/synthetic_genome_data

(Semi-) Synthetic Genome-Data Bundle

This repo holds an enriched genome data composed of multiple dataset publications enriched with profile data in close alignment with learned distributions.

Nowadays, data processing becomes more and more common. To enable testing, evaluation and development of data driven applications, this repository holds a script to generate large scale and high dimensional data sets which are created in close alignment with public data sets esp. their data distribution.

An examplary usage can be to evaluate new anonymization techniques which rely on non-anonymized data. Since nobody wants his PII data published, this fake but realistic data may be used to assess and evaluate such use cases.

Table of Contents

  • Composition
    • Data sources & origins
    • Attributes
      • Behavioral/Medical Attributes
      • User data
  • Related Links & Other Datasets

Composition

The following chapter shall briefly list and describe the include attributes for a single data record, including its source, type and distribution. All attributes shall be presented with examples.

Data sources & origins

Genome data:

COVID-19 specific:

Blood type distribution per country:

Diseases:

Drugs:

A Bundle of disease, SNP and genomic data:

ICD-9-CM Diagnosis and Procedure Codes:

Healthcare:

Other Healthcare specific:

Behavioral/Medical Attributes

The behavior attribute values include, but may not be limited to

  • blood type
  • drug usage
  • disease-gene relations
  • disease-disease relations
  • disease diagnosis
  • single-nucleotide polymorphis (SNP)
  • color

The raw data can be found in /2_behavior_medical_attribute_values .

Example Values

Attribute Type Example value
Blood Type String B+
Color String Purple

For drugs:

Attribute Type Example value
PRODUCTID String 0002-1200_e62214a4-82fd-4e06-90a0-577a32fea93f
PRODUCTTYPENAME String HUMAN PRESCRIPTION DRUG
PROPRIETARYNAME String Amyvid
PRODUCTNDC String 0002-1200
NONPROPRIETARYNAME String Florbetapir F 18
DOSAGEFORMNAME String INJECTION, SOLUTION
ROUTENAME String INTRAVENOUS
STARTMARKETINGDATE Date 20120601
MARKETINGCATEGORYNAME String NDA
APPLICATIONNUMBER String NDA202008
ACTIVE_NUMERATOR_STRENGTH Integer 51
ACTIVE_INGRED_UNIT String mCi/mL
PHARM_CLASSES String Radioactive Diagnostic Agent [EPC],Positron Emitting Activity [MoA]

For drug packages:

Attribute Type Example value
PRODUCTNDC String 0002-1200
NDCPACKAGECODE String 0002-1200-30
PACKAGEDESCRIPTION String 1 VIAL, MULTI-DOSE in 1 CAN (0002-1200-30) > 30 mL in 1 VIAL, MULTI-DOSE

For disease-disease relations:

Attribute Type Example value
Disease_1 String Yohimbine
Disease_2 String Disorder Of Male Reproductive System
relation Double 0

For disease-gene relations:

Attribute Type Example value
Concept ID String C0035243
Disease String Respiratory Tract Infections
Type String DEG
Gene String RNFT1

For symptoms:

Attribute Type Example value
symptom_name String Aging, Premature
disease_name String Acquired Immunodeficiency Syndrome
cooccurs Integer C0035243
tfidf_score Integer 3
disease_id Float 10.3936544686139
symptom_id String D000163
doid_code String DOID:635
doid_name String acquired immunodeficiency syndrome

For SNPs:

Attribute Type Example value
snpId String rs10004195
pubmedId Integer 25687912
geneId String 81793
TEST String TLR10
geneSymbol String umls:C0679408
sourceId String BeFree
diseaseName String Lesion of stomach
sentence String Three single-nucleotide polymorphisms, TLR1 rs4833095, TLR10 rs10004195, and TLR10 rs4129009 were genotyped by TaqMan SNP genotyping assay in 2553 participants with diverse gastric lesions.
score Float 0.000271441872080303
year Date 2015
geneSymbol_dbSNP String TLR10
CHROMOSOME String 4
POS String 38783103
REF String T
ALT String A

Attributes

The CRM attribute values originate from fakenamegenerator.com, which provides

  • in sum 487 million different region-sensitive names (108 million male names, 379 million female names)
  • addresses and its geocoordinates (latitude & longitude) for 31 countries
  • local telephone numbers
  • national identification numbers
  • birthday and age
  • email addresses, usernames, passwords, websites and browser user agents
  • (fake but consistent) Visa numbers, expiring dates, CVV2s
  • employment details including company and Occupation
  • height and weight

Further details regarding the statistics, the reader is kindly referred to the original source.

Example Values

Attribute Type Example value
Firstname String Shirley
Middlename String Time
Lastname String Coffey
Address String Sömmeringstr. 93
ZIP Integer 75172
City String Pforzheim Weststadt
GeoCoordinates String 48.884783, 8.690593
Phone String 07231 69 44 49
County Code Integer 49
Birthday Date August 2, 1941
Age Integer 75
Email Address String SebastianGottlieb@dayrep.com
Username String Topas1941
Password String vaiFaoz4
Browser user agent String Mozilla/5.0 (Windows NT 10.0; Win64; x64)
Visa Nr. String 4929 0844 9315 7600
Expiring Date Date 5/2019
CVV2 Integer 666
Company Integer Schaak Electronics
Occupation Integer Financial examiner
Height (in cm) Integer 173
Weight (in kg) Float 68.2

Composed Data set

A composed data set with 107 columns and nearly 1M rows can be found at here.

Related Links & Other Datasets

Aggregated & statistics: