dustine32
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| [ | |
| { | |
| "module_term": "GO:0048839", | |
| "annotations": [ | |
| { | |
| "ptn_id": "PTN002750520", | |
| "label": "HARMONIN", | |
| "term": "GO:0042491", | |
| "leaf_genes": [ | |
| { |
dustine32
/ metabolic_gocams2genes.rq
Created
July 28, 2022 23:49
Metabolic causal GO-CAMs-to-genes list query
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| PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX dc: <http://purl.org/dc/elements/1.1/> | |
| PREFIX gomodel: <http://model.geneontology.org/> | |
| PREFIX REACTO: <http://purl.obolibrary.org/obo/go/extensions/reacto.owl#> | |
| PREFIX MF: <http://purl.obolibrary.org/obo/GO_0003674> |
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| PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX dc: <http://purl.org/dc/elements/1.1/> | |
| PREFIX gomodel: <http://model.geneontology.org/> | |
| PREFIX MF: <http://purl.obolibrary.org/obo/GO_0003674> | |
| PREFIX causally_upstream_of_or_within: <http://purl.obolibrary.org/obo/RO_0002418> |
dustine32
/ slim_maker.py
Created
October 12, 2021 15:16
Generate the PANTHER slim given a list of IBDs in GAF format
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| from ontobio.ontol_factory import OntologyFactory | |
| from ontobio.assoc_factory import AssociationSetFactory | |
| from ontobio.io.ontol_renderers import GraphRenderer, OboFormatGraphRenderer | |
| from ontobio.io.gafparser import GafParser | |
| from ontobio.util.go_utils import GoAspector | |
| import argparse | |
| import json | |
| import os | |
| parser = argparse.ArgumentParser() |