> top > projects

Projects (159)

Name Description # Ann. Author Maintainer updated at Status
bionlp-st-id-2011-training The training dataset from the infectious diseases (ID) task in the BioNLP Shared Task 2011. <br> Entity types: <br>- Genes and gene products: gene, RNA, and protein name mentions. <br>- Two-component systems: mentions of the names of two-component regulatory systems, frequently embedding the names of the two Proteins forming the system.<br>- Chemicals: mentions of chemical compounds such as "NaCL".<br>- Organisms: mentions of organism names or organism specification through specific properties (e.g. "graRS mutant").<br>- Regulons/Operons: mentions of names of specific regulons and operons. 5,609 University of Tokyo Tsujii Laboratory, NaCTeM and Biocomplexity Institute of Virginia Tech Yue Wang 2017-04-18 Released
jnlpba-st-training The training data used in the task came from the GENIA version 3.02 corpus, This was formed from a controlled search on MEDLINE using the MeSH terms "human", "blood cells" and "transcription factors". From this search, 1,999 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus. For the shared task only the classes protein, DNA, RNA, cell line and cell type were used. The first three incorporate several subclasses from the original taxonomy while the last two are interesting in order to make the task realistic for post-processing by a potential template filling application. The publication year of the training set ranges over 1990~1999. 51,290 GENIA Yue Wang 2017-04-14 Released
AIMed The AIMed corpus is one of the most widely used corpora for protein-protein interaction extraction. The protein annotations are either parts of the protein interaction annotations, or are uninvolved in any protein interaction annotation.<br> Publication: http://www.cs.utexas.edu/~ml/papers/bionlp-aimed-04.pdf 4,042 The University of Texas at Austin Yue Wang 2017-04-14 Testing
AlvisNLP-Async-Test Test for the asynchronous AlvisNLP/ML annotator family. 0 Robert Bossy rbossy 2017-04-07 Testing
Allie An annotation set of abbreviations and expanded forms extracted from PubMed/MEDLINE by machines. 8,704,648 Database Center for Life Science Yasunori Yamamoto 2017-04-06 Developing
tagtog-demo demo documents produced by tagtog annotations 262 tagtog 2017-04-03 Developing
SCAI-Test A small corpus for the evaluation of dictionaries containing chemical entities. <br> Publication: http://www.scai.fraunhofer.de/fileadmin/images/bio/data_mining/paper/kolarik2008.pdf <br> Original source: https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/corpora-for-chemical-entity-recognition.html 1,206 CALBC Project Yue Wang 2017-04-03 Released
BioLarkPubmedHPO 228 abstracts manually annotated with Human Phenotype Ontology (HPO) concepts and harmonized by three curators, which can be used as a reference standard for free text annotation of human phenotypes. For more info, please see Groza et al. "Automatic concept recognition using the human phenotype ontology reference and test suite corpora", 2015. 7,236 Tudor Groza simon 2017-03-28 Released
Parkinson 54 Jin-Dong Kim 2017-03-11 Testing
FSU-PRGE A new broad-coverage corpus composed of 3,306 MEDLINE abstracts dealing with gene and protein mentions.<br> The annotation process was semi-automatic. <br> Publication: http://aclweb.org/anthology/W/W10/W10-1838.pdf 59,505 CALBC Project Yue Wang 2017-03-08 Released