[bioontology-support] Some Questions Related to RadLex 3.3.3

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[bioontology-support] Some Questions Related to RadLex 3.3.3

Nadin Kökciyan-2
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 <[hidden email]>
Date: 23 March 2011 00:24
Subject: Some Questions Related to RadLex 3.3.3
To: [hidden email]


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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Re: [bioontology-support] Some Questions Related to RadLex 3.3.3

Ray Fergerson

Nadin,

 

The same error in BioPortal that prevents visualization of some properties for RadLex is the one that is preventing the related classes from being linked. When we fix the underlying problem this should all work.

 

We are not “working” on RadLex. We simply display whatever ontologies people have loaded into BioPortal. I cannot comment about other versions of RadLex which are available on the web and why they do not show all of the relations. We are not directly involved in the development or distribution of this ontology and cannot answer questions specific to it.

 

Ray

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Nadin Kökciyan
Sent: Thursday, April 21, 2011 12:35 PM
To: [hidden email]
Subject: [bioontology-support] Some Questions Related to RadLex 3.3.3

 

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 <[hidden email]>
Date: 23 March 2011 00:24
Subject: Some Questions Related to RadLex 3.3.3
To: [hidden email]

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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