UCSDBioLit Discussions Rss Feed

New Post: Additional Database Resource Suggestions

blanchj — Wed, 27 Jul 2011 07:52:01 GMT

http://www.obofoundry.org/

http://www.imgt.org/IMGTeducation/Enseignements/_FR/FMBS312_MR2_TC3_290909.pdf (some biological ontologies descriptions)

New Post: Add-in not connecting to databases

AlexWade — Thu, 31 Mar 2011 18:53:26 GMT

Yes, it should be routing these http requests through your proxy configuration, but let me verify this and get back to you.

New Post: Add-in not connecting to databases

NBeyond — Thu, 31 Mar 2011 18:43:11 GMT

Thanks for responding so quickly! I'll look forward to trying the new version when it's ready. Quick question though while I have your ear: Should the data connector you're using work behind a proxy (as configured in iexplore)? Or will I need to try the add-in on a network that isn't proxified?

Thanks!

New Post: Add-in not connecting to databases

AlexWade — Thu, 31 Mar 2011 18:28:02 GMT

Nick,

Thanks for reaching out. There was a recent change to the NCBO ontology webservice that broke this add-in. Our engineers have the fix ready and should have this pushed out (in the binary and source code) in the next week. Apologies for the inconvenience!

---Alex

New Post: Add-in not connecting to databases

NBeyond — Thu, 31 Mar 2011 18:19:51 GMT

I'm hoping this project is still monitored. I tried installing this Add-in to see if it's something that we can adapt for our knowledge management initiative. When I bring up the configuration for the add-in I don't see any ontologies though. It will not let me load an obo file, and the form does not close when I click 'Ok'. I thought this might be my setup, as my workstation is behind a proxy, but I'm seeing the same behavior at home.

Is this expected with the add-in at the moment? Or did I miss something when installing it?

Thank you,

Nick Thorpe

New Post: add-in use for large text documents

rahularora25 — Tue, 09 Nov 2010 11:00:21 GMT

Hi,

Can you please let us know if our response solved your questions?

Regards,
Support Team

New Post: add-in use for large text documents

tcvinay — Fri, 15 Oct 2010 08:15:17 GMT

Hi,

Word add-in would work as expected when we annotate large documents. But it would be VERY slow to load and save and scan the document. This might be due to the reason that the word add-in has to analyze 900 pages and then annotate.

The above observation is based on the following environment:

1. Annotate a test document(contains 900 pages).

2. System Details:

Word 2010 32-bit

Windows 7 Enterprise 64-bit

4GB (3.9 Usable) RAM

Please let us know if this answers your question.

Thanks,

Support Team

New Post: add-in use for large text documents

endemoneus — Tue, 12 Oct 2010 15:23:02 GMT

I am afraid I cannot do that. I don't have the right to distribute it.

Thank you for your understanding.

New Post: add-in use for large text documents

tcvinay — Tue, 12 Oct 2010 06:14:24 GMT

Hi,

Can you please share the document (having 1000 pages) which you are using to annotate using word add-in? This will help to analyze the issue and come up with a solution.

Please let us know if you have any issues/concerns.
Thanks,
Support Team

New Post: add-in use for large text documents

tcvinay — Fri, 08 Oct 2010 13:30:09 GMT

Hi,

We are looking into your question. We will get back to you as soon as possible.

Please let us know if you have any further questions/issues.
Thanks,
Support Team

New Post: add-in use for large text documents

endemoneus — Thu, 07 Oct 2010 14:28:18 GMT

Can you please tell me if you can anticipate how the add-in would react when used to annotate large documents (e.g. a book of around 1000 pages)?

Thank you.

New Post: term highlighting+visualizing mark-ups

endemoneus — Thu, 07 Oct 2010 10:38:54 GMT

Seems to work just fine.

Thank you for your help.

New Post: term highlighting+visualizing mark-ups

tcvinay — Thu, 07 Oct 2010 09:31:39 GMT

Hi,

<<Term highlighting used to work at the beginning but now it doesn't work anymore>>
Yes, Term highlighting was used in the previous versions.

In later versions of Word, “custom XML” is automatically removed since it is no longer supported in Word. As a work around, the newer version of the Ontology add-in adds “Content Controls” to the word document.
In the new version of add-in, an option Highlight marked-up items is present under the Ontology tab. Also, Content Controls are created to contain the terms

<<Is there another way to check if the mark-ups have been created>>
Yes, You can check the mark-ups using these two methods:

You will need to enable the Developer tab in Microsoft Word 2010 and select the design mode property. This will highlight all your named-content.
In the XML, the mark-ups are stored with the named-content attribute

You can enable Developer tab using the following steps:

Open Microsoft Word 2010
Click on File -> Options
Select the Customize Ribbon option from the left pane
From the Choose commands drop-down menu, select on Main tabs
Select Developer and add it to the main tabs
The Developer tab appears on the main ribbon
select the Design Mode option to highlight all the named-content

Please let us know if this answers your questions.
Thanks,
Support Team

New Post: term highlighting+visualizing mark-ups

tcvinay — Wed, 06 Oct 2010 05:13:58 GMT

Hi,

We are working on your issue. We will get back to you as soon as possible.

Please let us know if you have any further comments/issues.
Regards,
Support Team

New Post: term highlighting+visualizing mark-ups

endemoneus — Tue, 05 Oct 2010 11:56:15 GMT

Hi,

I am testing the latest version of the add-in in Word 2010. Term highlighting used to work at the beginning but now it doesn't work anymore. Do you have a solution to this? Is there another way to check if the mark-ups have been created (without having to install the Article Authoring plug-in)? I have tried to visualize directly the content of my document as a ".zip" (in order to see the xml files behind), but couldn't manage to see the content...

Thank you.

New Post: Support for ".owl" ontologies

endemoneus — Wed, 29 Sep 2010 13:13:15 GMT

Hi,

Yes, it answers my question. Thank you.

New Post: Support for ".owl" ontologies

tcvinay — Tue, 28 Sep 2010 13:04:03 GMT

Hi,

We only support OBO ontologies for the time being. As of today we do not have any plans for supporting OWL ontologies.
However, this is something that should be relatively straightforward to implement if we have an OWL parser, as the source code for the Ontology add-in is available in codeplex.

I hope this answers your question.
Thanks,
Support Team

New Post: How to use relationship types

tcvinay — Mon, 27 Sep 2010 05:28:01 GMT

Hi,

Can you please give more details on what exactly are you trying to achieve and which tool are you using?

Thanks,
Support Team

New Post: How to use relationship types

endemoneus — Fri, 24 Sep 2010 14:20:18 GMT

Hi,

Thank you for your answer. In fact I wanted to translate my "owl" ontology into an "obo" one, in order to be able to test your tool using my own ontology. I read somewhere that you are discussing about providing support for owl ontologies. Can you please tell me if you plan to do so?

Thank you.

New Post: How to use relationship types

tcvinay — Thu, 23 Sep 2010 06:43:23 GMT

Hi,

We are working on your issue. We will get back to you as soon as possible.

Please let us know if you have any further comments/issues.
Regards,
Support Team