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moosa-r / rbioapi

rbioapi: User-Friendly R Interface to Biologic Web Services' API
https://rbioapi.moosa-r.com/
GNU General Public License v3.0
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Database Connection #6

Closed klpara closed 2 years ago

klpara commented 2 years ago

Hello,

I am trying to access PANTHER but the database is not responding, I restarted the R session but still having trouble accessing it. Is there some way to fix this?

Thank you!

rba_connection_test(print_output=TRUE) Checking Your connection to the Databases currently supported by rbioapi: --->>> Internet : +++ Connected to the Internet. --->>> Enrichr : +++ The server is responding. --->>> Ensembl : +++ The server is responding. --->>> JASPAR : +++ The server is responding. --->>> miEAA : +++ The server is responding. --->>> PANTHER : !!! failed with error: Error in curl::curl_fetch_memory(url, handle = handle) : Recv failure: Connection was reset --->>> Reactome Content Service : +++ The server is responding. --->>> Reactome Analysis Service : +++ The server is responding. --->>> STRING : +++ The server is responding. --->>> UniProt : +++ The server is responding.

rba_options() rbioapi_option current_value allowed_value 1 diagnostics FALSE Logical (TRUE/FALSE) 2 dir_name rbioapi Character 3 progress FALSE Logical (TRUE/FALSE) 4 retry_max 1 Numeric (0 or greater) 5 retry_wait 10 Numeric (0 or greater) 6 save_file FALSE Logical (TRUE/FALSE) 7 skip_error FALSE Logical (TRUE/FALSE) 8 timeout 90 Numeric (0.1 or greater) 9 verbose TRUE Logical (TRUE/FALSE

moosa-r commented 2 years ago

Dear @klpara

This is a network-related issue. Either PANTHER was down when you tried this or you/ your network is blocked by PANTHER. Currently, PANTHER seems to be down. I will check again after the website is up.

moosa-r commented 2 years ago

PANTHER is up again and rbioapi is communication with the server without issues. Feel free to re-open the issue if you have other problems.

rbioapi::rba_connection_test()
Checking Your connection to the Databases currently supported by rbioapi:
--->>> Internet :
+++ Connected to the Internet.
--->>> Enrichr :
+++ The server is responding.
--->>> Ensembl :
+++ The server is responding.
--->>> JASPAR :
+++ The server is responding.
--->>> miEAA :
+++ The server is responding.
--->>> PANTHER :
+++ The server is responding.
--->>> Reactome Content Service :
+++ The server is responding.
--->>> Reactome Analysis Service :
+++ The server is responding.
--->>> STRING :
+++ The server is responding.
--->>> UniProt :
+++ The server is responding.

As example:

rba_panther_enrich(genes = c("p53", "BRCA1", "cdk2", "Q99835", "CDC42",
        "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"),
    organism = 9606, annot_dataset = "GO:0008150",
    cutoff = 0.01)
Performing over-representation enrichment analysis of 10 input genes of organism 9606 against GO:0008150 datasets.
$reference
$reference$organism
[1] "Homo sapiens"

$reference$mapped_count
[1] 20589

$reference$unmapped_count
[1] 0

$input_list
$input_list$organism
[1] "Homo sapiens"

$input_list$mapped_count
[1] 10

$input_list$mapped_id
 [1] "CDC42"   "RACGAP1" "cdk2"    "PLK1"    "RAC2"    "CDK1"    "KIF23"   "BRCA1"   "Q99835"  "p53"    

$input_list$unmapped_count
[1] 0

$result
   number_in_list fold_enrichment          fdr    expected number_in_reference       pValue plus_minus    term.id   term.label
1               8       23.036643 1.470311e-06 0.347272816                 715 9.376385e-11          + GO:0010564   regulation of cell cycle process
........

$search
$search$search_type
[1] "overrepresentation"

$tool_release_date
[1] 20221013

$enrichment_test_type
[1] "FISHER"

$annotDataSet
[1] "GO:0008150"

$annot_version_release_date
[1] "GO Ontology database DOI:  10.5281/zenodo.6799722 Released 2022-07-01"

$correction
[1] "FDR"
klpara commented 2 years ago

Thanks a lot!

Best,

Kathyani

From: Moosa Rezwani @.> Sent: Thursday, October 20, 2022 11:03:09 AM To: moosa-r/rbioapi @.> Cc: Kathyani Parasram @.>; Mention @.> Subject: Re: [moosa-r/rbioapi] Database Connection (Issue #6)

PANTHER is up again and rbioapi is communication with the server without issues. Feel free to re-open the issue if you have other problems.

rbioapi::rba_connection_test()

Checking Your connection to the Databases currently supported by rbioapi: --->>> Internet : +++ Connected to the Internet. --->>> Enrichr : +++ The server is responding. --->>> Ensembl : +++ The server is responding. --->>> JASPAR : +++ The server is responding. --->>> miEAA : +++ The server is responding. --->>> PANTHER : +++ The server is responding. --->>> Reactome Content Service : +++ The server is responding. --->>> Reactome Analysis Service : +++ The server is responding. --->>> STRING : +++ The server is responding. --->>> UniProt : +++ The server is responding.

As example:

rba_panther_enrich(genes = c("p53", "BRCA1", "cdk2", "Q99835", "CDC42", "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"), organism = 9606, annot_dataset = "GO:0008150", cutoff = 0.01)

Performing over-representation enrichment analysis of 10 input genes of organism 9606 against GO:0008150 datasets. $reference $reference$organism [1] "Homo sapiens"

$reference$mapped_count [1] 20589

$reference$unmapped_count [1] 0

$input_list $input_list$organism [1] "Homo sapiens"

$input_list$mapped_count [1] 10

$input_list$mapped_id [1] "CDC42" "RACGAP1" "cdk2" "PLK1" "RAC2" "CDK1" "KIF23" "BRCA1" "Q99835" "p53"

$input_list$unmapped_count [1] 0

$result number_in_list fold_enrichment fdr expected number_in_reference pValue plus_minus term.id term.label 1 8 23.036643 1.470311e-06 0.347272816 715 9.376385e-11 + GO:0010564 regulation of cell cycle process ........

$search $search$search_type [1] "overrepresentation"

$tool_release_date [1] 20221013

$enrichment_test_type [1] "FISHER"

$annotDataSet [1] "GO:0008150"

$annot_version_release_date [1] "GO Ontology database DOI: 10.5281/zenodo.6799722 Released 2022-07-01"

$correction [1] "FDR"

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