[BioNLP] Annotated corpora containing anatomical and disease mentions?

Faisal Mahbub Chowdhury chowdhury at fbk.eu
Fri Apr 27 08:22:13 EDT 2012

Hi Phil,

You might also want to look at the Arizona Disease Corpus (AZDC)<http://diego.asu.edu/downloads/AZDC> (http://diego.asu.edu/downloads/AZDC/). It has 2856 PubMed abstracts annotated with disease names and mapped to UMLS CUIs.


From: bionlp-bounces at lists.ccs.neu.edu [bionlp-bounces at lists.ccs.neu.edu] on behalf of Mariana Neves [neves at informatik.hu-berlin.de]
Sent: Friday, April 27, 2012 1:29 PM
To: Natural language processing for biology
Subject: Re: [BioNLP] Annotated corpora containing anatomical and disease mentions?

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 :)


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


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