EnglishFrenchSpanish

Ad


OnWorks favicon

gmod_load_cvterms.plp - Online in the Cloud

Run gmod_load_cvterms.plp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gmod_load_cvterms.plp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


load_cvterms.pl - compares which terms are new in the file compared to the database and
inserts them

SYNOPSIS


Usage: perl load_cvterms.pl -H dbhost -D dbname [-vdntuFo] file

parameters

-g GMOD database profile name (can provide host, DB name, password, username, and
driver) Default: 'default'

-s database name for linking (must be in db table, e.g. GO )

-n controlled vocabulary name (e.g 'biological_process'). optional. If not given,
terms of all namespaces related with database name will be handled.

-F File format. Can be obo or go_flat and others supported by Bio::OntologyIO.
Default: obo

-u update all the terms. Without -u, the terms in the database won't be updated to
the contents of the file, in terms of definitions, etc. New terms will still be
added.

-v verbose output

-o outfile for writing errors and verbose messages (optional)

-t trial mode. Don't perform any store operations at all. (trial mode cannot test
inserting associated data for new terms)

The following options are required if not using GMOD profile

-H hostname for database [required if -p isn't used]

-D database name [required if -p isn't used]

-p password (if you need to provide a password to connect to your db)

-r username (if you need to provide a username to connect to your database)

-d driver name (e.g. 'Pg' for postgres). Driver name can be provided in gmod_config

The script parses the ontology in the file and the corresponding ontology in the database,
if present. It compares which terms are new in the file compared to the database and
inserts them, and compares all the relationships that are new and inserts them. It removes
the relationships that were not specified in the file from the database. It never removes
a term entry from the database.

This script works with Chado schema (see gmod.org) and accesse the following tables:

db
dbxref
cv
cvterm
cvterm_relationship
cvtermsynonym
cvterm_dbxref
cvtermprop

Terms that are in the database but not in the file are set to is_obsolete=1. All the
terms that are present in the database are updated (if using -u option) to reflect the
term definitions that are in the file. New terms that are in the file but not in the
database are stored. The following data are associated with each term insert/update:

Term name
Term definition
Relationships with other terms
Synonyms
Secondary ids
Definition dbxrefs
Comments

Use gmod_load_cvterms.plp online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

Linux commands

  • 1
    abidw
    abidw
    abidw - serialize the ABI of an ELF
    file abidw reads a shared library in ELF
    format and emits an XML representation
    of its ABI to standard output. The
    emitted ...
    Run abidw
  • 2
    abilint
    abilint
    abilint - validate an abigail ABI
    representation abilint parses the native
    XML representation of an ABI as emitted
    by abidw. Once it has parsed the XML
    represe...
    Run abilint
  • 3
    createhdf
    createhdf
    createhdf Create a blank IDE hard
    disk image inhdf format ...
    Run createhdf
  • 4
    CreateInterface
    CreateInterface
    CreateInterface Create a Java
    Interface definition from DBus
    introspection data. ...
    Run CreateInterface
  • 5
    gba3
    gba3
    gba3 - GAMBAS Archiver ...
    Run gba3
  • 6
    gbackground
    gbackground
    gbackground - interval-based gnome
    background changer SYNTAX: gbackground
    DESCRIPTION: This program allows to
    change periodically the gnome background
    in inter...
    Run gbackground
  • More »

Ad