From phamhha at gmail.com Mon Jun 20 03:26:12 2011 From: phamhha at gmail.com (Ha Pham) Date: Mon, 20 Jun 2011 00:26:12 -0700 Subject: [Kim-discussion] KIM server version 3.0-RC4 missing components? Message-ID: Hi All, I'm evaluating KIM and the only version I can download is 3.0RC4. Once downloaded and extracted, I run into a couple of issues: - the doc/html-documentation is completely empty. Is this the intended behaviour? - The doc/quick-start-guide/KIM_Getting_Started_Guide.pdf mention that there exist a folder call /sesame, which I also don't find in the unzipped package - When i follow the LatestNews_UI_Guide.pdf, there are a couple of places where results won't get shown, and there are error related to sesame. - There seems to be no documentation about how to programmatically interact with KIM. So I'd like to ask for some clarification on the above, and if possible, let me know where to download the package that's more complete or in sync with the documentation. Thanks & best regards, Ha. -------------- next part -------------- An HTML attachment was scrubbed... URL: From philip.alexiev at ontotext.com Mon Jun 20 04:28:05 2011 From: philip.alexiev at ontotext.com (Philip Alexiev @ Ontotext) Date: Mon, 20 Jun 2011 11:28:05 +0300 Subject: [Kim-discussion] KIM server version 3.0-RC4 missing components? In-Reply-To: References: Message-ID: Hi Pham, You can find the latest KIM documentation on the official web site: http://www.ontotext.com/kim . It includes the quick start guide and the system documentation. There you can get familiar with the interfaces to communicate with the KIM server and you can look at some examples how to do that. Please have in mind that the purpose of the Latest News server is not to provide a service, but rather to be used for demo purposes. The server is updated periodically and some of the examples may not be functional. You can use your own scenarios, according to the documents currently available there. Hope this helps. Philip Alexiev Software Engineer, KIM team On 20 Jun 2011, at 10:26 AM, Ha Pham wrote: > > Hi All, > > I'm evaluating KIM and the only version I can download is 3.0RC4. Once downloaded and extracted, I run into a couple of issues: > > - the doc/html-documentation is completely empty. Is this the intended behaviour? > - The doc/quick-start-guide/KIM_Getting_Started_Guide.pdf mention that there exist a folder call /sesame, which I also don't find in the unzipped package > - When i follow the LatestNews_UI_Guide.pdf, there are a couple of places where results won't get shown, and there are error related to sesame. > - There seems to be no documentation about how to programmatically interact with KIM. > > So I'd like to ask for some clarification on the above, and if possible, let me know where to download the package that's more complete or in sync with the documentation. > > Thanks & best regards, > Ha. > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion -------------- next part -------------- An HTML attachment was scrubbed... URL: From phamhha at gmail.com Mon Jun 20 11:55:35 2011 From: phamhha at gmail.com (Ha Pham) Date: Mon, 20 Jun 2011 08:55:35 -0700 Subject: [Kim-discussion] KIM server version 3.0-RC4 missing components? In-Reply-To: References: Message-ID: Hi Philip, Thanks for your email. Can you give me some pointer on how to programmatically interact with KIM, e.g. submit search queries from external system. thanks Ha. On Mon, Jun 20, 2011 at 1:28 AM, Philip Alexiev @ Ontotext < philip.alexiev at ontotext.com> wrote: > Hi Pham, > > You can find the latest KIM documentation on the official web site: > http://www.ontotext.com/kim . It includes the quick start guide and the > system documentation. There you can get familiar with the interfaces to > communicate with the KIM server and you can look at some examples how to do > that. > > Please have in mind that the purpose of the Latest News server is not to > provide a service, but rather to be used for demo purposes. The server is > updated periodically and some of the examples may not be functional. You > can use your own scenarios, according to the documents currently available > there. > > Hope this helps. > Philip Alexiev > Software Engineer, KIM team > > On 20 Jun 2011, at 10:26 AM, Ha Pham wrote: > > > Hi All, > > I'm evaluating KIM and the only version I can download is 3.0RC4. Once > downloaded and extracted, I run into a couple of issues: > > - the doc/html-documentation is completely empty. Is this the intended > behaviour? > - The doc/quick-start-guide/KIM_Getting_Started_Guide.pdf mention that > there exist a folder call /sesame, which I also don't find in the unzipped > package > - When i follow the LatestNews_UI_Guide.pdf, there are a couple of places > where results won't get shown, and there are error related to sesame. > - There seems to be no documentation about how to programmatically interact > with KIM. > > So I'd like to ask for some clarification on the above, and if possible, > let me know where to download the package that's more complete or in sync > with the documentation. > > Thanks & best regards, > Ha. > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From philip.alexiev at ontotext.com Tue Jun 21 04:11:12 2011 From: philip.alexiev at ontotext.com (Philip Alexiev @ Ontotext) Date: Tue, 21 Jun 2011 11:11:12 +0300 Subject: [Kim-discussion] KIM server version 3.0-RC4 missing components? In-Reply-To: References: Message-ID: Hi Ha On the bottom of the official page of the KIM project, you will find links to the documentation. Most particularly, you can download and examine the system documentation, where you will find descriptions and examples how to interact with the server using RMI and web services. hth philip On 20 Jun 2011, at 6:55 PM, Ha Pham wrote: > Thanks for your email. Can you give me some pointer on how to programmatically interact with KIM, e.g. submit search queries from external system. > From sreckojoksimovic at gmail.com Wed Jun 22 10:39:11 2011 From: sreckojoksimovic at gmail.com (Srecko Joksimovic) Date: Wed, 22 Jun 2011 16:39:11 +0200 Subject: [Kim-discussion] Extend proton ontology Message-ID: <001901cc30ea$27e60bd0$77b22370$@com> Hello everyone! I have extended Proton ontology, and created acm_proton.ttl file. This file contains my Concepts. When I annotate document, I want to see only these Concepts. I saw tutorial, I have read few posts, but I could not find the solution. I have edited kim/config/owlim.ttl file, and added new line in import section. And I also added new namespace. But when I run annotator, I do not see my Concepts. Please, I need quick help on this one. Best, - Lucky -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreckojoksimovic at gmail.com Wed Jun 22 11:29:53 2011 From: sreckojoksimovic at gmail.com (srecko joksimovic) Date: Wed, 22 Jun 2011 17:29:53 +0200 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> Message-ID: Hello Philip, I think that I could send you a part of this file. This is what I have defined: a protont:Topic ; protons:generatedBy ; protons:hasMainAlias < http://www.lornet.org/acm-ccs/proton#Alias_756db3b5-b66b-41fe-a82e-1012f18a6672> . < http://www.lornet.org/acm-ccs/proton#Alias_877dc2e2-c7cf-4188-a523-6ee9b7cbdd24 > a protons:Alias ; "Optimization at en" . < http://www.lornet.org/acm-ccs/proton#Alias_62107227-8c21-4ed8-99e0-bb2e4e1cb810 > a protons:Alias ; "Assistive Technologies For Persons With Disabilities at en" . a protont:Topic ; protons:generatedBy ; protons:hasMainAlias < http://www.lornet.org/acm-ccs/proton#Alias_ff0e0512-f2e8-4b14-9a37-71a675dcd2eb> . and many others... Could you please tell me what to do next? Best, Srecko On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext < philip.alexiev at gmail.com> wrote: > Hello Srecko, > > The steps are described in this guide: > http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . > > Depending on the specifics of your ontology, you could map it to proton or > not. If you can create a complete mapping to the proton classes, then > recognizing the new concepts in the texts will be a little easier. You just > need to create a statement for each new concept that it is generated by a > trusted source and also point its labels. > > If you decide not to map to proton, then some additional steps are required > . Create a new gazetteer with the query to get your concepts and their type > and label. Then use a Jape Transducer and create your custom jape rules to > convert the resulting Lookup annotations to some of the annotation types in > KIM's whitelist. This is also described in the guide. > > Hope this helps. > philip > > > On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote: > > Hello everyone!**** > ** ** > I have extended Proton ontology, and created acm_proton.ttl file. This file > contains my Concepts. When I annotate document, I want to see only these > Concepts.**** > I saw tutorial, I have read few posts, but I could not find the solution. I > have edited kim/config/owlim.ttl file, and added new line in import section. > And I also added new namespace. But when I run annotator, I do not see my > Concepts.**** > ** ** > Please, I need quick help on this one.**** > ** ** > Best,**** > - Lucky**** > ** ** > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From philip.alexiev at ontotext.com Wed Jun 22 11:44:12 2011 From: philip.alexiev at ontotext.com (Philip Alexiev @ Ontotext) Date: Wed, 22 Jun 2011 18:44:12 +0300 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> Message-ID: <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> Hi, 1. First make sure is declared as trusted. This is a statement from KIM's knowledge base: . You can either use some of the existing trusted sources, or declare yours as trusted. 2. Then create a jape rule to match the Lookup annotations with class feature "http://proton.semanticweb.org/2006/05/protont#Topic" and to create a Topic annotation. 3. Ad the Topic annotation type to the whitelist of annotations of KIM in KIM/config/nerc.properties in feature com.ontotext.kim.KIMConstants.IE_ANN_TYPES . 4. Delete the cache by removing the KIM/context/default/populated folder and start KIM again. You can start it with the Gate interface to check if your annotations are created. To do that run KIM/bin/kim gate . Hope this helps Philip On 22 Jun 2011, at 6:29 PM, srecko joksimovic wrote: > Hello Philip, > > I think that I could send you a part of this file. This is what I have defined: > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > > a protons:Alias ; > > "Optimization at en" . > > > a protons:Alias ; > > "Assistive Technologies For Persons With Disabilities at en" . > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > > and many others... Could you please tell me what to do next? > > Best, > Srecko > > On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext wrote: > Hello Srecko, > > The steps are described in this guide: > http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . > > Depending on the specifics of your ontology, you could map it to proton or not. If you can create a complete mapping to the proton classes, then recognizing the new concepts in the texts will be a little easier. You just need to create a statement for each new concept that it is generated by a trusted source and also point its labels. > > If you decide not to map to proton, then some additional steps are required . Create a new gazetteer with the query to get your concepts and their type and label. Then use a Jape Transducer and create your custom jape rules to convert the resulting Lookup annotations to some of the annotation types in KIM's whitelist. This is also described in the guide. > > Hope this helps. > philip > > > On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote: > >> Hello everyone! >> >> I have extended Proton ontology, and created acm_proton.ttl file. This file contains my Concepts. When I annotate document, I want to see only these Concepts. >> I saw tutorial, I have read few posts, but I could not find the solution. I have edited kim/config/owlim.ttl file, and added new line in import section. And I also added new namespace. But when I run annotator, I do not see my Concepts. >> >> Please, I need quick help on this one. >> >> Best, >> - Lucky >> >> _______________________________________________ >> Kim-discussion mailing list >> Kim-discussion at ontotext.com >> http://ontotext.com/mailman/listinfo/kim-discussion > > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreckojoksimovic at gmail.com Wed Jun 22 11:47:09 2011 From: sreckojoksimovic at gmail.com (Srecko Joksimovic) Date: Wed, 22 Jun 2011 17:47:09 +0200 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> Message-ID: <003501cc30f3$a694af50$f3be0df0$@com> Thank you Philip! This was a really brief answer. I will try to do what you said. Thank you again. Best, Srecko From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] Sent: Wednesday, June 22, 2011 5:44 PM To: srecko joksimovic Cc: kim-discussion at ontotext.com Subject: Re: [Kim-discussion] Extend proton ontology Hi, 1. First make sure is declared as trusted. This is a statement from KIM's knowledge base: . You can either use some of the existing trusted sources, or declare yours as trusted. 2. Then create a jape rule to match the Lookup annotations with class feature "http://proton.semanticweb.org/2006/05/protont#Topic" and to create a Topic annotation. 3. Ad the Topic annotation type to the whitelist of annotations of KIM in KIM/config/nerc.properties in feature com.ontotext.kim.KIMConstants.IE_ANN_TYPES . 4. Delete the cache by removing the KIM/context/default/populated folder and start KIM again. You can start it with the Gate interface to check if your annotations are created. To do that run KIM/bin/kim gate . Hope this helps Philip On 22 Jun 2011, at 6:29 PM, srecko joksimovic wrote: Hello Philip, I think that I could send you a part of this file. This is what I have defined: a protont:Topic ; protons:generatedBy ; protons:hasMainAlias . a protons:Alias ; "Optimization at en" . a protons:Alias ; "Assistive Technologies For Persons With Disabilities at en" . a protont:Topic ; protons:generatedBy ; protons:hasMainAlias . and many others... Could you please tell me what to do next? Best, Srecko On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext wrote: Hello Srecko, The steps are described in this guide: http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . Depending on the specifics of your ontology, you could map it to proton or not. If you can create a complete mapping to the proton classes, then recognizing the new concepts in the texts will be a little easier. You just need to create a statement for each new concept that it is generated by a trusted source and also point its labels. If you decide not to map to proton, then some additional steps are required . Create a new gazetteer with the query to get your concepts and their type and label. Then use a Jape Transducer and create your custom jape rules to convert the resulting Lookup annotations to some of the annotation types in KIM's whitelist. This is also described in the guide. Hope this helps. philip On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote: Hello everyone! I have extended Proton ontology, and created acm_proton.ttl file. This file contains my Concepts. When I annotate document, I want to see only these Concepts. I saw tutorial, I have read few posts, but I could not find the solution. I have edited kim/config/owlim.ttl file, and added new line in import section. And I also added new namespace. But when I run annotator, I do not see my Concepts. Please, I need quick help on this one. Best, - Lucky _______________________________________________ Kim-discussion mailing list Kim-discussion at ontotext.com http://ontotext.com/mailman/listinfo/kim-discussion _______________________________________________ Kim-discussion mailing list Kim-discussion at ontotext.com http://ontotext.com/mailman/listinfo/kim-discussion -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreckojoksimovic at gmail.com Wed Jun 22 12:32:19 2011 From: sreckojoksimovic at gmail.com (Srecko Joksimovic) Date: Wed, 22 Jun 2011 18:32:19 +0200 Subject: [Kim-discussion] Extend proton ontology References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> Message-ID: <004201cc30f9$f5e24b20$e1a6e160$@com> Hi Philip, I have one more question for now... I am beginning to doubt if I know, but let's assume that I know how to do what you said in your last answer (point 3 and 4). I know what should JAPE rule be, and I will probably be able to do that. But how to make sure that is declared as trusted? This could be funny question, but I am not sure what to do. Best, Srecko From: Srecko Joksimovic [mailto:sreckojoksimovic at gmail.com] Sent: Wednesday, June 22, 2011 5:47 PM To: 'Philip Alexiev @ Ontotext' Cc: 'kim-discussion at ontotext.com' Subject: RE: [Kim-discussion] Extend proton ontology Thank you Philip! This was a really brief answer. I will try to do what you said. Thank you again. Best, Srecko From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] Sent: Wednesday, June 22, 2011 5:44 PM To: srecko joksimovic Cc: kim-discussion at ontotext.com Subject: Re: [Kim-discussion] Extend proton ontology Hi, 1. First make sure is declared as trusted. This is a statement from KIM's knowledge base: . You can either use some of the existing trusted sources, or declare yours as trusted. 2. Then create a jape rule to match the Lookup annotations with class feature "http://proton.semanticweb.org/2006/05/protont#Topic" and to create a Topic annotation. 3. Ad the Topic annotation type to the whitelist of annotations of KIM in KIM/config/nerc.properties in feature com.ontotext.kim.KIMConstants.IE_ANN_TYPES . 4. Delete the cache by removing the KIM/context/default/populated folder and start KIM again. You can start it with the Gate interface to check if your annotations are created. To do that run KIM/bin/kim gate . Hope this helps Philip On 22 Jun 2011, at 6:29 PM, srecko joksimovic wrote: Hello Philip, I think that I could send you a part of this file. This is what I have defined: a protont:Topic ; protons:generatedBy ; protons:hasMainAlias . a protons:Alias ; "Optimization at en" . a protons:Alias ; "Assistive Technologies For Persons With Disabilities at en" . a protont:Topic ; protons:generatedBy ; protons:hasMainAlias . and many others... Could you please tell me what to do next? Best, Srecko On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext wrote: Hello Srecko, The steps are described in this guide: http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . Depending on the specifics of your ontology, you could map it to proton or not. If you can create a complete mapping to the proton classes, then recognizing the new concepts in the texts will be a little easier. You just need to create a statement for each new concept that it is generated by a trusted source and also point its labels. If you decide not to map to proton, then some additional steps are required . Create a new gazetteer with the query to get your concepts and their type and label. Then use a Jape Transducer and create your custom jape rules to convert the resulting Lookup annotations to some of the annotation types in KIM's whitelist. This is also described in the guide. Hope this helps. philip On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote: Hello everyone! I have extended Proton ontology, and created acm_proton.ttl file. This file contains my Concepts. When I annotate document, I want to see only these Concepts. I saw tutorial, I have read few posts, but I could not find the solution. I have edited kim/config/owlim.ttl file, and added new line in import section. And I also added new namespace. But when I run annotator, I do not see my Concepts. Please, I need quick help on this one. Best, - Lucky _______________________________________________ Kim-discussion mailing list Kim-discussion at ontotext.com http://ontotext.com/mailman/listinfo/kim-discussion _______________________________________________ Kim-discussion mailing list Kim-discussion at ontotext.com http://ontotext.com/mailman/listinfo/kim-discussion -------------- next part -------------- An HTML attachment was scrubbed... URL: From philip.alexiev at ontotext.com Wed Jun 22 14:17:05 2011 From: philip.alexiev at ontotext.com (Philip Alexiev @ Ontotext) Date: Wed, 22 Jun 2011 21:17:05 +0300 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: <004201cc30f9$f5e24b20$e1a6e160$@com> References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> Message-ID: <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> Hi Srecko, You state that a source is trusted by importing a statement like this in owlim: . You can either add this to your custom RDF or you can use the already predefined trusted sources (they are defined with similar statements in KIM/context/default/kb/wkb.nt ) . You can read about JAPE in the official GATE documentation. The documentation is very comprehensive and helpful: http://gate.ac.uk/sale/tao/splitch8.html#chap:jape GATE is the semantic annotation platform KIM uses. If you want to customize the default KIM information extraction process, getting familiar with GATE will be very helpful. HTH Philip On 22 Jun 2011, at 7:32 PM, Srecko Joksimovic wrote: > Hi Philip, > > I have one more question for now... I am beginning to doubt if I know, but let?s assume that I know how to do what you said in your last answer (point 3 and 4). I know what should JAPE rule be, and I will probably be able to do that. > But how to make sure that is declared as trusted? > > This could be funny question, but I am not sure what to do. > > Best, > Srecko > > From: Srecko Joksimovic [mailto:sreckojoksimovic at gmail.com] > Sent: Wednesday, June 22, 2011 5:47 PM > To: 'Philip Alexiev @ Ontotext' > Cc: 'kim-discussion at ontotext.com' > Subject: RE: [Kim-discussion] Extend proton ontology > > Thank you Philip! > This was a really brief answer. I will try to do what you said. Thank you again. > > Best, > Srecko > > From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > Sent: Wednesday, June 22, 2011 5:44 PM > To: srecko joksimovic > Cc: kim-discussion at ontotext.com > Subject: Re: [Kim-discussion] Extend proton ontology > > Hi, > > 1. First make sure is declared as trusted. This is a statement from KIM's knowledge base: > . > You can either use some of the existing trusted sources, or declare yours as trusted. > > 2. Then create a jape rule to match the Lookup annotations with class feature "http://proton.semanticweb.org/2006/05/protont#Topic" and to create a Topic annotation. > > 3. Ad the Topic annotation type to the whitelist of annotations of KIM in KIM/config/nerc.properties in feature com.ontotext.kim.KIMConstants.IE_ANN_TYPES . > > 4. Delete the cache by removing the KIM/context/default/populated folder and start KIM again. You can start it with the Gate interface to check if your annotations are created. To do that run KIM/bin/kim gate . > > > Hope this helps > Philip > > On 22 Jun 2011, at 6:29 PM, srecko joksimovic wrote: > > > Hello Philip, > > I think that I could send you a part of this file. This is what I have defined: > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > > a protons:Alias ; > > "Optimization at en" . > > > a protons:Alias ; > > "Assistive Technologies For Persons With Disabilities at en" . > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > > and many others... Could you please tell me what to do next? > > Best, > Srecko > > On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext wrote: > Hello Srecko, > > The steps are described in this guide: > http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . > > Depending on the specifics of your ontology, you could map it to proton or not. If you can create a complete mapping to the proton classes, then recognizing the new concepts in the texts will be a little easier. You just need to create a statement for each new concept that it is generated by a trusted source and also point its labels. > > If you decide not to map to proton, then some additional steps are required . Create a new gazetteer with the query to get your concepts and their type and label. Then use a Jape Transducer and create your custom jape rules to convert the resulting Lookup annotations to some of the annotation types in KIM's whitelist. This is also described in the guide. > > Hope this helps. > philip > > > On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote: > > Hello everyone! > > I have extended Proton ontology, and created acm_proton.ttl file. This file contains my Concepts. When I annotate document, I want to see only these Concepts. > I saw tutorial, I have read few posts, but I could not find the solution. I have edited kim/config/owlim.ttl file, and added new line in import section. And I also added new namespace. But when I run annotator, I do not see my Concepts. > > Please, I need quick help on this one. > > Best, > - Lucky > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreckojoksimovic at gmail.com Wed Jun 22 14:54:37 2011 From: sreckojoksimovic at gmail.com (Srecko Joksimovic) Date: Wed, 22 Jun 2011 20:54:37 +0200 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> Message-ID: <005b01cc310d$d6d7e230$8487a690$@com> Thank you Philip. I know something about GATE, but I have to learn more. Ok, this means that I have step 2. to solve... Best, Srecko From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] Sent: Wednesday, June 22, 2011 8:17 PM To: Srecko Joksimovic Cc: kim-discussion at ontotext.com Subject: Re: [Kim-discussion] Extend proton ontology Hi Srecko, You state that a source is trusted by importing a statement like this in owlim: . You can either add this to your custom RDF or you can use the already predefined trusted sources (they are defined with similar statements in KIM/context/default/kb/wkb.nt ) . You can read about JAPE in the official GATE documentation. The documentation is very comprehensive and helpful: http://gate.ac.uk/sale/tao/splitch8.html#chap:jape GATE is the semantic annotation platform KIM uses. If you want to customize the default KIM information extraction process, getting familiar with GATE will be very helpful. HTH Philip On 22 Jun 2011, at 7:32 PM, Srecko Joksimovic wrote: Hi Philip, I have one more question for now... I am beginning to doubt if I know, but let's assume that I know how to do what you said in your last answer (point 3 and 4). I know what should JAPE rule be, and I will probably be able to do that. But how to make sure that is declared as trusted? This could be funny question, but I am not sure what to do. Best, Srecko From: Srecko Joksimovic [mailto:sreckojoksimovic at gmail.com] Sent: Wednesday, June 22, 2011 5:47 PM To: 'Philip Alexiev @ Ontotext' Cc: 'kim-discussion at ontotext.com' Subject: RE: [Kim-discussion] Extend proton ontology Thank you Philip! This was a really brief answer. I will try to do what you said. Thank you again. Best, Srecko From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] Sent: Wednesday, June 22, 2011 5:44 PM To: srecko joksimovic Cc: kim-discussion at ontotext.com Subject: Re: [Kim-discussion] Extend proton ontology Hi, 1. First make sure is declared as trusted. This is a statement from KIM's knowledge base: . You can either use some of the existing trusted sources, or declare yours as trusted. 2. Then create a jape rule to match the Lookup annotations with class feature "http://proton.semanticweb.org/2006/05/protont#Topic" and to create a Topic annotation. 3. Ad the Topic annotation type to the whitelist of annotations of KIM in KIM/config/nerc.properties in feature com.ontotext.kim.KIMConstants.IE_ANN_TYPES . 4. Delete the cache by removing the KIM/context/default/populated folder and start KIM again. You can start it with the Gate interface to check if your annotations are created. To do that run KIM/bin/kim gate . Hope this helps Philip On 22 Jun 2011, at 6:29 PM, srecko joksimovic wrote: Hello Philip, I think that I could send you a part of this file. This is what I have defined: a protont:Topic ; protons:generatedBy ; protons:hasMainAlias . a protons:Alias ; "Optimization at en" . a protons:Alias ; "Assistive Technologies For Persons With Disabilities at en" . a protont:Topic ; protons:generatedBy ; protons:hasMainAlias . and many others... Could you please tell me what to do next? Best, Srecko On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext wrote: Hello Srecko, The steps are described in this guide: http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . Depending on the specifics of your ontology, you could map it to proton or not. If you can create a complete mapping to the proton classes, then recognizing the new concepts in the texts will be a little easier. You just need to create a statement for each new concept that it is generated by a trusted source and also point its labels. If you decide not to map to proton, then some additional steps are required . Create a new gazetteer with the query to get your concepts and their type and label. Then use a Jape Transducer and create your custom jape rules to convert the resulting Lookup annotations to some of the annotation types in KIM's whitelist. This is also described in the guide. Hope this helps. philip On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote: Hello everyone! I have extended Proton ontology, and created acm_proton.ttl file. This file contains my Concepts. When I annotate document, I want to see only these Concepts. I saw tutorial, I have read few posts, but I could not find the solution. I have edited kim/config/owlim.ttl file, and added new line in import section. And I also added new namespace. But when I run annotator, I do not see my Concepts. Please, I need quick help on this one. Best, - Lucky _______________________________________________ Kim-discussion mailing list Kim-discussion at ontotext.com http://ontotext.com/mailman/listinfo/kim-discussion _______________________________________________ Kim-discussion mailing list Kim-discussion at ontotext.com http://ontotext.com/mailman/listinfo/kim-discussion -------------- next part -------------- An HTML attachment was scrubbed... URL: From philip.alexiev at ontotext.com Wed Jun 22 15:17:24 2011 From: philip.alexiev at ontotext.com (Philip Alexiev @ Ontotext) Date: Wed, 22 Jun 2011 22:17:24 +0300 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: <005b01cc310d$d6d7e230$8487a690$@com> References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> <005b01cc310d$d6d7e230$8487a690$@com> Message-ID: For step 2, you can take a look at the already existing grammars, who transform Lookup annotations to meaningful annotations. One such is KIM/context/default/resources/grammar/main/gazrules.jape . Your grammar for Topic will look like this: Phase: GazTopic Input: Lookup Options: control = appelt Rule: GazTopic ( {Lookup.class == "http://proton.semanticweb.org/2006/05/protont#Topic"} ):topic --> :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } You can add such a rule for each class you are interested in. Just remember to add "Topic" to KIM's annotation types whitelist. best philip On 22 Jun 2011, at 9:54 PM, Srecko Joksimovic wrote: > Thank you Philip. I know something about GATE, but I have to learn more. > Ok, this means that I have step 2. to solve... > > Best, > Srecko > > From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > Sent: Wednesday, June 22, 2011 8:17 PM > To: Srecko Joksimovic > Cc: kim-discussion at ontotext.com > Subject: Re: [Kim-discussion] Extend proton ontology > > Hi Srecko, > > You state that a source is trusted by importing a statement like this in owlim: > > . > > You can either add this to your custom RDF or you can use the already predefined trusted sources (they are defined with similar statements in KIM/context/default/kb/wkb.nt ) . > > You can read about JAPE in the official GATE documentation. The documentation is very comprehensive and helpful: > http://gate.ac.uk/sale/tao/splitch8.html#chap:jape > > GATE is the semantic annotation platform KIM uses. If you want to customize the default KIM information extraction process, getting familiar with GATE will be very helpful. > > HTH > Philip > > > On 22 Jun 2011, at 7:32 PM, Srecko Joksimovic wrote: > > > Hi Philip, > > I have one more question for now... I am beginning to doubt if I know, but let?s assume that I know how to do what you said in your last answer (point 3 and 4). I know what should JAPE rule be, and I will probably be able to do that. > But how to make sure that is declared as trusted? > > This could be funny question, but I am not sure what to do. > > Best, > Srecko > > From: Srecko Joksimovic [mailto:sreckojoksimovic at gmail.com] > Sent: Wednesday, June 22, 2011 5:47 PM > To: 'Philip Alexiev @ Ontotext' > Cc: 'kim-discussion at ontotext.com' > Subject: RE: [Kim-discussion] Extend proton ontology > > Thank you Philip! > This was a really brief answer. I will try to do what you said. Thank you again. > > Best, > Srecko > > From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > Sent: Wednesday, June 22, 2011 5:44 PM > To: srecko joksimovic > Cc: kim-discussion at ontotext.com > Subject: Re: [Kim-discussion] Extend proton ontology > > Hi, > > 1. First make sure is declared as trusted. This is a statement from KIM's knowledge base: > . > You can either use some of the existing trusted sources, or declare yours as trusted. > > 2. Then create a jape rule to match the Lookup annotations with class feature "http://proton.semanticweb.org/2006/05/protont#Topic" and to create a Topic annotation. > > 3. Ad the Topic annotation type to the whitelist of annotations of KIM in KIM/config/nerc.properties in feature com.ontotext.kim.KIMConstants.IE_ANN_TYPES . > > 4. Delete the cache by removing the KIM/context/default/populated folder and start KIM again. You can start it with the Gate interface to check if your annotations are created. To do that run KIM/bin/kim gate . > > > Hope this helps > Philip > > On 22 Jun 2011, at 6:29 PM, srecko joksimovic wrote: > > > Hello Philip, > > I think that I could send you a part of this file. This is what I have defined: > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > > a protons:Alias ; > > "Optimization at en" . > > > a protons:Alias ; > > "Assistive Technologies For Persons With Disabilities at en" . > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > > and many others... Could you please tell me what to do next? > > Best, > Srecko > > On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext wrote: > Hello Srecko, > > The steps are described in this guide: > http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . > > Depending on the specifics of your ontology, you could map it to proton or not. If you can create a complete mapping to the proton classes, then recognizing the new concepts in the texts will be a little easier. You just need to create a statement for each new concept that it is generated by a trusted source and also point its labels. > > If you decide not to map to proton, then some additional steps are required . Create a new gazetteer with the query to get your concepts and their type and label. Then use a Jape Transducer and create your custom jape rules to convert the resulting Lookup annotations to some of the annotation types in KIM's whitelist. This is also described in the guide. > > Hope this helps. > philip > > > On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote: > > Hello everyone! > > I have extended Proton ontology, and created acm_proton.ttl file. This file contains my Concepts. When I annotate document, I want to see only these Concepts. > I saw tutorial, I have read few posts, but I could not find the solution. I have edited kim/config/owlim.ttl file, and added new line in import section. And I also added new namespace. But when I run annotator, I do not see my Concepts. > > Please, I need quick help on this one. > > Best, > - Lucky > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion -------------- next part -------------- An HTML attachment was scrubbed... URL: From philip.alexiev at ontotext.com Mon Jun 27 04:30:25 2011 From: philip.alexiev at ontotext.com (Philip Alexiev @ Ontotext) Date: Mon, 27 Jun 2011 11:30:25 +0300 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: <001701cc3356$0132c410$03984c30$@com> References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> <005b01cc310d$d6d7e230$8487a690$@com> <006301cc3114$35501750$9ff045f0$@com> <5A9E35B2-3215-4876-94A5-830219D7A109@ontotext.com> <001701cc3356$0132c410$03984c30$@com> Message-ID: Hi Srecko, I will explain this RHS : > :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } This means, that an annotation will be created of type Topic which has the offsets of the topic binding set, matched from the LHS. The annotation will have a feature inst, which will be the same as the inst feature of the Lookup annotation in the same binding set. The same is true for the class feature. inst and class are features of the Lookup annotations that the gazetteer creates. They serve to link the annotations in text with their representations in the semantic repository. Lookups are based on the entities in owlim, and the features denote the class and the instance URI of those entities. You can read more about setting feature values from matched annotations in this part of the gate documentation: 8.3.2 Copying Feature Values from the LHS to the RHS You do not need to change the expression in the brackets. In this form, it simply means the new Topic annotation will copy its features from the Lookup, based on which it is created. Hope this helps. Please feel free to ask for more clarification. Philip On 25 Jun 2011, at 7:36 PM, Srecko Joksimovic wrote: > Hi Philip! > I think I really need your help. The project I am working on has two parts. And it doesn?t go as I expected. I am still reading (when I catch free time) about GATE and JAPE, but I also still have a problem with this JAPE rule. > > I understand left side, right side and other stuff, but, you sent me an example: > > Phase: GazTopic > Input: Lookup > Options: control = appelt > > Rule: GazTopic > ( > {Lookup.class == "http://proton.semanticweb.org/2006/05/protont#Topic"} > ):topic > --> > :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } > > This "http://proton.semanticweb.org/2006/05/protont#Topic" part is ok. Could you please tell me what to do with ?{inst = :topic.Lookup.inst , class = :topic.Lookup.class}?? I have many instances, and I?m not sure what should be in this part... > > This is part of document: > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > > a protons:Alias ; > > "Optimization at en" . > > > a protons:Alias ; > > "Assistive Technologies For Persons With Disabilities at en" . > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > Excuse me for wasting your time, but I?m out of time :( > > From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > Sent: Wednesday, June 22, 2011 9:43 PM > To: Srecko Joksimovic > Subject: Re: [Kim-discussion] Extend proton ontology > > Hi Srecko, > > I am glad I was of help. Feel free to ask if something escapes you. > > Best, > Philip > > On 22 Jun 2011, at 10:40 PM, Srecko Joksimovic wrote: > > > Hi Philip, > > This is very helpful! I will continue reading about GATE, but this was very useful. I will try this. > > Best, > Srecko > > From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > Sent: Wednesday, June 22, 2011 9:17 PM > To: Srecko Joksimovic > Cc: kim-discussion at ontotext.com > Subject: Re: [Kim-discussion] Extend proton ontology > > For step 2, you can take a look at the already existing grammars, who transform Lookup annotations to meaningful annotations. One such is KIM/context/default/resources/grammar/main/gazrules.jape . > > Your grammar for Topic will look like this: > > Phase: GazTopic > Input: Lookup > Options: control = appelt > > Rule: GazTopic > ( > {Lookup.class == "http://proton.semanticweb.org/2006/05/protont#Topic"} > ):topic > --> > :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } > > > You can add such a rule for each class you are interested in. Just remember to add "Topic" to KIM's annotation types whitelist. > > best > philip > > > On 22 Jun 2011, at 9:54 PM, Srecko Joksimovic wrote: > > > > Thank you Philip. I know something about GATE, but I have to learn more. > Ok, this means that I have step 2. to solve... > > Best, > Srecko > > From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > Sent: Wednesday, June 22, 2011 8:17 PM > To: Srecko Joksimovic > Cc: kim-discussion at ontotext.com > Subject: Re: [Kim-discussion] Extend proton ontology > > Hi Srecko, > > You state that a source is trusted by importing a statement like this in owlim: > > . > > You can either add this to your custom RDF or you can use the already predefined trusted sources (they are defined with similar statements in KIM/context/default/kb/wkb.nt ) . > > You can read about JAPE in the official GATE documentation. The documentation is very comprehensive and helpful: > http://gate.ac.uk/sale/tao/splitch8.html#chap:jape > > GATE is the semantic annotation platform KIM uses. If you want to customize the default KIM information extraction process, getting familiar with GATE will be very helpful. > > HTH > Philip > > > On 22 Jun 2011, at 7:32 PM, Srecko Joksimovic wrote: > > > > > Hi Philip, > > I have one more question for now... I am beginning to doubt if I know, but let?s assume that I know how to do what you said in your last answer (point 3 and 4). I know what should JAPE rule be, and I will probably be able to do that. > But how to make sure that is declared as trusted? > > This could be funny question, but I am not sure what to do. > > Best, > Srecko > > From: Srecko Joksimovic [mailto:sreckojoksimovic at gmail.com] > Sent: Wednesday, June 22, 2011 5:47 PM > To: 'Philip Alexiev @ Ontotext' > Cc: 'kim-discussion at ontotext.com' > Subject: RE: [Kim-discussion] Extend proton ontology > > Thank you Philip! > This was a really brief answer. I will try to do what you said. Thank you again. > > Best, > Srecko > > From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > Sent: Wednesday, June 22, 2011 5:44 PM > To: srecko joksimovic > Cc: kim-discussion at ontotext.com > Subject: Re: [Kim-discussion] Extend proton ontology > > Hi, > > 1. First make sure is declared as trusted. This is a statement from KIM's knowledge base: > . > You can either use some of the existing trusted sources, or declare yours as trusted. > > 2. Then create a jape rule to match the Lookup annotations with class feature "http://proton.semanticweb.org/2006/05/protont#Topic" and to create a Topic annotation. > > 3. Ad the Topic annotation type to the whitelist of annotations of KIM in KIM/config/nerc.properties in feature com.ontotext.kim.KIMConstants.IE_ANN_TYPES . > > 4. Delete the cache by removing the KIM/context/default/populated folder and start KIM again. You can start it with the Gate interface to check if your annotations are created. To do that run KIM/bin/kim gate . > > > Hope this helps > Philip > > On 22 Jun 2011, at 6:29 PM, srecko joksimovic wrote: > > > Hello Philip, > > I think that I could send you a part of this file. This is what I have defined: > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > > a protons:Alias ; > > "Optimization at en" . > > > a protons:Alias ; > > "Assistive Technologies For Persons With Disabilities at en" . > > > a protont:Topic ; > protons:generatedBy ; > protons:hasMainAlias > . > > > and many others... Could you please tell me what to do next? > > Best, > Srecko > > On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext wrote: > Hello Srecko, > > The steps are described in this guide: > http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . > > Depending on the specifics of your ontology, you could map it to proton or not. If you can create a complete mapping to the proton classes, then recognizing the new concepts in the texts will be a little easier. You just need to create a statement for each new concept that it is generated by a trusted source and also point its labels. > > If you decide not to map to proton, then some additional steps are required . Create a new gazetteer with the query to get your concepts and their type and label. Then use a Jape Transducer and create your custom jape rules to convert the resulting Lookup annotations to some of the annotation types in KIM's whitelist. This is also described in the guide. > > Hope this helps. > philip > > > On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote: > > Hello everyone! > > I have extended Proton ontology, and created acm_proton.ttl file. This file contains my Concepts. When I annotate document, I want to see only these Concepts. > I saw tutorial, I have read few posts, but I could not find the solution. I have edited kim/config/owlim.ttl file, and added new line in import section. And I also added new namespace. But when I run annotator, I do not see my Concepts. > > Please, I need quick help on this one. > > Best, > - Lucky > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreckojoksimovic at gmail.com Mon Jun 27 08:52:58 2011 From: sreckojoksimovic at gmail.com (srecko joksimovic) Date: Mon, 27 Jun 2011 14:52:58 +0200 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> <005b01cc310d$d6d7e230$8487a690$@com> <006301cc3114$35501750$9ff045f0$@com> <5A9E35B2-3215-4876-94A5-830219D7A109@ontotext.com> <001701cc3356$0132c410$03984c30$@com> Message-ID: Hi Philip, And thank you for the explanation. I thought so, but I didn't try to test what I have done. As I understood, I should create a new .jape file, and copy to kim3.0/plugins/ANNIE/resources/NE? Or another folder...? Best, Srecko On Mon, Jun 27, 2011 at 10:30 AM, Philip Alexiev @ Ontotext < philip.alexiev at ontotext.com> wrote: > Hi Srecko, > > I will explain this RHS : > > :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } > > > This means, that an annotation will be created of type *Topic* which has > the offsets of the *topic* binding set, matched from the LHS. The > annotation will have a feature *inst*, which will be the same as the *inst > * feature of the Lookup annotation in the same binding set. The same is > true for the *class* feature. *inst* and *class* are features of the > Lookup annotations that the gazetteer creates. They serve to link the > annotations in text with their representations in the semantic repository. > Lookups are based on the entities in owlim, and the features denote the > class and the instance URI of those entities. > > You can read more about setting feature values from matched annotations in > this part of the gate documentation: > 8.3.2 Copying Feature Values from the LHS to the RHS > > You do not need to change the expression in the brackets. In this form, it > simply means the new *Topic* annotation will copy its features from the * > Lookup*, based on which it is created. > > Hope this helps. > Please feel free to ask for more clarification. > Philip > > > On 25 Jun 2011, at 7:36 PM, Srecko Joksimovic wrote: > > Hi Philip! > I think I really need your help. The project I am working on has two parts. > And it doesn?t go as I expected. I am still reading (when I catch free time) > about GATE and JAPE, but I also still have a problem with this JAPE rule.* > *** > ** ** > I understand left side, right side and other stuff, but, you sent me an > example:**** > ** ** > Phase: GazTopic**** > Input: Lookup**** > Options: control = appelt**** > **** > Rule: GazTopic**** > (**** > {Lookup.class == "http://proton.semanticweb.org/2006/05/protont#Topic"}*** > * > ):topic**** > -->**** > :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } > **** > ** ** > This "http://proton.semanticweb.org/2006/05/protont#Topic" part is ok. > Could you please tell me what to do with ?{inst = :topic.Lookup.inst , class > = :topic.Lookup.class}?? I have many instances, and I?m not sure what should > be in this part...**** > ** ** > This is part of document:**** > ** ** > **** > a protont:Topic ;**** > protons:generatedBy > ;**** > protons:hasMainAlias**** > < > http://www.lornet.org/acm-ccs/proton#Alias_756db3b5-b66b-41fe-a82e-1012f18a6672> > .**** > **** > < > http://www.lornet.org/acm-ccs/proton#Alias_877dc2e2-c7cf-4188-a523-6ee9b7cbdd24 > >**** > a protons:Alias ;**** > **** > "Optimization at en" .**** > **** > < > http://www.lornet.org/acm-ccs/proton#Alias_62107227-8c21-4ed8-99e0-bb2e4e1cb810 > >**** > a protons:Alias ;**** > **** > "Assistive Technologies For Persons With Disabilities at en" .* > *** > **** > **** > a protont:Topic ;**** > protons:generatedBy > ;**** > protons:hasMainAlias**** > < > http://www.lornet.org/acm-ccs/proton#Alias_ff0e0512-f2e8-4b14-9a37-71a675dcd2eb> > .**** > ** ** > Excuse me for wasting your time, but I?m out of time :(**** > ** ** > *From:* Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > *Sent:* Wednesday, June 22, 2011 9:43 PM > *To:* Srecko Joksimovic > *Subject:* Re: [Kim-discussion] Extend proton ontology**** > ** ** > Hi Srecko,**** > ** ** > I am glad I was of help. Feel free to ask if something escapes you.**** > ** ** > Best,**** > Philip**** > ** ** > On 22 Jun 2011, at 10:40 PM, Srecko Joksimovic wrote:**** > > > **** > Hi Philip,**** > **** > This is very helpful! I will continue reading about GATE, but this was very > useful. I will try this.**** > **** > Best,**** > Srecko**** > **** > *From:* Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > *Sent:* Wednesday, June 22, 2011 9:17 PM > *To:* Srecko Joksimovic > *Cc:* kim-discussion at ontotext.com > *Subject:* Re: [Kim-discussion] Extend proton ontology**** > **** > For step 2, you can take a look at the already existing grammars, who > transform Lookup annotations to meaningful annotations. One such is > KIM/context/default/resources/grammar/main/gazrules.jape .**** > **** > Your grammar for Topic will look like this:**** > **** > Phase: GazTopic**** > Input: Lookup**** > Options: control = appelt**** > **** > Rule: GazTopic**** > (**** > {Lookup.class == "http://proton.semanticweb.org/2006/05/protont#Topic"}*** > * > ):topic**** > -->**** > :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } > **** > **** > **** > You can add such a rule for each class you are interested in. Just remember > to add "Topic" to KIM's annotation types whitelist.**** > **** > best**** > philip**** > **** > **** > On 22 Jun 2011, at 9:54 PM, Srecko Joksimovic wrote:**** > > > > **** > Thank you Philip. I know something about GATE, but I have to learn more.** > ** > Ok, this means that I have step 2. to solve...**** > **** > Best,**** > Srecko**** > **** > *From:* Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > *Sent:* Wednesday, June 22, 2011 8:17 PM > *To:* Srecko Joksimovic > *Cc:* kim-discussion at ontotext.com > *Subject:* Re: [Kim-discussion] Extend proton ontology**** > **** > Hi Srecko,**** > **** > You state that a source is trusted by importing a statement like this in > owlim:**** > **** > < > http://www.w3.org/1999/02/22-rdf-syntax-ns#type> < > http://proton.semanticweb.org/2006/05/protons#Trusted> .**** > **** > You can either add this to your custom RDF or you can use the already > predefined trusted sources (they are defined with similar statements in > KIM/context/default/kb/wkb.nt ) .**** > **** > You can read about JAPE in the official GATE documentation. The > documentation is very comprehensive and helpful: **** > http://gate.ac.uk/sale/tao/splitch8.html#chap:jape**** > **** > GATE is the semantic annotation platform KIM uses. If you want to customize > the default KIM information extraction process, getting familiar with GATE > will be very helpful.**** > **** > HTH**** > Philip**** > **** > **** > On 22 Jun 2011, at 7:32 PM, Srecko Joksimovic wrote:**** > > > > > **** > Hi Philip,**** > **** > I have one more question for now... I am beginning to doubt if I know, but > let?s assume that I know how to do what you said in your last answer (point > 3 and 4). I know what should JAPE rule be, and I will probably be able to do > that.**** > But how to make sure that < > http://www.lornet.org/acm-ccs/proton#TrustedSrc> is declared as trusted?** > ** > **** > This could be funny question, but I am not sure what to do.**** > **** > Best,**** > Srecko**** > **** > *From:* Srecko Joksimovic [mailto:sreckojoksimovic at gmail.com] > *Sent:* Wednesday, June 22, 2011 5:47 PM > *To:* 'Philip Alexiev @ Ontotext' > *Cc:* 'kim-discussion at ontotext.com' > *Subject:* RE: [Kim-discussion] Extend proton ontology**** > **** > Thank you Philip!**** > This was a really brief answer. I will try to do what you said. Thank you > again.**** > **** > Best,**** > Srecko**** > **** > *From:* Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] > *Sent:* Wednesday, June 22, 2011 5:44 PM > *To:* srecko joksimovic > *Cc:* kim-discussion at ontotext.com > *Subject:* Re: [Kim-discussion] Extend proton ontology**** > **** > Hi,**** > **** > 1. First make sure is > declared as trusted. This is a statement from KIM's knowledge base:**** > < > http://www.w3.org/1999/02/22-rdf-syntax-ns#type> < > http://proton.semanticweb.org/2006/05/protons#Trusted> .**** > You can either use some of the existing trusted sources, or declare yours > as trusted.**** > **** > 2. Then create a jape rule to match the Lookup annotations with class > feature "http://proton.semanticweb.org/2006/05/protont#Topic" and to > create a Topic annotation.**** > **** > 3. Ad the Topic annotation type to the whitelist of annotations of KIM in > KIM/config/nerc.properties in feature > com.ontotext.kim.KIMConstants.IE_ANN_TYPES .**** > **** > 4. Delete the cache by removing the KIM/context/default/populated folder > and start KIM again. You can start it with the Gate interface to check if > your annotations are created. To do that run KIM/bin/kim gate .**** > **** > **** > Hope this helps**** > Philip**** > **** > On 22 Jun 2011, at 6:29 PM, srecko joksimovic wrote:**** > > **** > Hello Philip,**** > **** > I think that I could send you a part of this file. This is what I have > defined:**** > **** > **** > a protont:Topic ;**** > protons:generatedBy > ;**** > protons:hasMainAlias**** > < > http://www.lornet.org/acm-ccs/proton#Alias_756db3b5-b66b-41fe-a82e-1012f18a6672> > .**** > **** > < > http://www.lornet.org/acm-ccs/proton#Alias_877dc2e2-c7cf-4188-a523-6ee9b7cbdd24 > >**** > a protons:Alias ;**** > **** > "Optimization at en" .**** > **** > < > http://www.lornet.org/acm-ccs/proton#Alias_62107227-8c21-4ed8-99e0-bb2e4e1cb810 > >**** > a protons:Alias ;**** > **** > "Assistive Technologies For Persons With Disabilities at en" .* > *** > **** > **** > a protont:Topic ;**** > protons:generatedBy > ;**** > protons:hasMainAlias**** > < > http://www.lornet.org/acm-ccs/proton#Alias_ff0e0512-f2e8-4b14-9a37-71a675dcd2eb> > .**** > **** > **** > and many others... Could you please tell me what to do next?**** > **** > Best, **** > Srecko**** > **** > On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext < > philip.alexiev at gmail.com> wrote:**** > Hello Srecko,**** > **** > The steps are described in this guide:**** > http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . **** > **** > Depending on the specifics of your ontology, you could map it to proton or > not. If you can create a complete mapping to the proton classes, then > recognizing the new concepts in the texts will be a little easier. You just > need to create a statement for each new concept that it is generated by a > trusted source and also point its labels.**** > **** > If you decide not to map to proton, then some additional steps are required > . Create a new gazetteer with the query to get your concepts and their type > and label. Then use a Jape Transducer and create your custom jape rules to > convert the resulting Lookup annotations to some of the annotation types in > KIM's whitelist. This is also described in the guide.**** > **** > Hope this helps.**** > philip**** > **** > **** > On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote:**** > **** > > Hello everyone!**** > **** > I have extended Proton ontology, and created acm_proton.ttl file. This file > contains my Concepts. When I annotate document, I want to see only these > Concepts.**** > I saw tutorial, I have read few posts, but I could not find the solution. I > have edited kim/config/owlim.ttl file, and added new line in import section. > And I also added new namespace. But when I run annotator, I do not see my > Concepts.**** > **** > Please, I need quick help on this one.**** > **** > Best,**** > - Lucky**** > **** > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion**** > > **** > **** > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion**** > **** > **** > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion**** > **** > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From philip.alexiev at ontotext.com Mon Jun 27 09:32:30 2011 From: philip.alexiev at ontotext.com (Philip Alexiev @ Ontotext) Date: Mon, 27 Jun 2011 16:32:30 +0300 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> <005b01cc310d$d6d7e230$8487a690$@com> <006301cc3114$35501750$9ff045f0$@com> <5A9E35B2-3215-4876-94A5-830219D7A109@ontotext.com> <001701cc3356$0132c410$03984c30$@com> Message-ID: <82864263-3874-429D-8216-AAB27C57D98F@ontotext.com> Hi, The folder does not matter. You set the path to the .jape file when you create the Jape transducer processing resource in the GATE interface. greetings, philip On 27 Jun 2011, at 3:52 PM, srecko joksimovic wrote: > Hi Philip, > > And thank you for the explanation. I thought so, but I didn't try to test what I have done. > As I understood, I should create a new .jape file, and copy to kim3.0/plugins/ANNIE/resources/NE? Or another folder...? > > Best, > Srecko > > On Mon, Jun 27, 2011 at 10:30 AM, Philip Alexiev @ Ontotext wrote: > Hi Srecko, > > I will explain this RHS : >> :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } > > This means, that an annotation will be created of type Topic which has the offsets of the topic binding set, matched from the LHS. The annotation will have a feature inst, which will be the same as the inst feature of the Lookup annotation in the same binding set. The same is true for the class feature. inst and class are features of the Lookup annotations that the gazetteer creates. They serve to link the annotations in text with their representations in the semantic repository. Lookups are based on the entities in owlim, and the features denote the class and the instance URI of those entities. > > You can read more about setting feature values from matched annotations in this part of the gate documentation: > 8.3.2 Copying Feature Values from the LHS to the RHS > > > You do not need to change the expression in the brackets. In this form, it simply means the new Topic annotation will copy its features from the Lookup, based on which it is created. > > Hope this helps. > Please feel free to ask for more clarification. > Philip > > > On 25 Jun 2011, at 7:36 PM, Srecko Joksimovic wrote: > >> Hi Philip! >> I think I really need your help. The project I am working on has two parts. And it doesn?t go as I expected. I am still reading (when I catch free time) about GATE and JAPE, but I also still have a problem with this JAPE rule. >> >> I understand left side, right side and other stuff, but, you sent me an example: >> >> Phase: GazTopic >> Input: Lookup >> Options: control = appelt >> >> Rule: GazTopic >> ( >> {Lookup.class == "http://proton.semanticweb.org/2006/05/protont#Topic"} >> ):topic >> --> >> :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } >> >> This "http://proton.semanticweb.org/2006/05/protont#Topic" part is ok. Could you please tell me what to do with ?{inst = :topic.Lookup.inst , class = :topic.Lookup.class}?? I have many instances, and I?m not sure what should be in this part... >> >> This is part of document: >> >> >> a protont:Topic ; >> protons:generatedBy ; >> protons:hasMainAlias >> . >> >> >> a protons:Alias ; >> >> "Optimization at en" . >> >> >> a protons:Alias ; >> >> "Assistive Technologies For Persons With Disabilities at en" . >> >> >> a protont:Topic ; >> protons:generatedBy ; >> protons:hasMainAlias >> . >> >> Excuse me for wasting your time, but I?m out of time :( >> >> From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] >> Sent: Wednesday, June 22, 2011 9:43 PM >> To: Srecko Joksimovic >> Subject: Re: [Kim-discussion] Extend proton ontology >> >> Hi Srecko, >> >> I am glad I was of help. Feel free to ask if something escapes you. >> >> Best, >> Philip >> >> On 22 Jun 2011, at 10:40 PM, Srecko Joksimovic wrote: >> >> >> Hi Philip, >> >> This is very helpful! I will continue reading about GATE, but this was very useful. I will try this. >> >> Best, >> Srecko >> >> From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] >> Sent: Wednesday, June 22, 2011 9:17 PM >> To: Srecko Joksimovic >> Cc: kim-discussion at ontotext.com >> Subject: Re: [Kim-discussion] Extend proton ontology >> >> For step 2, you can take a look at the already existing grammars, who transform Lookup annotations to meaningful annotations. One such is KIM/context/default/resources/grammar/main/gazrules.jape . >> >> Your grammar for Topic will look like this: >> >> Phase: GazTopic >> Input: Lookup >> Options: control = appelt >> >> Rule: GazTopic >> ( >> {Lookup.class == "http://proton.semanticweb.org/2006/05/protont#Topic"} >> ):topic >> --> >> :topic.Topic = { inst = :topic.Lookup.inst , class = :topic.Lookup.class } >> >> >> You can add such a rule for each class you are interested in. Just remember to add "Topic" to KIM's annotation types whitelist. >> >> best >> philip >> >> >> On 22 Jun 2011, at 9:54 PM, Srecko Joksimovic wrote: >> >> >> >> Thank you Philip. I know something about GATE, but I have to learn more. >> Ok, this means that I have step 2. to solve... >> >> Best, >> Srecko >> >> From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] >> Sent: Wednesday, June 22, 2011 8:17 PM >> To: Srecko Joksimovic >> Cc: kim-discussion at ontotext.com >> Subject: Re: [Kim-discussion] Extend proton ontology >> >> Hi Srecko, >> >> You state that a source is trusted by importing a statement like this in owlim: >> >> . >> >> You can either add this to your custom RDF or you can use the already predefined trusted sources (they are defined with similar statements in KIM/context/default/kb/wkb.nt ) . >> >> You can read about JAPE in the official GATE documentation. The documentation is very comprehensive and helpful: >> http://gate.ac.uk/sale/tao/splitch8.html#chap:jape >> >> GATE is the semantic annotation platform KIM uses. If you want to customize the default KIM information extraction process, getting familiar with GATE will be very helpful. >> >> HTH >> Philip >> >> >> On 22 Jun 2011, at 7:32 PM, Srecko Joksimovic wrote: >> >> >> >> >> Hi Philip, >> >> I have one more question for now... I am beginning to doubt if I know, but let?s assume that I know how to do what you said in your last answer (point 3 and 4). I know what should JAPE rule be, and I will probably be able to do that. >> But how to make sure that is declared as trusted? >> >> This could be funny question, but I am not sure what to do. >> >> Best, >> Srecko >> >> From: Srecko Joksimovic [mailto:sreckojoksimovic at gmail.com] >> Sent: Wednesday, June 22, 2011 5:47 PM >> To: 'Philip Alexiev @ Ontotext' >> Cc: 'kim-discussion at ontotext.com' >> Subject: RE: [Kim-discussion] Extend proton ontology >> >> Thank you Philip! >> This was a really brief answer. I will try to do what you said. Thank you again. >> >> Best, >> Srecko >> >> From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at ontotext.com] >> Sent: Wednesday, June 22, 2011 5:44 PM >> To: srecko joksimovic >> Cc: kim-discussion at ontotext.com >> Subject: Re: [Kim-discussion] Extend proton ontology >> >> Hi, >> >> 1. First make sure is declared as trusted. This is a statement from KIM's knowledge base: >> . >> You can either use some of the existing trusted sources, or declare yours as trusted. >> >> 2. Then create a jape rule to match the Lookup annotations with class feature "http://proton.semanticweb.org/2006/05/protont#Topic" and to create a Topic annotation. >> >> 3. Ad the Topic annotation type to the whitelist of annotations of KIM in KIM/config/nerc.properties in feature com.ontotext.kim.KIMConstants.IE_ANN_TYPES . >> >> 4. Delete the cache by removing the KIM/context/default/populated folder and start KIM again. You can start it with the Gate interface to check if your annotations are created. To do that run KIM/bin/kim gate . >> >> >> Hope this helps >> Philip >> >> On 22 Jun 2011, at 6:29 PM, srecko joksimovic wrote: >> >> >> Hello Philip, >> >> I think that I could send you a part of this file. This is what I have defined: >> >> >> a protont:Topic ; >> protons:generatedBy ; >> protons:hasMainAlias >> . >> >> >> a protons:Alias ; >> >> "Optimization at en" . >> >> >> a protons:Alias ; >> >> "Assistive Technologies For Persons With Disabilities at en" . >> >> >> a protont:Topic ; >> protons:generatedBy ; >> protons:hasMainAlias >> . >> >> >> and many others... Could you please tell me what to do next? >> >> Best, >> Srecko >> >> On Wed, Jun 22, 2011 at 5:01 PM, Philip Alexiev @ Ontotext wrote: >> Hello Srecko, >> >> The steps are described in this guide: >> http://www.ontotext.com/sites/default/files/Customizing%20KIM3.pdf . >> >> Depending on the specifics of your ontology, you could map it to proton or not. If you can create a complete mapping to the proton classes, then recognizing the new concepts in the texts will be a little easier. You just need to create a statement for each new concept that it is generated by a trusted source and also point its labels. >> >> If you decide not to map to proton, then some additional steps are required . Create a new gazetteer with the query to get your concepts and their type and label. Then use a Jape Transducer and create your custom jape rules to convert the resulting Lookup annotations to some of the annotation types in KIM's whitelist. This is also described in the guide. >> >> Hope this helps. >> philip >> >> >> On 22 Jun 2011, at 5:39 PM, Srecko Joksimovic wrote: >> >> Hello everyone! >> >> I have extended Proton ontology, and created acm_proton.ttl file. This file contains my Concepts. When I annotate document, I want to see only these Concepts. >> I saw tutorial, I have read few posts, but I could not find the solution. I have edited kim/config/owlim.ttl file, and added new line in import section. And I also added new namespace. But when I run annotator, I do not see my Concepts. >> >> Please, I need quick help on this one. >> >> Best, >> - Lucky >> >> _______________________________________________ >> Kim-discussion mailing list >> Kim-discussion at ontotext.com >> http://ontotext.com/mailman/listinfo/kim-discussion >> >> >> _______________________________________________ >> Kim-discussion mailing list >> Kim-discussion at ontotext.com >> http://ontotext.com/mailman/listinfo/kim-discussion >> >> >> _______________________________________________ >> Kim-discussion mailing list >> Kim-discussion at ontotext.com >> http://ontotext.com/mailman/listinfo/kim-discussion >> >> > > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreckojoksimovic at gmail.com Tue Jun 28 03:12:40 2011 From: sreckojoksimovic at gmail.com (srecko joksimovic) Date: Tue, 28 Jun 2011 09:12:40 +0200 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: <82864263-3874-429D-8216-AAB27C57D98F@ontotext.com> References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> <005b01cc310d$d6d7e230$8487a690$@com> <006301cc3114$35501750$9ff045f0$@com> <5A9E35B2-3215-4876-94A5-830219D7A109@ontotext.com> <001701cc3356$0132c410$03984c30$@com> <82864263-3874-429D-8216-AAB27C57D98F@ontotext.com> Message-ID: Hi Philip, I've decided to go step by step, to learn, and to see what I did wrong. I created kim/context/default/kb/acm folder, and copied my acm.ttl file. I configured owlim.ttl, and added one more import. Then I created folder kim/context/default/kb/acm and file query.txt with content like this: prefix rdfs: prefix protont: PREFIX protons: SELECT ?la ?entity ?cl WHERE { ?entity a ?cl ; rdfs:label ?la ; protons:generatedBy . ?cl rdfs:subClassOf protont:Topic . OPTIONAL { ?sc rdfs:subClassOf ?cl. ?entity a ?sc . filter(?cl != ?sc) } filter (!bound(?sc) && isURI (?cl)) } I also deleted populated folder and tried to start kim. There was only one problem, and here is part of the output: [INFO] Adding ontology kb/wkbx.nt... [INFO] Adding ontology kb/acm/acm-ccs_proton.ttl... [Fatal Error] proton#:1:1: Content is not allowed in prolog. [ERROR] Parsing failed org.openrdf.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1] at org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:533) at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:267) at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:244) at com.ontotext.trree.OwlimSchemaRepository._addThisOntology(OwlimSchemaRepository.java:820) at com.ontotext.trree.OwlimSchemaRepository.doLocalInit(OwlimSchemaRepository.java:768) at com.ontotext.trree.OwlimSchemaRepository.initialize(OwlimSchemaRepository.java:555) at org.openrdf.repository.sail.SailRepository.initialize(SailRepository.java:84) at com.ontotext.kim.semanticrepository.UnmanagedRepositoryFactory.reconnect(UnmanagedRepositoryFactory.java:40) at com.ontotext.kim.KIMServiceImpl.getSemanticRepositoryAPI(KIMServiceImpl.java:228) at com.ontotext.kim.KIMServiceImpl.getSemanticRepositoryAPI(KIMServiceImpl.java:198) at com.ontotext.kim.KIMServiceImpl$ServerComponentStarter.run(KIMServiceImpl.java:82) Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog. at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:260) ... 9 more [INFO] Labels are loaded from aliases. [INFO] Waking Up GATE... Probably, the problem is with labels. Maybe I'm wrong, but as I understand, in query above I'm looking for label, but if you remember, in my rdf file I use alias... and, here is the part of my file: < http://www.lornet.org/acm-ccs/proton#Alias_07c6001f-8f5c-49e1-ae3c-92c9121b4297 > a protons:Alias ; "Convex Programming at en" . < http://www.lornet.org/acm-ccs/proton#Alias_63786f1d-7b3c-4872-b4e0-8227de53c015 > a protons:Alias ; "Document and Text Processing at en" . a protont:Topic ; protons:generatedBy ; protons:hasMainAlias < http://www.lornet.org/acm-ccs/proton#Alias_dee6eec3-b503-4d3e-a98d-ecdde5d5ee1a> . < http://www.lornet.org/acm-ccs/proton#Alias_ff639082-2cc4-484e-92f7-5f0f09898d2d > a protons:Alias ; "Store and Forward Networks at en" . < http://www.lornet.org/acm-ccs/proton#Alias_7f00cebc-8828-4415-83b3-2eb53ae3b0b6 > a protons:Alias ; "Integral Equations at en" . < http://www.lornet.org/acm-ccs/proton#Alias_08a8af20-311b-4a43-b996-7d4a8c034636 > a protons:Alias ; "Information Filtering at en" . The good thing is that I want to learn, and the bad thing is that I ask to much :) Thank you in advance! Srecko -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreckojoksimovic at gmail.com Tue Jun 28 05:14:21 2011 From: sreckojoksimovic at gmail.com (srecko joksimovic) Date: Tue, 28 Jun 2011 11:14:21 +0200 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: <862155F6-7D1F-4D28-A397-95026CC6C1E4@ontotext.com> References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> <005b01cc310d$d6d7e230$8487a690$@com> <006301cc3114$35501750$9ff045f0$@com> <5A9E35B2-3215-4876-94A5-830219D7A109@ontotext.com> <001701cc3356$0132c410$03984c30$@com> <82864263-3874-429D-8216-AAB27C57D98F@ontotext.com> <862155F6-7D1F-4D28-A397-95026CC6C1E4@ontotext.com> Message-ID: Hi Philip, looks like the first problem was because of file extension. When I changed from ttl to nt, everything went fine. Now I'll try JVisualVM. Thank you for your help! Best, Srecko On Tue, Jun 28, 2011 at 9:27 AM, Philip Alexiev @ Ontotext < philip.alexiev at gmail.com> wrote: > Hi Srecko, > > The log indicates, that the RDF in kb/acm/acm-ccs_proton.ttl is not > valid. You can use some tool to validate it. A good one is an online service > at: http://www.rdfabout.com/demo/validator/ . > > After you fix this and KIM starts and loads your RDF, you can use > JVisualVM to connect to the server and try what the gazetteer query will > return. This is the easiest way to construct a correct gazetteer query that > fills its dictionary. I am attaching a screenshot how this is done: > Hope this helps. > Philip > > > > On 28 Jun 2011, at 10:12 AM, srecko joksimovic wrote: > > Hi Philip, > > I've decided to go step by step, to learn, and to see what I did wrong. > I created kim/context/default/kb/acm folder, and copied my acm.ttl file. I > configured owlim.ttl, and added one more import. Then I created folder > kim/context/default/kb/acm and file query.txt with content like this: > > prefix rdfs: > prefix protont: > PREFIX protons: > SELECT ?la ?entity ?cl > WHERE { > ?entity a ?cl ; > rdfs:label ?la ; > protons:generatedBy . > ?cl rdfs:subClassOf protont:Topic . > OPTIONAL > { > ?sc rdfs:subClassOf ?cl. > ?entity a ?sc . > filter(?cl != ?sc) > } > filter (!bound(?sc) && isURI (?cl)) > } > > I also deleted populated folder and tried to start kim. There was only one > problem, and here is part of the output: > > [INFO] Adding ontology kb/wkbx.nt... > [INFO] Adding ontology kb/acm/acm-ccs_proton.ttl... > [Fatal Error] proton#:1:1: Content is not allowed in prolog. > [ERROR] Parsing failed > org.openrdf.rio.RDFParseException: Content is not allowed in prolog. [line > 1, column 1] > at > org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:533) > at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:267) > at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:244) > at > com.ontotext.trree.OwlimSchemaRepository._addThisOntology(OwlimSchemaRepository.java:820) > at > com.ontotext.trree.OwlimSchemaRepository.doLocalInit(OwlimSchemaRepository.java:768) > at > com.ontotext.trree.OwlimSchemaRepository.initialize(OwlimSchemaRepository.java:555) > at > org.openrdf.repository.sail.SailRepository.initialize(SailRepository.java:84) > at > com.ontotext.kim.semanticrepository.UnmanagedRepositoryFactory.reconnect(UnmanagedRepositoryFactory.java:40) > at > com.ontotext.kim.KIMServiceImpl.getSemanticRepositoryAPI(KIMServiceImpl.java:228) > at > com.ontotext.kim.KIMServiceImpl.getSemanticRepositoryAPI(KIMServiceImpl.java:198) > at > com.ontotext.kim.KIMServiceImpl$ServerComponentStarter.run(KIMServiceImpl.java:82) > Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog. > at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) > at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown > Source) > at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:260) > ... 9 more > [INFO] Labels are loaded from aliases. > [INFO] Waking Up GATE... > > > Probably, the problem is with labels. Maybe I'm wrong, but as I understand, > in query above I'm looking for label, but if you remember, in my rdf file I > use alias... > > and, here is the part of my file: > > < > http://www.lornet.org/acm-ccs/proton#Alias_07c6001f-8f5c-49e1-ae3c-92c9121b4297 > > > a protons:Alias ; > > "Convex Programming at en" . > > < > http://www.lornet.org/acm-ccs/proton#Alias_63786f1d-7b3c-4872-b4e0-8227de53c015 > > > a protons:Alias ; > > "Document and Text Processing at en" . > > > a protont:Topic ; > protons:generatedBy > ; > protons:hasMainAlias > < > http://www.lornet.org/acm-ccs/proton#Alias_dee6eec3-b503-4d3e-a98d-ecdde5d5ee1a> > . > > < > http://www.lornet.org/acm-ccs/proton#Alias_ff639082-2cc4-484e-92f7-5f0f09898d2d > > > a protons:Alias ; > > "Store and Forward Networks at en" . > > < > http://www.lornet.org/acm-ccs/proton#Alias_7f00cebc-8828-4415-83b3-2eb53ae3b0b6 > > > a protons:Alias ; > > "Integral Equations at en" . > > < > http://www.lornet.org/acm-ccs/proton#Alias_08a8af20-311b-4a43-b996-7d4a8c034636 > > > a protons:Alias ; > > "Information Filtering at en" . > > The good thing is that I want to learn, and the bad thing is that I ask to > much :) > > Thank you in advance! > > Srecko > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion > > > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: not available Type: image/png Size: 144897 bytes Desc: not available URL: From sreckojoksimovic at gmail.com Tue Jun 28 06:22:59 2011 From: sreckojoksimovic at gmail.com (srecko joksimovic) Date: Tue, 28 Jun 2011 12:22:59 +0200 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> <005b01cc310d$d6d7e230$8487a690$@com> <006301cc3114$35501750$9ff045f0$@com> <5A9E35B2-3215-4876-94A5-830219D7A109@ontotext.com> <001701cc3356$0132c410$03984c30$@com> <82864263-3874-429D-8216-AAB27C57D98F@ontotext.com> <862155F6-7D1F-4D28-A397-95026CC6C1E4@ontotext.com> Message-ID: Hi Philip, I hope that you are still wiling to help me :) I finished the first part - started KIM and installed JVisualVM. I didn't have any problem to get it up and running, but I couldn't get MBeans because of: "Data not available because JMX connection to the JMX agent could not be established." I tried "Add JMX Connection..." and I got this message: "Cannot connect to localhost:8080 using service:jmx:rmi://jndi/rmi://localhost:8080/jmxrmi" I probably missed something again... could you please tell me what? -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreckojoksimovic at gmail.com Tue Jun 28 10:18:53 2011 From: sreckojoksimovic at gmail.com (Srecko Joksimovic) Date: Tue, 28 Jun 2011 16:18:53 +0200 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> <005b01cc310d$d6d7e230$8487a690$@com> <006301cc3114$35501750$9ff045f0$@com> <5A9E35B2-3215-4876-94A5-830219D7A109@ontotext.com> <001701cc3356$0132c410$03984c30$@com> <82864263-3874-429D-8216-AAB27C57D98F@ontotext.com> <862155F6-7D1F-4D28-A397-95026CC6C1E4@ontotext.com> Message-ID: <002d01cc359e$50665390$f132fab0$@com> Hi Philip, Yes I have. It is exactly same as in your screenshot. When I select MBeans, all I see is this message: "Data not available because JMX connection to the JMX agent could not be established." Maybe I should do something to enable this JMX agent? Best, Srecko -----Original Message----- From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at gmail.com] Sent: Tuesday, June 28, 2011 12:32 To: srecko joksimovic Cc: kim-discussion at ontotext.com mailing-list Subject: Re: [Kim-discussion] Extend proton ontology Hi Srecko Have you activated the MBeans extension in JVisualVM ? Once you do it, when you select the KIM server process, you will be able to see the list of registered MBeans and choose from them as you see in my screenshot. Hth, Philip On 28 Jun 2011, at 1:22 PM, srecko joksimovic wrote: > Hi Philip, > > I hope that you are still wiling to help me :) > > I finished the first part - started KIM and installed JVisualVM. I didn't have any problem to get it up and running, but I couldn't get MBeans because of: > > "Data not available because JMX connection to the JMX agent could not be established." > > I tried "Add JMX Connection..." and I got this message: > > "Cannot connect to localhost:8080 using service:jmx:rmi://jndi/rmi://localhost:8080/jmxrmi" > > I probably missed something again... could you please tell me what? > > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion From philip.alexiev at ontotext.com Tue Jun 28 10:38:48 2011 From: philip.alexiev at ontotext.com (Philip Alexiev @ Ontotext) Date: Tue, 28 Jun 2011 17:38:48 +0300 Subject: [Kim-discussion] Extend proton ontology In-Reply-To: <002d01cc359e$50665390$f132fab0$@com> References: <001901cc30ea$27e60bd0$77b22370$@com> <17070B9A-06C9-4167-A620-953E8BF40DE1@ontotext.com> <2A4787D1-EEF0-4C93-998D-B735FFB0C3E3@ontotext.com> <004201cc30f9$f5e24b20$e1a6e160$@com> <02A439F2-0DD7-49DB-9662-5E339E13CCE9@ontotext.com> <005b01cc310d$d6d7e230$8487a690$@com> <006301cc3114$35501750$9ff045f0$@com> <5A9E35B2-3215-4876-94A5-830219D7A109@ontotext.com> <001701cc3356$0132c410$03984c30$@com> <82864263-3874-429D-8216-AAB27C57D98F@ontotext.com> <862155F6-7D1F-4D28-A397-95026CC6C1E4@ontotext.com> <002d01cc359e$50665390$f132fab0$@com> Message-ID: Hi Srecko, Have you run the KIM server? Is it on your local machine? Are you accessing it through a proxy ? best, philip On 28 Jun 2011, at 5:18 PM, Srecko Joksimovic wrote: > Hi Philip, > > Yes I have. It is exactly same as in your screenshot. When I select MBeans, > all I see is this message: > "Data not available because JMX connection to the JMX agent could not be > established." > > Maybe I should do something to enable this JMX agent? > > Best, > Srecko > > -----Original Message----- > From: Philip Alexiev @ Ontotext [mailto:philip.alexiev at gmail.com] > Sent: Tuesday, June 28, 2011 12:32 > To: srecko joksimovic > Cc: kim-discussion at ontotext.com mailing-list > Subject: Re: [Kim-discussion] Extend proton ontology > > Hi Srecko > > Have you activated the MBeans extension in JVisualVM ? Once you do it, when > you select the KIM server process, you will be able to see the list of > registered MBeans and choose from them as you see in my screenshot. > > Hth, > Philip > > > On 28 Jun 2011, at 1:22 PM, srecko joksimovic wrote: > >> Hi Philip, >> >> I hope that you are still wiling to help me :) >> >> I finished the first part - started KIM and installed JVisualVM. I didn't > have any problem to get it up and running, but I couldn't get MBeans because > of: >> >> "Data not available because JMX connection to the JMX agent could not be > established." >> >> I tried "Add JMX Connection..." and I got this message: >> >> "Cannot connect to localhost:8080 using > service:jmx:rmi://jndi/rmi://localhost:8080/jmxrmi" >> >> I probably missed something again... could you please tell me what? >> >> >> _______________________________________________ >> Kim-discussion mailing list >> Kim-discussion at ontotext.com >> http://ontotext.com/mailman/listinfo/kim-discussion > > _______________________________________________ > Kim-discussion mailing list > Kim-discussion at ontotext.com > http://ontotext.com/mailman/listinfo/kim-discussion