bhklab / annotationgx Goto Github PK

queryUnichem is currently only one at a time and makes the user apply across a list.

Include an option with a list input

AnnotationGx::getPubchemCompound(ids= 'PUGREST.BadRequest', from = 'cid', to = 'property', properties = c('Title', 'MolecularFormula', 'InChIKey', 'CanonicalSMILES'))
   property/Title,MolecularFormula,InChIKey,CanonicalSMILES
                                                     <char>
1:                                       PUGREST.BadRequest

whereas a good CID returns:

AnnotationGx::getPubchemCompound(ids= '100016', from = 'cid', to = 'property', properties = c('Title', 'MolecularFormula', 'InChIKey', 'CanonicalSMILES'))
      CID MolecularFormula                   CanonicalSMILES
    <int>           <char>                            <char>
1: 100016        C9H12N2O5 C1=CN(C(=O)N=C1)C2C(C(C(O2)CO)O)O
                      InChIKey      Title
                        <char>     <char>
1: RPQZTTQVRYEKCR-WCTZXXKLSA-N Zebularine

Basic functionality implemented, create vignette with the example.

Add the annotation step in a pipeline?

from ccle pipeline:

# treatment_annotations$pubchem.CID[20] 
# which is 60838

AnnotationGx::annotatePubchemCompound("60838", "CAS")
Error in if (is.character(txt) && length(txt) == 1 && nchar(txt, type = "bytes") <  : 
  missing value where TRUE/FALSE needed

This is how I run the query:
pubchem_r2 = lapply(paste0("clean", seq(9)) ,function(col){ pubchem_query = getPubChemCompound(na.omit(unlist(drugnames_df[,col])), from='name', to='property', properties=c('Title'), batch=FALSE) })

I usually get blacklisted after "clean2".
Each queried vector contains 821 drug names.

Here is the error I get:
<simpleError: PubChem Server returned Black status! You could be black listed. The returned state message is:
Request Count status: Black (265%), Request Time status: Green (0%), Service status: Green (7%),
Remaining blocking time: 0:0:2.>

• Review Zenodo API documentation
• Write an R wrapper function which allows data submission to Zenodo via POST request

remotes::install_github(
"bhklab/AnnotationGx",
build_manual=TRUE,
build_vignettes=TRUE
)

Downloading GitHub repo bhklab/AnnotationGx@HEAD
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Enter one or more numbers, or an empty line to skip updates:
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/8x/mq9t1w4d4kxdbj1837xwsx_m0000gn/T/RtmpgShzxp/remotes122a2268168fc/bhklab-AnnotationGx-27cbafe/DESCRIPTION’ (578ms)
─ preparing ‘AnnotationGx’:
✔ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes
E creating vignettes (1m 3.9s)
--- re-building ‘Cellosaurus.Rmd’ using rmarkdown
--- finished re-building ‘Cellosaurus.Rmd’

--- re-building ‘ChEMBL.Rmd’ using rmarkdown
--- finished re-building ‘ChEMBL.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "1. Introduction to AnnotationGx", and the latter is "Introduction to AnnotationGx". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘OncoTree.Rmd’ using rmarkdown

Quitting from lines 62-63 [getCancerSubtypes] (OncoTree.Rmd)
Error: processing vignette 'OncoTree.Rmd' failed with diagnostics:
replacement has 0 rows, data has 885
--- failed re-building ‘OncoTree.Rmd’

--- re-building ‘PubChemAPI.Rmd’ using rmarkdown
--- finished re-building ‘PubChemAPI.Rmd’

--- re-building ‘Unichem.Rmd’ using rmarkdown
--- finished re-building ‘Unichem.Rmd’

SUMMARY: processing the following file failed:
‘OncoTree.Rmd’

Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'AnnotationGx' from GitHub:
! System command 'R' failed

Initially it asked to install 'sessioninfo'

need to explain how to annotate to other fields:
example from the gdsc pipeline

field_map <- list(
    "id" = "id",
    "ac" = "accession",
    "sy" = "synonyms",
    "misspelling" = "misspellings",
    "di" = "diseases",
    "ca" = "category",
    "sx" = "sexOfCell",
    "ag" = "ageAtSampling",
    "derived-from-site" = "samplingSite"
)

fields <- names(field_map)

sampleMetadata[, paste0("cellosaurus.", fields) := {
    mapped <- AnnotationGx::mapCell2Accession(
        as.character(GDSC.COSMIC_ID), 
        from = "dr",
        to = fields,
        BPPARAM = BPPARAM
    )
    return(mapped[, 1:length(fields)])
    }
    

Write a function to fetch annotations from OncoTree
See API - http://oncotree.mskcc.org/#/home?tab=api

1. add parameter in function call to not return the query and query:ac columns

• Validate that data.table assignment operations to fields are possible and streamlined

2. QOL feature to map the api column names i.e sy, di to their real names synonyms disease