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phenoscape-nlp

Source for EQ-Generating CharaParser application, which uses unsupervised lexicon learning and natural language processing to propose EQ-based phenotype annotations. The software is currently being developed as part of the Phenoscape project (http://phenoscape.org/). It is useful for character descriptions written in the style similar to the example below:

Distal end of cleithrum

  1. is not bifurcate, bearing only an anterior process
  2. bifurcate

The input to EQ-Generating CharaParser is

  1. character descriptions in NeXML format
  2. a (may be empty) glossary of the related domain
  3. ontologies for EQs

Some algorithms used in CharaParser are reported in:

  1. Cui, H., Boufford, D., & Selden, P. (2010). Semantic Annotation of Biosystematics Literature without Training Examples. Journal of American Society of Information Science and Technology. 61 (3): 522-542 doi:10.1002/asi.21246

  2. Cui, H. (2012). CharaParser for fine-grained semantic annotation of organism morphological descriptions. Journal of American Society of Information Science and Technology. 63(4) doi:10.1002/asi.22618

License

EQ-Generating CharaParser source code can be used, modified, and distributed under the terms of the MIT License. Please see the file LICENSE for details.

How to cite

If you use EQ-Generating CharaParser in your research, please cite the following publications:

• Cui, H., Dahdul, W., Dececchi, A., Ibrahim, N., Mabee, P., Balhoff, J., Gopalakrishnan, H. (2015) CharaPaser+EQ: Performance Evaluation Without Gold Standard. Annual Meeting of the Association for Information Science and Technology, Nov 6-10, St Louis, Missouri, 2015. (Full paper, acceptance rate: 36.%) https://www.asist.org/files/meetings/am15/proceedings/openpage15.html