mathelab / ramp-db Goto Github PK

I try to install rmysql but could not, do you have any suggestions?
https://stackoverflow.com/questions/24537257/installing-rmysql-in-mavericks

Hi there,
I am wondering why the application service is unavailable. Is this due to COVID or for other reasons?
Thanks!

Please include formatting guidelines for inputting sourceids (i.e. Pubchem IDs need "pubchem:" appended, HMDB IDs need 7 digits, not 5)

Error messages (e.g. pathway analysis on creatinine and leucine), should be better displayed.

Work on improving the speed of the pathway enrichment analysis.

In Unix/linux environment, the function rampFindSynonymFromSynonym listed in rampQueryHelper.R file meets an error. In fact, the table’s name used is ‘analyteSynonym’ while the table’s name in the database is ‘analytesynonym’. The function meets a case sensitive problem.

one among other faulty lines :

Advantages:

• has normalized metabolite IDs
• has ontology tagging (e.g. Pathway Ontology)
• normalized various types of interactions

cc @DeniseSl22

Hello Mathelab,

Thank you for this wonderful app. I was running an analysis of KEGG IDs and I noticed a strange analyte showing up as a result of kegg:C00089. Instead of Sucrose, which corresponds to C00089, a compound named Furan takes its place. Furan is entry number C14275. Please let me know if you are able to resolve kegg:C00089 being wrongfully identified as the analyte Furan.

Thank you,
Manjot Virdee

Hello,
I've installed RaMP today, it got installed well and i could launch the web services from R. Now, i would like to perform the section "Retrieve pathway from given analytes" using a list of genes and a list of metabolites, but in R, so using RaMP R functions. I didn't find any documentation to do this though... Also, i noticed that when i use this command line, all these RaMP functions appear :
head(ls(getNamespace("RaMP")), n = 100) [1] "analyte_result" "compute_overlap_matrix" "connectToRaMP" [4] "FilterFishersResults" "findAnalyteHasPathway" "findCluster" [7] "genes_result" "getAnalyteFromPathway" "getMetaFromOnto" [10] "getOntoFromMeta" "getPathwayFromAnalyte" "hmdb_gene" [13] "hmdb_metab" "kegg_gene" "kegg_metab" [16] "metabolites_result" "plotCataNetwork" "processData" [19] "rampFastCata" "rampFastPathFromSource" "rampFileOfAnalytes_tab4" [22] "rampFindSourceFromId" "rampFindSourceRampId" "rampFindSynonymFromSynonym" [25] "reactome_gene" "reactome_metab" "runCombinedFisherTest" [28] "runFisherTest" "runRaMPapp" "sysdataObject" [31] "updateOverlapMatrices" "updateOverlapMatrix" "wiki_gene" [34] "wiki_metab" "write_FishersResults" "writePathwaysToCSV"
However, most of them are unvailable, so when i try to use them R doesn't recognize them. I precise that i used this code before testing the functions :
library(RaMP) connectToRaMP(dbname = "ramp", username = "root", conpass = "mycode",host = "localhost")
Another precision, I use MySQL and R in windows 8.1.

How could I perform my analysis using R functions, and why most of them aren't recognized ?
Thanks in advance for your help !

The following functions connect to the database, but do not close the connection:

• RaMP::getPathwayFromAnalyte
• runCombinedFisherTest

When the functions are run multiple times, this causes the following error in RStudio: Cannot allocate a new connection: 16 connections already opened

All id types should be prepended to all compound and gene ids.

Here are the id types currently in RaMP:
mysql> select distinct(IDtype) from source where geneOrCompound ="compound";
+------------+
| IDtype |
+------------+
| kegg |
| CAS |
| chebi |
| chemspider |
| hmdb |
| LIPIDMAPS |
| pubchem |
+------------+
7 rows in set (0.14 sec)

mysql> select distinct(IDtype) from source where geneOrCompound ="gene";
+--------------------+
| IDtype |
+--------------------+
| enzymeNomenclature |
| kegg |
| uniprot |
| ensembl |
| entrez |
| hmdb |
+--------------------+
6 rows in set (0.08 sec)

Hello,

I recently upgraded to R version 4.0.0. I am trying to reinstall the RaMP R package on my system but getting the following error:

devtools::install_github("mathelab/RAMP-DB", force = TRUE)

Downloading GitHub repo mathelab/RAMP-DB@master
✓ checking for file ‘/private/var/folders/s6/smq8l3gx6dvb78q6c47kxz480000gn/T/RtmpWCklX4/remotes48c52b79554d/Mathelab-RaMP-DB-3a96ed8/DESCRIPTION’ (371ms)
─ preparing ‘RaMP’:
✓ checking DESCRIPTION meta-information ...
Warning in grepl(e, files, perl = TRUE, ignore.case = TRUE) :
PCRE pattern compilation error
'unrecognized character follows '
at 'img/.$'
Error in grepl(e, files, perl = TRUE, ignore.case = TRUE) :
invalid regular expression '^\img/.$'
Execution halted
Error: Failed to install 'RaMP' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr:
E> * checking for file ‘/private/var/folders/s6/smq8l3gx6dvb78q6c47kxz480000gn/T/RtmpWCklX4/remotes48c52b79554d/Mathelab-RaMP-DB-3a96ed8/DESCRIPTION’ ... OK
E> * preparing ‘RaMP’:
E> * checking DESCRIPTION meta-information ... OK
E> Warning in grepl(e, files, perl = TRUE, ignore.case = TRUE) :
E> PCRE pattern compilation error
E> 'unrecognized character follows '
E> at 'img/.$'
E> Error in grepl(e, files, perl = TRUE, ignore.case = TRUE) :
E> invalid regular expression '^\img/.$'
E> Execution halted

Session info:
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] IntLIM_0.1.0

Any help greatly appreciated.

The search result of source ID in the data table is not shown.

When using the RaMP implementation at rampdb.ncats.io I ran into this issue when inputting multiple analytes as a batch query to retrieve relevant associated pathways. I clicked Run Pathway Analysis and the system returned the error: "DataTables warning: tableid = DataTables_Table_2 - Requested unknown parameter '1' for row 44, column 1.

Clustering throws an error message if you attempt to cluster with a short list of metabolite pathways (e.g. glucose, cholesterol), and then crashes if you retry clustering

After user input the list of metabolites, let the user see the plot of Ubiquitness (appear in how many pathways). Then users should have the choices to select metabolites they want to filter and only run the analysis on the metabolites with the frequency appearance less than the cutoff

Got the following error message when I tried to run pathway enrichment on the attached metabolite list:
Warning: Error in stats::fisher.test: all entries of 'x' must be nonnegative and finite
ChemRICH metabolites.txt

How many super classes, classes, and sub classes are stored in HMDB? Can we readily extract this information?

On the UI, we should remind all users that their ids should be prepended by the source type.
For example, for HMDB id, prepend 'hmdb:'; for ChEBI, prepend 'chebi:'.

For all the datatableOutput, we want the source ID column to have the prefix deleted since previously we manually prepend ID type to each ID.

The following warning shows up. It's probably bc it's looking for an input to grep but there is none to start of with.

runRaMPapp()

Listening on http://127.0.0.1:5501
Warning in grepl(input$CataInput, kw_analyte, ignore.case = TRUE) :
input string 60211 is invalid in this locale
Warning in grepl(input$CataInput, kw_analyte, ignore.case = TRUE) :
input string 119030 is invalid in this locale
Warning in grepl(input$CataInput, kw_analyte, ignore.case = TRUE) :
input string 246819 is invalid in this locale

Tried to make networks with "Glucose" in individual metabolite input and "Glucose" and "Cholesterol" in batch input for tab 4. Got the same error in both instances:

Warning: Error in %>%: could not find function "%>%"
| Stack trace (innermost first):
| 80: RaMP::plotCataNetwork
| 79: func [server/tab4.R#135]
| 78: origRenderFunc
| 77: output$networkmulti
| 2: shiny::runApp
| 1: runRaMPapp