Ontology Term Annotation

Phenex is an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves... Platforms: Windows

GO::Model::Term is a term or concept in an ontology. SYNOPSIS # From a file use GO::Parser; my $parser = new GO::Parser({handler=>obj}); # create parser object $parser->parse("gene_ontology.obo"); # parse file -> objects my $graph = $parser->handler->graph; # get L object my $term =... Platforms: *nix

Bio::Ontology::Ontology is a standard implementation of an Ontology. SYNOPSIS use Bio::Ontology::Ontology; # create ontology object my $ont = Bio::Ontology::Ontology->new(-name => "OBF"); # add terms, relationships ... my $bp = Bio::Ontology::Term->new(-name => "Bioperl"); my $obf =... Platforms: *nix

GO::View is a Perl module that creates a gif or png image for visualizing the GO DAG. This perl module generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the GO::TermFinder perl module created by the Stanford... Platforms: *nix

Bio::Ontology::GOterm is a representation of GO terms. SYNOPSIS $term = Bio::Ontology::GOterm->new ( -go_id => "GO:0016847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); $term->add_definition_references(... Platforms: *nix

Term::VT102 is a class to emulate a DEC VT102 terminal. SYNOPSIS use Term::VT102; my $vt = Term::VT102->new (cols => 80, rows => 24); while (<>) { $vt->process ($_); } The VT102 class provides emulation of most of the functions of a DEC VT102 terminal. Once initialised, data passed to a... Platforms: *nix

Term::ANSIScreen is a Perl module for terminal control using ANSI escape sequences. SYNOPSIS # qw/:color/ is exported by default, i.e. color() & colored() use Term::ANSIScreen qw/:color :cursor :screen :keyboard/; print setmode(1), setkey(a,b); print "40x25 mode now, with a mapped to... Platforms: *nix

Bio::Ontology::Relationship is a relationship for an ontology. SYNOPSIS $rel = Bio::Ontology::Relationship->new( -identifier => "16847", -subject_term => $subj, -object_term => $obj, -predicate_term => $pred ); This is a basic implementation of Bio::Ontology::RelationshipI. The... Platforms: *nix

dtRdr::Annotation::IO::YAML is a Perl module to read/write annotations from/to yml files. Methods init $io->init; items_for Return the hashrefs for a given book. @items = $io->items_for($book); insert $io->insert($object, %args); delete $io->delete($object, %args); update... Platforms: *nix

Term::ReadLine::Gnu is a Perl extension for the GNU Readline/History Library. SYNOPSIS use Term::ReadLine; $term = new Term::ReadLine ProgramName; while ( defined ($_ = $term->readline(prompt>)) ) { ... } This is an implementation of Term::ReadLine using the GNU Readline/History... Platforms: *nix

Term::GnuplotTerminals is a Perl documentation of gnuplot output devices. aed767 The aed512 and aed767 terminal drivers support AED graphics terminals. The two drivers differ only in their horizontal ranges, which are 512 and 768 pixels, respectively. Their vertical range is 575 pixels. There... Platforms: *nix

Term::ANSIMenu is an infrastructure for creating menus in ANSI capable terminals. SYNOPSIS use Term::ANSIMenu; my $menu = Term::ANSIMenu->new( width => 40, help => [[, &standard_help], [hint 1, &help_item], [ undef, &standard_help], [hint 3, undef] ], title => title, items => [[1,... Platforms: *nix

Term::Animation is a Perl module that provides a framework to produce sprite animations using ASCII art. Each ASCII sprite is given one or more frames, and placed into the animation as an animation entity. An animation entity can have a callback routine that controls the position and frame of... Platforms: *nix

Term::Prompt is a Perl extension for prompting a user for information. SYNOPSIS use Term::Prompt; $value = &prompt(...); use Term::Prompt qw(termwrap); print &termwrap(...); $Term::Prompt::MULTILINE_INDENT = ; PREREQUISITES You must have Text::Wrap and Term::ReadKey available on... Platforms: *nix

Term::Shell is a simple command-line shell framework. SYNOPSIS package MyShell; use base qw(Term::Shell); sub run_command1 { print "command 1!n"; } sub smry_command1 { "what does command1 do?" } sub help_command1 { < Platforms: *nix

OntologyEngineI is a Perl interface a minimal Ontology implementation should satisfy. This describes the minimal interface an ontology query engine should provide. It intentionally doesnt make explicit references to the ontology being a DAG, nor does it mandate that the ontology be a... Platforms: *nix

Term::TtyRec::Player is a Perl module that playbacks ttyrec data. SYNOPSIS use Term::TtyRec::Player; use FileHandle; # $handle is any IO::* object my $handle = FileHandle->new(file.tty); my $player = Term::TtyRec::Player->new($handle); # options can be set as hashref my $player =... Platforms: *nix

Term::ShellUI is a fully-featured shell-like command line environment. SYNOPSIS use Term::ShellUI; my $term = new Term::ShellUI( commands => { "cd" => { desc => "Change to directory DIR", maxargs => 1, args => sub { shift->complete_onlydirs(@_); }, proc => sub { chdir($_[0] ||... Platforms: *nix

Term::GDBUI is a fully-featured shell-like command line environment. SYNOPSIS use Term::GDBUI; my $term = new Term::GDBUI(commands => get_commands()); # (see below for the code to get_commands) $term->run(); Term::GDBUI uses the history and autocompletion features of Term::ReadLine to... Platforms: *nix

Term::TtyRec::Plus is a Perl module to read a ttyrec. SYNOPSIS Term::TtyRec::Plus is a module that lets you read ttyrec files. The related module, Term::TtyRec is designed more for simple interactions. Term::TtyRec::Plus gives you more information and, using a callback, lets you munge the... Platforms: *nix