PhenCards Project (2019)
For this Project, I applied PySpark to merge databases from several sources and used Docker to build images of the project. Here is an overview of the data sorces I used:
| INDEX | EXTERNAL-DATABASE-NAME | SOURCE-LINK | INSTRUCTIONS | COMMENTS |
|---|---|---|---|---|
| 1 | ICD-10 | ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD10CM/2020/icd10cm_order_2020.txt | No permission required | Use the link to download |
| 2 | ICD-9 | ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD-9/ucod.txt | No permission required | Use the link to download |
| 3 | ICD-O | https://github.com/philipsales/icdoncology-3/blob/master/icd-oncology.v3.json | No permission required | Use the link to download |
| 4 | SNOMEDCT_US | https://download.nlm.nih.gov/umls/kss/IHTSDO20200131/SnomedCT_InternationalRF2_PRODUCTION_20200131T120000Z.zip | If account/password is needed, use the following: / | Need account information for download permission, around 500M |
| 5 | UMLS | https://download.nlm.nih.gov/umls/kss/2019AB/umls-2019AB-full.zip | If account/password is needed, use the following: / | Need account information for download permission, around 4GB; here is a useful tool to download using cluster: https://askubuntu.com/questions/29079/how-do-i-provide-a-username-and-password-to-wget |
| 6 | MeSH | ftp://nlmpubs.nlm.nih.gov/online/mesh/MESH_FILES/xmlmesh/desc2020.gz | No permission required | Use the link to download |
| 7 | DOID | http://purl.obolibrary.org/obo/doid.owl | No permission required | This is an HTML format file, need attention for parsing |