GMOD_LOAD_CVTERMS(1p)

💖 GMOD_LOAD_CVTERMS 💖

okay bestie, gather round, because we're talking about load_cvterms.pl, a lil Perl script from the User Contributed Perl Documentation corner of the internet, and honestly? it's giving ontology-wrangling main character energy. 🧚

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✨ NAME ✨

load_cvterms.pl — bestie, this script literally compares which terms are new in the file compared to the database, and then inserts them. that's the whole vibe. 🦋

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🌸 SYNOPSIS 🌸

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

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🎀 parameters 🎀

• -g — the GMOD database profile name. it can hand over the host, DB name, password, username, and driver all at once, iconic behavior honestly. Default: 'default'
• -s — database name for linking (it must be in the db table, e.g. GO). no cap.
• -n — controlled vocabulary name (e.g. 'biological_process'). optional! if you don't give it, terms of all namespaces related with the database name will be handled. she's flexible like that 💅
• -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. but new terms will still be added. so like, half the job, bestie 🫶
• -v — verbose output. she will talk.
• -o — outfile for writing errors and verbose messages (optional)
• -t — trial mode. don't perform any store operations at all.

⚠️ heads up: trial mode cannot test inserting associated data for new terms. so it's a vibe check, not a full dress rehearsal. 😭

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🔥 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

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🌈 DESCRIPTION 🌈

okay so here's what she actually does:

The script parses the ontology in the file and the corresponding ontology in the database, if present. she 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. she removes the relationships that were not specified in the file from the database. and listen — it never removes a term entry from the database. ever. she's not like that. 💜

This script works with Chado schema (see gmod.org) and accesses 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 the -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

like, she keeps receipts on every single one of those. periodt. 👑

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👑 AUTHOR 👑

• Lukas Mueller <lam87@cornell.edu>
• Naama Menda <nm249@cornell.edu>

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⭐ VERSION AND DATE ⭐

Version 0.15, September 2010.

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and that's the whole page, bestie!! 🍓 this was documented by perl v5.30.0, dated 2019-12-05, under the manual name GMOD_LOAD_CVTERMS(1p) — go forth and load those cvterms, you absolute icon 💖✨