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Projects (159)

Name Description # Ann. Author Maintainer updated at Status
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
CellFinder CellFinder corpus 4,754 Mariana Neves, Alexander Damaschun, Andreas Kurtz, Ulf Leser Mariana Neves 2015-11-25 Released
2015-BEL-Sample-2 The 295 BEL statements for sample set used for the 2015 BioCreative challenge. 11,430 Fabio Rinaldi Nico Colic 2016-05-25 Released
CoMAGC In 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. 1,528 Lee et al Hee-Jin Lee 2015-02-24 Released
SPECIES800 SPECIES 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. <br> Described in: <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065390" target="blank">The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text.</a> Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, et al. (2013). PLoS ONE, 2013, 8(6): e65390. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065390" target="blank">doi:10.1371/journal.pone.0065390</a> 3,708 Evangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensen evangelos 2015-11-20 Released
tmVarCorpus Wei C-H, Harris BR, Kao H-Y, Lu Z (2013) tmVar: A text mining approach for extracting sequence variants in biomedical literature, Bioinformatics, 29(11) 1433-1439, doi:10.1093/bioinformatics/btt156. 1,431 Chih-Hsuan Wei , Bethany R. Harris , Hung-Yu Kao and Zhiyong Lu Chih-Hsuan Wei 2015-08-06 Released
NCBIDiseaseCorpus The 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. 6,881 Rezarta Islamaj Doğan,Robert Leaman,Zhiyong Lu Chih-Hsuan Wei 2015-08-06 Released
CyanoBase Cyanobacteria are prokaryotic organisms that have served as important model organisms for studying oxygenic photosynthesis and have played a significant role in the Earthfs history as primary producers of atmospheric oxygen.<br> Publication: http://www.aclweb.org/anthology/W12-2430 1,101 Kazusa DNA Research Institute and Database Center for Life Science (DBCLS) Yue Wang 2016-05-17 Released
AnEM_abstracts 250 documents selected randomly from citation abstracts <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_full-texts">AnEM_full-texts</a>, it is probably the largest manually annotated corpus on anatomical entities. 1,946 NaCTeM Yue Wang 2016-06-07 Released
spacy-test Random 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. 136,597 Nico Colic Nico Colic 2016-05-25 Released