dataset links

[jd-coderepos]

Thank you for releasing this software with the community. 👍 💯 A small concern: would it be possible that the BioNLP dataset links are now broken?

[jd-coderepos]

It could be then that the old datasets are retired...

[yanyk13]

Any ideas where to get these datasets?

[jd-coderepos]

Not really. If they are retired perhaps then they are not publicly available anymore. But this is just my assumption.

[HevOHel]

I've tried Genia-2011 from official website of BioNLP, but there is still something wrong which is showed as file missing.

[jd-coderepos]

I have attempted to survey here the working links https://www.orkg.org/orkg/comparison/R165702 for BioNLP NER and https://www.orkg.org/orkg/comparison/R165866 for BioNLP Event Extraction.

[trieuhl]

I think you may need to contact the workshop's organizers. I found this, but not sure the data is same as the original or not:
https://sites.google.com/site/bionlpst2013/tasks/cancer-genetics-cg-task

[yanyk13]

I got 404 error when opening the data links...

[yanyk13]

https://www.orkg.org/orkg/comparison/R165866

There are no BioNLP-2013 data download links on this page

[trieuhl]

I am sorry to hear that. Maybe you need to contact the workshop organizer:
https://aclanthology.org/W13-2008.pdf

[yanyk13]

I wrote an email to Dr.Kim two months ago, he said the website works well for him. I wrote another email with a detailed description of the data links... However, he did not reply. Got no idea where to download the data...

[jd-coderepos]

I think you may need to contact the workshop's organizers. I found this, but not sure the data is same as the original or not: https://sites.google.com/site/bionlpst2013/tasks/cancer-genetics-cg-task

Indeed I see a 404 error too for the data links on the page.

[jd-coderepos]

Here is a link I found on PubMed https://www.ncbi.nlm.nih.gov/research/bionlp/Data/ . Sharing in case it may be helpful to someone.

[OStars]

Do you get the GE2013 now? Are there some alternative datasets for biomedical event extraction?

[jd-coderepos]

Some listed here 'Surveying BioNLP Shared Tasks Corpora for Event Extraction' https://orkg.org/comparison/R165866/ . For those without links, maybe the authors need to be contacted directly. If you get it could you please let us know... :)

[OStars]

I find GE2013 dataset which is the same as GE2016. GE2016 reuse the GE2013, which is re-complemented and re-designed for evaluation from KB construction perspective. For details, you could read the paper: Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task

[OStars]

I find GE2013 dataset which is the same as GE2016. GE2016 reuse the GE2013, which is re-complemented and re-designed for evaluation from KB construction perspective. For details, you could read the paper: Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task

GE2016 is now available at: http://pubannotation.org/collections/bionlp-st-ge-2016

[yanyk13]

cool, thx a lot

[barthfab]

Not sure if this is still relevant but there is a git repo containing all bionlp datasets used by DeepEventMine (openbiocorpora) except for GE2016. Also, the bigbio library provides biomedical dataloaders for over 126+ biomedical datasets.