Current state
(master) a -> b -> c
|
(itrb) -> d
Idea: Create a new branch from b, merge that into (test)
1. Go to the commit
David Koslicki dkoslicki
dkoslicki
/ ComplicatedWorkflow.json
Created
June 24, 2022 18:26
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| { | |
| "workflow": [ | |
| { | |
| "id": "fill", | |
| "parameters": { "allowlist": ["infores:cohd"], | |
| "qedge_keys": [ | |
| "e0" | |
| ] | |
| } | |
| }, |
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| { | |
| "message": { | |
| "query_graph": { | |
| "nodes": { | |
| "disease": { | |
| "ids": ["MONDO:0004975"] | |
| }, | |
| "chemical": { | |
| "categories": ["biolink:ChemicalEntity"] | |
| } |
dkoslicki
/ query_to_chp.json
Created
July 5, 2022 17:58
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| { | |
| "message": { | |
| "query_graph": { | |
| "edges": { | |
| "e1": { | |
| "object": "n1", | |
| "predicates": [ | |
| "biolink:expressed_in" | |
| ], | |
| "subject": "n2" |
dkoslicki
/ CHP_response.json
Created
July 5, 2022 18:34
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| { | |
| "message": { | |
| "query_graph": { | |
| "nodes": { | |
| "n1": { | |
| "ids": [ | |
| "UBERON:0001235", | |
| "UBERON:0001274", | |
| "UBERON:0002116", | |
| "UBERON:0034969", |
dkoslicki
/ Merge_from_the_middle.md
Last active
July 8, 2022 17:32
Query:
curl -X 'POST' \
'https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes' \
-H 'accept: application/json' \
-H 'Content-Type: application/json' \
-d '{
"curies": [
"CHEMBL.COMPOUND:CHEMBL1201567"
],
dkoslicki
/ small_nodes.csv
Created
June 27, 2023 14:27
We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 8 columns, instead of 11 in line 1.
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| node_id,node_type,all_names,description,knowledge_source,link,synonyms,is_pathogen | |
| Microbe:1,biolink:OrganismTaxon,['Archaea'],[('rank', 'superkingdom'), ('taxid', '2157')],['GTDB'],['https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2157'],['GTDB:Archaea'],False | |
| Microbe:2,biolink:OrganismTaxon,['Halobacteriota'],[('taxid', ''), ('rank', 'phylum')],['GTDB'],[],['GTDB:Halobacteriota'],False | |
| Microbe:3,biolink:OrganismTaxon,['Methanosarcinia'],[('taxid', ''), ('rank', 'class')],['GTDB'],[],['GTDB:Methanosarcinia'],False | |
| Microbe:4,biolink:OrganismTaxon,['Methanosarcinales'],[('taxid', '94695'), ('rank', 'order')],['GTDB'],['https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=94695'],['GTDB:Methanosarcinales'],False | |
| Microbe:5,biolink:OrganismTaxon,['Methanosarcinaceae'],[('taxid', '2206'), ('rank', 'family')],['GTDB'],['https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2206'],['GTDB:Methanosarcinaceae'],False | |
| Microbe:6,biolink:OrganismTaxon,['Methanosarcina |
dkoslicki
/ small_nodes.tsv
Created
June 27, 2023 14:40
We can make this file beautiful and searchable if this error is corrected: It looks like row 7 should actually have 8 columns, instead of 3 in line 6.
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| node_id node_type all_names description knowledge_source link synonyms is_pathogen | |
| Microbe:1 biolink:OrganismTaxon ['Archaea'] [('rank', 'superkingdom'), ('taxid', '2157')] ['GTDB'] ['https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2157'] ['GTDB:Archaea'] False | |
| Microbe:2 biolink:OrganismTaxon ['Halobacteriota'] [('taxid', ''), ('rank', 'phylum')] ['GTDB'] [] ['GTDB:Halobacteriota'] False | |
| Microbe:3 biolink:OrganismTaxon ['Methanosarcinia'] [('taxid', ''), ('rank', 'class')] ['GTDB'] [] ['GTDB:Methanosarcinia'] False | |
| Microbe:4 biolink:OrganismTaxon ['Methanosarcinales'] [('taxid', '94695'), ('rank', 'order')] ['GTDB'] ['https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=94695'] ['GTDB:Methanosarcinales'] False | |
| Microbe:5 biolink:OrganismTaxon ['Methanosarcinaceae'] [('taxid', '2206'), ('rank', 'family')] ['GTDB'] ['https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2206'] ['GTDB:Methanosarcinaceae'] False | |
| Microbe:6 biolink:OrganismTaxon ['Methanosarcina |
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| import requests | |
| import os | |
| import json | |
| import glob | |
| import re | |
| query_classes = ['ameliorates','CPIC','drug_treats_rare_disease','DrugCentral_creative', | |
| 'GTRx','OOPD','RareDisease','three_hop','treats'] | |
| aras = ["aragorn", "arax", "bte", 'improving'] | |
| ara_pattern = re.compile(fr"({'|'.join(aras)})") | |
| query_pattern = re.compile(fr"({'|'.join(query_classes)})") |
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