A tool to generate prioritized genes using phenotype information.
- Available at: http://molgenis.org/vibe
- Source code: https://github.com/molgenis/molgenis-app-vibe
- Download vibe .jar file
- Download and extract TDB
- Make sure you have Java 8 or higher
- Open a terminal and run VIBE.
java -jar vibe-with-dependencies.jar -v -t TDB/ -o results.tsv -p HP:0002996 -p HP:0001377
Instructions regarding building/testing the app can be found here and how to create a TDB for the app can be found here.
* = Only required when certain arguments are used.
java -jar vibe-with-dependencies.jar [-h] [-v] -t <FILE> [-w <FILE> -n <NAME> -m <NUMBER>] [-o <FILE>] [-l] [-u] -p <HPO ID> [-p <HPO ID>]...
Using only the user-defined phenotypes:
java -jar vibe-with-dependencies.jar -v -t TDB/ -o results.tsv -p HP:0002996 -p HP:0001377
Using the user-defined phenotypes and phenotypes that are related to them with a maximum distance of 1:
java -jar vibe-with-dependencies.jar -v -t TDB/ -w hp.owl -n distance -m 1 -o results.tsv -p HP:0002996
Using the user-defined phenotypes and their (grand)children with a maximum distance of 2:
java -jar vibe-with-dependencies.jar -v -t TDB/ -w hp.owl -n children -m 2 -o results.tsv -p HP:0002996
There are currently 2 options for the output. By default the output will look something like:
gene (NCBI) gene symbol (HGNC) highest GDA score diseases (UMLS) with sources per disease
1311 COMP 1.0 C0410538 (1.0):10405447,10753957,10852928,11084047,11691584,11745002,11746044,11746045,11782471,11891674,11968079,12479386,12483304,12483437,12768438,12792737,12819015,14580238,15094116,15183431,15266613,15337766,15551305,15579310,15694129,15756302,15880723,16199550,16514635,16520029,17200202,17307347,17394206,17570134,17579668,17588960,18193163,18546327,19762713,20301660,20578249,20819661,20936634,21042783,21599986,21922596,22006726,23562786,24194321,24595329,24892720,24997222,29104872,7670471,7670472,9021009,9184241,9188668,9388247,9452026,9452063,9463320,9632164,9749943,9880218,9887340,9921895,9923655|C1838280 (0.74):10405447,11084047,11565064,11782471,12483304,12819015,14684695,20301302,21922596,7670472,9021009,9184241,9452026,9463320,9887340,9921895,9923655|C0026760 (0.6):10364514,10655510,11084047,11479597,11528506,11565064,11782471,11968079,12479386,12483304,12819015,15183431,15337766,15694129,15756302,15880723,16199550,16514635,17133256,17200202,17570134,18193163,18682400,19808781,20578249,20936634,21922596,24595329,24997222,7670472,9184241,9463320,9921895,9923655|C0013336 (0.13):11691584,12483304,15472220|C1867103 (0.1)|C0029422 (0.03):11891674,12768438,17579668
4010 LMX1B 1.0 C0027341 (1.0):10425280,10537763,10571942,10660670,10767331,10854116,11668639,11956244,11978876,12215822,12792813,12819019,15562281,15638822,15774843,15785774,15928687,16825280,17166916,17431898,17515884,17657578,17710881,18414507,18535845,18538102,18562181,18595794,18634531,18952915,19147669,19222527,19721866,20199424,20531206,20568247,21184584,21850167,22211385,23687361,24042019,24720768,25380522,25898926,26380986,26560070,28335748,9590287,9590288,9618165,9664684,9837817|C0029422 (0.11):10767331|C1867103 (0.1)|C1867439 (0.1)
Here, each row represents a gene. Each row consists out of several (tab-seperated) fields. First is the NCBI gene id, then the highest found gene-disease association score found in DisGeNET for that gene, and finally all found associated diseases with the gene-disease association score specific for that gene-disease combination followed by the evidence IDs (pubmed if no URL is shown) for it.
Alternatively, the option -l can be added when running the tool. If this is done, the output will only contain the genes (separated by comma's). The example output above would look like:
1311,4010
The -u option changes the output to use URI's instead of ID's for certain fields. As this strongly increases the output size, in general it is not advised to use this option.
Q: It takes forever to retrieve information from the TDB.
A: Depending on the how much information needs to be retrieved from the TDB based on the input genes, this process may indeed take a while. However, there are ways to speed up this process. Examples include using an SSD instead HDD and using a 64-bit JVM.