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NameTDescription# Ann.AuthorMaintainerUpdated_atStatus

1-20 / 172 すべて表示
bionlp-st-ge-2016-test-proteinsProtein annotations to the benchmark test data set of the BioNLP-ST 2016 GE task. A participant of the GE task may import the documents and annotations of this project to his/her own project, to begin with producing event annotations. For more details, please refer to the benchmark test data set (bionlp-st-ge-2016-test). 4.34 KDBCLSJin-Dong Kim2016-05-04公開中
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 Wang2016-12-06公開中
bionlp-st-ge-2016-corefCoreference annotation to the benchmark data set (reference and test) of BioNLP-ST 2016 GE task. For detailed information, please refer to the benchmark reference data set (bionlp-st-ge-2016-reference) and benchmark test data set (bionlp-st-ge-2016-test).853DBCLSJin-Dong Kim2016-05-23公開中
bionlp-st-ge-2016-test-teesNER and event extraction produced by TEES (with the default GE11 model) for the 14 full papers used in the BioNLP 2016 GE task test corpus.9.17 KNico ColicNico Colic2016-05-25公開中
AnEM_abstracts250 documents selected randomly from citation abstracts 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 Together with AnEM_full-texts, it is probably the largest manually annotated corpus on anatomical entities.1.95 KNaCTeMYue Wang2016-06-07公開中
bionlp-st-pc-2013-traingThe training dataset from the pathway curation (PC) task in the BioNLP Shared Task 2013. The entity types defined in the PC task are simple chemical, gene or gene product, complex and cellular component.7.86 KNaCTeM and KISTIYue Wang2016-12-06公開中
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 Grozasimon2017-03-28公開中
tmVarCorpusWei 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/btt156.1.43 KChih-Hsuan Wei , Bethany R. Harris , Hung-Yu Kao and Zhiyong LuChih-Hsuan Wei2015-08-06公開中
bionlp-st-ge-2016-reference-teesNER and event extraction produced by TEES (with the default GE11 model) for the 20 full papers used in the BioNLP 2016 GE task reference corpus.14.6 KNico Colic Nico Colic2016-05-25公開中
bionlp-st-cg-2013-trainingThe training dataset from the cancer genetics task in the BioNLP Shared Task 2013. Composed of anatomical and molecular entities.10.9 KNaCTeMYue Wang2016-12-06公開中
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 Lee2015-02-24公開中
CellFinderCellFinder corpus4.75 KMariana Neves, Alexander Damaschun, Andreas Kurtz, Ulf LeserMariana Neves2015-11-25公開中
bionlp-st-ge-2016-referenceIt is the benchmark reference data set of the BioNLP-ST 2016 GE task. It includes Genia-style event annotations to 20 full paper articles which are about NFκB proteins. The task is to develop an automatic annotation system which can produce annotation similar to the annotation in this data set as much as possible. For evaluation of the performance of a participating system, the system needs to produce annotations to the documents in the benchmark test data set (bionlp-st-ge-2016-test). GE 2016 benchmark data set is provided as multi-layer annotations which include: bionlp-st-ge-2016-reference: benchmark reference data set (this project) bionlp-st-ge-2016-test: benchmark test data set (annotations are blined) bionlp-st-ge-2016-test-proteins: protein annotation to the benchmark test data set Following is supporting resources: bionlp-st-ge-2016-coref: coreference annotation bionlp-st-ge-2016-uniprot: Protein annotation with UniProt IDs. pmc-enju-pas: dependency parsing result produced by Enju UBERON-AE: annotation for anatomical entities as defined in UBERON ICD10: annotation for disease names as defined in ICD10 GO-BP: annotation for biological process names as defined in GO GO-CC: annotation for cellular component names as defined in GO A SPARQL-driven search interface is provided at http://bionlp.dbcls.jp/sparql.14.4 KDBCLSJin-Dong Kim2016-05-23公開中
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 Colic2016-05-25公開中
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 Jensenevangelos2015-11-20公開中
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 Wei2015-08-06公開中
CyanoBaseCyanobacteria 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. Publication: http://www.aclweb.org/anthology/W12-24301.1 KKazusa DNA Research Institute and Database Center for Life Science (DBCLS)Yue Wang2016-05-17公開中
2015-BEL-Sample-2The 295 BEL statements for sample set used for the 2015 BioCreative challenge.11.4 KFabio RinaldiNico Colic2016-05-25公開中
bionlp-st-ge-2016-testIt is the benchmark test data set of the BioNLP-ST 2016 GE task. It includes Genia-style event annotations to 14 full paper articles which are about NFκB proteins. For testing purpose, however, annotations are all blinded, which means users cannot see the annotations in this project. Instead, annotations in any other project can be compared to the hidden annotations in this project, then the annotations in the project will be automatically evaluated based on the comparison. A participant of GE task can get the evaluation of his/her result of automatic annotation, through following process: Create a new project. Import documents from the project, bionlp-st-2016-test-proteins to your project. Import annotations from the project, bionlp-st-2016-test-proteins to your project. At this point, you may want to compare you project to this project, the benchmark data set. It will show that protein annotations in your project is 100% correct, but other annotations, e.g., events, are 0%. Produce event annotations, using your system, upon the protein annotations. Upload your event annotations to your project. Compare your project to this project, to get evaluation. GE 2016 benchmark data set is provided as multi-layer annotations which include: bionlp-st-ge-2016-reference: benchmark reference data set bionlp-st-ge-2016-test: benchmark test data set (this project) bionlp-st-ge-2016-test-proteins: protein annotation to the benchmark test data set Following is supporting resources: bionlp-st-ge-2016-coref: coreference annotation bionlp-st-ge-2016-uniprot: Protein annotation with UniProt IDs. pmc-enju-pas: dependency parsing result produced by Enju UBERON-AE: annotation for anatomical entities as defined in UBERON ICD10: annotation for disease names as defined in ICD10 GO-BP: annotation for biological process names as defined in GO GO-CC: annotation for cellular component names as defined in GO A SPARQL-driven search interface is provided at http://bionlp.dbcls.jp/sparql.7.99 KDBCLSJin-Dong Kim2016-05-22公開中
bionlp-st-id-2011-trainingThe training dataset from the infectious diseases (ID) task in the BioNLP Shared Task 2011. Entity types: - Genes and gene products: gene, RNA, and protein name mentions. - Two-component systems: mentions of the names of two-component regulatory systems, frequently embedding the names of the two Proteins forming the system.- Chemicals: mentions of chemical compounds such as "NaCL".- Organisms: mentions of organism names or organism specification through specific properties (e.g. "graRS mutant").- Regulons/Operons: mentions of names of specific regulons and operons.5.61 KUniversity of Tokyo Tsujii Laboratory, NaCTeM and Biocomplexity Institute of Virginia TechYue Wang2017-04-18公開中
NameT# Ann.AuthorMaintainerUpdated_atStatus

1-20 / 172 すべて表示
bionlp-st-ge-2016-test-proteins4.34 KDBCLSJin-Dong Kim2016-05-04公開中
PennBioIE23.9 KUPenn Biomedical Information Extraction ProjectYue Wang2016-12-06公開中
bionlp-st-ge-2016-coref853DBCLSJin-Dong Kim2016-05-23公開中
bionlp-st-ge-2016-test-tees9.17 KNico ColicNico Colic2016-05-25公開中
AnEM_abstracts1.95 KNaCTeMYue Wang2016-06-07公開中
bionlp-st-pc-2013-traing7.86 KNaCTeM and KISTIYue Wang2016-12-06公開中
BioLarkPubmedHPO7.24 KTudor Grozasimon2017-03-28公開中
tmVarCorpus1.43 KChih-Hsuan Wei , Bethany R. Harris , Hung-Yu Kao and Zhiyong LuChih-Hsuan Wei2015-08-06公開中
bionlp-st-ge-2016-reference-tees14.6 KNico Colic Nico Colic2016-05-25公開中
bionlp-st-cg-2013-training10.9 KNaCTeMYue Wang2016-12-06公開中
CoMAGC1.53 KLee et alHee-Jin Lee2015-02-24公開中
CellFinder4.75 KMariana Neves, Alexander Damaschun, Andreas Kurtz, Ulf LeserMariana Neves2015-11-25公開中
bionlp-st-ge-2016-reference14.4 KDBCLSJin-Dong Kim2016-05-23公開中
spacy-test137 KNico ColicNico Colic2016-05-25公開中
SPECIES8003.71 KEvangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensenevangelos2015-11-20公開中
NCBIDiseaseCorpus6.88 KRezarta Islamaj Doğan,Robert Leaman,Zhiyong LuChih-Hsuan Wei2015-08-06公開中
CyanoBase1.1 KKazusa DNA Research Institute and Database Center for Life Science (DBCLS)Yue Wang2016-05-17公開中
2015-BEL-Sample-211.4 KFabio RinaldiNico Colic2016-05-25公開中
bionlp-st-ge-2016-test7.99 KDBCLSJin-Dong Kim2016-05-22公開中
bionlp-st-id-2011-training5.61 KUniversity of Tokyo Tsujii Laboratory, NaCTeM and Biocomplexity Institute of Virginia TechYue Wang2017-04-18公開中