W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > February 2008

partial review of SenseLab doc

From: Eric Prud'hommeaux <eric@w3.org>
Date: Mon, 11 Feb 2008 18:57:59 -0500
To: public-semweb-lifesci@w3.org
Message-ID: <20080211235759.GF16996@w3.org>
I changed some words in the abstract, and a few other places. Also, I
flagged some spans with the ever-popular pink issue class. Take a look,
cast your votes.

Here are the diffs so you can look:
--- Overview.html.~1.63~	2008-02-11 18:46:48.000000000 -0500
+++ Overview.html	2008-02-11 18:25:50.000000000 -0500
@@ -32,6 +32,8 @@
 table.dbsTable { border-collapse: collapse; border-color: #000000; }
 table.dbsTable td:first-child { vertical-align: top; }
 table.dbsTable td { padding: 2px 5px 2px 5px; }
+.at-issue {text-decoration: underline;}
+.issue {background-color: #fcc;}
       /*]]>*/
   </style>
   <!-- link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/TR/Note" / -->
@@ -93,10 +95,10 @@
 <h2 class="notoc" id="abstract">Abstract</h2>
 
 <p>SenseLab is a collection of databases for neuroscientific research. This
-document describes how we converted some of the SenseLab databases to the
-Resource Description Framework (RDF) and the Web Ontology Language (OWL), the
-considerations we made and the advantages and potential disadvantages of the
-conversion to RDF/OWL we identified. We will also try to give suggestions to
+document describes how we represented some of the SenseLab databases in
+Resource Description Framework (RDF) and Web Ontology Language (OWL), 
+and discusses the advantages and disadvantages of
+our mapping. We also give suggestions to
 database administrators who consider doing a conversion to RDF/OWL.</p>
 </div>
 
@@ -161,8 +163,8 @@
 divided into a number of specialised databases, of which we have converted
 three to Semantic Web formats. These databases are NeuronDB, BrainPharm and
 ModelDB. NeuronDB contains descriptions of anatomic locations, cell
-architecture and physiologic parameters of neuronal cells based on
-compartmental models of neurons. The pilot BrainPharm database is intended to
+architecture and physiologic parameters of neuronal cells<span class="at-issue"> based on
+compartmental models of neurons</span><span class="issue"> Unclear if one or all three are based on a compartmental model. Can we strike this?</span>. The pilot BrainPharm database is intended to
 support research on drugs for the treatment of neurological disorders. It
 enhances the descriptions in a portion of NeuronDB with descriptions of the
 actions of pathological and pharmacological agents. ModelDB is a large
@@ -176,7 +178,7 @@
 <p>The databases are based on the "entity-attribute-value with classes and
 relationships" (EAV/CR) schema [<a href="#ref-EAV-CR">EAV-CR</a>]. The data
 can also be downloaded from the SenseLab Semantic Web developments portal [<a
-href="#ref-SENSELAB-SW">SENSELAB-SW</a>] as a database dump in MDB format and
+href="#ref-SENSELAB-SW">SENSELAB-SW</a>] as a database dump in MDB<span class="issue"> [as in <a href="http://mdbtools.sourceforge.net/">MDB Tools</a>?]</span> format and
 as text.</p>
 
 <h3 id="first">Initial RDF and OWL conversions</h3>
@@ -193,20 +195,20 @@
 
 <h4 id="Process">Process</h4>
 
-<p>We developed a converter application in Java that by queried the SenseLab
+<p>We developed a converter application in Java that queried the SenseLab
 database and wrote RDF/XML files. The conversion was fully automatic for the
 RDF version, but required some manual editing for the OWL version.</p>
 
 <h4 id="Outcome">Outcome </h4>
 
-<p>These conversions reflected a lot of the local database structure, which
+<p>These conversions were too tied to the original database structure, which
 resulted in inconsistent OWL ontologies. Some shortcomings of the first
 conversion to OWL were: </p>
 <ul>
-  <li>'Part of' relations were wrongly represented as subclass relations.
+  <li>'Part of' relations were incorrectly represented as subclass relations.
     This seems to be one of the most common mistakes in ontology development
     in general. </li>
-  <li>Class disjoints were missing which made it hard to find inconsistencies
+  <li>Class disjoints<a id="disjoint-ref" href="#disjoint">¹</a> were missing which made it hard to find inconsistencies
     and data entry errors. </li>
   <li>After disjoints were introduced, we found some previously unidentified
     inconsistencies with the help of OWL reasoners: some classes (e.g.
@@ -223,13 +225,15 @@
     was the label of the "distal part of the dendrite". </li>
 </ul>
 
+  <p id="disjoint"><a href="#disjoin-ref">¹</a> Disjoint classes are used in OWL to assert that they have no members in common. Inferences from this can be used to flag an inconsistent models.</a>
+
 <h3 id="revised">Revised OWL conversions</h3>
 
 <p>The revised OWL conversion was based on the first OWL conversions. The
-design of the SenseLab ontologies was oriented on the view of ontological
-realism [<a href="#ref-SMITH-2004">SMITH-2004</a>]. This means that the
+design of the SenseLab ontologies follows the "ontological
+realism" approach [<a href="#ref-SMITH-2004">SMITH-2004</a>]. This means that the
 ontologies are focused on direct representations of physical objects and
-processes (e.g., neuronal cells, ionic currents) in reality, and not on their
+processes (e.g., neuronal cells, ionic currents), and not on their
 abstractions (e.g., concepts or database entries). </p>
 
 <h4 id="Motivation1">Motivation</h4>
@@ -261,7 +265,7 @@
 </ul>
 
 <p>Based on this manually created basic ontology, the data from the SenseLab
-databases were then automatically converted to OWL using programs written in
+databases <span class="at-issue">were</span><span class="issue"> while technically correct, there are five people in the world who remember that "data" is a plural 3rd declension neuter noun. Six now.</span> then automatically converted to OWL using programs written in
 Java and Python. The automated export scripts extended the manually created
 basic ontology through the creation of subclasses, OWL property restrictions
 and individuals. The resulting ontologies show no clearly distinguishable

-- 
-eric

office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
mobile: +1.617.599.3509

(eric@w3.org)
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Received on Monday, 11 February 2008 23:58:10 GMT

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