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Dénes Türei Retrieve the list of kinases and phosphatases from OmniPath

Updated by Dénes Türei
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File kinases.r Modified

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 # Collect kinases and phosphatases from various resources
 # using OmniPath and the OmnipathR R package
 # https://github.com/saezlab/OmnipathR
+#
+# To see the list of resources: get_annotation_resources()
 
 if(!('OmnipathR' %in% installed.packages())){
Updated by Dénes Türei
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File kinases.r Modified

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     kinasecom_kinases,
     dgidb_kinases,
     hgnc_kinases
-)
+) %>% unique
 
 
 all_phosphatases <- c(
     uniprot_phosphatases,
     hgnc_phosphatases,
     dgidb_phosphatases
-)
+) %>% unique
Created by Dénes Türei
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File kinases.r Added

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+#!/usr/bin/env Rscript
+
+# Author: Denes Turei
+# turei.denes@gmail.com
+#
+# Collect kinases and phosphatases from various resources
+# using OmniPath and the OmnipathR R package
+# https://github.com/saezlab/OmnipathR
+
+if(!('OmnipathR' %in% installed.packages())){
+
+    require(devtools)
+    devtools::install_github('saezlab/OmnipathR')
+
+}
+
+require(dplyr)
+require(OmnipathR)
+
+uniprot_kinases <-
+    import_omnipath_annotations(
+        resources = 'UniProt_keyword',
+        wide = TRUE
+    ) %>%
+    filter(
+        keyword == 'Kinase' &
+        entity_type == 'protein'
+    ) %>%
+    pull(uniprot)
+
+
+kinasecom_kinases <-
+    import_omnipath_annotations(
+        resources = 'kinase.com',
+        entity_types = 'protein',
+        wide = TRUE
+    ) %>%
+    pull(uniprot)
+
+
+dgidb_kinases <-
+    import_omnipath_annotations(
+        resources = 'DGIdb',
+        entity_types = 'protein',
+        wide = TRUE
+    ) %>%
+    filter(
+        category == 'KINASE'
+    ) %>%
+    pull(uniprot)
+
+
+hgnc_kinases <- import_omnipath_annotations(
+        resources = 'HGNC',
+        wide = TRUE
+    ) %>%
+    filter(
+        grepl('kinase', mainclass, ignore.case = TRUE) &
+        entity_type == 'protein'
+    ) %>%
+    pull(uniprot) %>%
+    unique()
+
+
+uniprot_phosphatases <-
+    import_omnipath_annotations(
+        resources = 'UniProt_keyword',
+        wide = TRUE
+    ) %>%
+    filter(
+        keyword == 'Protein phosphatase' &
+        entity_type == 'protein'
+    ) %>%
+    pull(uniprot)
+
+
+hgnc_phosphatases <-
+    import_omnipath_annotations(
+        resources = 'HGNC',
+        wide = TRUE
+    ) %>%
+    filter(
+        grepl('rotein phosphatase', mainclass, fixed = TRUE) &
+        entity_type == 'protein'
+    ) %>%
+    pull(uniprot) %>%
+    unique()
+
+
+dgidb_phosphatases <-
+    import_omnipath_annotations(
+        resources = 'DGIdb',
+        entity_types = 'protein',
+        wide = TRUE
+    ) %>%
+    filter(
+        category == 'PROTEIN PHOSPHATASE'
+    ) %>%
+    pull(uniprot)
+
+
+all_kinases <- c(
+    uniprot_kinases,
+    kinasecom_kinases,
+    dgidb_kinases,
+    hgnc_kinases
+)
+
+
+all_phosphatases <- c(
+    uniprot_phosphatases,
+    hgnc_phosphatases,
+    dgidb_phosphatases
+)
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