Full download from clue

cycle20 commented 2 years ago

[x] raw list of HUGO, UNIPROT_KB_ID pairs
[x] merge raw list and reduced duplication list
[x] double check GeneName - UniProt ACC pairs, when there is only one hit
[x] cache with UniProt data
[x] https://open.fda.gov/apis/downloads/ (https://www.accessdata.fda.gov/scripts/cder/ndc/index.cfm)
[ ] cache with FDA data (2023. dec. 19.)
- records with no openfda data?
[ ] cache with [ pert_iname, label id ] pairs (lookup table for faster search)
[ ] FDA search function

cycle20 commented 1 year ago

full_target_list.csv

cycle20 commented 1 year ago

2 IDs were not mapped: CDO-1 MMP23A

cycle20 commented 1 year ago

full_list.csv

cycle20 commented 1 year ago

[x] https://uniprot.org/uniprotkb/P49588/entry#names_and_taxonomy ; # of p.names: 1 HUGO: AARS first name: AARS1
[x] https://uniprot.org/uniprotkb/P25098/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ADRBK1 first name: GRK2
[x] https://uniprot.org/uniprotkb/P35626/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ADRBK2 first name: GRK3
[x] https://uniprot.org/uniprotkb/P30520/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ADSS first name: ADSS2
[x] https://uniprot.org/uniprotkb/Q8N142/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ADSSL1 first name: ADSS1
[x] https://uniprot.org/uniprotkb/P10696/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ALPPL2 first name: ALPG
[x] https://uniprot.org/uniprotkb/O43681/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ASNA1 first name: GET3
[x] https://uniprot.org/uniprotkb/P25705/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ATP5A1 first name: ATP5F1A
[x] https://uniprot.org/uniprotkb/P06576/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ATP5B first name: ATP5F1B
[x] https://uniprot.org/uniprotkb/P36542/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ATP5C1 first name: ATP5F1C
[x] https://uniprot.org/uniprotkb/P30049/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ATP5D first name: ATP5F1D
[x] https://uniprot.org/uniprotkb/P24539/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ATP5F1 first name: ATP5PB
[x] https://uniprot.org/uniprotkb/Q9Y3I0/entry#names_and_taxonomy ; # of p.names: 1 HUGO: C22orf28 first name: RTCB
[x] https://uniprot.org/uniprotkb/P49589/entry#names_and_taxonomy ; # of p.names: 1 HUGO: CARS first name: CARS1
[x] https://uniprot.org/uniprotkb/Q16773/entry#names_and_taxonomy ; # of p.names: 1 HUGO: CCBL1 first name: KYAT1
[x] https://uniprot.org/uniprotkb/Q6YP21/entry#names_and_taxonomy ; # of p.names: 1 HUGO: CCBL2 first name: KYAT3
[x] https://uniprot.org/uniprotkb/P12532/entry#names_and_taxonomy ; # of p.names: 2 HUGO: CKMT1A first name: CKMT1A
[x] https://uniprot.org/uniprotkb/P14868/entry#names_and_taxonomy ; # of p.names: 1 HUGO: DARS first name: DARS1
[x] https://uniprot.org/uniprotkb/P07814/entry#names_and_taxonomy ; # of p.names: 1 HUGO: EPRS first name: EPRS1
[x] https://uniprot.org/uniprotkb/Q86YB8/entry#names_and_taxonomy ; # of p.names: 1 HUGO: ERO1LB first name: ERO1B
[x] https://uniprot.org/uniprotkb/P41250/entry#names_and_taxonomy ; # of p.names: 1 HUGO: GARS first name: GARS1
[x] https://uniprot.org/uniprotkb/P04062/entry#names_and_taxonomy ; # of p.names: 1 HUGO: GBA first name: GBA1
[x] https://uniprot.org/uniprotkb/Q86Y34/entry#names_and_taxonomy ; # of p.names: 1 HUGO: GPR97 first name: ADGRG3
[x] https://uniprot.org/uniprotkb/Q8TF76/entry#names_and_taxonomy ; # of p.names: 1 HUGO: GSG2 first name: HASPIN
[x] https://uniprot.org/uniprotkb/Q02108/entry#names_and_taxonomy ; # of p.names: 1 HUGO: GUCY1A3 first name: GUCY1A1
[x] https://uniprot.org/uniprotkb/Q02153/entry#names_and_taxonomy ; # of p.names: 1 HUGO: GUCY1B3 first name: GUCY1B1
[x] https://uniprot.org/uniprotkb/P69905/entry#names_and_taxonomy ; # of p.names: 2 HUGO: HBA1 first name: HBA1
[x] https://uniprot.org/uniprotkb/P52758/entry#names_and_taxonomy ; # of p.names: 1 HUGO: HRSP12 first name: RIDA
[x] https://uniprot.org/uniprotkb/Q15046/entry#names_and_taxonomy ; # of p.names: 1 HUGO: KARS first name: KARS1
[x] https://uniprot.org/uniprotkb/Q9P2J5/entry#names_and_taxonomy ; # of p.names: 1 HUGO: LARS first name: LARS1
[x] https://uniprot.org/uniprotkb/O60502/entry#names_and_taxonomy ; # of p.names: 1 HUGO: MGEA5 first name: OGA
[x] https://uniprot.org/uniprotkb/Q969V6/entry#names_and_taxonomy ; # of p.names: 1 HUGO: MKL1 first name: MRTFA
[x] https://uniprot.org/uniprotkb/P49959/entry#names_and_taxonomy ; # of p.names: 1 HUGO: MRE11A first name: MRE11
[x] https://uniprot.org/uniprotkb/P22033/entry#names_and_taxonomy ; # of p.names: 1 HUGO: MUT first name: MMUT
[x] https://uniprot.org/uniprotkb/O43776/entry#names_and_taxonomy ; # of p.names: 1 HUGO: NARS first name: NARS1
[x] https://uniprot.org/uniprotkb/P55769/entry#names_and_taxonomy ; # of p.names: 1 HUGO: NHP2L1 first name: SNU13
[x] https://uniprot.org/uniprotkb/Q9P286/entry#names_and_taxonomy ; # of p.names: 1 HUGO: PAK7 first name: PAK5
[x] https://uniprot.org/uniprotkb/O15530/entry#names_and_taxonomy ; # of p.names: 1 HUGO: PDK1 first name: PDPK1
[x] https://uniprot.org/uniprotkb/Q9Y646/entry#names_and_taxonomy ; # of p.names: 1 HUGO: PGCP first name: CPQ
[x] https://uniprot.org/uniprotkb/O94903/entry#names_and_taxonomy ; # of p.names: 1 HUGO: PROSC first name: PLPBP
[x] https://uniprot.org/uniprotkb/Q53H96/entry#names_and_taxonomy ; # of p.names: 1 HUGO: PYCRL first name: PYCR3
[x] https://uniprot.org/uniprotkb/Q16637/entry#names_and_taxonomy ; # of p.names: 2 HUGO: SMN1 first name: SMN1
[x] https://uniprot.org/uniprotkb/P26639/entry#names_and_taxonomy ; # of p.names: 1 HUGO: TARS first name: TARS1
[x] https://uniprot.org/uniprotkb/Q13630/entry#names_and_taxonomy ; # of p.names: 1 HUGO: TSTA3 first name: GFUS
[x] https://uniprot.org/uniprotkb/P23381/entry#names_and_taxonomy ; # of p.names: 1 HUGO: WARS first name: WARS1
[x] https://uniprot.org/uniprotkb/P54577/entry#names_and_taxonomy ; # of p.names: 1 HUGO: YARS first name: YARS1

cycle20 commented 1 year ago

An example: adaptavir: CCR5: versus https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=62 https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=11692 https://www.uniprot.org/uniprotkb/P51681/entry#disease_variants https://drugcentral.org/?q=CCR5&approval= https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL274/

cycle20 commented 1 year ago

Corrupted label records at FDA:

  matchLevel ingrLength year  splEffDate setId                                ndcCodes             applicationNumber submitter                             
       <dbl>      <int> <chr> <chr>      <chr>                                <chr>                <chr>             <chr>                                 
1          1          1 NA    20070330   346af8fe-3816-49de-bfd3-5a7425e728f9 57664-291; 57664-292 NA                CARACO PHARMACEUTICAL LABORATORIES LTD
2          1          1 NA    20060104   f133fe04-1550-4fa4-9dc4-652c27936bf2 0091-3351; 0091-3352 NA                SCHWARZ PHARMA

curl  'https://api.fda.gov/drug/ndc.json?search=product_ndc:57664-291&limit=1'
curl  'https://api.fda.gov/drug/ndc.json?search=product_ndc:57664-292&limit=1'
curl  'https://api.fda.gov/drug/ndc.json?search=product_ndc:0091-3351&limit=1'
curl  'https://api.fda.gov/drug/ndc.json?search=product_ndc:0091-3352&limit=1'

{
  "error": {
    "code": "NOT_FOUND",
    "message": "No matches found!"
  }
}

cycle20 / EZCancerTarget

Full download from clue #54