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articles Added rest of the files except for obo files Apr 30, 2018
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README.md

The Colorado Richly Annotated Full-Text (CRAFT) Corpus

The contents of this repository consist of the v3.1 release of the CRAFT Corpus. This release consists of 67 articles from the PubMed Central Open Access subset, each of which has been annotated along a number of different axes. Please see the CRAFT Wiki for further details on the corpus distribution.

Concept annotation

Concepts mentioned in these articles have been mapped (“normalized”) to specific ontology classes, relying on ten Open Biomedical Ontologies. For additional details see this README.

For details of the concept annotations and citation, please see:
Bada, M., Eckert, M., Evans, D., Garcia, K., Shipley, K., Sitnikov, D., Baumgartner Jr., W. A., Cohen, K. B., Verspoor, K., Blake, J. A., and Hunter, L. E. (2012) Concept annotation in the CRAFT corpus. BMC Bioinformatics 12:161. [link]

For an overview of the concept annotation guidelines, please see:
Bada, M., Eckert, M., Palmer, M., and Hunter, L.E. (2010) An overview of the CRAFT annotation guidelines. Proceedings of the Fourth Linguistic Annotation Workshop, ACL 2010, pp. 207-211. [link]

For details of the Uberon anatomical annotations, please see:
Bada, M., Vasilevsky, N., Baumgartner Jr., W.A., Haendel, M., and Hunter, L.E. (2017) Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. Database, Volume 2017, bax087. [link]

For evaluation of concept recognition tools on the concept annotations, please see:
Funk, C., Baumgartner, W.A., Garcia, B., Roeder, C., Bada, M., Cohen, K.B., Hunter, L.E., and Verspoor, K. (2014) Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics 15:59. [link]

Coreference annotation

The corpus has been annotated with coreference relations, including identity and appositives, for all coreferring base noun phrases.

For details of the coreference annotations, please see:
Cohen, K.B., Lanfranchi, A., Choi, M.J., Bada, M., Baumgartner Jr., W.A., Panteleyeva, N., Verspoor, K., Palmer, M., and Hunter, L.E. (2017) Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinformatics 18:372. [link]

Structural annotation

All sentences have been marked up with respect to sentence segmentation, tokenization, part-of-speech tags, grammatical dependency, and treebanking. Document section boundaries and typography (e.g., italics, boldface, subscript, superscript) have also been extracted from the source document files.

The following article explores syntactic tool performance over CRAFT:
Verspoor, K., Cohen, K.B., Lanfranchi, A., Warner, C., Johnson, H.L., Roeder, C., Choi, J.D., Funk, C., Malenkiy, Y., Eckert, M., Xue, N., Baumgartner Jr., W.A., Bada, M., Palmer, M., Hunter L.E. (2012) A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinformatics 13:207. [link]

Feedback

Please direct comments, questions, and suggestions to the Issues section of the CRAFT GitHub page, or send e-mail to Mike Bada at mike.bada@ucdenver.edu.

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