Re: Ontology Annotator to the sandbox
Ahmed, people are busy getting the release ready, which is I guess mostly why you're not getting much feedback. Maybe you could ping us again after the release is out? --Thilo Ahmed Abdeen Hamed wrote: Hello UIMA-developers, I am just following up on the original note that I sent about donating obo-annotator to the sandbox. I hope you have had some time to review and decide whether or not etc. I understand that my code does not perhaps live to the high standards of the developers here. This is because we built the application over time for research purposes and it was not intended to be used by other communities. However, after playing with it for a while now, I believe this application will add so much value to the current UIMA projects. So, please don't let my messy code push you away from getting it ready for a nice and decent incubator release :-) To make the decision easier, I can schedule a a live demo to show you what this application can do. I can use screen-share since I am a mac user but I can use other technologies if that works best for any of you. Please let me know what you one way or the other. Thanks, Ahmed On Tue, Aug 18, 2009 at 9:43 AM, Ahmed Abdeen Hamedahmed.elma...@gmail.com wrote: Hi Jörn, Yes, I just remembered that the documentation was also on the website as well. Here is also the link to the demo application that we developed for ASU Embryo Project that used the tool. The tool was pointed to manually curated ontologies by domain experts in Purble Sea Urchin and annotated the each MEDLINE abstract with the Concepts, Organizations and People entities. You will see the terms highlighted when you click on the abstracts provided: http://enuvis07.fulton.asu.edu:3000/abstracts/ Please let me know if you have any further questions. Ahmed On Tue, Aug 18, 2009 at 3:41 AM, Jörn Kottmann kottm...@gmail.com wrote: Ahmed Abdeen Hamed wrote: Attached is the documentation to the old version and I will point you a PEAR file once I finish refactoring. You cannot send attachments to this list. http://obo-annotator.svn.sourceforge.net/viewvc/obo-annotator/obo-annotator/OBO-Annotator.pdf?view=log Is this the link to the documentation you attached ? Jörn
Re: Ontology Annotator to the sandbox
Sure, sounds good Thilo. Good luck with the release! Ahmed On Tue, Aug 25, 2009 at 10:04 AM, Thilo Goetztwgo...@gmx.de wrote: Ahmed, people are busy getting the release ready, which is I guess mostly why you're not getting much feedback. Maybe you could ping us again after the release is out? --Thilo Ahmed Abdeen Hamed wrote: Hello UIMA-developers, I am just following up on the original note that I sent about donating obo-annotator to the sandbox. I hope you have had some time to review and decide whether or not etc. I understand that my code does not perhaps live to the high standards of the developers here. This is because we built the application over time for research purposes and it was not intended to be used by other communities. However, after playing with it for a while now, I believe this application will add so much value to the current UIMA projects. So, please don't let my messy code push you away from getting it ready for a nice and decent incubator release :-) To make the decision easier, I can schedule a a live demo to show you what this application can do. I can use screen-share since I am a mac user but I can use other technologies if that works best for any of you. Please let me know what you one way or the other. Thanks, Ahmed On Tue, Aug 18, 2009 at 9:43 AM, Ahmed Abdeen Hamedahmed.elma...@gmail.com wrote: Hi Jörn, Yes, I just remembered that the documentation was also on the website as well. Here is also the link to the demo application that we developed for ASU Embryo Project that used the tool. The tool was pointed to manually curated ontologies by domain experts in Purble Sea Urchin and annotated the each MEDLINE abstract with the Concepts, Organizations and People entities. You will see the terms highlighted when you click on the abstracts provided: http://enuvis07.fulton.asu.edu:3000/abstracts/ Please let me know if you have any further questions. Ahmed On Tue, Aug 18, 2009 at 3:41 AM, Jörn Kottmann kottm...@gmail.com wrote: Ahmed Abdeen Hamed wrote: Attached is the documentation to the old version and I will point you a PEAR file once I finish refactoring. You cannot send attachments to this list. http://obo-annotator.svn.sourceforge.net/viewvc/obo-annotator/obo-annotator/OBO-Annotator.pdf?view=log Is this the link to the documentation you attached ? Jörn
Re: Ontology Annotator to the sandbox
Hello UIMA-developers, I am just following up on the original note that I sent about donating obo-annotator to the sandbox. I hope you have had some time to review and decide whether or not etc. I understand that my code does not perhaps live to the high standards of the developers here. This is because we built the application over time for research purposes and it was not intended to be used by other communities. However, after playing with it for a while now, I believe this application will add so much value to the current UIMA projects. So, please don't let my messy code push you away from getting it ready for a nice and decent incubator release :-) To make the decision easier, I can schedule a a live demo to show you what this application can do. I can use screen-share since I am a mac user but I can use other technologies if that works best for any of you. Please let me know what you one way or the other. Thanks, Ahmed On Tue, Aug 18, 2009 at 9:43 AM, Ahmed Abdeen Hamedahmed.elma...@gmail.com wrote: Hi Jörn, Yes, I just remembered that the documentation was also on the website as well. Here is also the link to the demo application that we developed for ASU Embryo Project that used the tool. The tool was pointed to manually curated ontologies by domain experts in Purble Sea Urchin and annotated the each MEDLINE abstract with the Concepts, Organizations and People entities. You will see the terms highlighted when you click on the abstracts provided: http://enuvis07.fulton.asu.edu:3000/abstracts/ Please let me know if you have any further questions. Ahmed On Tue, Aug 18, 2009 at 3:41 AM, Jörn Kottmann kottm...@gmail.com wrote: Ahmed Abdeen Hamed wrote: Attached is the documentation to the old version and I will point you a PEAR file once I finish refactoring. You cannot send attachments to this list. http://obo-annotator.svn.sourceforge.net/viewvc/obo-annotator/obo-annotator/OBO-Annotator.pdf?view=log Is this the link to the documentation you attached ? Jörn
Re: Ontology Annotator to the sandbox
Ahmed Abdeen Hamed wrote: Attached is the documentation to the old version and I will point you a PEAR file once I finish refactoring. You cannot send attachments to this list. http://obo-annotator.svn.sourceforge.net/viewvc/obo-annotator/obo-annotator/OBO-Annotator.pdf?view=log Is this the link to the documentation you attached ? Jörn
Re: Ontology Annotator to the sandbox
Hi Jörn, Yes, I just remembered that the documentation was also on the website as well. Here is also the link to the demo application that we developed for ASU Embryo Project that used the tool. The tool was pointed to manually curated ontologies by domain experts in Purble Sea Urchin and annotated the each MEDLINE abstract with the Concepts, Organizations and People entities. You will see the terms highlighted when you click on the abstracts provided: http://enuvis07.fulton.asu.edu:3000/abstracts/ Please let me know if you have any further questions. Ahmed On Tue, Aug 18, 2009 at 3:41 AM, Jörn Kottmann kottm...@gmail.com wrote: Ahmed Abdeen Hamed wrote: Attached is the documentation to the old version and I will point you a PEAR file once I finish refactoring. You cannot send attachments to this list. http://obo-annotator.svn.sourceforge.net/viewvc/obo-annotator/obo-annotator/OBO-Annotator.pdf?view=log Is this the link to the documentation you attached ? Jörn
Ontology Annotator to the sandbox
Hello UIMA developers and engineers, I have been developing an Ontology-Based Annotator UIMA component for over a year now. The Annotator is based on the ConceptMapper that was first released last year. I have been successfully using the ontology annotator for a while. Also some of the collaborators at Indiana University have successfully used it for the BioCreativeII.5 and Arizona State University for their Embryo Project. Our school here has been thinking of donating the project to the UIMA community and create a sandbox for it. Please let me know if this is something that would be good the UIMA/NLP community and where I should start if everyone votes yet. Sincerely, Ahmed Ahmed Abdeen Hamed Scientific Informatics Project Leader Marine Biological Laboratoty, Wood Hole MA And Center of Clinical and Transactional Sciences University of Vermont, Burlington VT
Re: Ontology Annotator to the sandbox
Sounds interesting. If possible, can you post some links to more information about what it is? -Marshall Ahmed Abdeen Hamed wrote: Hello UIMA developers and engineers, I have been developing an Ontology-Based Annotator UIMA component for over a year now. The Annotator is based on the ConceptMapper that was first released last year. I have been successfully using the ontology annotator for a while. Also some of the collaborators at Indiana University have successfully used it for the BioCreativeII.5 and Arizona State University for their Embryo Project. Our school here has been thinking of donating the project to the UIMA community and create a sandbox for it. Please let me know if this is something that would be good the UIMA/NLP community and where I should start if everyone votes yet. Sincerely, Ahmed Ahmed Abdeen Hamed Scientific Informatics Project Leader Marine Biological Laboratoty, Wood Hole MA And Center of Clinical and Transactional Sciences University of Vermont, Burlington VT
