A couple of tips for you writing parsers.
1.
Hypertext links are usually added into documents by writing a $href into
srsdb.i file and invoked from icarus productions using the $Rep
function. Instead of writing a new $href for every a new database link
and cluttering the srsdb.i file, you could use a generic one which is
already defined (in v. 5.1.0.):
$href:[entryR link:"<A HREF=wgetz?-e+[%s-%s:%s]>%s</A>"]
and call that from SRS e.g.
h_pt: ~ {$In:[fields c:pt t:html]}
'PT' (word {$Rep:{$ParStr:entryR 'rebase' 'id' $Ct $Ct}}
|noword)* ~
to parse line like
PT HindIII
2.
Whenever you have a literature reference containing the name or
standardized abbreviation of the journal, volume and first page of the
article, you can create a link PubMed using a predefined link.
$href:[pubmedR link: |<A
HREF="http://www.ncbi.nlm.nih.gov/htbin-post/\
|PubMed/wgetcit?display=abstract&journal=%s&\
|volume=%s&page=%s">%s</A>\
]
h_ref: ~ {$In:[fields c:rl t:html] $Out }
# journal vol first page
/..[ ]+/ (/([^0-9]+)([0-9]+): ?([0-9]+)[^\n]+/
{$j=$StrRep:[$1 from:'.' to:'+']
$j=$StrRep:[$j from:'&' to:'']
$j=$StrRep:[$j from:' ' to:'+']
$j=$StrRep:[$j from:'++' to:'+']
$j=$Trim:[$j skip:'+']
$Rep:{$ParStr:pubmedR $j $2 $3 $Ct}} |/./)*
~
to add hypertext link to a line like:
RL J. Mol. Biol. 132:133-139(1979).
More information and other options of the NCBI Citation Matcher page at
http://www.ncbi.nlm.nih.gov/PubMed/citmatch.html
Have fun,
-Heikki
--
______ _/ _/_____________________________________________________
_/ _/ http://www2.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho heikki at ebi.ac.uk
_/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
_/ _/ _/ Wellcome Trust Genome Campus, Hinxton
_/ _/ _/ Cambs. CB10 1SD, United Kingdom
_/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________
