There is a bug when bern recognize the 'Excerpt' section in some papers, shown below.

Open SongbiaoZhu opened this issue 5 years ago • 3 comments

There are some articles with 'Excerpt' section, instead of 'Abstract' section.

For example, these pimids, ['29787038', '30844201', '31643199', '31643392', '31643562', '31855378', '31869126'].

Error output

BERN returned the html text on this kind of pmid, as [{"project":"BERN","sourcedb":"PubMed","sourceid":"31869126","text":"error: tmtool: PubTatorBioC.key","denotations":[],"timestamp":"Sat Apr 11 04:43:19 +0000 2020"}] Please have a notice. Besides, BERN is such a nice tool and good job!

Apr 11 '20 04:04 SongbiaoZhu

Is anybody reading this?

Apr 22 '20 23:04 amalic

The cases you reported occur in very recent PMIDs and are caused by an external dependency, tmTool, of BERN.

I recommend you to use a HTTPS POST call (i.e., API for raw text) for very recent PMIDs.

Apr 23 '20 14:04 donghyeonk

API call for raw text does not work either

See Github issue https://github.com/dmis-lab/bern/issues/17

May 03 '20 04:05 amalic