Ensure toggled fields get their own column for Cellosaurus output

[mattbocc]

As it stands, all of the extra fields you toggle on for a cellosaurus query are all dumped into the "comments" section. A huge improvement would be for them to have their own columns if toggled on.

Ex.

> CVCL_0001 <- annotateCellAccession("CVCL_0001", to = c("id", "sy", "idsy", "ac", "acas", "dr", "ww", "genome-ancestry", "hla", "registration", "sequence-variation", "anecdotal", "biotechnology", "breed", "caution", "cell-type", "characteristics", "donor-info", "derived-from-site", "discontinued", "doubling-time", "from", "group", "karyotype", "knockout", "msi", "miscellaneous", "misspelling", "mab-isotype", "mab-target", "omics", "part-of", "population", "problematic", "resistance", "senescence", "integrated", "transformant", "virology", "cc", "str", "di", "din", "dio", "ox", "sx", "ag", "oi", "hi", "ch", "ca", "dt", "dtc", "dtu", "dtv"))

[14:48:40][INFO][AnnotationGx::annotateCellAccession] Building Cellosaurus requests...
[14:48:40][INFO][AnnotationGx::annotateCellAccession] Performing Requests...
[14:48:40][INFO][AnnotationGx::annotateCellAccession] Parsing Responses...

> CVCL_0001

cellLineName accession category

1: HEL CVCL_0001 Cancer cell line
date ageAtSampling

1: Created: 04-04-12; Last updated: 14-08-25; Version: 49 30Y
sexOfCell synonyms diseases crossReferences hierarchy comments

1: Male Hel, GM0.... C7152; E.... BTO_0000.... list(c("....

> CVCL_0001$comments

[[1]]
[[1]]$Cell type
[[1]]$Cell type[[1]]
[1] "Erythroblast" "CL=CL_0000765."

[[1]]$Derived from site
[[1]]$Derived from site[[1]]
[1] "In situ" "Peripheral blood" "UBERON=UBERON_0000178."

[[1]]$Donor information
[[1]]$Donor information[[1]]
[1] "Originally the patient was suffering from Hodgkin lymphoma."

[[1]]$Doubling time
[[1]]$Doubling time[[1]]
[1] "~24 hours (PubMed=6177045)"
[2] "17.8 +- 1.8 hours (Note=In serum-containing medium), 23.3 +- 0.8 hours (Note=In serum-free medium) (PubMed=7538619)"
[3] "~36 hours (DSMZ=ACC-11)."

[[1]]$Genome ancestry
[[1]]$Genome ancestry[[1]]
[1] "African=2.4%"
[2] "Native American=1.79%"
[3] "East Asian, North=3.9%"
[4] "East Asian, South=0%"
[5] "South Asian=5.12%"
[6] "European, North=13.33%"
[7] "European, South=73.45% (PubMed=30894373)."

[[1]]$HLA typing
[[1]]$HLA typing[[1]]
[1] "A03:01,32:01" "B35:08,35:08"
[3] "C04:01,04:01" "DQA105:01,05:01"
[5] "DRB1*03:38,13:03 (PubMed=26589293)."

[[1]]$HLA typing[[2]]
[1] "A03:01:01,32:01:01"
[2] "B35:08:01,35:01:01"
[3] "C04:01:01,04:01:01"
[4] "DPA101:03:01,01:03:01"
[5] "DPB1*04:01:01,02:01:02 (DSMZCellDive=ACC-11)."

[[1]]$Microsatellite instability
[[1]]$Microsatellite instability[[1]]
[1] "Stable (MSS) (PubMed=10739008" "PubMed=11226526"
[3] "Sanger)."

[[1]]$Omics
[[1]]$Omics[[1]]
[1] "Genomics" "DNA methylation analysis."

[[1]]$Omics[[2]]
[1] "Genomics" "Whole exome sequencing."

[[1]]$Omics[[3]]
[1] "Phenotyping" "Drug screening."

[[1]]$Omics[[4]]
[1] "Proteomics"
[2] "Expression"
[3] "Large antibody panel staining analysis."

[[1]]$Omics[[5]]
[1] "Proteomics" "Quantitative."

[[1]]$Omics[[6]]
[1] "Transcriptomics" "Microarray."

[[1]]$Omics[[7]]
[1] "Transcriptomics" "RNAseq."

[[1]]$Omics[[8]]
[1] "Variations" "SNP array analysis."

[[1]]$Part of
[[1]]$Part of[[1]]
[1] "Cancer Dependency Map project (DepMap) (includes Cancer Cell Line Encyclopedia - CCLE)."

[[1]]$Part of[[2]]
[1] "COSMIC cell lines project."

[[1]]$Part of[[3]]
[1] "Human Protein Atlas, Cell Atlas panel."

[[1]]$Part of[[4]]
[1] "LL-100 blood cancer cell line panel."

[[1]]$Population
[[1]]$Population[[1]]
[1] "Caucasian."

[[1]]$Sequence variation
[[1]]$Sequence variation[[1]]
[1] "Mutation"
[2] "HGNC"
[3] "HGNC:6192"
[4] "JAK2"
[5] "Simple"
[6] "p.Val617Phe (c.1849G>T)"
[7] "ClinVar=VCV000014662"
[8] "Zygosity=Homozygous (PubMed=16408098)."

[[1]]$Sequence variation[[2]]
[1] "Mutation"
[2] "HGNC"
[3] "HGNC:11998"
[4] "TP53"
[5] "Simple"
[6] "p.Met133Lys (c.398T>A)"
[7] "ClinVar=VCV002430159"
[8] "Zygosity=Homozygous (Cosmic-CLP=907053"
[9] "DepMap=ACH-000004)."