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[bioontology-support] Some Questions Related to RadLex 3.3.3

Nadin Kökciyan nadin.kokciyan at boun.edu.tr
Thu Apr 21 12:35:06 PDT 2011


Dear Sir/Madam,

I sent an email a while ago to RSNA support team, but I have still no
answers from them.. As we still continue to explore RadLex, we realized that
there are two different versions to explore RadLex on web. First one is
provided by you, which contains all information related to the ontology.
Second is provided by radlex,org site, where we can access only "is a"
relations between concepts, which offers very restricted information about
the ontology. Are teams working on RadLex different?

And we have one suggestion. It is great to see on web all relationships
described in RadLex ontology, we think that it could be a good idea to have
property values clickable. Let's take an example: liver. When browsing
RadLex, we see that liver "has regional part" 'right lobe of liver'. But we
are not able to click on 'right lobe of liver', because its a text only area
and not a link. It is not user friendly to copy this text, type in search
box and search again.

Our other questions are listed below(see forwarded mail), we will be happy
if we can have feedback from you, or anyone working on RadLex. Note that our
project team's focus is on "liver" related concepts.

Best regards,
Nadin Kökciyan


---------- Forwarded message ----------
From: Nadin Kökciyan <nadin.kokciyan at boun.edu.tr>
Date: 23 March 2011 00:24
Subject: Some Questions Related to RadLex 3.3.3
To: radlexfeedback at rsna.org


Dear Sir/Madam,

My name is Nadin Kökciyan. I'm a MS student at Computer Engineering
Department in Bogazici University, Istanbul/Turkey. We are currently working
on development of an ontology related to liver and liver diseases. On the
other hand, there is another team working on image processing of liver
cases. Our aim is to find similar cases given a specific case of a liver
patient; thus, this system will optimize results among hundreds of records
and help doctors to make a decision about a specific case.

We are happy to see all development related to RadLex. We are using the term
browser online, also exploring RadLex as a Protege project, and sometimes
using the visual editor to see hierarchies between concepts. We have some
questions that we want to ask, and we will be happy if you ever can find
some time to answer them.

1. Online term browser allows us to see only one relation: "is-a" relation.
Is that intentional? In Protege, we can see that there are different
relations defined such as "has Part", "has regional part" etc.
2. We have difficulties to browse RadLex in Protege. All class names are
beginning with "RID" and it is difficult to have some idea about a concept
by only looking at this id information. Is there a way to replace "RID"
names with "Preffered name" property of a class? Same as we see in online
term browser.
3. As our aim is to build an ontology, and cover RadLex liver related terms,
our focus is on all relationships. As we examine the ontology, we had
difficulties to understand some parts of it. Let me give an example.
*RID58(liver)
has Part RID74 and RID69*. But we realized that duplicated values are
present in that part. For "has Part" relation, RID74 and RID69 classes are
added twice. Or another example that we came up with is, *RID69 part of
RID58*. Again we have duplicated values, RID58 is added twice for this
relation. Is that intentional?
4. In "lobe of liver" class, we can see that "quadrate lobe" is a subtype.
Then, we have two subclasses for "lobe of liver": "right lobe of liver" and
"left lobe of liver". But then, we realize that, quadrate lobe is part of
"left lobe of liver". If this is the case,  the information "quadrate lobe"
defined as a subtype in superclass "lobe of liver" is not correct, since
quadrate lobe is not a subtype for "right lobe of liver" but only for "left
lobe of liver". It seemed a little bit ambigious, right?
5. Is(are) there any application(s) using RadLex? We really want to check
them out and see how RadLex is used.
6. Finally, we have some difficulties to understand the nature of properties
defined within the ontology such as "has subtype", "has regional part" etc.
Is there any manual, or technical report where we can find information about
the nature of these relationships?

As a conclusion, we want to use RadLex in our project, and we really try to
understand it. We appreciate your help, thanks in advance.

Best regards,
Nadin Kökciyan
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