为什么做这件事？ 初衷是用于做基因的注释，后来发现有些数据库多多少少有些问题，比如基因名错了、基因ID过时了等等，为了方便重复使用数据库，所以将常用的数据库整理好了，方便重复调用。数据库预处理的原则是简单又灵活。
软件功能： 基因水平的注释。
library(devtools)
options(options(timeout = max(600, getOption("timeout")))) # install size about 500Mb
install_github("fentouxungui/BiologyDB")如果下载不下来，建议下载Release里的文件，然后本地安装。
如果仅仅是使用整理好的数据，建议安装fentouxungui/BiologyDBLight包。
library(devtools)
install_github("fentouxungui/BiologyDBLight")首先，由于各种各样的原因，并非所有的数据都整理的很好【更新到最新ID】。另外，建议在注释本地数据时，先更新本地基因数据到最新的ID。
-
人的话，用HGNC提供的在线工具Multi-symbol checker进行更新，然后用ZhangRtools包里的 Check_hgnc_hits 对匹配结果预处理。gtf version: Gencode v45
-
小鼠的话，用MGI提供的在线工具MGI Batch Query进行基因ID更新。gtf version: Gencode vM34
-
果蝇的话，用Flybase提供的在线工具Batch Download或ID Validator进行ID更新。gtf version: flybase r6.56
library(BiologyDB)
d <- data(package = "BiologyDB")
d$results[,"Item"]
#> [1] "AnimalTFDB_Fly_TF"
#> [2] "AnimalTFDB_Fly_TFCofactors"
#> [3] "AnimalTFDB_Human_TF"
#> [4] "AnimalTFDB_Human_TFCofactors"
#> [5] "AnimalTFDB_Mouse_TF"
#> [6] "AnimalTFDB_Mouse_TFCofactors"
#> [7] "CellChat_Human_LigandReceptorsInteractions"
#> [8] "CellChat_Human_Ligands"
#> [9] "CellChat_Human_Receptors"
#> [10] "CellChat_Mouse_LigandReceptorsInteractions"
#> [11] "CellChat_Mouse_Ligands"
#> [12] "CellChat_Mouse_Receptors"
#> [13] "CellPhoneDB_Human_Interactions"
#> [14] "CellPhoneDB_Human_Ligands"
#> [15] "CellPhoneDB_Human_Receptors"
#> [16] "CellTalkDB_Human_Interactions"
#> [17] "CellTalkDB_Mouse_Interactions"
#> [18] "Flybase_Fly_AutomatedGeneSummary"
#> [19] "Flybase_Fly_BestGeneSummary"
#> [20] "Flybase_Fly_GeneSnapshots"
#> [21] "Flybase_Fly_Genes"
#> [22] "GENCODE_Human_Genes"
#> [23] "GENCODE_Mouse_Genes"
#> [24] "GENEONTOLOGY_Fly"
#> [25] "GENEONTOLOGY_Human"
#> [26] "GENEONTOLOGY_Mouse"
#> [27] "HPA_Human_102Genes_SecretedAndFDAApprovedDrugTargets"
#> [28] "HPA_Human_12631Genes_NotSecretedOrMembraneBound"
#> [29] "HPA_Human_1708Genes_BothSecretedAndMembraneBound"
#> [30] "HPA_Human_1708Genes_Secreted"
#> [31] "HPA_Human_19670Genes_GODiseaseDistributionLocation"
#> [32] "HPA_Human_429Genes_MembraneBoundAndHasFDAApprovedDrugTargets"
#> [33] "HPA_Human_5520Genes_MembraneBound"
#> [34] "HPA_Human_754Genes_FDAApprovedDrugTargets"
#> [35] "HPA_Human_ProteinClass_CD"
#> [36] "HPA_Human_ProteinClass_GPCR"
#> [37] "HPA_Human_ProteinClass_Plasma"
#> [38] "HPA_Human_ProteinClass_Transporters"
#> [39] "HPA_Human_ProteinClass_VoltageGatedIonChannels"
#> [40] "Human_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull"
#> [41] "Human_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull_Expanded"
#> [42] "Human_GuideToPHARMACOLOGY_Interactions_OnlyTargetsFull_Expanded"
#> [43] "Human_GuideToPHARMACOLOGY_LigandsPeptides"
#> [44] "Human_GuideToPHARMACOLOGY_Targets"
#> [45] "Mouse_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull"
#> [46] "Mouse_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull_Expanded"
#> [47] "Mouse_GuideToPHARMACOLOGY_Interactions_OnlyTargetsFull_Expanded"
#> [48] "Mouse_GuideToPHARMACOLOGY_LigandsPeptides"
#> [49] "Mouse_GuideToPHARMACOLOGY_Targets"
#> [50] "NCBI_Human_GeneSummary"
#> [51] "NCBI_Mouse_GeneSummary"
#> [52] "TheHumanTranscriptionFactors"
#> [53] "UniProt_Human_GeneFunction"
#> [54] "UniProt_Mouse_GeneFunction"
#> [55] "UniProt_ProteinFamily_AllSpecies"
#> [56] "UniProt_ProteinFamily_Human"
#> [57] "UniProt_ProteinFamily_Mouse"
#> [58] "VerSeDa_Mouse_SecretomePrediction"人：tutorials/Prepare-Human-Database.Rmd
小鼠：tutorials/Prepare-Mouse-Database.Rmd
果蝇：tutorials/Prepare-Fly-Database.Rmd
sessionInfo()
#> R version 4.4.1 (2024-06-14 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 22631)
#>
#> Matrix products: default
#>
#>
#> locale:
#> [1] LC_COLLATE=Chinese (Simplified)_China.utf8
#> [2] LC_CTYPE=Chinese (Simplified)_China.utf8
#> [3] LC_MONETARY=Chinese (Simplified)_China.utf8
#> [4] LC_NUMERIC=C
#> [5] LC_TIME=Chinese (Simplified)_China.utf8
#>
#> time zone: Asia/Shanghai
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] BiologyDB_0.0.0.9000
#>
#> loaded via a namespace (and not attached):
#> [1] compiler_4.4.1 fastmap_1.2.0 cli_3.6.3 tools_4.4.1
#> [5] htmltools_0.5.8.1 rstudioapi_0.16.0 yaml_2.3.8 rmarkdown_2.27
#> [9] knitr_1.47 xfun_0.45 digest_0.6.36 rlang_1.1.4
#> [13] evaluate_0.24.0