| FA_Top100Plus-GeneProtein | | Top100＋本来Top100に入るべきだった７レビューの計、107レビュー中101レビュー。
5414, 6076, 6930, 8403, 9643, 18544は、0denotationでドキュメント自体登録していない。
attributesの詳細はconfig参照。
ドキュメントのソースDBが@AikoHIRAKIとなっているものはTypo修正がPubAnnotationの公式FirstAuthorsドキュメントに反映された段階で置き換えます。
| 10.4 K | | yucca | 2023-11-29 | Uploading | |
| LitCoin-MeSH-Disease-2 | | Flase Negative全部入れてみた | 4.08 K | | yucca | 2023-11-29 | | |
| LitCoin-Chemical-MeSH-CHEBI | | ChemicalEntity:
Annotated by PD-MeSH2022_CHEBI_tuned-B | 3.84 K | | yucca | 2023-11-29 | Testing | |
| LitCoin-Disease-Tuning-1 | | Annotator=PD-MeSH2022_C_F03_plus_allFN-B | 6.98 K | | yucca | 2023-11-29 | | |
| LitCoin-Disease-MeSH | | MeSH C and F03, plus false negatives that appear in two or more documents in LitCoin-entities | 3.56 K | | yucca | 2023-11-29 | Testing | |
| PMC-KEGG | | Documents from PMC including the word KEGG, with names of software tools and databases marked. | 27 | | yucca | 2023-11-28 | Developing | |
| TEST-ChemicalEntity | | ChemicalEntity : Annotated by PD-MeSH2022_CHEBI_tuned-B | 827 | | yucca | 2023-11-29 | Beta | |
| 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.
Publication: http://www.aclweb.org/anthology/W12-2430 | 1.1 K | Kazusa DNA Research Institute and Database Center for Life Science (DBCLS) | Yue Wang | 2023-11-26 | Released | |
| AnEM_full-texts | | 250 documents selected randomly from full-text papers
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_abstracts, it is probably the largest manually annotated corpus on anatomical entities. | 687 | NaCTeM | Yue Wang | 2023-11-29 | Uploading | |
| 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 K | NaCTeM | Yue Wang | 2023-11-29 | Released | |
| funRiceGenes-all | | | 1.51 K | PubDictionaries | Yue Wang | 2023-11-29 | Developing | |
| 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 K | UPenn Biomedical Information Extraction Project | Yue Wang | 2023-11-26 | Released | |
| 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 K | INRA | Yue Wang | 2023-11-29 | Released | |
| PIR-corpus1 | | The Protein Information Resource (PIR) is not biased towards any particular biomedical domain, and is expected to provide more diverse protein names in a given sample size.
Annotation category: protein, compound-protein, acronym. | 4.44 K | University of Delaware and Georgetown University Medical Center | Yue Wang | 2023-11-27 | Released | |
| TEST0 | | | 3.37 M | | Yue Wang | 2023-11-24 | | |
| 2_test | | | 145 M | | Yue Wang | 2023-11-24 | | |
| 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 K | GENIA Project | Yue Wang | 2023-11-29 | Released | |
| 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 K | NaCTeM | Yue Wang | 2023-11-28 | Released | |
| 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 K | GENIA | Yue Wang | 2023-11-29 | Released | |
| AIMed | | The AIMed corpus is one of the most widely used corpora for protein-protein interaction extraction. The protein annotations are either parts of the protein interaction annotations, or are uninvolved in any protein interaction annotation.
Publication: http://www.cs.utexas.edu/~ml/papers/bionlp-aimed-04.pdf | 4.04 K | The University of Texas at Austin | Yue Wang | 2023-11-27 | Testing | |
