Changes between Initial Version and Version 1 of TermServer


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Timestamp:
05/08/06 13:34:25 (12 years ago)
Author:
trac
Comment:

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  • TermServer

    v1 v1  
     1The FMS TermServer is a interface to the FMA written in lisp.  
     2There are two versions, a very old one written in perl and a newer 
     3one written in Java by Peter Mork that works with OQAFMA. 
     4Both are in CVS (the `perl` and `java` directories, the rest 
     5is OQAFMA itself and an ancient `kbd`) at  
     6http://sig.biostr.washington.edu/viewcvs/viewcvs.cgi/src/symkb/server/ 
     7 
     8== New java FMS == 
     9 
     10Same lisp API as old FMS, just talks to current FMA via OQAFMA. 
     11An example query is: 
     12{{{ 
     13(fms-get-children "Heart" "lymphatic drainage") 
     14}}} 
     15 
     16So an entire example session might be: 
     17{{{ 
     18tricycle:~>telnet quad.biostr.washington.edu 8098 
     19> Trying 128.95.228.16... 
     20> Connected to 128.95.228.16 (128.95.228.16). 
     21> Escape character is '^]'. 
     22> connected 
     23> 3 
     24> (fms-get-children "Heart" "lymphatic drainage") 
     25> received 
     26> 4 
     27> ( "Left cardiac tributary of tracheobronchial lymphatic tree"  "Right 
     28> cardiac tributary of brachiocephalic lymphatic tree" ) 
     29> 3 
     30> (fms-get-ancestors "Left cardiac tributary of tracheobronchial lymphatic 
     31> tree" "tributary") 
     32> received 
     33> 4 
     34> () 
     35> 3 
     36> (quit) 
     37}}} 
     38 
     39 
     40== Old perl FMS == 
     41 
     42The old currently lives at `tela:/usr/local/lib/ts/` and needs 
     43`/var/run/fm/` to exist for PIDs and maybe logs in debug mode. 
     44It uses the `fm_master` mysql database, a pre-Protege copy of the FMA. 
     45The Dynamic SceneGenerator uses the old FMS. 
     46 
     47To get it running on sphenoid, I did this: 
     48{{{ 
     49cp -a /usr/local/data/i386-linux/lib/ts/ /usr/local/lib 
     50mkdir /var/run/fm 
     51wget http://dag.wieers.com/packages/perl-IO-stringy/perl-IO-stringy-2.109-1.2.el4.rf.noarch.rpm 
     52wget http://dag.wieers.com/packages/perl-IO-Tty/perl-IO-Tty-1.02-1.2.el4.rf.i386.rpm 
     53rpm -Uhv perl-IO*rpm 
     54}}} 
     55After importing the database and lightly editing a couple of files, it worked.