These are exciting times for biomedical natural language processing. The number of conferences and workshops in which research from this community is presented is so large as to have been difficult to imagine 10 years ago. This page sketches the conference ecosystem of our field.
BioNLP workshops at the Association for Computational Linguistics annual meeting
The Association for Computational Linguistics has hosted a workshop on biomedical natural language processing since 2002, known as BioNLP. Since 2008, it has also served as the official meeting of the SIGBIOMED special interest group. As compared to other venues, this workshop tends towards work with more linguistic bent, including work that is interesting from a linguistic perspective but does not yet yield high performance numbers on language processing tasks.
American Medical Informatics Association annual meeting
The AMIA annual meeting tends to be especially receptive to clinically-oriented work. A typical AMIA natural language processing paper might be a system for mining smoking status from the health records of homeless military veterans.
The Association for Computational Linguistics has been hosting an annual workshop on natural language processing in the psychology/psychiatry/mental health domains for the past 5 years. You can learn more about the exciting work going on there at the CLPsych web site.
Intelligent Systems for Molecular Biology
The ISMB annual meeting tends to publish work on completed systems that report high performance. A system that does information extraction for some focussed genomics domain, publicly available through a web interface, would be an example of a typical ISMB natural language processing paper.
Pacific Symposium on Biocomputing
The PSB conference tends to publish work on relatively focussed topics, and those topics change at least every three years, making it difficult to predict what kinds of papers will get accepted there. Historically, quite a bit of the work at the intersection between biomedical ontologies and natural language processing has been published there.