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NameTDescription# Ann.AuthorMaintainerUpdated_atStatus

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SPECIES800SPECIES 800 (S800): an abstract-based manually annotated corpus. S800 comprises 800 PubMed abstracts in which organism mentions were identified and mapped to the corresponding NCBI Taxonomy identifiers. Described in: The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, et al. (2013). PLoS ONE, 2013, 8(6): e65390. doi:10.1371/journal.pone.00653903.71 KEvangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensenevangelos2015-11-20Released
BioLarkPubmedHPO228 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", 2015.7.24 KTudor Grozasimon2017-03-28Released
NCBIDiseaseCorpusThe NCBI disease corpus is fully annotated at the mention and concept level to serve as a research resource for the biomedical natural language processing community.6.88 KRezarta Islamaj Doğan,Robert Leaman,Zhiyong LuChih-Hsuan Wei2015-08-06Released
CellFinderCellFinder corpus4.75 KMariana Neves, Alexander Damaschun, Andreas Kurtz, Ulf LeserMariana Neves2015-11-25Released
CoMAGCIn order to access the large amount of information in biomedical literature about genes implicated in various cancers both efficiently and accurately, the aid of text mining (TM) systems is invaluable. Current TM systems do target either gene-cancer relations or biological processes involving genes and cancers, but the former type produces information not comprehensive enough to explain how a gene affects a cancer, and the latter does not provide a concise summary of gene-cancer relations. In order to support the development of TM systems that are specifically targeting gene-cancer relations but are still able to capture complex information in biomedical sentences, we publish CoMAGC, a corpus with multi- faceted annotations of gene-cancer relations. In CoMAGC, a piece of annotation is composed of four semantically orthogonal concepts that together express 1) how a gene changes, 2) how a cancer changes and 3) the causality between the gene and the cancer. The multi-faceted annotations are shown to have high inter-annotator agreement. In addition, the annotations in CoMAGC allow us to infer the prospective roles of genes in cancers and to classify the genes into three classes according to the inferred roles. We encode the mapping between multi-faceted annotations and gene classes into 10 inference rules. The inference rules produce results with high accuracy as measured against human annotations. CoMAGC consists of 821 sentences on prostate, breast and ovarian cancers. Currently, the corpus deals with changes in gene expression levels among other types of gene changes.1.53 KLee et alHee-Jin Lee2015-02-24Released
spacy-testRandom set of articles used for testing in the development of the RESTful spaCy parsing web service. Since development is now finished, they are released for the community to use.137 KNico ColicNico Colic2016-05-25Released
bionlp-st-epi-2011-trainingThe training dataset from the Epigenetics and Post-translational Modifications (EPI) task in the BioNLP Shared Task 2011. The core entities of the task are genes and gene products (RNA and proteins), identified in the data simply as "Protein" annotations. 7.6 KGENIAYue Wang2016-12-06Released
FSU-PRGEA new broad-coverage corpus composed of 3,306 MEDLINE abstracts dealing with gene and protein mentions. The annotation process was semi-automatic. Publication: http://aclweb.org/anthology/W/W10/W10-1838.pdf59.5 KCALBC ProjectYue Wang2017-03-08Released
PennBioIEThe PennBioIE corpus (0.9) covers two domains of biomedical knowledge. One is the inhibition of the cytochrome P450 family of enzymes (CYP450 or CYP for short) , and the other domain is the molecular genetics of dance (oncology or onco for short).23.9 KUPenn Biomedical Information Extraction ProjectYue Wang2016-12-06Released
DisGeNETDisease-Gene association annotation.3.12 MNuria Queralt Jin-Dong Kim2016-01-28Beta
NEUROSESThis 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.2.15 Mnestoralvaro2016-02-24Beta
QFMC_MEDLINEQuaero French Medical Corpus: Annotation of MEDLINE titles5.97 KAurélie NévéolPierre Zweigenbaum2016-02-03Beta
PubCasesHPOHPO annotation in PubCases0Toyofumi Fujiwara2017-07-25Beta
bionlp-st-ge-2016-uniprotUniProt protein annotation to the benchmark data set of BioNLP-ST 2016 GE task: reference data set (bionlp-st-ge-2016-reference) and test data set (bionlp-st-ge-2016-test). The annotations are produced based on a dictionary 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). For detailed information about BioNLP-ST GE 2016 task data sets, please refer to the benchmark reference data set (bionlp-st-ge-2016-reference) and benchmark test data set (bionlp-st-ge-2016-test). 16.2 KDBCLSJin-Dong Kim2016-05-22Beta
CRAFT-treebankPenn Treebank markup for each sentence of the Colorado Richly Annotated Full Text Corpus (CRAFT).844 KUColoradoJin-Dong Kim2015-11-19Beta
craftTest bed for PubAnnotation query development.53 KKevin Bretonnel CohenKevinBretonnelCohen2015-10-13Beta
Ab3P-abbreviationsThis 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: 10.1186/1471-2105-9-4022.34 KSunghwan Sohn, Donald C Comeau, Won Kim and W John Wilburcomeau2016-07-29Beta
PubmedHPOHuman phenotype annotation to PubMed abstracts, based on the HPO ontology12.4 MTudor Grozatudor2017-07-24Beta
IMDB-NLPAnnotations for chunking and semantic role labeling based on in-memory databases.02016-05-06Uploading
CoGe_Citation_AnnotationsAnnotated 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 0Heather Lenthclent2016-10-11Uploading
NameT# Ann.AuthorMaintainerUpdated_atStatus

21-40 / 170 show all
SPECIES8003.71 KEvangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensenevangelos2015-11-20Released
BioLarkPubmedHPO7.24 KTudor Grozasimon2017-03-28Released
NCBIDiseaseCorpus6.88 KRezarta Islamaj Doğan,Robert Leaman,Zhiyong LuChih-Hsuan Wei2015-08-06Released
CellFinder4.75 KMariana Neves, Alexander Damaschun, Andreas Kurtz, Ulf LeserMariana Neves2015-11-25Released
CoMAGC1.53 KLee et alHee-Jin Lee2015-02-24Released
spacy-test137 KNico ColicNico Colic2016-05-25Released
bionlp-st-epi-2011-training7.6 KGENIAYue Wang2016-12-06Released
FSU-PRGE59.5 KCALBC ProjectYue Wang2017-03-08Released
PennBioIE23.9 KUPenn Biomedical Information Extraction ProjectYue Wang2016-12-06Released
DisGeNET3.12 MNuria Queralt Jin-Dong Kim2016-01-28Beta
NEUROSES2.15 Mnestoralvaro2016-02-24Beta
QFMC_MEDLINE5.97 KAurélie NévéolPierre Zweigenbaum2016-02-03Beta
PubCasesHPO0Toyofumi Fujiwara2017-07-25Beta
bionlp-st-ge-2016-uniprot16.2 KDBCLSJin-Dong Kim2016-05-22Beta
CRAFT-treebank844 KUColoradoJin-Dong Kim2015-11-19Beta
craft53 KKevin Bretonnel CohenKevinBretonnelCohen2015-10-13Beta
Ab3P-abbreviations2.34 KSunghwan Sohn, Donald C Comeau, Won Kim and W John Wilburcomeau2016-07-29Beta
PubmedHPO12.4 MTudor Grozatudor2017-07-24Beta
CoGe_Citation_Annotations0Heather Lenthclent2016-10-11Uploading