Bio::A...erence(3pm)

NAME ✨

Bio::Annotation::Reference — a specialised DBLink object for Literature References 💖

Like, it's a database link but make it bibliography. Periodt.

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SYNOPSIS 🎀

$reg = Bio::Annotation::Reference->new( -title    => 'title line',
                                        -location => 'location line',
                                        -authors  => 'author line',
                                        -medline  => 998122 );

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DESCRIPTION 🌸

Okay so bestie, this object presents a literature reference. It's considered to be a specialised form of database link, iykyk. The extra methods it gives you are all just set/get methods to store strings that are commonly associated with references — specifically title, location (that's the journal page, btw) and the authors line.

And here's the vibe check: there is no attempt to do anything more than store these things as strings for processing elsewhere. Why? Because parsing these things sucks 😭 and generally it's specific to the specific format you're using. To give you an easy route to go format --> object --> format without losing data, we keep them as strings. Feel free to post the list for a better solution, but in general this gets very messy very fast...

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AUTHOR - Ewan Birney 🫶

Email birney@ebi.ac.uk

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APPENDIX 💅

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 🫣

new 🐣

• Title: new
• Usage:

$ref = Bio::Annotation::Reference->new( -title => 'title line',
                          -authors => 'author line',
                          -location => 'location line',
                          -medline => 9988812);

• Function: (nothing here in the original, bestie — it's just vibes)
• Example: (also empty, not me leaving it blank 🙈)
• Returns: a new Bio::Annotation::Reference object
• Args: a hash with optional title, authors, location, medline, pubmed, start, end, consortium, rp and rg attributes

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AnnotationI implementing functions 🧚

as_text

• Title: as_text
• Usage: (blank in the original, no cap)
• Function: (blank)
• Example: (blank)
• Returns: (blank)
• Args: (blank)

Just a heads-up: this one is a placeholder in the docs, okay? No tea to spill here 💀

display_text

• Title: display_text
• Usage:

my $str = $ann->display_text();

• Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation.

One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned

• Example: (empty, sadly)
• Returns: a string
• Args: [optional] callback

Yes, the original really says "te specific implementation" — I'm not fixing it, I'm preserving the artifact 🏛️

hash_tree

• Title: hash_tree
• Usage: (blank)
• Function: (blank)
• Example: (blank)
• Returns: (blank)
• Args: (blank)

tagname

• Title: tagname
• Usage:

$obj->tagname($newval)

• Function: Get/set the tagname for this annotation value.

Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already.

• Example: (blank)
• Returns: value of tagname (a scalar)
• Args: new value (a scalar, optional)

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Specific accessors for References 👑

start

• Title: start
• Usage:

$self->start($newval)

• Function: Gives the reference start base
• Example: (blank)
• Returns: value of start
• Args: newvalue (optional)

end

• Title: end
• Usage:

$self->end($newval)

• Function: Gives the reference end base
• Example: (blank)
• Returns: value of end
• Args: newvalue (optional)

rp

• Title: rp
• Usage:

$self->rp($newval)

• Function: Gives the RP line. No attempt is made to parse this line.
• Example: (blank)
• Returns: value of rp
• Args: newvalue (optional)

rg

• Title: rg
• Usage:

$obj->rg($newval)

• Function: Gives the RG line. This is Swissprot/Uniprot specific, and if set will usually be identical to the authors attribute, but the swissprot manual does allow both RG and RA (author) to be present for the same reference.
• Example: (blank)
• Returns: value of rg (a scalar)
• Args: on set, new value (a scalar or undef, optional)

authors

• Title: authors
• Usage:

$self->authors($newval)

• Function: Gives the author line. No attempt is made to parse the author line.
• Example: (blank)
• Returns: value of authors
• Args: newvalue (optional)

location

• Title: location
• Usage:

$self->location($newval)

• Function: Gives the location line. No attempt is made to parse the location line.
• Example: (blank)
• Returns: value of location
• Args: newvalue (optional)

title

• Title: title
• Usage:

$self->title($newval)

• Function: Gives the title line (if exists)
• Example: (blank)
• Returns: value of title
• Args: newvalue (optional)

medline

• Title: medline
• Usage:

$self->medline($newval)

• Function: Gives the medline number
• Example: (blank)
• Returns: value of medline
• Args: newvalue (optional)

pubmed

• Title: pubmed
• Usage:

$refobj->pubmed($newval)

• Function: Get/Set the PubMed number, if it is different from the MedLine number.
• Example: (blank)
• Returns: value of medline (yes, medline — that's literally what the original says, I'm just the messenger 😭*)*
• Args: newvalue (optional)

database

• Title: database
• Usage: (blank)
• Function: Overrides DBLink database to be hard coded to 'MEDLINE' (or 'PUBMED' if only pubmed id has been supplied), unless the database has been set explicitly before.
• Example: (blank)
• Returns: (blank)
• Args: (blank)

primary_id

• Title: primary_id
• Usage: (blank)
• Function: Overrides DBLink primary_id to provide medline number, or pubmed number if only that has been defined
• Example: (blank)
• Returns: (blank)
• Args: (blank)

optional_id

• Title: optional_id
• Usage: (blank)
• Function: Overrides DBLink optional_id to provide the PubMed number.
• Example: (blank)
• Returns: (blank)
• Args: (blank)

publisher

• Title: publisher
• Usage:

$self->publisher($newval)

• Function: Gives the publisher line. No attempt is made to parse the publisher line.
• Example: (blank)
• Returns: value of publisher
• Args: newvalue (optional)

editors

• Title: editors
• Usage:

$self->editors($newval)

• Function: Gives the editors line. No attempt is made to parse the editors line.
• Example: (blank)
• Returns: value of editors
• Args: newvalue (optional)

encoded_ref

• Title: encoded_ref
• Usage:

$self->encoded_ref($newval)

• Function: Gives the encoded_ref line. No attempt is made to parse the encoded_ref line. (this is added for reading PDB records (REFN record), where this contains ISBN/ISSN/ASTM code)
• Example: (blank)
• Returns: value of encoded_ref
• Args: newvalue (optional)

doi

• Title: doi
• Usage:

$self->doi($newval)

• Function: Gives the DOI (Digital Object Identifier) from the International DOI Foundation (http://www.doi.org/), which can be used to resolve URL links for the full-text documents using:

http://dx.doi.org/<doi>

• Example: (blank)
• Returns: value of doi
• Args: newvalue (optional)

consortium

• Title: consortium
• Usage:

$self->consortium($newval)

• Function: Gives the consortium line. No attempt is made to parse the consortium line.
• Example: (blank)
• Returns: value of consortium
• Args: newvalue (optional)

gb_reference

• Title: gb_reference
• Usage:

$obj->gb_reference($newval)

• Function: Gives the generic GenBank REFERENCE line. This is GenBank-specific. If set, this includes everything on the reference line except the REFERENCE tag and the reference count. This is mainly a fallback for the few instances when REFERENCE lines have unusual additional information such as split sequence locations, feature references, etc. See Bug 2020 in Bugzilla for more information.
• Example: (blank)
• Returns: value of gb_reference (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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okay that's the whole page, you ate that 💅✨

This was the Bio::Annotation::Reference page from the User Contributed Perl Documentation set, and it's tagged perl v5.32.1, dated 2021-08-15. Bye bestie, go cite something responsibly 🦋🎀💖