docking-org/oicr-zinc

Exported files from ZINC for use in OICR ICGC DCC and Collaboratory

oicr-zinc's Issues

atc_classifications split into two fields

Before moving to GitHub, there is one field for atc code:

   "atc_classifications": [
      {
           "level4": "L01AA",
           "level4_description": "Nitrogen mustard analogues",
           "level5": "L01AA07",
           "who_name": "trofosfamide"
       }
   ],

What's in the git repo now:

   "atc_codes": [
       {
           "code": "L01AA",
           "description": "Nitrogen mustard analogues"
       }
   ],
   "atc_level5_codes": [
       "L01AA07"
   ],

Can we merge these two into one field as before?

Remove non-HUMAN entries in genes.ldjson

Drug Class appears to be inchikey

Example for first drug in drugs.ldjson:

"inchikey": "AAKJLRGGTJKAMG-UHFFFAOYSA-N"
...
"drug_class": "AAKJLRGGTJKAMG-UHFFFAOYSA-N

ATC values: atc_codes vs atc_classifications

Hi!

We were going over the latest data from our import of the drug data and noticed we were missing ATC information for some drugs. Turns out we were not accounting for a structure that it sometimes present in the JSON.

We were expecting something like this:

"atc_level5_codes": ["L01AD07"], "atc_codes": [{"code": "L01AD", "description": "Nitrosoureas"}]

But instead got something like this:

"atc_classifications": [{"who_name": "abiraterone", "level4": "L02BX", "level5": "L02BX03", "level4_description": "Other hormone antagonists and related agents"}]

I've made the appropriate changes in our import process to handle this, but I was curious if there is going to be a consolidation in the future to a single structure or maybe there was a reason for having differing structures?

Loading of Initial Data

We need to add the initial export data (and any scripts used to generate it).

Remove drugs-L01.ldjson drugs-L02.ldjson in exports folder

These two files are causing some confusing, should be removed.