AIIA-GMT
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AIIA-GMT version 0.01
=====================
AIIA::GMT is a XML-RPC client of a web-service server, AIIA gene mention tagger, which provides the service to recognize named entities in the biomedical articles.
AIIA gene mention tagger, developed by Adaptive Internet Intelligent Agents Lab, Institute of Information Science, Academia Sinica, Taiwan and I-Fang Chung's Lab, Institute of Bioinformatics, National Yang-Ming University, Taiwan, is a named entity r...
This module is developed to help those who want to use this remote service with XML-RPC, rather than with its web interface. Finally, this module and service is released under a GPLv3 License. You're free to use it for both academic or personal use.
INSTALLATION
To install this module type the following:
perl Makefile.PL
make
make test
lib/AIIA/GMT.pm view on Meta::CPAN
use AIIA::GMT;
$result = &text2entity('less than 3000 words');
print Dump $result;
=head1 DESCRIPTION
AIIA::GMT is a XML-RPC client of a web-service server, AIIA gene mention tagger, which provides the service to recognize named entities in the biomedical articles.
AIIA gene mention tagger, developed by Adaptive Internet Intelligent Agents Lab, Institute of Information Science, Academia Sinica, Taiwan and I-Fang Chung's Lab, Institute of Bioinformatics, National Yang-Ming University, Taiwan, is a named entity r...
This module is developed to help those who want to use this remote service with XML-RPC, rather than with its web interface. Finally, this module and service is released under a GPLv3 License. You're free to use it for both academic or personal use.
=head1 METHODS
=over 4
=item text2entity('less than 3000 words');
Return a ARRAY reference which contains all of the entities recognized from your input with its position information, for example: '20 seperated-by-tab human protein-tyrosine-phosphatase'.
For a global function, use:
#define NEED_function_GLOBAL
Note that you mustn't have more than one global request for one
function in your project.
Function Static Request Global Request
-----------------------------------------------------------------------------------------
eval_pv() NEED_eval_pv NEED_eval_pv_GLOBAL
grok_bin() NEED_grok_bin NEED_grok_bin_GLOBAL
grok_hex() NEED_grok_hex NEED_grok_hex_GLOBAL
grok_number() NEED_grok_number NEED_grok_number_GLOBAL
grok_numeric_radix() NEED_grok_numeric_radix NEED_grok_numeric_radix_GLOBAL
grok_oct() NEED_grok_oct NEED_grok_oct_GLOBAL
newCONSTSUB() NEED_newCONSTSUB NEED_newCONSTSUB_GLOBAL
newRV_noinc() NEED_newRV_noinc NEED_newRV_noinc_GLOBAL
sv_2pv_nolen() NEED_sv_2pv_nolen NEED_sv_2pv_nolen_GLOBAL
sv_2pvbyte() NEED_sv_2pvbyte NEED_sv_2pvbyte_GLOBAL
sv_catpvf_mg() NEED_sv_catpvf_mg NEED_sv_catpvf_mg_GLOBAL
hints => 1,
changes => 1,
cplusplus => 0,
filter => 1,
);
my($ppport) = $0 =~ /([\w.]+)$/;
my $LF = '(?:\r\n|[\r\n])'; # line feed
my $HS = "[ \t]"; # horizontal whitespace
eval {
require Getopt::Long;
Getopt::Long::GetOptions(\%opt, qw(
help quiet diag! filter! hints! changes! cplusplus
patch=s copy=s diff=s compat-version=s
list-provided list-unsupported api-info=s
)) or usage();
};
if ($@ and grep /^-/, @ARGV) {
usage() if "@ARGV" =~ /^--?h(?:elp)?$/;
die "Getopt::Long not found. Please don't use any options.\n";
}
usage() if $opt{help};
if (exists $opt{'compat-version'}) {
my($r,$v,$s) = eval { parse_version($opt{'compat-version'}) };
if ($@) {
die "Invalid version number format: '$opt{'compat-version'}'\n";
}
die "Only Perl 5 is supported\n" if $r != 5;
die "Invalid version number: $opt{'compat-version'}\n" if $v >= 1000 || $s >= 1000;
$opt{'compat-version'} = sprintf "%d.%03d%03d", $r, $v, $s;
}
else {
$opt{'compat-version'} = 5;
}
check_uni|||
checkcomma|||
checkposixcc|||
ck_anoncode|||
ck_bitop|||
ck_concat|||
ck_defined|||
ck_delete|||
ck_die|||
ck_eof|||
ck_eval|||
ck_exec|||
ck_exists|||
ck_exit|||
ck_ftst|||
ck_fun|||
ck_glob|||
ck_grep|||
ck_index|||
ck_join|||
ck_lengthconst|||
do_trans_count_utf8|||
do_trans_count|||
do_trans_simple_utf8|||
do_trans_simple|||
do_trans|||
do_vecget|||
do_vecset|||
do_vop|||
docatch_body|||
docatch|||
doeval|||
dofile|||
dofindlabel|||
doform|||
doing_taint||5.008001|n
dooneliner|||
doopen_pm|||
doparseform|||
dopoptoeval|||
dopoptolabel|||
dopoptoloop|||
dopoptosub_at|||
dopoptosub|||
dounwind|||
dowantarray|||
dump_all||5.006000|
dump_eval||5.006000|
dump_fds|||
dump_form||5.006000|
dump_indent||5.006000|v
dump_mstats|||
dump_packsubs||5.006000|
dump_sub||5.006000|
dump_vindent||5.006000|
dumpuntil|||
dup_attrlist|||
emulate_eaccess|||
eval_pv|5.006000||p
eval_sv|5.006000||p
expect_number|||
fbm_compile||5.005000|
fbm_instr||5.005000|
fd_on_nosuid_fs|||
filter_add|||
filter_del|||
filter_gets|||
filter_read|||
find_beginning|||
find_byclass|||
my @files;
my @srcext = qw( xs c h cc cpp );
my $srcext = join '|', @srcext;
if (@ARGV) {
my %seen;
@files = grep { -f && !exists $seen{$_} } map { glob $_ } @ARGV;
}
else {
eval {
require File::Find;
File::Find::find(sub {
$File::Find::name =~ /\.($srcext)$/i
and push @files, $File::Find::name;
}, '.');
};
if ($@) {
@files = map { glob "*.$_" } @srcext;
}
}
}
else {
error("Cannot open '$tmp' for writing: $!");
}
return undef;
}
sub can_use
{
eval "use @_;";
return $@ eq '';
}
sub rec_depend
{
my $func = shift;
my %seen;
return () unless exists $depends{$func};
grep !$seen{$_}++, map { ($_, rec_depend($_)) } @{$depends{$func}};
}
# define call_pv perl_call_pv
#endif
#ifndef call_argv
# define call_argv perl_call_argv
#endif
#ifndef call_method
# define call_method perl_call_method
#endif
#ifndef eval_sv
# define eval_sv perl_eval_sv
#endif
/* Replace: 0 */
/* Replace perl_eval_pv with eval_pv */
/* eval_pv depends on eval_sv */
#ifndef eval_pv
#if defined(NEED_eval_pv)
static SV* DPPP_(my_eval_pv)(char *p, I32 croak_on_error);
static
#else
extern SV* DPPP_(my_eval_pv)(char *p, I32 croak_on_error);
#endif
#ifdef eval_pv
# undef eval_pv
#endif
#define eval_pv(a,b) DPPP_(my_eval_pv)(aTHX_ a,b)
#define Perl_eval_pv DPPP_(my_eval_pv)
#if defined(NEED_eval_pv) || defined(NEED_eval_pv_GLOBAL)
SV*
DPPP_(my_eval_pv)(char *p, I32 croak_on_error)
{
dSP;
SV* sv = newSVpv(p, 0);
PUSHMARK(sp);
eval_sv(sv, G_SCALAR);
SvREFCNT_dec(sv);
SPAGAIN;
sv = POPs;
PUTBACK;
if (croak_on_error && SvTRUE(GvSV(errgv)))
croak(SvPVx(GvSV(errgv), na));
return sv;
( run in 1.965 second using v1.01-cache-2.11-cpan-98e64b0badf )