R/mapNaive.R
liberalMap.RdProduce a data.frame with a set of naive terms mapped to all matching ontology ids and their formal terms
liberalMap(terms, onto, useAgrep = FALSE, ...)character() vector, can use grep-compatible regular expressions
an instance of ontologyIndex::ontology_index
logical(1) if TRUE, agrep will be used
passed to agrep if used
a data.frame
cands = c("astrocyte$", "oligodendrocyte", "oligodendrocyte precursor",
"neoplastic", "^neuron$", "^vascular", "badterm")
#co = ontoProc::getCellOnto()
co = getOnto("cellOnto", year_added="2023")
#> loading from cache
liberalMap(cands, co)
#> input ontoid
#> 1 astrocyte$ CL:0000127
#> 2 astrocyte$ CL:0002604
#> 3 astrocyte$ CL:0002626
#> 4 astrocyte$ CL:0002627
#> 5 oligodendrocyte CL:0000128
#> 6 oligodendrocyte CL:0002453
#> 7 oligodendrocyte CL:2000025
#> 8 oligodendrocyte CL:4023059
#> 9 oligodendrocyte GO:0014003
#> 10 oligodendrocyte GO:0022032
#> 11 oligodendrocyte GO:0048709
#> 12 oligodendrocyte GO:0048713
#> 13 oligodendrocyte GO:0048714
#> 14 oligodendrocyte GO:0048715
#> 15 oligodendrocyte GO:0070444
#> 16 oligodendrocyte GO:0070445
#> 17 oligodendrocyte GO:0070446
#> 18 oligodendrocyte GO:0070447
#> 19 oligodendrocyte GO:0097252
#> 20 oligodendrocyte GO:1900141
#> 21 oligodendrocyte GO:1900142
#> 22 oligodendrocyte GO:1900143
#> 25 neoplastic CHEBI:35610
#> 26 neoplastic CL:0001063
#> 27 neoplastic PATO:0002011
#> 28 neoplastic PATO:0002097
#> 29 ^neuron$ CL:0000540
#> 30 ^vascular CL:0000359
#> 31 ^vascular CL:0005022
#> 32 ^vascular CL:4023051
#> 33 ^vascular CL:4023056
#> 34 ^vascular GO:0003018
#> 35 ^vascular GO:0005172
#> 36 ^vascular GO:0010232
#> 37 ^vascular GO:0035886
#> 38 ^vascular GO:0043184
#> 39 ^vascular GO:0072360
#> 40 ^vascular GO:0097084
#> 41 ^vascular GO:0101023
#> 42 ^vascular GO:1904738
#> 43 ^vascular GO:1905288
#> 44 ^vascular GO:1990874
#> 45 ^vascular PR:000001971
#> 46 ^vascular PR:000002112
#> 47 ^vascular PR:000048096
#> 48 ^vascular PR:P35918
#> 49 ^vascular PR:P35968
#> 50 ^vascular UBERON:0005629
#> 51 ^vascular UBERON:0006965
#> 52 ^vascular UBERON:0007798
#> 53 ^vascular UBERON:0009536
#> 54 ^vascular UBERON:0009537
#> 55 badterm badterm
#> term
#> 1 astrocyte
#> 2 hippocampal astrocyte
#> 3 immature astrocyte
#> 4 mature astrocyte
#> 5 oligodendrocyte
#> 6 oligodendrocyte precursor cell
#> 7 spinal cord oligodendrocyte
#> 8 differentiation-committed oligodendrocyte precursor
#> 9 oligodendrocyte development
#> 10 telencephalon oligodendrocyte cell migration
#> 11 oligodendrocyte differentiation
#> 12 regulation of oligodendrocyte differentiation
#> 13 positive regulation of oligodendrocyte differentiation
#> 14 negative regulation of oligodendrocyte differentiation
#> 15 oligodendrocyte progenitor proliferation
#> 16 regulation of oligodendrocyte progenitor proliferation
#> 17 negative regulation of oligodendrocyte progenitor proliferation
#> 18 positive regulation of oligodendrocyte progenitor proliferation
#> 19 oligodendrocyte apoptotic process
#> 20 regulation of oligodendrocyte apoptotic process
#> 21 negative regulation of oligodendrocyte apoptotic process
#> 22 positive regulation of oligodendrocyte apoptotic process
#> 25 antineoplastic agent
#> 26 neoplastic cell
#> 27 neoplastic
#> 28 neoplastic, malignant
#> 29 neuron
#> 30 vascular associated smooth muscle cell
#> 31 vascular lymphangioblast
#> 32 vascular leptomeningeal cell
#> 33 vascular leptomeningeal cell (Mmus)
#> 34 vascular process in circulatory system
#> 35 vascular endothelial growth factor receptor binding
#> 36 vascular transport
#> 37 vascular associated smooth muscle cell differentiation
#> 38 vascular endothelial growth factor receptor 2 binding
#> 39 vascular cord development
#> 40 vascular associated smooth muscle cell development
#> 41 vascular endothelial cell proliferation
#> 42 vascular associated smooth muscle cell migration
#> 43 vascular associated smooth muscle cell apoptotic process
#> 44 vascular associated smooth muscle cell proliferation
#> 45 vascular endothelial growth factor receptor
#> 46 vascular endothelial growth factor receptor 2
#> 47 vascular endothelial growth factor receptor 2, signal peptide removed form (human)
#> 48 vascular endothelial growth factor receptor 2 (mouse)
#> 49 vascular endothelial growth factor receptor 2 (human)
#> 50 vascular plexus
#> 51 vascular cord
#> 52 vascular system
#> 53 vascular element of left lung
#> 54 vascular element of right lung
#> 55 <NA>