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Projects (159)

Name Description # Ann. Author Maintainer updated at Status
NEUROSES This corpus is composed of PubMed articles containing cognitive enhancers and anti-depressants drug mentions. The selected sentences are automatically annotated using the NCBO Annotator with the Chemical Entities of Biological Interest (CHEBI) and Phenotypic Quality Ontology (PATO) ontologies, we also produced annotations using PhenoMiner ontology via a dictionary-based tagger. 2,151,082 nestoralvaro 2016-02-24 Beta
bionlp-st-ge-2016-uniprot <p>UniProt protein annotation to the benchmark data set of BioNLP-ST 2016 GE task: reference data set (<a href="http://pubannotation.org/projects/bionlp-st-ge-2016-reference">bionlp-st-ge-2016-reference</a>) and test data set (<a href="http://pubannotation.org/projects/bionlp-st-ge-2016-test">bionlp-st-ge-2016-test</a>).</p> <p>The annotations are produced based on a <a href="http://pubdictionaries.org/dictionaries/nfkb-rel-proteins">dictionary</a> which is semi-automatically compiled for the 34 full paper articles included in the benchmark data set (20 in the reference data set + 14 in the test data set).</p> <p>For detailed information about BioNLP-ST GE 2016 task data sets, please refer to the benchmark reference data set (<a href="http://pubannotation.org/projects/bionlp-st-ge-2016-reference">bionlp-st-ge-2016-reference</a>) and benchmark test data set (<a href="http://pubannotation.org/projects/bionlp-st-ge-2016-test">bionlp-st-ge-2016-test</a>).</p> 16,198 DBCLS Jin-Dong Kim 2016-05-22 Beta
Ab3P-abbreviations This corpus was developed during the creation of the Ab3P abbreviation definition identification tool. It includes 1250 manually annotated MEDLINE records. This gold standard includes 1221 abbreviation-definition pairs. Abbreviation definition identification based on automatic precision estimates Sunghwan Sohn, Donald C Comeau, Won Kim and W John Wilbur BMC Bioinformatics20089:402 DOI: 10.1186/1471-2105-9-402 2,342 Sunghwan Sohn, Donald C Comeau, Won Kim and W John Wilbur comeau 2016-07-29 Beta
CRAFT-treebank Penn Treebank markup for each sentence of the Colorado Richly Annotated Full Text Corpus (CRAFT). 844,123 UColorado Jin-Dong Kim 2015-11-19 Beta
PubmedHPO Human phenotype annotation to PubMed abstracts, based on the HPO ontology 12,437,742 Tudor Groza tudor 2016-12-06 Beta
craft Test bed for PubAnnotation query development. 52,960 Kevin Bretonnel Cohen KevinBretonnelCohen 2015-10-13 Beta
IMDB-NLP Annotations for chunking and semantic role labeling based on in-memory databases. 0 2016-05-06 Uploading
CoGe_Citation_Annotations Annotated PMC abstracts+full articles, that cite the "CoGe" papers (PMID: 18952863, 18269575). Total Num Citations: 165 Total Num Unique Citations: 141 Total Num Abstracts: 165 Total Num Whole Articles: 165 0 Heather Lent hclent 2016-10-11 Uploading
AnEM_full-texts 250 documents selected randomly from full-text papers <br> Entity types: organism subdivision, anatomical system, organ, multi-tissue structure, tissue, cell, developing anatomical structure, cellular component, organism substance, immaterial anatomical entity and pathological formation<br> Together with <a href="http://pubannotation.org/projects/AnEM_abstracts">AnEM_abstracts</a>, it is probably the largest manually annotated corpus on anatomical entities. 689 NaCTeM Yue Wang 2016-07-27 Uploading
uniprot-mouse Protein annotation based on UniProt 11,461 Jin-Dong Kim 2016-04-27 Developing