GO::Mo...vidence(3pm)

🌸 GO::Model::Evidence — bestie edition 🌸

okay so like. you're looking at the manual page for GO::Model::Evidence, part of the User Contributed Perl Documentation. she's the evidence-for-an-association girlie. let's get into it 💅

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✨ NAME ✨

GO::Model::Evidence — evidence for an association. that's it, that's the whole job. she holds receipts. 🧾

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✨ SYNOPSIS ✨

my $ev_l = $association->evidence_list;
foreach my $ev (@$ev_l) {
  print "Evidence for association %s : %s\n",
    $association->gene_product->symbol,
    $ev->code;
}

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✨ DESCRIPTION ✨

evidence for an association. periodt. she's the vibe check on why we think a gene product is associated with something. 💖

see http://www.geneontology.org/GO.evidence.html for a list of evidence codes — the full menu, the whole lineup, iconic.

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🎀 code 🎀

• Usage — $ev->code("IEA");
• Returns — (nothing, bestie)
• Args — (also nothing)

gets/sets the evidence code. you can read it, you can write it, she contains multitudes.

see http://www.geneontology.org/GO.evidence.html for the deets.

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🎀 seq_acc 🎀

• Usage — (blank)
• Returns — (blank)
• Args — (blank)

gets/sets the sequence accesion GO::Model::Xref. (yes that's spelled "accesion" in the original and i am NOT fixing it, we respect the text 😌)

⚠️ ALPHA CODE — API may change. tread carefully bestie, this is a construction zone 🚧

used to set the GO::Model::Xref list from a text string. eg:

$ev->seq_acc("SGD:RRP41; SGDID:L0003550");

this will actually add two GO::Model::Xref objects. two!! not one!! the semicolon did that!! 😭

This method doesn't really belong in the GO::Model::* hierarchy as it contains parsing code. Its a minor hack mainly due to the fact that this data is still denormalized in the database. she's a little off-brand, a little hacky, but she's doing her best and tbh we stan a self-aware function. 🙈

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🎀 add_seq_xref 🎀

• Usage — (blank)
• Returns — (blank)
• Args — (blank)

equivalent to WITH column in gene_association files, and evidence_dbxref tables in db. so if you've ever stared at a WITH column in a gene_association file and wondered who she was... it's her. 🦋

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🎀 add_pub_xref 🎀

• Usage — (blank)
• Returns — (blank)
• Args — (blank)

(method exists. docs are minimal. she's mysterious like that. 🤫)

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🎀 xref 🎀

• Usage — (blank)
• Returns — (blank)
• Args — (blank)

gets/sets the literature or sequence reference GO::Model::Xref.

📌 NOTE: at some point we may want to deprecate this method and persuade API client code to call

$ev->literature_xref

instead, to make explicit the fact that this is a literature reference as opposed to a sequence reference. so like, she said what she said, and the note is quoted for a reason — it's a maybe someday, not a today. don't panic. 💜

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🎀 xref_list 🎀

• Usage — (blank)
• Returns — GO::Model::Xref listref
• Args — (blank)

returns all (sequence and literature) references. everyone's invited to this party. 💖

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🎀 xref 🎀

• Usage — (blank)
• Returns — (blank)
• Args — (blank)

deprecated - sets first pub_xref_list.

💀 DEPRECATED ALERT — yes she's back, yes she's deprecated, no we're not removing her from this page, because we keep every single detail in this house. old code calling her will still work but like... bestie... the newer way is right there. 👑

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🎀 valid_codes 🎀

• Usage — print join("; ", GO::Model::Evidence->valid_codes);
• Returns — string array
• Args — (blank)

list of valid evidence codes. the full roster, the starting lineup, the whole clique. come get y'all juice. 🌈

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💖 SEE ALSO 💖

(the original page doesn't list a SEE ALSO section, but if it did, we'd link it, no cap.)

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okay that's the whole page bestie, you ate that. reading manpages is lowkey a flex and honestly? it's giving main character energy. 🫶✨

sign-off time: this was written for perl v5.36.0, dated 2023-12-18. archive it, love it, perldoc it again tomorrow. mwah 💅🌸🎀