Eric Czech eric-czech

## export_pmdb_pub_dates.py
(
    pd.read_gbq(
        "SELECT pmid, EXTRACT(YEAR from pub_date) AS pub_year FROM `pmdb-bq.pmdb.article` WHERE pub_date IS NOT NULL",
        use_bqstorage_api=True
    )
    .to_parquet("pub_years.parquet")
)

## ukb_gwas_poc.ipynb

      
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                / ukb_gwas_poc.ipynb
            
            
              Created
              January 25, 2024 20:23
            
              
                UK Biobank sgkit GWAS POC
              
          
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## gpt4_linreg.ipynb

      
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                / gpt4_linreg.ipynb
            
            
              Created
              April 7, 2023 13:52
            
              
                Linear regression for GWAS created by GPT4
              
          
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## mlb_top_hitter_prediction.ipynb
playerID,yearID,stint,teamID,lgID,G,AB,R,H,2B,3B,HR,RBI,SB,CS,BB,SO,IBB,HBP,SH,SF,GIDP
abercda01,1871,1,TRO,NA,1,4,0,0,0,0,0,0,0,0,0,0,,,,,0
addybo01,1871,1,RC1,NA,25,118,30,32,6,0,0,13,8,1,4,0,,,,,0
allisar01,1871,1,CL1,NA,29,137,28,40,4,5,0,19,3,1,2,5,,,,,1
allisdo01,1871,1,WS3,NA,27,133,28,44,10,2,2,27,1,1,0,2,,,,,0
ansonca01,1871,1,RC1,NA,25,120,29,39,11,3,0,16,6,2,2,1,,,,,0
armstbo01,1871,1,FW1,NA,12,49,9,11,2,1,0,5,0,1,0,1,,,,,0
barkeal01,1871,1,RC1,NA,1,4,0,1,0,0,0,2,0,0,1,0,,,,,0
barnero01,1871,1,BS1,NA,31,157,66,63,10,9,0,34,11,6,13,1,,,,,1
barrebi01,1871,1,FW1,NA,1,5,1,1,1,0,0,1,0,0,0,0,,,,,0

## baseball-stats.csv
playerID,yearID,stint,teamID,lgID,G,AB,R,H,2B,3B,HR,RBI,SB,CS,BB,SO,IBB,HBP,SH,SF,GIDP
abercda01,1871,1,TRO,NA,1,4,0,0,0,0,0,0,0,0,0,0,,,,,0
addybo01,1871,1,RC1,NA,25,118,30,32,6,0,0,13,8,1,4,0,,,,,0
allisar01,1871,1,CL1,NA,29,137,28,40,4,5,0,19,3,1,2,5,,,,,1
allisdo01,1871,1,WS3,NA,27,133,28,44,10,2,2,27,1,1,0,2,,,,,0
ansonca01,1871,1,RC1,NA,25,120,29,39,11,3,0,16,6,2,2,1,,,,,0
armstbo01,1871,1,FW1,NA,12,49,9,11,2,1,0,5,0,1,0,1,,,,,0
barkeal01,1871,1,RC1,NA,1,4,0,1,0,0,0,2,0,0,1,0,,,,,0
barnero01,1871,1,BS1,NA,31,157,66,63,10,9,0,34,11,6,13,1,,,,,1
barrebi01,1871,1,FW1,NA,1,5,1,1,1,0,0,1,0,0,0,0,,,,,0

## Top MLB hitters.ipynb

      
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                / Top MLB hitters.ipynb
            
            
              Last active
              June 13, 2022 00:03
            
              
                Top MLB hitters
              
          
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## ncbi_human_genes.csv
taxon_id,gene_id,gene_symbol
9606,109951028,A-GAMMA3'E
9606,1,A1BG
9606,503538,A1BG-AS1
9606,29974,A1CF
9606,2,A2M
9606,144571,A2M-AS1
9606,144568,A2ML1
9606,100874108,A2ML1-AS1
9606,106478979,A2ML1-AS2

## hgnc_gene_lookup.ipynb

      
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              Last active
              September 23, 2021 13:06
            
              
                Google patents HGNC normalizations
              
          
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## zooma.py
import requests
from urllib.parse import quote_plus

def get_info(disease):
    url_fmt = 'http://www.ebi.ac.uk/spot/zooma/v2/api/services/annotate?propertyValue={disease}&propertyType=disease&filter=ontologies:[efo]'
    url = url_fmt.format(disease=quote_plus(disease))
    print(url)
    res = requests.get(url).json()
    if len(res) == 0:
        return None

## search_efo_ols.py
def search_efo(disease):
    import requests
    from urllib.parse import quote_plus
    res = requests.get(f"https://www.ebi.ac.uk/ols/api/select?q={quote_plus(disease)}&ontology=efo")
    res = res.json()
    docs = res['response']['docs']
    if len(docs) == 0:
        return None
    return docs[0]
	(
	pd.read_gbq(
	"SELECT pmid, EXTRACT(YEAR from pub_date) AS pub_year FROM `pmdb-bq.pmdb.article` WHERE pub_date IS NOT NULL",
	use_bqstorage_api=True
	)
	.to_parquet("pub_years.parquet")
	)
	playerID,yearID,stint,teamID,lgID,G,AB,R,H,2B,3B,HR,RBI,SB,CS,BB,SO,IBB,HBP,SH,SF,GIDP
	abercda01,1871,1,TRO,NA,1,4,0,0,0,0,0,0,0,0,0,0,,,,,0
	addybo01,1871,1,RC1,NA,25,118,30,32,6,0,0,13,8,1,4,0,,,,,0
	allisar01,1871,1,CL1,NA,29,137,28,40,4,5,0,19,3,1,2,5,,,,,1
	allisdo01,1871,1,WS3,NA,27,133,28,44,10,2,2,27,1,1,0,2,,,,,0
	ansonca01,1871,1,RC1,NA,25,120,29,39,11,3,0,16,6,2,2,1,,,,,0
	armstbo01,1871,1,FW1,NA,12,49,9,11,2,1,0,5,0,1,0,1,,,,,0
	barkeal01,1871,1,RC1,NA,1,4,0,1,0,0,0,2,0,0,1,0,,,,,0
	barnero01,1871,1,BS1,NA,31,157,66,63,10,9,0,34,11,6,13,1,,,,,1
	barrebi01,1871,1,FW1,NA,1,5,1,1,1,0,0,1,0,0,0,0,,,,,0
	taxon_id,gene_id,gene_symbol
	9606,109951028,A-GAMMA3'E
	9606,1,A1BG
	9606,503538,A1BG-AS1
	9606,29974,A1CF
	9606,2,A2M
	9606,144571,A2M-AS1
	9606,144568,A2ML1
	9606,100874108,A2ML1-AS1
	9606,106478979,A2ML1-AS2
	import requests
	from urllib.parse import quote_plus

	def get_info(disease):
	url_fmt = 'http://www.ebi.ac.uk/spot/zooma/v2/api/services/annotate?propertyValue={disease}&propertyType=disease&filter=ontologies:[efo]'
	url = url_fmt.format(disease=quote_plus(disease))
	print(url)
	res = requests.get(url).json()
	if len(res) == 0:
	return None
	def search_efo(disease):
	import requests
	from urllib.parse import quote_plus
	res = requests.get(f"https://www.ebi.ac.uk/ols/api/select?q={quote_plus(disease)}&ontology=efo")
	res = res.json()
	docs = res['response']['docs']
	if len(docs) == 0:
	return None
	return docs[0]