---
name: "gmod_make_cvtermpath.pl"
section: "1p"
platform: "linux"
package: "chado-utils"
version: "1.31-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmod_make_cvtermpath.pl"
---

# gmod\_make\_cvtermpath.pl(1p)

calculates the transitive closure on the ontology terms in the cvterm table

## NAME

gmod\_make\_cvtermpath.pl - calculates the transitive closure on the ontology terms in the cvterm table

## USAGE

```
 perl gmod_make_cvtermpath.pl -H [dbhost] -D [dbname]  [-vt] -c cvname
 perl gmod_make_cvtermpath.pl -g [GMODConf_profile] -c cvname
```

### Parameters

- \-c

  Name of ontology (cv.name) to compute the transitive closure on. (Required)

- \-v

  Verbose output

- \-t

  Trial mode. Do not perform any store operations at all. (Not implemented)

- \-o

  outfile for writing errors and verbose messages (optional)

- \-g

  GMOD database profile name (can provide host and DB name) Default: 'default'

### If not using a GMOD database profile (option -g) then you must provide the following parameters

- \-D

  Database name

- \-H

  Hostname

- \-d

  Database driver name (e.g. 'Pg' for postgres)

- \-u

  \[Optional- if default user is not used\] Database user name

- \-p

  \[Optional- if you need a password to connect to your database\] Password for your user to connect to the database

## DESCRIPTION

This script calculates the transitive closure on the ontology terms in the cvterm table.  As this is a computationaly intensive operation, doing so on a large cv like the Gene Ontology can take several hours.  For more information on what a transative closure is, please see:

```
  http://www.geneontology.org/GO.database.shtml#graphs
```

## AUTHOR

Naama Menda \<nm249@cornell.edu\>

## VERSION AND DATE

Version 1.2, Feb. 2011.