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Commented Issue: Unable to load OBO ontology [9298]

reach2raziq — Mon, 05 Sep 2011 14:48:24 GMT

After doing a fresh install of the Add-in (Word 2010), I am not able to load an ontology for use with the Add-in. The select menu on the left-hand side of the Add-in does not display any ontologies and after manually downloading an ontology and using the file chooser on the right-hand side of the Add-in the ontology is not loaded.
Comments: ** Comment from web user: reach2raziq **

Hi,

In current version of Word Add-in For Ontology Recognition, Apikey was not required to pass along with URI for user authentication. You need to wait until the new version of Word Add-in For Ontology Recognition that matches the latest changes of BioLit Web services.

We are working on the latest release and we will notify the community users when the new release is available for download.

Regards,
Abdul Raziq
MSR ER Customer Support Team

Commented Issue: Unable to load OBO ontology [9298]

whetzel — Fri, 02 Sep 2011 21:37:26 GMT

The BioLit project (http://biolit.ucsd.edu/doc/) is now working, however there seems to still be issues with the Add-in. Can you confirm whether the Add-in is working in your environment?

Thanks!
Trish

Commented Issue: Unable to load OBO ontology [9298]

jlfink — Fri, 19 Aug 2011 03:08:39 GMT

I suspect that we need to use an NCBO API key in the URL queries now. I have obtained the key and forwarded it to others that are more capable in editing the code. Hopefully, this will fix the issue.

Commented Issue: Unable to load OBO ontology [9298]

reach2raziq — Fri, 12 Aug 2011 06:51:20 GMT

Hi,
Thanks for showing interest on Word Add-in For Ontology Recognition.

The UCSD Biolit Server is down which is causing this problem. We have a constant track on this and update you once the server is up.

Regards,
MSR ER Support Team

Commented Issue: Unable to load OBO ontology [9298]

whetzel — Thu, 11 Aug 2011 07:54:54 GMT

Screenshot uploaded.

Created Issue: Unable to load OBO ontology [9298]

whetzel — Thu, 11 Aug 2011 07:49:10 GMT

Commented Issue: Ontology Add-in may not load if there is a conflict with other add-ins [1431]

cnprakash — Thu, 16 Dec 2010 12:26:03 GMT

When other add-ins are installed (such as the Article Authoring Add-in or Math Add-in for Microsoft Office Word, for example), the ontology add-in may not load. This problem can also happen with other add-ins.

The current belief is that the problem is related to this:

http://blogs.msdn.com/vsod/archive/2008/11/01/vsto-2008-throws-cannotcreatecustomizationdomainexception-when-microsoft-word-math-add-in-is-installed.aspx

From the description “this issue only reproduces when you have another Add-in installed that implements IDTExtensibility2 interface … this is related with one of the CLR bugs and the only way to avoid this is shiming the COM Add-in For e.g.(The Microsoft Math Add-in for Microsoft Office Word 2007) using the COM shim wizard and register the shimmed dll on the problem machine)."

Changes will likely have to be made to this and other add-ins to avoid this problem.
Comments: ** Comment from web user: cnprakash **

Hi,

We were able to reproduce this issue in our test machine. The issue is being caused as the Ontology add-in is not able to access the Ontology REST Web Services. Can you please check if you are able to access the following Ontology web-services from your browser: http://rest.bioontology.org/bioportal/ontologies ?

In case you are able to access the Ontology web services from your browser, please follow either of two solutions given below to resolve this issue.

Solution 1:
Configure internet explorer to use a Proxy server. For more details on how to configure the Internet Explorer to use a proxy server please refer the link below.
http://support.microsoft.com/kb/135982
Solution 2 :
Create an Exception for Microsoft Word in Windows Firewall. For more details on how to create Exception in windows firewall please refer the link below.
http://www.sevenforums.com/tutorials/542-windows-firewall-add-remove-exception.html

Please let us know if our solution helps in solving your issue.
Regards,
Support Team

Commented Issue: Ontology Add-in may not load if there is a conflict with other add-ins [1431]

cnprakash — Fri, 10 Dec 2010 13:34:43 GMT

Hi,

We are currently working on this issue ,we will keep you posted on the updates.

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

Commented Issue: Ontology Add-in may not load if there is a conflict with other add-ins [1431]

KirtChristensen — Thu, 09 Dec 2010 15:45:44 GMT

The addin installed and loaded the first time. However, it would not load the OBO files. The dialog for selecting them would not provide the Ontology terms in a list or let me select a local OBO file and load it. Clicking the OK button had no effect. Only cancel would work. The next time that Word was loaded the Ontology Addin was listed as disabled. I have tried to remove and reload it without success.

1. Office 2007 is being used.
2. Lots of COM and Smart Tag addins. Here is a list:

Active Add-Ins
No Active Add-ins
Inactive Add-ins
ActionsPane C:\....O\ActionsPane.xsd XML Schema
ActionsPane3 C:\..AActionsPane3.xsd XML Schema
ClearCase Word Integration C:\...in\ccmsoaddin,dll COM Add-in
Custom XML Data C:\,..icel2\OFFRHDDLL Document Inspector
Date (Smart tag lists) C:\...art Tag\MOFL.DLL Smart Tag
Financial Symbol (Smart tag lists) C:\..art Tag\MOFLDLL Smart Tag
Google Desktop Office Addin C:\..,DesktopOffice.dll COM Add-in
Headers, Footers, and Watermarks C:\...icel2\OFFRHD.DLL Document Inspector
Hidden Text C:\...icel2\OFFRHD.DLL Document Inspector
Measurement Converter (Measurement Converter) C:\...Tag\METCONV.DLL Smart Tag
Microsoft Actions Pane — XML Expansion Pack
Microsoft Actions Pane 3 a XML Expansion Pack
Microsoft Visual Studio 2008 Tools for Office Design-Time Adaptor for Word 2003 C:\...rd2003Adaptor.dll COM Add-in
Microsoft Visual Studio 2008 Tools for Office Design-Time Adaptor for Word 2007 C:\...rd200lAdaptor,dll COM Add-in
Person (Lotus Notes Recognizer) C:\...otes\smarttags.dll Smart Tag
Person (Outlook e-mail recipients) C:\...rt Tag\FNAMEDLL Smart Tag
Telephone Number (Smart tag lists) CA...art Tag\MOFLDLL Smart Tag
Time (Smart tag lists) C:\...art Tag\MOFL.DLL Smart Tag
Disabled Add-ins
Word Add in For Ontology Recognition C:\.,,ioLit.vstolvstolocal COM Add-in

Commented Issue: Ontology Add-in may not load if there is a conflict with other add-ins [1431]

cnprakash — Wed, 08 Dec 2010 12:54:33 GMT

Hi,

We were not able to reproduce this issue on our test machine. Can you please share the repro steps and the following details with us:
1. The version of Office being used by you.
2. The add-ins you have installed prior to the installation of ontology add-in .
Also, can you please let us know the exact error you are getting when You are installing ontology add-in .

Please let us know in case you have any questions/concerns.
Regards,
Support Team

Commented Issue: Ontology Add-in may not load if there is a conflict with other add-ins [1431]

KirtChristensen — Tue, 07 Dec 2010 20:46:06 GMT

I have downloaded the lastest version and installed. I appear to be having a similiar problem. Feel free to contact me directly if you have advise on how to eliminate these conflicts. I'm removing other addins currently.

Created Issue: Feature Req: add support for Synonyms [6093]

AlexWade — Mon, 10 May 2010 21:17:13 GMT

The add-in should recognize term synonyms and allow markup. Perhaps even with the option to mark-up the synonym or to use the preferred term instead.

Commented Issue: Ontology Add-in may not load if there is a conflict with other add-ins [1431]

erteam — Sat, 08 May 2010 00:15:10 GMT

We made some significant changes to interoperability with other add-ins for the beta 2 release. Please try it and let us know if that fixes the issue.

Thanks

Commented Issue: Ontology Add-in may not load if there is a conflict with other add-ins [1431]

erteam — Sat, 08 May 2010 00:15:08 GMT

We made some significant changes to interoperability with other add-ins for the beta 2 release. Please try it and let us know if that fixes the issue.

Thanks

Closed Issue: BioLit Info Pane / Search Terms case-sensitive and only matches whole terms [1556]

erteam — Fri, 07 May 2010 23:59:54 GMT

If I enter a term in the Search Terms tab of the Info Pane, I can only find a term if I enter the exact term (which mostly defeats the purpose of this feature).

This search needs to be case-insensitive and it should match partial strings.

For example, "Diabetes" should match "diabetes mellitus", "diabetes insipidus", etc.

It would also be good to have a "no results found" message in those instances.
Comments:

Fixed in Beta 2

Commented Issue: Ontology Browser needs to be cleared after ontologies are deleted [1558]

erteam — Fri, 07 May 2010 23:59:37 GMT

If an ontology is displayed in the BROWSER and then it is deleted in the config panel, the BROWSER still displays that ontology (and it is navigable and is listed in the drop-down menu). When an existing ontology is selected instead, the deleted ontology finally goes away.
Comments: ** Comment from web user: erteam **

This should be fixed in beta 2. Please try it and let us know.

Thanks

Commented Issue: Database ID recognition does not toggle [2069]

erteam — Fri, 07 May 2010 23:58:16 GMT

If I have PDB ID turned on and I type a PDB ID, it is recognized. If I turn off PDB ID recognition in the config panel, the ID is still recognized. The behaviour I would expect is for the recognition for those IDs to stop.
Comments: ** Comment from web user: erteam **

This should be fixed in Beta 2. Please try it and let us know.

Thanks

Commented Issue: Highlight Terms is faulty [2384]

erteam — Fri, 07 May 2010 23:57:33 GMT

After terms are marked-up and highlighting is turned on, the highlights never go away even when Highlight Terms is toggled. Also some terms never get highlighted even though they are marked-up.
I can give you the document I was using if you can't replicate this.
Comments: ** Comment from web user: erteam **

This should be fixed in Beta 2. Please try it and let us know.

Thanks

Closed Issue: "Ontologies" add-in randomly deactivated [2386]

erteam — Fri, 07 May 2010 23:56:52 GMT

Sometimes, the "Ontologies" tab disappears after Word is closed and reopened. It appears to be inactivated in the Add-in Options menu. I tried reactivating it, but that didn't work. This issue seems to be unique to the latest release. Reinstall fixes it.
Comments:

Fixed in Beta 2

Commented Issue: Need smarttag option for marking-up all database IDs [5587]

erteam — Fri, 07 May 2010 23:55:00 GMT

There is a menu option that allows automatic mark-up of all future instances of ontology terms, but it doesn't exist for the database IDs.
Comments: ** Comment from web user: erteam **

Please check to see if this is still true in Beta 2.
Thanks