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Projects (159)

Name Description # Ann. Author Maintainer updated at Status
EVEXDB 11,219,321 EVEXDB smp 2016-01-28 Testing
Allie An annotation set of abbreviations and expanded forms extracted from PubMed/MEDLINE by machines. 8,704,648 Database Center for Life Science Yasunori Yamamoto 2017-04-06 Developing
PubmedHPO Human phenotype annotation to PubMed abstracts, based on the HPO ontology 12,437,742 Tudor Groza tudor 2016-12-06 Beta
BioPortalExp 11,831,167 tudor 2015-09-16 Testing
DisGeNET Disease-Gene association annotation. 3,117,504 Nuria Queralt Jin-Dong Kim 2016-01-28 Beta
NEUROSES This 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. 2,151,082 nestoralvaro 2016-02-24 Beta
pubmed-enju-pas Annotating PubMed abstracts for predicate-argument structure (PAS). Enju 2.4.2 is used to automatically compute PAS. 735,773 Enju Jin-Dong Kim 2016-01-31 Developing
CRAFT-treebank Penn Treebank markup for each sentence of the Colorado Richly Annotated Full Text Corpus (CRAFT). 844,123 UColorado Jin-Dong Kim 2015-11-19 Beta
bionlp-st-ge-2016-spacy-parsed Dependency parses produced by spaCy parser, and part-of-speech tags produced by Stanford tagger (with the wsj-0-18-left3words-nodistsim model). The exact procedure is described <a href="http://spacy.dbcls.jp/spacy_rest">here</a>. Data set contains the 34 full paper articles used in the BioNLP 2016 GE task. 225,680 Nico Colic Nico Colic 2016-05-25 Released
pmc-enju-pas <p>Predicate-argument structure annotation produced by <a href="http://kmcs.nii.ac.jp/enju/">Enju</a>. This data set is initially produced as a supporting resource for <a href="http://bionlp.dbcls.jp/projects/bionlp-st-ge-2016/">BioNLP-ST 2016 GE task</a>. As so, it currently includes the 34 full paper articles that are in the benchmark data sets of GE 2016 task, reference data set (<a href="http://pubannotation.org/projects/bionlp-st-ge-2016-reference">bionlp-st-ge-2016-reference</a>) and test data set (<a href="http://pubannotation.org/projects/bionlp-st-ge-2016-test">bionlp-st-ge-2016-test</a>), but will be extended to include more papers from the <a href="http://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/">PubMed Central Open Access subset (PMCOA)</a>.</p> 205,061 DBCLS Jin-Dong Kim 2016-05-22 Developing