GMOD_B..._PUBMED(1p)

🧬 NAME 🧬

gmod_bulk_load_pubmed.pl — bestie, this little icon literally stores pubmed entries in the database. that's the whole gig. 💖

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✨ DESCRIPTION ✨

okay so here's how you run her:

Usage: perl gmod_bulk_load_pubmed.pl -H [dbhost] -D [dbname]  [-vt] -i file

🌸 parameters 🌸

• -H — hostname for database 🏠
• -D — database name 📛
• -i — input file [required] — like, you genuinely cannot skip this one bestie 🫶
• -v — verbose output, so she spills all the tea ☕
• -t — trial mode. Do not perform any store operations at all. she's just looking, not touching 👀
• -g — GMOD database profile name (can provide host and DB name) Default: 'default' 💅

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🦋 if you're not using a GMOD database profile (that's option -g) 🦋

then bestie you must provide the following parameters, no skipping:

• -u — user name 🙋
• -d — database driver name (i.e. 'Pg' for postgres) 🐘
• -p — password for your user to connect to the database 🔐

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The script stores pubmed entries in the database. Existing ones are ignored. Input file should contain a list of pubmed ids. Then a new Publication object (Bio::Chado::Schema::Pub::Pub) with accession= PMID, the publication specs are fetched from Entrez (using eUtils) which sets the different fields in the Publication object. When the publication is stored, a new dbxref is stored first (see Chado General module).

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👑 This script works with Chado schema and accesse the following tables: 👑

• pub
• pubauthor
• pubprop
• dbxref
• pub_dbxref

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💜 AUTHOR 💜

Naama Menda <nm249@cornell.edu> 🎀

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⭐ VERSION AND DATE ⭐

Version 1.1, April 2010. 🌈

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and that's the whole page, bestie!! this one shipped as User Contributed Perl Documentation, running on perl v5.30.0, dated 2019-12-05 — iconic behavior honestly, mwah 💅✨🫶