[BioNLP] Annotated corpora containing anatomical and disease mentions?

Mariana Neves neves at informatik.hu-berlin.de
Fri Apr 27 07:29:59 EDT 2012

Dear Phil,

we have recently made available the CellFinder corpus (to be presented 
at the LREC next month) which contains 10 full papers and anatomical 
annotations related to the stem cell domain. I guess there are also some 
body parts and tissues annotated in the GENIA corpus. Regarding 
diseases, there are some in the BioText corpus. All of them are 
available for visualization in our corpora repository and for download 
in the corresponding website, by clicking on the name of the corpus.


Not (yet) included in our repository, you might want to have a look at 
the EBI corpus for disease 
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2352871/). The CALBC silver 
corpus which also contains diseases ( http://www.calbc.eu/).

Although I am afraid none contains both diseases and anatomical 
annotations. I hope it helps you.



On 04/27/2012 01:03 PM, Phil Gooch wrote:
> (reply to self) I've found this useful resource: 
> http://www.nactem.ac.uk/resources.php?view=9 although it's just noun 
> phrases rather than complete sentences/paragraphs. Being able to 
> identify 'body' in a list of noun phrases is a bit different to 
> correctly identifying and disambiguating 'body' in it's anatomical 
> context in free text :)
> Phil
> On Fri, Apr 27, 2012 at 11:10 AM, Phil Gooch <philgooch at gmail.com 
> <mailto:philgooch at gmail.com>> wrote:
>     Hi all
>     Is anyone aware of any biomedical corpora (such as Medline
>     abstracts) freely available that have been annotated for
>     anatomical and disease concepts? I have some clinical notes, but
>     it would be good to have some more general biomedical resources also.
>     Many thanks
>     Phil
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