nitration events" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - 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Overexpression of MARK4 led to tau hyperphosphorylation, reduced expression of synaptic markers, and loss of dendritic spines and synapses, phenotypes also observed after A\u03b2 treatment." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "soluble amyloid-\u03b2 oligomers" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "reduced expression of synaptic markers" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "27623715.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Using primary cultures of rat hippocampal neurons as a model system, we show that the partitioning defective-1 (PAR-1)/microtubule affinity-regulating kinase (MARK) family kinases act as critical mediators of A\u03b2 toxicity on synapses and dendritic spines. 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Overexpression of MARK4 led to tau hyperphosphorylation, reduced expression of synaptic markers, and loss of dendritic spines and synapses, phenotypes also observed after A\u03b2 treatment." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "soluble amyloid-\u03b2 oligomers" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "loss of synapses" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "27623715.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Importantly, expression of a non-phosphorylatable form of tau with the PAR-1/MARK site mutated blocked the synaptic toxicity induced by MARK4 overexpression or A\u03b2 treatment." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "soluble amyloid-\u03b2 oligomers" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "synaptic toxicity" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "27623715.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "To probe the involvement of endogenous MARK kinases in mediating the synaptic toxicity of A\u03b2, we employed a peptide inhibitor capable of effectively and specifically inhibiting the activities of all PAR-1/MARK family members. This inhibitor abrogated the toxic effects of A\u03b2 oligomers on dendritic spines and synapses as assayed at the morphological and electrophysiological levels." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "soluble amyloid-\u03b2 oligomers" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "synaptic toxicity" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "27623715.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Our results reveal a critical role for PAR-1/MARK kinases in AD pathogenesis and suggest PAR-1/MARK inhibitors as potential therapeutics for AD and possibly other tauopathies where aberrant tau hyperphosphorylation is involved." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "soluble amyloid-\u03b2 oligomers" - } - ] - ] - }, - { - "relation": "causes_no_change" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "synaptic toxicity" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "27671637.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "APOE4 is the greatest genetic risk factor for Alzheimer's disease (AD)." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "HGNC", - "name": "APOE4" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "DO", - "name": "Alzheimer's disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "27671637.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "APOE4 is particularly associated with increased levels of amyloid-\u03b2 (A\u03b2)." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "amyloid-\u03b2" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "HGNC", - "name": "APOE4" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "27671637.0", - "pub_date": "", - "author_list": "", - "comment": "" - 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] - } - }, - { - "evidence": "Post-translational modifications (PTMs) of proteins are becoming the focus of intense research due to their implications in a broad spectrum of neurodegenerative diseases." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "MESH", - "name": "neurodegenerative diseases" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "protein post-translational modification" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "30985105.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Post-translational modifications (PTMs) of proteins are becoming the focus of intense research due to their implications in a broad spectrum of neurodegenerative diseases." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Post-translational modifications" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "GO", - "name": "protein modifications" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "30985105.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Post-translational modifications (PTMs) of proteins are becoming the focus of intense research due to their implications in a broad spectrum of neurodegenerative diseases." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "PTMs" - 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{ - "citation": { - "type": "PubMed", - "title": "", - "ref": "30985105.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "In Alzheimer's disease (AD), dysregulated phosphorylation is reported to promote pathogenic processing of the microtubule-associated tau protein." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "phosphorylation" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "pathogenic processing of tau protein" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "30985105.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Among the PTMs, the enzymatic addition of N-acetyl-d-glucosamine (GlcNAc) residues to Ser/Thr residues is reported to deliver protective effects against the pathogenic processing of both amyloid precursor protein (APP) and tau." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "N-acetyl-d-glucosamine" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "pathogenic processing of amyloid precursor protein" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "30985105.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Among the PTMs, the enzymatic addition of N-acetyl-d-glucosamine (GlcNAc) residues to Ser/Thr residues is reported to deliver protective effects against the pathogenic processing of both amyloid precursor protein (APP) and tau." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "N-acetyl-d-glucosamine" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "pathogenic processing of tau protein" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "30985105.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Modification of tau with as few as one single O-GlcNAc residue inhibits its toxic self-assembly." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau protein" - } - ] - ] - }, - { - "relation": "directly_decreases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "toxic self-assembly" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "30985105.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Modification of tau with as few as one single O-GlcNAc residue inhibits its toxic self-assembly." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "tau protein" - } - ] - ] - }, - { - "relation": "directly_decreases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "toxic self-assembly" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "30985105.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "This modification also has the same effect on the assembly of the Parkinson's disease (PD) associated \u03b1-synuclein (ASyn) protein." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Parkinson's disease" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "neurodegenerative diseases" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "7667312.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Here we describe the in vitro assembly of recombinant tau protein and constructs derived from it into PHFs. 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{ - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "directly_decreases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "PHF assembly" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "7667312.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "PHF assembly was enabled again by mutating Cys-291 for Ala." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "directly_increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - 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} - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "PHF assembly" - } - ] - ] - }, - { - "relation": "regulates" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "redox potential in the neuron" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The major protein subunit of the paired helical filaments (PHF) of Alzheimer disease (AD) is the microtubule-associated protein tau." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "is_a" - 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"title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Tau is a family of phosphopolypeptides that are abnormally phosphorylated in PHF." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "GO", - "name": "phosphopolypeptide" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Tau is a family of phosphopolypeptides that are abnormally phosphorylated in PHF." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "paired helical filaments" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Tau is a family of phosphopolypeptides that are abnormally phosphorylated in PHF." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - 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"chatGPT" - ] - } - }, - { - "evidence": "In this study, a non-PHF pool of tau abnormally phosphorylated at Ser-199/202, and tau not phosphorylated at this site (AD P-tau and AD tau, respectively) were isolated from the 27,000 x g to 200,000 x g fraction of AD brain homogenate by extraction in 8 M urea, followed by dialysis against Tris buffer." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "GO", - "name": "phosphopolypeptide" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "AD P-tau and AD tau were further purified and separated from each other by acid precipitation, glial fibrillary acidic protein affinity chromatography, and phosphocellulose chromatography." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "GO", - "name": "phosphopolypeptide" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The resulting AD P-tau and AD tau preparations were free of cytoskeletal proteins, ubiquitin, and beta-amyloid peptide." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "GO", - "name": "phosphopolypeptide" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Immunochemical and morphological analysis of AD P-tau preparations revealed that most of the protein was of non-PHF origin." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "GO", - "name": "phosphopolypeptide" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The AD P-tau was about 3-4-fold (approximately 8 mol P04/mol protein, M(r) 41,318) more phosphorylated than cytosolic tau from AD and control brains." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "GO", - "name": "phosphopolypeptide" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Unlike PHF, the AD P-tau lacked ubiquitin." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "GO", - "name": "phosphopolypeptide" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "In AD brain the levels of cytosolic tau were about half of those in control aged cases." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "decreases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "cytosolic tau" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8226987.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "These findings suggest that the abnormal phosphorylation of tau in AD occurs in the cytosol." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8391280.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Most ubiquitin in paired helical filaments occurred as a monoubiquitinated form, and only a small proportion of ubiquitin formed multiubiquitin chains." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "paired helical filaments" - } - ] - ] - }, - { - "relation": "has_modification" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "HGNC", - "name": "ubiquitin" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8391280.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "There was a ubiquitin-negative smear, in which tau was much less processed in the amino-terminal portion." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "paired helical filaments" - } - ] - ] - }, - { - "relation": "has_modification" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "HGNC", - "name": "tau" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8702879.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Upon phosphorylation with MAP kinase, synapsin I showed reduced F-actin bundling activity." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "synapsin I" - } - ] - ] - }, - { - "relation": "decreases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "F-actin bundling activity" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8726973.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Western blot analysis of the immunoprecipitate showed both cdk5 and p67 (Munc-18), a putative regulator molecule of the kinase. Addition of p67 fusion protein enhanced the kinase activity of the immunoprecipitate by 60% above the basal activity." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "HGNC", - "name": "CDK5" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "p67 (Munc-18)" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8985134.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The purpose of this investigation was to identify and localize tissue transglutaminase (TGase) within neurons from the hippocampi of normal aged individuals and of those with confirmed Alzheimer's disease (AD). This enzyme may be a factor in the molecular mechanisms of neurodegeneration and formation of insoluble macromolecular complexes found in the neurons of normal aged and AD brain tissue." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer's disease" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "neurodegeneration" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8985134.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The purpose of this investigation was to identify and localize tissue transglutaminase (TGase) within neurons from the hippocampi of normal aged individuals and of those with confirmed Alzheimer's disease (AD). This enzyme may be a factor in the molecular mechanisms of neurodegeneration and formation of insoluble macromolecular complexes found in the neurons of normal aged and AD brain tissue." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer's disease" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "formation of insoluble macromolecular complexes" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8985134.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "An antibody made to the extracellular TGase, coagulation factor XIIIa, was found to be specific for purified intracellular guinea pig liver tissue TGase. The specificity for liver tissue TGase has enabled us to identify tissue TGase(s) within rat hippocampal neurons and within neurons from normal aged and AD hippocampal tissues." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "HGNC", - "name": "TGM2" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "MESH", - "name": "tissue transglutaminase" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8985134.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Degenerating neurons from the AD hippocampus, compared to neurons from the normal aged hippocampus, exhibited increased immunoreactivity for TGase and demonstrated co-labeling for PHF1 and anti-TGase. Our results suggest that TGase may be associated with the neurofibrillary degeneration observed in AD, thereby implicating TGase as a potential factor in the pathogenesis of Alzheimer's disease." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer's disease" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "abundance" - } - }, - [ - { - "namespace": "HGNC", - "name": "TGM2" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8985176.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The microtubule-associated protein tau is the main component of the paired helical filaments (PHFs) of Alzheimer's disease." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "is_a" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "paired helical filament assembly" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8985176.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Here we report that PHF assembly is strongly enhanced by RNA." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "process", - "name": "biological_process" - } - }, - [ - { - "namespace": "GO", - "name": "paired helical filament assembly" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "rna" - } - }, - [ - { - "namespace": "miRBase", - "name": "RNA" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8985176.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "The RNA-induced assembly of PHFs includes the dimerization of tau as an early intermediate." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "8985176.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Three-repeat constructs polymerize most efficiently, two repeat constructs are the minimum number required for assembly, and even all six full-length isoforms of tau can be induced to form PHFs by RNA." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "MAPT" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "9099822.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Total transglutaminase activity was significantly higher in the Alzheimer's disease prefrontal cortex compared to control." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "TGM2" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "Alzheimer's disease" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "9099822.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Because the neurofibrillary tangles in Alzheimer's disease have similar characteristics, and because tau protein, the major component of these tangles is an excellent substrate of transglutaminase in vitro." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "TGM2" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "neurofibrillary tangles" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "9099822.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "it can be suggested that transglutaminase could be a contributing factor in neurofibrillary tangle formation." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "TGM2" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "neurofibrillary tangle formation" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "9099822.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "Because the elevation of transglutaminase in the Alzheimer's disease samples occurred in the prefrontal cortex, where neurofibrillary pathology is usually abundant." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "TGM2" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "prefrontal cortex" - } - ] - ] - } - ] - }, - { - "sets": [ - { - "citation": { - "type": "PubMed", - "title": "", - "ref": "9099822.0", - "pub_date": "", - "author_list": "", - "comment": "" - } - }, - { - "set": { - "DataSource": [ - "chatGPT" - ] - } - }, - { - "evidence": "There were no significant differences in transglutaminase activity or levels in the cerebellum between control and Alzheimer's disease cases." - } - ] - }, - { - "statement": [ - { - "subject": [ - { - "function": { - "type": "abundance", - "name": "protein" - } - }, - [ - { - "namespace": "HGNC", - "name": "TGM2" - } - ] - ] - }, - { - "relation": "increases" - }, - { - "object": [ - { - "function": { - "type": "process", - "name": "pathology" - } - }, - [ - { - "namespace": "MESH", - "name": "cerebellum" - } - ] - ] - } - ] - } - ] - } -] \ No newline at end of file diff --git a/neo4j-import.py b/neo4j-import.py index 61ce9cb..78f09e5 100644 --- a/neo4j-import.py +++ b/neo4j-import.py @@ -14,6 +14,6 @@ n4jbel = Neo4jBel(client=neo) -n4jbel.import_json([gpt3_5_json]) -#n4jbel.import_json([sherpa_json, gpt3_5_json]) +#n4jbel.import_json([gpt3_5_json]) +n4jbel.import_json([sherpa_json, gpt3_5_json]) print("Done") \ No newline at end of file From 1bcb9c42ec57e1bf480d0652e8d1a7242e801922 Mon Sep 17 00:00:00 2001 From: Babaiha <66859895+NeginBabaiha@users.noreply.github.com> Date: Tue, 5 Sep 2023 10:05:20 +0200 Subject: [PATCH 4/9] update --- .bumpversion.cfg | 2 +- .../site/python3.7/greenlet/greenlet.h | 164 ++++++++++++++++++ ebel/Scripts/Activate.ps1 | 51 ++++++ ebel/Scripts/activate | 76 ++++++++ ebel/Scripts/activate.bat | 33 ++++ ebel/Scripts/deactivate.bat | 21 +++ ebel/Scripts/easy_install-3.7.exe | Bin 0 -> 106383 bytes ebel/Scripts/easy_install.exe | Bin 0 -> 106383 bytes ebel/Scripts/f2py.exe | Bin 0 -> 106369 bytes ebel/Scripts/normalizer.exe | Bin 0 -> 106397 bytes ebel/Scripts/pip.exe | Bin 0 -> 106374 bytes ebel/Scripts/pip3.7.exe | Bin 0 -> 106374 bytes ebel/Scripts/pip3.exe | Bin 0 -> 106374 bytes ebel/Scripts/python.exe | Bin 0 -> 501264 bytes ebel/Scripts/pythonw.exe | Bin 0 -> 500240 bytes ebel/Scripts/tqdm.exe | Bin 0 -> 106360 bytes ebel/__init__.py | 2 +- ebel/grammar/grammar_bel_2_1.bnf | 10 +- ebel/manager/neo4j/n4j_importer.py | 32 ++-- ebel/manager/neo4j/n4j_structure.py | 1 + ebel/manager/orientdb/biodbs/bel.py | 2 +- ebel/manager/orientdb/biodbs/biogrid.py | 2 +- ebel/manager/orientdb/biodbs/kegg.py | 2 +- ebel/manager/orientdb/importer.py | 2 +- ebel/manager/orientdb/odb_defaults.py | 112 ++++++++++++ ebel/manager/orientdb/odb_structure.py | 3 +- ebel/pyvenv.cfg | 3 + ebel/transformers.py | 12 +- mkdocs.yml | 2 +- neo4j-import.py | 13 +- requirements.txt | 3 +- setup.cfg | 3 +- 32 files changed, 507 insertions(+), 44 deletions(-) create mode 100644 ebel/Include/site/python3.7/greenlet/greenlet.h create mode 100644 ebel/Scripts/Activate.ps1 create mode 100644 ebel/Scripts/activate create mode 100644 ebel/Scripts/activate.bat create mode 100644 ebel/Scripts/deactivate.bat create mode 100644 ebel/Scripts/easy_install-3.7.exe create mode 100644 ebel/Scripts/easy_install.exe create mode 100644 ebel/Scripts/f2py.exe create mode 100644 ebel/Scripts/normalizer.exe create mode 100644 ebel/Scripts/pip.exe create mode 100644 ebel/Scripts/pip3.7.exe create mode 100644 ebel/Scripts/pip3.exe create mode 100644 ebel/Scripts/python.exe create mode 100644 ebel/Scripts/pythonw.exe create mode 100644 ebel/Scripts/tqdm.exe create mode 100644 ebel/pyvenv.cfg diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 64c0ea6..14c2618 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.0.25 +current_version = 1.0.28 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(?:-(?P[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))? diff --git a/ebel/Include/site/python3.7/greenlet/greenlet.h b/ebel/Include/site/python3.7/greenlet/greenlet.h new file mode 100644 index 0000000..d02a16e --- /dev/null +++ b/ebel/Include/site/python3.7/greenlet/greenlet.h @@ -0,0 +1,164 @@ +/* -*- indent-tabs-mode: nil; tab-width: 4; -*- */ + +/* Greenlet object interface */ + +#ifndef Py_GREENLETOBJECT_H +#define Py_GREENLETOBJECT_H + + +#include + +#ifdef __cplusplus +extern "C" { +#endif + +/* This is deprecated and undocumented. It does not change. */ +#define GREENLET_VERSION "1.0.0" + +#ifndef GREENLET_MODULE +#define implementation_ptr_t void* +#endif + +typedef struct _greenlet { + PyObject_HEAD + PyObject* weakreflist; + PyObject* dict; + implementation_ptr_t pimpl; +} PyGreenlet; + +#define PyGreenlet_Check(op) (op && PyObject_TypeCheck(op, &PyGreenlet_Type)) + + +/* C API functions */ + +/* Total number of symbols that are exported */ +#define PyGreenlet_API_pointers 12 + +#define PyGreenlet_Type_NUM 0 +#define PyExc_GreenletError_NUM 1 +#define PyExc_GreenletExit_NUM 2 + +#define PyGreenlet_New_NUM 3 +#define PyGreenlet_GetCurrent_NUM 4 +#define PyGreenlet_Throw_NUM 5 +#define PyGreenlet_Switch_NUM 6 +#define PyGreenlet_SetParent_NUM 7 + +#define PyGreenlet_MAIN_NUM 8 +#define PyGreenlet_STARTED_NUM 9 +#define PyGreenlet_ACTIVE_NUM 10 +#define PyGreenlet_GET_PARENT_NUM 11 + +#ifndef GREENLET_MODULE +/* This section is used by modules that uses the greenlet C API */ +static void** _PyGreenlet_API = NULL; + +# define PyGreenlet_Type \ + (*(PyTypeObject*)_PyGreenlet_API[PyGreenlet_Type_NUM]) + +# define PyExc_GreenletError \ + ((PyObject*)_PyGreenlet_API[PyExc_GreenletError_NUM]) + +# define PyExc_GreenletExit \ + ((PyObject*)_PyGreenlet_API[PyExc_GreenletExit_NUM]) + +/* + * PyGreenlet_New(PyObject *args) + * + * greenlet.greenlet(run, parent=None) + */ +# define PyGreenlet_New \ + (*(PyGreenlet * (*)(PyObject * run, PyGreenlet * parent)) \ + _PyGreenlet_API[PyGreenlet_New_NUM]) + +/* + * PyGreenlet_GetCurrent(void) + * + * greenlet.getcurrent() + */ +# define PyGreenlet_GetCurrent \ + (*(PyGreenlet * (*)(void)) _PyGreenlet_API[PyGreenlet_GetCurrent_NUM]) + +/* + * PyGreenlet_Throw( + * PyGreenlet *greenlet, + * PyObject *typ, + * PyObject *val, + * PyObject *tb) + * + * g.throw(...) + */ +# define PyGreenlet_Throw \ + (*(PyObject * (*)(PyGreenlet * self, \ + PyObject * typ, \ + PyObject * val, \ + PyObject * tb)) \ + _PyGreenlet_API[PyGreenlet_Throw_NUM]) + +/* + * PyGreenlet_Switch(PyGreenlet *greenlet, PyObject *args) + * + * g.switch(*args, **kwargs) + */ +# define PyGreenlet_Switch \ + (*(PyObject * \ + (*)(PyGreenlet * greenlet, PyObject * args, PyObject * kwargs)) \ + _PyGreenlet_API[PyGreenlet_Switch_NUM]) + +/* + * PyGreenlet_SetParent(PyObject *greenlet, PyObject *new_parent) + * + * g.parent = new_parent + */ +# define PyGreenlet_SetParent \ + (*(int (*)(PyGreenlet * greenlet, PyGreenlet * nparent)) \ + _PyGreenlet_API[PyGreenlet_SetParent_NUM]) + +/* + * PyGreenlet_GetParent(PyObject* greenlet) + * + * return greenlet.parent; + * + * This could return NULL even if there is no exception active. + * If it does not return NULL, you are responsible for decrementing the + * reference count. + */ +# define PyGreenlet_GetParent \ + (*(PyGreenlet* (*)(PyGreenlet*)) \ + _PyGreenlet_API[PyGreenlet_GET_PARENT_NUM]) + +/* + * deprecated, undocumented alias. + */ +# define PyGreenlet_GET_PARENT PyGreenlet_GetParent + +# define PyGreenlet_MAIN \ + (*(int (*)(PyGreenlet*)) \ + _PyGreenlet_API[PyGreenlet_MAIN_NUM]) + +# define PyGreenlet_STARTED \ + (*(int (*)(PyGreenlet*)) \ + _PyGreenlet_API[PyGreenlet_STARTED_NUM]) + +# define PyGreenlet_ACTIVE \ + (*(int (*)(PyGreenlet*)) \ + _PyGreenlet_API[PyGreenlet_ACTIVE_NUM]) + + + + +/* Macro that imports greenlet and initializes C API */ +/* NOTE: This has actually moved to ``greenlet._greenlet._C_API``, but we + keep the older definition to be sure older code that might have a copy of + the header still works. */ +# define PyGreenlet_Import() \ + { \ + _PyGreenlet_API = (void**)PyCapsule_Import("greenlet._C_API", 0); \ + } + +#endif /* GREENLET_MODULE */ + +#ifdef __cplusplus +} +#endif +#endif /* !Py_GREENLETOBJECT_H */ diff --git a/ebel/Scripts/Activate.ps1 b/ebel/Scripts/Activate.ps1 new file mode 100644 index 0000000..7535a11 --- /dev/null +++ b/ebel/Scripts/Activate.ps1 @@ -0,0 +1,51 @@ +function global:deactivate ([switch]$NonDestructive) { + # Revert to original values + if (Test-Path function:_OLD_VIRTUAL_PROMPT) { + copy-item function:_OLD_VIRTUAL_PROMPT function:prompt + remove-item function:_OLD_VIRTUAL_PROMPT + } + + if (Test-Path env:_OLD_VIRTUAL_PYTHONHOME) { + copy-item env:_OLD_VIRTUAL_PYTHONHOME env:PYTHONHOME + remove-item env:_OLD_VIRTUAL_PYTHONHOME + } + + if (Test-Path env:_OLD_VIRTUAL_PATH) { + copy-item env:_OLD_VIRTUAL_PATH env:PATH + remove-item env:_OLD_VIRTUAL_PATH + } + + if (Test-Path env:VIRTUAL_ENV) { + remove-item env:VIRTUAL_ENV + } + + if (!$NonDestructive) { + # Self destruct! + remove-item function:deactivate + } +} + +deactivate -nondestructive + +$env:VIRTUAL_ENV="C:\Users\nbabaiha\Documents\GitHub\ebel\ebel" + +if (! $env:VIRTUAL_ENV_DISABLE_PROMPT) { + # Set the prompt to include the env name + # Make sure _OLD_VIRTUAL_PROMPT is global + function global:_OLD_VIRTUAL_PROMPT {""} + copy-item function:prompt function:_OLD_VIRTUAL_PROMPT + function global:prompt { + Write-Host -NoNewline -ForegroundColor Green '(ebel) ' + _OLD_VIRTUAL_PROMPT + } +} + +# Clear PYTHONHOME +if (Test-Path env:PYTHONHOME) { + copy-item env:PYTHONHOME env:_OLD_VIRTUAL_PYTHONHOME + remove-item env:PYTHONHOME +} + +# Add the venv to the PATH +copy-item env:PATH env:_OLD_VIRTUAL_PATH +$env:PATH = "$env:VIRTUAL_ENV\Scripts;$env:PATH" diff --git a/ebel/Scripts/activate b/ebel/Scripts/activate new file mode 100644 index 0000000..b1a7148 --- /dev/null +++ b/ebel/Scripts/activate @@ -0,0 +1,76 @@ +# This file must be used with "source bin/activate" *from bash* +# you cannot run it directly + +deactivate () { + # reset old environment variables + if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then + PATH="${_OLD_VIRTUAL_PATH:-}" + export PATH + unset _OLD_VIRTUAL_PATH + fi + if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then + PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}" + export PYTHONHOME + unset _OLD_VIRTUAL_PYTHONHOME + fi + + # This should detect bash and zsh, which have a hash command that must + # be called to get it to forget past commands. Without forgetting + # past commands the $PATH changes we made may not be respected + if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then + hash -r + fi + + if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then + PS1="${_OLD_VIRTUAL_PS1:-}" + export PS1 + unset _OLD_VIRTUAL_PS1 + fi + + unset VIRTUAL_ENV + if [ ! "${1:-}" = "nondestructive" ] ; then + # Self destruct! + unset -f deactivate + fi +} + +# unset irrelevant variables +deactivate nondestructive + +VIRTUAL_ENV="C:\Users\nbabaiha\Documents\GitHub\ebel\ebel" +export VIRTUAL_ENV + +_OLD_VIRTUAL_PATH="$PATH" +PATH="$VIRTUAL_ENV/Scripts:$PATH" +export PATH + +# unset PYTHONHOME if set +# this will fail if PYTHONHOME is set to the empty string (which is bad anyway) +# could use `if (set -u; : $PYTHONHOME) ;` in bash +if [ -n "${PYTHONHOME:-}" ] ; then + _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}" + unset PYTHONHOME +fi + +if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then + _OLD_VIRTUAL_PS1="${PS1:-}" + if [ "x(ebel) " != x ] ; then + PS1="(ebel) ${PS1:-}" + else + if [ "`basename \"$VIRTUAL_ENV\"`" = "__" ] ; then + # special case for Aspen magic directories + # see http://www.zetadev.com/software/aspen/ + PS1="[`basename \`dirname \"$VIRTUAL_ENV\"\``] $PS1" + else + PS1="(`basename \"$VIRTUAL_ENV\"`)$PS1" + fi + fi + export PS1 +fi + +# This should detect bash and zsh, which have a hash command that must +# be called to get it to forget past commands. Without forgetting +# past commands the $PATH changes we made may not be respected +if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then + hash -r +fi diff --git a/ebel/Scripts/activate.bat b/ebel/Scripts/activate.bat new file mode 100644 index 0000000..108c7ee --- /dev/null +++ b/ebel/Scripts/activate.bat @@ -0,0 +1,33 @@ +@echo off + +rem This file is UTF-8 encoded, so we need to update the current code page while executing it +for /f "tokens=2 delims=:." %%a in ('"%SystemRoot%\System32\chcp.com"') do ( + set _OLD_CODEPAGE=%%a +) +if defined _OLD_CODEPAGE ( + "%SystemRoot%\System32\chcp.com" 65001 > nul +) + +set VIRTUAL_ENV=C:\Users\nbabaiha\Documents\GitHub\ebel\ebel + +if not defined PROMPT set PROMPT=$P$G + +if defined _OLD_VIRTUAL_PROMPT set PROMPT=%_OLD_VIRTUAL_PROMPT% +if defined _OLD_VIRTUAL_PYTHONHOME set PYTHONHOME=%_OLD_VIRTUAL_PYTHONHOME% + +set _OLD_VIRTUAL_PROMPT=%PROMPT% +set PROMPT=(ebel) %PROMPT% + +if defined PYTHONHOME set _OLD_VIRTUAL_PYTHONHOME=%PYTHONHOME% +set PYTHONHOME= + +if defined _OLD_VIRTUAL_PATH set PATH=%_OLD_VIRTUAL_PATH% +if not defined _OLD_VIRTUAL_PATH set _OLD_VIRTUAL_PATH=%PATH% + +set PATH=%VIRTUAL_ENV%\Scripts;%PATH% + +:END +if defined _OLD_CODEPAGE ( + "%SystemRoot%\System32\chcp.com" %_OLD_CODEPAGE% > nul + set _OLD_CODEPAGE= +) diff --git a/ebel/Scripts/deactivate.bat b/ebel/Scripts/deactivate.bat new file mode 100644 index 0000000..1205c61 --- /dev/null +++ b/ebel/Scripts/deactivate.bat @@ -0,0 +1,21 @@ +@echo off + +if defined _OLD_VIRTUAL_PROMPT ( + set "PROMPT=%_OLD_VIRTUAL_PROMPT%" +) +set _OLD_VIRTUAL_PROMPT= + +if defined _OLD_VIRTUAL_PYTHONHOME ( + set "PYTHONHOME=%_OLD_VIRTUAL_PYTHONHOME%" + set _OLD_VIRTUAL_PYTHONHOME= +) + +if defined _OLD_VIRTUAL_PATH ( + set "PATH=%_OLD_VIRTUAL_PATH%" +) + +set _OLD_VIRTUAL_PATH= + +set VIRTUAL_ENV= + +:END diff --git a/ebel/Scripts/easy_install-3.7.exe b/ebel/Scripts/easy_install-3.7.exe new file mode 100644 index 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