Getting started: bumps in the road

Feb 7, 2009 at 10:29 PM
I managed to get the add-in installed, adjusted its settings, and loaded some ontologies,
and am now trying to make it do something.

One problem is that if you add an ontology to the existing set, all ontologies
are reloaded, even if they were loaded previously. This is a problem when
one of them is a large ontology such as biological process.

In the release notes it says "
  • Open the test document from the Releases tab and follow the instructions in the page "
    The test document, assuming I found the right one, does not seem to have any
    instructions.

    The dotted underlining is almost invisible - I didn't notice it the first few times I
    visited the sample file. It appears under words that I wouldn't expect to find in
    my selected ontologies; but perhaps my settings are incorrect and it is looking
    outside of BioLit.

    I loaded IDO (among others) and attached a two-button mouse, clicked right on
    'epidemic', selected BioLit markup selection, and got a blank 'MarkupAliasing'
    window with no instructions.

    Not sure how to proceed. Please advise.

    Best
    Jonathan
  • Developer
    Feb 8, 2009 at 12:20 AM
    Hi Jonathan,

    Thank you so much for trying the add-in and for giving us feedback! It is early stages still so there are indeed some bumps in the road. I address your comments below.

    One problem is that if you add an ontology to the existing set, all ontologies
    are reloaded, even if they were loaded previously. This is a problem when
    one of them is a large ontology such as biological process.

    Yes, this is a known issue and has been submitted for fixing.

    In the release notes it says "
  • Open the test document from the Releases tab and follow the instructions in the page "
    The test document, assuming I found the right one, does not seem to have any
    instructions.


    I think you have the right one. There aren't really instructions (I edited the web page to remove that part); the header mentions that you need to download the Human Disease ontology to see some terms being recognized (although probably some other ontologies will work as well).

    The dotted underlining is almost invisible - I didn't notice it the first few times I
    visited the sample file. It appears under words that I wouldn't expect to find in
    my selected ontologies; but perhaps my settings are incorrect and it is looking
    outside of BioLit.


    I don't think there is much we can do about the underlining. I agree that it is extremely subtle. I will let the Microsoft guys comment on this since they know about this than I do.

    The unfortunate aspect of this entire enterprise is that the ontologies were not created for this purpose. Therefore, they contain a lot of words that you wouldn't think to select in your article and a lot of words that you would select if you used the exact term that the ontology used for that concept (which may be much more formal or lengthy than what is commonly used). There are some ways of improving this, primarily by also using the synonyms for the terms in the ontologies, but this is a surprisingly complicated venture. Hopefully, in future versions we can attempt this. Until then, however, there are not many feasible alternatives for addressing this problem. You can choose to have the add-in ignore terms that you feel are unnecessarily highlighted.

    The add-in will definitely not look outside of the ontologies that you have downloaded.

    I loaded IDO (among others) and attached a two-button mouse, clicked right on
    'epidemic', selected BioLit markup selection, and got a blank 'MarkupAliasing'
    window with no instructions.

    In order to make the Smart Tag appear, you need to hover the mouse cursor over the term. Right-clicking is a different function (and also one that has been submitted for fixing since it doesn't appear to work properly).

    I have written a draft of a User's Guide, but I didn't want to post it until the other team members had a chance to make their edits and additions. I made a draft version for you to look at for now, but I can't see how to attach it here. If you email me directly (biolit@ucsd.edu) I can send you the PDF. Otherwise, you can wait until we post the official version which will hopefully be early next week.

    Best regards,
    Lynn