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David Koslicki dkoslicki

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@dkoslicki
dkoslicki / score_ars_by_g_score.py
Created December 7, 2023 22:22
score_ars_by_g_score.py
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)})")
@dkoslicki
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.
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
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.
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
dkoslicki / query_and_results.md
Created May 31, 2023 17:26
Example SRI NN

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
dkoslicki / Merge_from_the_middle.md
Last active July 8, 2022 17:32

Current state

(master) a -> b -> c
         |
(itrb)     -> d

Idea: Create a new branch from b, merge that into (test)

1. Go to the commit

@dkoslicki
dkoslicki / CHP_response.json
Created July 5, 2022 18:34
{
"message": {
"query_graph": {
"nodes": {
"n1": {
"ids": [
"UBERON:0001235",
"UBERON:0001274",
"UBERON:0002116",
"UBERON:0034969",
@dkoslicki
dkoslicki / query_to_chp.json
Created July 5, 2022 17:58
{
"message": {
"query_graph": {
"edges": {
"e1": {
"object": "n1",
"predicates": [
"biolink:expressed_in"
],
"subject": "n2"
@dkoslicki
dkoslicki / Inferred_example.json
Created June 29, 2022 16:58
XDTD example
{
"message": {
"query_graph": {
"nodes": {
"disease": {
"ids": ["MONDO:0004975"]
},
"chemical": {
"categories": ["biolink:ChemicalEntity"]
}
@dkoslicki
dkoslicki / ComplicatedWorkflow.json
Created June 24, 2022 18:26
{
"workflow": [
{
"id": "fill",
"parameters": { "allowlist": ["infores:cohd"],
"qedge_keys": [
"e0"
]
}
},
@dkoslicki
dkoslicki / response.json
Last active May 17, 2022 20:11
Creative DTD answer
This file has been truncated, but you can view the full file.
{
"results": [
{
"node_bindings": {
"drug": [
{
"id": "CHEMBL.COMPOUND:CHEMBL1337"
}
],
"disease": [