lsw changes

Revision 1

Mon, 27 Feb 2006 02:40:26 -0000 (alanr)

initial

Revision 2

Mon, 27 Feb 2006 02:58:58 -0000 (alanr)

Revision 3

Mon, 27 Feb 2006 04:05:00 -0000 (alanr)

externals

Revision 4

Mon, 27 Feb 2006 04:50:32 -0000 (alanr)

up to date

Revision 5

Mon, 27 Feb 2006 05:12:31 -0000 (alanr)

manually constructed mapping of compounds

Revision 6

Mon, 27 Feb 2006 05:47:56 -0000 (alanr)

Revision 7

Mon, 27 Feb 2006 06:02:28 -0000 (alanr)

suggest owl-load-combined vs. individual database loads

Revision 8

Wed, 01 Mar 2006 08:36:53 -0000 (alanr)

Basic readme

Revision 9

Wed, 01 Mar 2006 17:08:42 -0000 (alanr)

clean up text a bit.

Revision 10

Wed, 01 Mar 2006 23:21:30 -0000 (alanr)

add instructions on how to download

Revision 11

Thu, 02 Mar 2006 04:00:02 -0000 (alanr)

remove paris attribution

Revision 12

Thu, 02 Mar 2006 05:49:15 -0000 (alanr)

add pointer to rss, test post-commit hook

Revision 13

Fri, 03 Mar 2006 22:46:18 -0000 (jeremy)

Changed iJR904-id to abbreviation instead of simpheny id

Revision 14

Sat, 04 Mar 2006 04:09:13 -0000 (alanr)

Started biopax folder, with demo folder proto. first example about using annotation properties

Revision 15

Sat, 04 Mar 2006 04:17:19 -0000 (alanr)

fix a path

Revision 16

Wed, 08 Mar 2006 23:00:55 -0000 (alanr)

New feature: lisp syntax for owl abstract syntax. See examples in
lisp-syntax.lisp, infinite-people-finite-ssn.lisp,
unfilled-slot-warning.lisp and documentation at top of lisp-syntax.lisp, and uri.lisp

Add a patch directory and a patch so that abcl uses print-object on clos classes.

Little clean up to sparql-stringify so it only includes the reasoning prefix if necessary.

misc other.

Revision 17

Wed, 08 Mar 2006 23:09:43 -0000 (alanr)

an eval-when was missing, and there was a compilation order issue (set-macro-character evaluates function too early)

Revision 18

Thu, 09 Mar 2006 05:27:59 -0000 (alanr)

add "partial", "complete" owl terms and fix owl class definitions to use them, as specified.

add consistent-infinite-infinite ontology, which causes pellet to go
into an infinite loop with latest version. Don't bother updating pellet.jar
until that's fixed.

Revision 19

Fri, 10 Mar 2006 04:43:09 -0000 (alanr)

Modified the startup command to check the java version and complain if it isn't 1.5.
Let someone set ABCL_JAVA to the java to use.

Modified the README to state that java 1.5 is needed.

Make sparql queries understand ! syntax for URIs, and modify existing
queries to do that (but more cleanup work needed for URIs).

Revision 20

Mon, 13 Mar 2006 06:58:21 -0000 (alanr)

owl/lisp-syntax.lisp

"Annotation" is a different term than "annotation". The former is 
for an ontology property and the latter is for an annotation property.
Annotation becomes ontology-property in lisp syntax. Modify define-owl-term 
to handle specifying the lisp syntax explicitly.

Add a few more terms I missed.

****************************************************************
owl/uri.lisp

More work on this. Fix so that unabbreviate-namespace happens at run
time, not read time. Define eval-uri-reader-macro for those situations
where you are reading uris within a quoted form.

****************************************************************
owl/query.lisp

Add :trace keyword, which if passed a string, prints the string, and the 
sparql query. For demos.

****************************************************************
extlib/commons-codec-1.3.jar
extlib/commons-httpclient-3.0.jar
extlib/xmlrpc-2.0.1.jar
server/lsw-server.asd
server/xmlrpc.lisp

Beginnings of an xmlrpc server so we can have perl and other non-lisp
clients. Works, except for exceptions. Not loaded yet.

****************************************************************
start.lisp

Add server to asdf central registry.

****************************************************************
extlib/pellet.jar

new version with infinite chain fixed.

****************************************************************
owl/describe.lisp

Bug fixes. 
 - reversed sense of direct/all for sub/superproperties
 - handle empty range
 - fix inverse property query

****************************************************************
README.txt

add apache license

****************************************************************
trunk/biopax/proto/pathway-participants.lisp

Examples against extension of biopax that makes the following changes:
Define property PARTICIPANTS*
Make PARTICIPANTS, PATHWAY-COMPONENTS, STEP-INTERACTIONS, subproperty of PARTICIPANTS*
Make PARTICIPANTS* transitive.

Enables one to query for pathways that have a protein in some interaction that is part of 
the pathway, and for pathways that a protein participates in .

Revision 21

Sat, 18 Mar 2006 05:36:08 -0000 (mt)

Mike Travers' fix to sparql with negative integer. 
Alan: uri's returned from sparql are now uri structs.
Testing check in with Mike's user and password

Revision 22

Mon, 20 Mar 2006 05:50:11 -0000 (alanr)

In owl/

* lisp-syntax.lisp: 

The ontology name doesn't have to be the same as the base, so 
add an :about keyword and slot. 

Add function (literal value-as-string type) for specifying the type of
a literal. e.g. (literal "foo" !xsd:string)

Keep track of keywords, versus functions, and a couple of lookup tables to
support owl-to-lisp-syntax.lisp

* owl-to-lisp-syntax.lisp

New. (pprint-owl-lisp-syntax  "http://www.biopax.org/release/biopax-level2.owl" 'biopax-level-2)
will print out a form which can be evaluated to and create an instance of owl-ontology bound to 
the variable biopax-level-2

* namespace.lisp

Add reactome: proto: xsd: namespaces.

uri.lisp

Support calling reader macro with first character #\< too.

* describe.lisp

Various cleanups/bug fixes.

(describe !bp2:control) now dispatches to (describe-entity "bp2:control")

* owl.asd

Add owl-to-lisp-syntax.lisp

* query.lisp

Fix :union. Can now write, e.g. 

(sparql 
     '(:select (?mol1) () 
	(:union 
	 ((?mol1 !bug:hasCharge -1))
         ((:union
            ((?mol1 !bug:hasCharge 1))
	    ((?mol1 !bug:hasCharge 0)))))))

* pellet.lisp

Add has-entity? function

* patches/abcl-trace.lisp, patches/patches.asd

New. Fix abcl not adequately protecting *trace-level* from interrupts.

* jss/invoke.lisp

Fix bug in resolving full class name (said it was ambiguous when it wasn't)

Revision 23

Mon, 20 Mar 2006 22:10:28 -0000 (alanr)

fix bug in kb method reported by Jeremy.

Revision 24

Mon, 20 Mar 2006 23:31:39 -0000 (alanr)

New example, from discussion with Andrea. 
fix "value" in abstract syntax

Revision 25

Tue, 21 Mar 2006 05:22:34 -0000 (alanr)

New test/example inconsistencies.lisp

Both property value on an individual and has value constraint in a restriction
are written value(..). Work around this by defining has-value for the latter.
Need to fix owl-to-lisp-syntax.lisp to properly parse this. 

Add with-ontology form for short-lived ontologies that you don't want to set
a global variable to.

Revision 26

Tue, 21 Mar 2006 07:09:01 -0000 (alanr)

* pellet.lisp

define kb-unsatisfiable-classes to return them.
Add !owl:Thing, !owl:Nothing to the list of known classes for a kb

* describe.lisp

Accept a uri as an argument to describe-entity.
If a class is unsatisfiable, then say so when describing.

* lisp-syntax.lisp

Add methods on ontology: 
(consistent ontology) return t if the ontology is consistent
(satisfiable ontology) return t if the ontology is satisfiable
(unsatisfiable-classes ontology) return a list of unsatisfiable classes.
(check ontology) returns t if an ontology is both satisfiable and consistent.

Revision 27

Tue, 21 Mar 2006 07:12:45 -0000 (alanr)

add unsatisfiable example

Revision 28

Tue, 21 Mar 2006 07:53:36 -0000 (alanr)

!owl:Nothing is, by definition, unsatisfiable. When checking if an ontology is
satisfiable, therefore, don't pay attention to it.

Revision 29

Tue, 21 Mar 2006 20:58:33 -0000 (alanr)

Some load dependencies fixed. 
print patch was clobbering sensible error messages in the debugger (abcl bug, methinks). Fixed now.

Revision 30

Wed, 22 Mar 2006 18:23:20 -0000 (jeremy)

Problem set 1. Create an ontology with a transitive slot, an inconsistent ontology, and an unsatisfiable class. In addition, be inconsistent in several ways

Revision 31

Mon, 27 Mar 2006 06:54:54 -0000 (alanr)

:a synonym for !rdf:type, as in (?protein :a !bp2:protein)
Fix filter clause to infix "<" and ">"

Revision 32

Mon, 27 Mar 2006 06:58:37 -0000 (alanr)

Show equivalent classes when describing.

Revision 33

Wed, 29 Mar 2006 19:43:41 -0000 (alanr)

Add blank/non-distinguished variables to sparql.

Use blank node for them. Lisp syntax is [](no space) or :_ (translates to []) 
or :_foo (translates to _:foo). [:p v] syntax not supported yet.

For now, pellet needs these to be named variables with
PelletOptions.TREAT_ALL_VARS_DISTINGUISHED to nil, so I handle this in
the rendering of lisp syntax to string. When pellet uses blank nodes as
non-distinguished queries will stay the same and renderer will change. 

tests/non-distinguished-variable.lisp is an example of how this works.

Also, sparql :trace is a little cleaner, with results printed too.

Revision 34

Thu, 30 Mar 2006 07:00:24 -0000 (alanr)

jss/invoke.lisp: fix but in set-java-field

owl/lisp-syntax.lisp,owl/namespace.lisp,owl/query.lisp : changes to
make abstract syntax and SPARQL queries look nicer by generating
qnames and appropriate PREFIX and Namespace statements. This isn't quite ready
in that it needs to make sure not to generate a qname when the URI has 
characters that are illegal in a qname. (setq *use-qnames* nil) to turn this feature
off (e.g. for debugging the bug work)

Revision 35

Sat, 08 Apr 2006 04:05:44 -0000 (alanr)

Changes to make it run under cygwin

Revision 36

Sat, 08 Apr 2006 13:33:29 -0000 (alanr)

a function needs to create file:// urls, so we can special case cygwin.

Revision 37

Sat, 08 Apr 2006 23:20:39 -0000 (alanr)

Joanne's example

Revision 38

Sun, 09 Apr 2006 00:08:40 -0000 (alanr)

emacs help

Revision 39

Sun, 09 Apr 2006 00:13:24 -0000 (alanr)

Add Joanne's demo to start.lisp, fix a bug in generating sames for debugging the bug