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[bioontology-support] Radlex Bioportal files

Ray Fergerson ray.fergerson at
Wed Aug 10 15:52:36 PDT 2011


My understanding is that we fixed the “synonym subslot” problem some time
ago. What should happen is that you specify the synonym super-slot and
then all values of all subslots of synonym automatically get used. Have
you tried this recently and found that it does not work? If so then this
is a bug that we should fix.

I am unclear about this preprocessing (flattening) step. Is this something
that someone on your end runs or is this something that someone here has
developed? (I have been here only a year and may have missed some

It is true that the BioPortal UI does not handle instances. In any case
you would probably want the system to pick up strings rather than
instances as labels. That way they will get used for such things as
annotation, autocomplete, and search. Perhaps it would be best to use the
preprocessing to create different language versions and load them into
BioPortal as views. This would provide a more natural browsing experience
for the language specific versions.

We can provide the original files for download rather than the processed
ones. We do this in other similar cases.


From: Collins, Beverly [mailto:Beverly.Collins at]
Sent: Thursday, August 04, 2011 2:26 PM
To: ray.fergerson at
Subject: Radlex Bioportal files

Hi Ray,

I’ve been investigating some things that happen with Radlex when it goes
into Bioportal,

and I have discovered a couple things.   One is that the Protégé is being
“flattened” for upload

to Bioportal, so that certain features don’t carry over, such as the slots
we have as sub-slots

of other slots are no longer in that relation, and the values don’t carry
up to the superslot.

We had subslots of Synonym so that we could distinguish, for instance,
“unsanctioned” synonyms,

misspellings, and so on.

One solution to that would be to allow for the Bioportal search function
to search in more slots than

just Preferred_Name and Synonym.  For now we think we have handled this by

pre-processor that overtly put the values into the Synonym slot from the
others, so that they will

show up in both places, but please let me know if there come to be options
for specifying a greater

number of search slots.

Another issue is that our terms originally are created as instances, so
that they can have a

slot indicating what language the term is.  (We have, e.g. German
translations of term names.)

The flattening process converts these to strings, so that the language
information is lost.

I’m not sure there is anything you can do about that, except to make the
original version available

to users.

However, the files that are available for upload from Bioportal are the
flattened versions,

so we wonder whether we can either replace that with the original protégé
files or have

the download link go to a Radlex site that will host the protégé files. I
don’t know how flexible

the Bioportal setup is.  If it is such that the files that go into
Bioportal must be the ones that are

made available, then can we somehow put a note indicating that this is a
converted file, and

that the originals are available at (I think we would also
need to provide some plugin files

if users are to use the originals.)

Finally, I see that the text description on the Bioportal Radlex homepage
gets cut off at the right side, at least

on my browser.  It shows:

RadLex is a controlled terminology for radiology-a single unified source
of radiology te

radiology practice, education, and research. For liscence information see


If I cut and paste the content, I get the whole phrase, but I’m not sure
why it isn’t displaying properly.

(Also, license is misspelled, our fault no doubt, but I’d be grateful if
you could fix it!)

Oh, actually one more: is it possible to get our programmer’s test Notes
deleted?  that would be, I think,

all the notes except the one I posted, the one from Daumke, and the one
someone posted today.

Thanks so much for your time on this.


Beverly Spejewski Collins, PhD

Grant coordinator, UPenn Radiology

RadLex coordinator, RSNA

P: 215-615-0429

F: 215-662-3093

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