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gaurav / request-from-babel.sparql
Created Mar 1, 2022
Code to replicate error on Ubergraph
View request-from-babel.sparql
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
SELECT ?cls ?pred ?val
from <http://reasoner.renci.org/ontology>
WHERE
{ ?cls ?pred ?val ;
a owl:Class .
FILTER (
?pred = oboInOwl:hasRelatedSynonym ||
View commands.sh
# Commands used to generate the other two files
head -n 70 medmentions.json | tail -n 1 > medmentions-line-70.json
head -n 2 pubmed_ds/split_0.txt | tail -n 1 > pubmed-line-2.json
View keybase.md

Keybase proof

I hereby claim:

  • I am gaurav on github.
  • I am mrvaidya (https://keybase.io/mrvaidya) on keybase.
  • I have a public key ASAvem26jsIZR6NjpVs9WeJv0Pz7wwYK1cOBUVhqIVSwtAo

To claim this, I am signing this object:

@gaurav
gaurav / crdch_model_pr_112_vs_v1.0.1.diff
Last active Sep 16, 2021
Diff between CRDCH model in PR 112 vs v1.0.1
View crdch_model_pr_112_vs_v1.0.1.diff
--- ccdhmodel.yaml 2021-09-16 14:57:11.000000000 -0400
+++ crdch_model.yaml 2021-09-16 14:56:48.000000000 -0400
@@ -1,84 +1,84 @@
name: CRDC-H
notes:
- Derived from [CDM_Dictionary_v1 (Active)](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4)
-id: https://example.org/ccdh
-version: v1.0-3-g99ffd30c-dirty
+id: https://example.org/crdch
+version: v0.2-346-g2a758251
@gaurav
gaurav / Shell output
Last active May 12, 2021
linkml-classes-bug
View Shell output
$ pipenv install linkml==0.0.7
Creating a Pipfile for this project...
Installing linkml==0.0.7...
Adding linkml to Pipfile's [packages]...
✔ Installation Succeeded
Pipfile.lock not found, creating...
Locking [dev-packages] dependencies...
Locking [packages] dependencies...
Building requirements...
Resolving dependencies...
View PFB dd_100.avro metadata.json
{
"nodes": [
{
"name": "root",
"ontology_reference": "",
"values": {},
"links": [],
"properties": []
},
{
@gaurav
gaurav / CGEX_CtxAll010-shex-validation.json
Created Jan 14, 2020
ShEx validation of example validation for CGEX_CtxAll010
View CGEX_CtxAll010-shex-validation.json
{
"type": "Failure",
"node": "http://dataexchange.clinicalgenome.org/CGEX_CtxAll010",
"shape": "http://dataexchange.clinicalgenome.org/interpretation/shacl/shapes/ContextualAllele",
"errors": [
{
"type": "TypeMismatch",
"triple": {
"type": "TestedTriple",
"subject": "http://dataexchange.clinicalgenome.org/CGEX_CtxAll010",
@gaurav
gaurav / field_summaries.2019-nov-4
Created Nov 4, 2019
List of fields used in PubMed Annual Baseline 2019
View field_summaries.2019-nov-4
# '.' indicates XML nodes
# '/' indicates XML attributes
# '#' are XML values, but only for some fields
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText,34722040)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.mn,2)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.mrow.mi,7)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.mrow.mo,6)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.mrow.msub.mi,4)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.msup.mi,1)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.msup.mrow.mi,1)
View batman bares bear arms
Jon Jon Wendt gives Gene Valgene his hooded cloak.
Gene Valgene: ...
Gene Valgene: [Batman voice] I'm the Batman now.
Jon Jon Wendt: Batman!
Gene Valgene: Batman.
Jon Jon Wendt: Batman! Batman! Batman!
Gene Valgene: BAAAAAAAAAT
Gene Valgene: MAAAAAAAAAAN
Jon Jon Wendt: That's the spirit!
Gene Valgene: [Batman voice] Hmm.
View .vimrc
" Activate pathogen.
call pathogen#infect()
call pathogen#helptags()
" These are a few of my favourite settings.
syntax on
set background=dark
set hlsearch
set incsearch
set smartindent