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NameTDescription# Ann.AuthorMaintainerUpdated_atStatus

1-20 / 491 show all
LitCovid-OGER-BB Using OGER (www.ontogene.com) and Biobert to obtain annotations for 10 different vocabularies.308 KFabio RinaldiNico Colic2021-05-27Released
LitCovid-OGER Using OGER (http://www.ontogene.org/resources/oger) to detect entities from 10 different vocabularies9.31 KFabio RinaldiNico Colic2021-05-27Released
2015-BEL-Sample-2 The 295 BEL statements for sample set used for the 2015 BioCreative challenge.11.4 KFabio RinaldiNico Colic2021-03-11Released
DisGeNET5_gene_disease The file contains gene-disease associations obtained by text mining MEDLINE abstracts using the BeFree system including the gene and disease off sets.2.04 MIBI GroupYue Wang2021-03-11Released
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.131 KNico ColicNico Colic2021-03-10Released
PubMed_ArguminSci Predictions for PubMed automatically extracted with the ArguminSci tool (https://github.com/anlausch/ArguminSci).777 Kzebet2021-03-10Released
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.6.85 KRezarta Islamaj Doğan,Robert Leaman,Zhiyong LuChih-Hsuan Wei2021-03-10Released
GENIAcorpus multi_cell (1,782) mono_cell (222) virus (2,136) protein_family_or_group (8,002) protein_complex (2,394) protein_molecule (21,290) protein_subunit (942) protein_substructure (129) protein_domain_or_region (1,044) protein_other (97) peptide (521) amino_acid_monomer (784) DNA_family_or_group (332) DNA_molecule (664) DNA_substructure (2) DNA_domain_or_region (39) DNA_other (16) RNA_family_or_group (1,545) RNA_molecule (554) RNA_substructure (106) RNA_domain_or_region (8,237) RNA_other (48) polynucleotide (259) nucleotide (243) lipid (2,375) carbohydrate (99) other_organic_compound (4,113) body_part (461) tissue (706) cell_type (7,473) cell_component (679) cell_line (4,129) other_artificial_source (211) inorganic (258) atom (342) other (21,056) 78.9 KGENIA ProjectYue Wang2021-03-10Released
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 1990~1999.51.1 KGENIAYue Wang2021-03-10Released
pubmed-sentences-benchmark A benchmark data for text segmentation into sentences. The source of annotation is the GENIA treebank v1.0. Following is the process taken. began with the GENIA treebank v1.0. sentence annotations were extracted and converted to PubAnnotation JSON. uploaded. 12 abstracts met alignment failure. among the 12 failure cases, 4 had a dot('.') character where there should be colon (':'). They were manually fixed then successfully uploaded: 7903907, 8053950, 8508358, 9415639. among the 12 failed abstracts, 8 were "250 word truncation" cases. They were manually fixed and successfully uploaded. During the fixing, manual annotations were added for the missing pieces of text. 30 abstracts had extra text in the end, indicating copyright statement, e.g., "Copyright 1998 Academic Press." They were annotated as a sentence in GTB. However, the text did not exist anymore in PubMed. Therefore, the extra texts were removed, together with the sentence annotation to them. 18.4 KGENIA projectJin-Dong Kim2021-03-10Released
PubMed_Structured_Abstracts Sections (zones) as retrieved from PubMed.131 Kzebet2021-03-10Released
PennBioIE The 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).23.8 KUPenn Biomedical Information Extraction ProjectYue Wang2021-03-10Released
AnEM_abstracts 250 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.1.91 KNaCTeMYue Wang2021-03-10Released
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", 2015.7.16 KTudor Grozasimon2021-03-10Released
bionlp-st-bb3-2016-training Entity (bacteria, habitats and geographical places) annotation to the training dataset of the BioNLP-ST 2016 BB task. For more information, please refer to bionlp-st-bb3-2016-development and bionlp-st-bb3-2016-test. Bacteria Bacteria entities are annotated as contiguous spans of text that contains a full unambiguous prokaryote taxon name, the type label is Bacteria. The Bacteria type is a taxon, at any taxonomic level from phylum (Eubacteria) to strain. The category that the text entities have to be assigned to is the most specific and unique category of the NCBI taxonomy resource. In case a given strain, or a group of strains is not referenced by NCBI, it is assigned with the closest taxid in the taxonomy. Habitat Habitat entities are annotated as spans of text that contains a complete mention of a potential habitat for bacteria, the type label is Habitat. Habitat entities are assigned one or several concepts from the habitat subpart of the OntoBiotope ontology. The assigned concepts are as specific as possible. OntoBiotope defines most relevant microorganism habitats from all areas considered by microbial ecology (hosts, natural environment, anthropized environments, food, medical, etc.). Habitat entities are rarely referential entities, they are usually noun phrases including properties and modifiers. There are rare cases of habitats referred with adjectives or verbs. The spans are generally contiguous but some of them are discontinuous in order to cope with conjunctions. Geographical Geographical entities are geographical and organization places denoted by official names.1.28 KINRAYue Wang2021-03-10Released
bionlp-st-cg-2013-training The training dataset from the cancer genetics task in the BioNLP Shared Task 2013. Composed of anatomical and molecular entities.10.9 KNaCTeMYue Wang2021-03-10Released
bionlp-st-epi-2011-training The 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. 7.59 KGENIAYue Wang2021-03-10Released
c_corpus Documents included in the c_corpus: https://github.com/SMAFIRA/c_corpus/blob/master/SMAFIRAc_0.4_Annotations.csv107 K2021-01-27Released
AGAC_sample AGAC track samples in BioNLP-OST 2019, Hong Kong874xiajingbo2021-01-19Released
AGAC_training AGAC track training set in BioNLP-OST 2019, Hong Kong3.32 Kxiajingbo2021-01-19Released
NameT# Ann.AuthorMaintainerUpdated_atStatus

1-20 / 491 show all
LitCovid-OGER-BB 308 KFabio RinaldiNico Colic2021-05-27Released
LitCovid-OGER 9.31 KFabio RinaldiNico Colic2021-05-27Released
2015-BEL-Sample-2 11.4 KFabio RinaldiNico Colic2021-03-11Released
DisGeNET5_gene_disease 2.04 MIBI GroupYue Wang2021-03-11Released
spacy-test 131 KNico ColicNico Colic2021-03-10Released
PubMed_ArguminSci 777 Kzebet2021-03-10Released
NCBIDiseaseCorpus 6.85 KRezarta Islamaj Doğan,Robert Leaman,Zhiyong LuChih-Hsuan Wei2021-03-10Released
GENIAcorpus 78.9 KGENIA ProjectYue Wang2021-03-10Released
jnlpba-st-training 51.1 KGENIAYue Wang2021-03-10Released
pubmed-sentences-benchmark 18.4 KGENIA projectJin-Dong Kim2021-03-10Released
PubMed_Structured_Abstracts 131 Kzebet2021-03-10Released
PennBioIE 23.8 KUPenn Biomedical Information Extraction ProjectYue Wang2021-03-10Released
AnEM_abstracts 1.91 KNaCTeMYue Wang2021-03-10Released
BioLarkPubmedHPO 7.16 KTudor Grozasimon2021-03-10Released
bionlp-st-bb3-2016-training 1.28 KINRAYue Wang2021-03-10Released
bionlp-st-cg-2013-training 10.9 KNaCTeMYue Wang2021-03-10Released
bionlp-st-epi-2011-training 7.59 KGENIAYue Wang2021-03-10Released
c_corpus 107 K2021-01-27Released
AGAC_sample 874xiajingbo2021-01-19Released
AGAC_training 3.32 Kxiajingbo2021-01-19Released