jorainer
commented
1 year ago I assume you are using Bioconductor release 3.15 packages? With Bioconductor release 3.16 (AnnotationHub version 3.6.0) it is available:
> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2022-10-31
> query(ah, "MassBank")
AnnotationHub with 2 records
# snapshotDate(): 2022-10-31
# $dataprovider: MassBank
# $species: NA
# $rdataclass: CompDb
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH107048"]]'
title
AH107048 | MassBank CompDb for release 2021.03
AH107049 | MassBank CompDb for release 2022.06
So, MassBank was not removed, but only added recently (and is thus not available for older Bioconductor/AnnotationHub versions).
pratarora
I am trying to use Massbank for annotation but it seems Annotation hub has removed Massbank?
MassBank release "2022.06" not found in AnnotationHub
unique(ah$dataprovider) [1] "UCSC"
[2] "Ensembl"
[3] "RefNet"
[4] "Inparanoid8"
[5] "NHLBI"
[6] "ChEA"
[7] "Pazar"
[8] "NIH Pathway Interaction Database"
[9] "Haemcode"
[10] "BroadInstitute"
[11] "PRIDE"
[12] "Gencode"
[13] "CRIBI"
[14] "Genoscope"
[15] "MISO, VAST-TOOLS, UCSC"
[16] "UWashington"
[17] "Stanford"
[18] "dbSNP"
[19] "BioMart"
[20] "GeneOntology"
[21] "KEGG"
[22] "URGI"
[23] "EMBL-EBI"
[24] "MicrosporidiaDB"
[25] "FungiDB"
[26] "TriTrypDB"
[27] "ToxoDB"
[28] "AmoebaDB"
[29] "PlasmoDB"
[30] "PiroplasmaDB"
[31] "CryptoDB"
[32] "TrichDB"
[33] "GiardiaDB"
[34] "The Gene Ontology Consortium"
[35] "ENCODE Project"
[36] "SchistoDB"
[37] "NCBI/UniProt"
[38] "GENCODE"
[39] "http://www.pantherdb.org"
[40] "RMBase v2.0"
[41] "snoRNAdb"
[42] "tRNAdb"
[43] "NCBI"
[44] "DrugAge, DrugBank, Broad Institute"
[45] "DrugAge"
[46] "DrugBank"
[47] "Broad Institute"
[48] "HMDB, EMBL-EBI, EPA"
[49] "STRING"
[50] "OMA"
[51] "OrthoDB"
[52] "PathBank"
[53] "EBI/EMBL"
[54] "NCBI,DBCLS"
[55] "FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,ENSEMBL,CELLPHONEDB,BADERLAB,SINGLECELLSIGNALR,HOMOLOGENE" [56] "WikiPathways"
[57] "UCSC Jaspar"
[58] "VAST-TOOLS"
[59] "pyGenomeTracks "
[60] "NA"
[61] "UoE"
[62] "mitra.stanford.edu/kundaje/akundaje/release/blacklists/"
[63] "ENCODE"
[64] "TargetScan,miRTarBase,USCS,ENSEMBL"
[65] "TargetScan"
[66] "QuickGO"
[67] "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/"
sessionInfo() R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.5 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_CH.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_CH.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_CH.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] AnnotationHub_3.4.0 BiocFileCache_2.4.0 dbplyr_2.3.0 MsBackendMassbank_1.4.0 RSQLite_2.2.20 RMariaDB_1.2.2
[7] forcats_0.5.2 stringr_1.5.0 dplyr_1.0.10 purrr_1.0.1 readr_2.1.3 tidyr_1.2.1
[13] tibble_3.1.8 ggplot2_3.4.0 tidyverse_1.3.2 MetaboCoreUtils_1.7.0 MetaboAnnotation_1.3.0 Spectra_1.9.6
[19] ProtGenerics_1.29.1 BiocParallel_1.30.4 CompoundDb_1.3.1 S4Vectors_0.34.0 BiocGenerics_0.42.0 AnnotationFilter_1.20.0
loaded via a namespace (and not attached): [1] googledrive_2.0.0 colorspace_2.0-3 rjson_0.2.21 ellipsis_0.3.2
[5] XVector_0.36.0 GenomicRanges_1.48.0 base64enc_0.1-3 fs_1.5.2
[9] clue_0.3-63 rstudioapi_0.14 MultiAssayExperiment_1.22.0 DT_0.27
[13] bit64_4.0.5 AnnotationDbi_1.58.0 interactiveDisplayBase_1.34.0 fansi_1.0.3
[17] lubridate_1.9.0 xml2_1.3.3 codetools_0.2-18 cachem_1.0.6
[21] knitr_1.41 jsonlite_1.8.4 broom_1.0.2 cluster_2.1.4
[25] png_0.1-8 shiny_1.7.4 BiocManager_1.30.19 compiler_4.2.2
[29] httr_1.4.4 backports_1.4.1 assertthat_0.2.1 Matrix_1.5-3
[33] fastmap_1.1.0 lazyeval_0.2.2 gargle_1.2.1 cli_3.6.0
[37] later_1.3.0 htmltools_0.5.4 tools_4.2.2 igraph_1.3.5
[41] gtable_0.3.1 glue_1.6.2 GenomeInfoDbData_1.2.8 rappdirs_0.3.3
[45] rsvg_2.4.0 Rcpp_1.0.9 Biobase_2.56.0 cellranger_1.1.0
[49] Biostrings_2.64.1 vctrs_0.5.1 xfun_0.36 rvest_1.0.3
[53] mime_0.12 timechange_0.2.0 lifecycle_1.0.3 googlesheets4_1.0.1
[57] zlibbioc_1.42.0 MASS_7.3-58.1 scales_1.2.1 promises_1.2.0.1
[61] hms_1.1.2 MatrixGenerics_1.8.1 parallel_4.2.2 SummarizedExperiment_1.26.1
[65] yaml_2.3.6 curl_5.0.0 memoise_2.0.1 gridExtra_2.3
[69] QFeatures_1.9.3 stringi_1.7.12 BiocVersion_3.15.2 filelock_1.0.2
[73] GenomeInfoDb_1.32.4 rlang_1.0.6 pkgconfig_2.0.3 matrixStats_0.63.0
[77] bitops_1.0-7 lattice_0.20-45 ChemmineR_3.48.0 htmlwidgets_1.6.1
[81] bit_4.0.5 tidyselect_1.2.0 magrittr_2.0.3 R6_2.5.1
[85] IRanges_2.30.1 generics_0.1.3 DelayedArray_0.22.0 DBI_1.1.3
[89] pillar_1.8.1 haven_2.5.1 withr_2.5.0 MsCoreUtils_1.11.3
[93] KEGGREST_1.36.3 RCurl_1.98-1.9 modelr_0.1.10 crayon_1.5.2
[97] utf8_1.2.2 tzdb_0.3.0 grid_4.2.2 readxl_1.4.1
[101] data.table_1.14.6 blob_1.2.3 reprex_2.0.2 digest_0.6.31
[105] xtable_1.8-4 httpuv_1.6.8 munsell_0.5.0