| Preeclampsia | | A collection of titles and abstracts of "Preeclampsia"-related papers. They were extracted from PubMed using the MeSH term "Preeclampsia" and specifying the language to be "English, on 11th September, 2017.
The texts were then annotated by PubDictionaries using the dictionary "Preeclampsia". | 58.9 K | | callahan_tiff | 2019-01-30 | Developing | |
| craft-sa-dev | | Development data for CRAFT SA shared task. This project contains the development (training) annotations for the Structural Annotation task of the CRAFT Shared Task 2019. This particular set contains token and sentence annotations with tokens linked via dependency relations. These dependency relations were automatically generated using the manually curated CRAFT constituency treebank files as input. | 512 K | University of Colorado Anschutz Medical Campus | craft-st | 2019-03-25 | Released | |
| SPECIES800_autotagged | | This project comprises the SPECIES800 corpus documents automatically annotated by the Jensenlab tagger.
Annotated entity types are:
Genes/proteins from the mentioned organisms (and any human ones)
PubChem Compound identifiers
NCBI Taxonomy entries
Gene Ontology cellular component terms
BRENDA Tissue Ontology terms
Disease Ontology terms
Environment Ontology terms
The SPECIES 800 (S800) comprises 800 PubMed abstracts. In its original form species mentions were manually 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.0065390.
The manually annotated corpus is also available as a PubAnnotation project (see here).
| 0 | Evangelos Pafilis, Sampo Pyysalo, Lars Juhl Jensen | evangelos | 2015-11-20 | Testing | |
| glycosmos-test-structure-v1 | | | 471 | | ISSAKU YAMADA | 2019-06-11 | Testing | |
| glycosmos-test-glycan-structure | | | 448 | | ISSAKU YAMADA | 2019-06-11 | Testing | |
| GlycoBiology-GO | | GO-based annotation to GlycoBiology abstracts | 0 | | Jin-Dong Kim | 2016-06-11 | Testing | |
| bionlp-st-ge-2016-reference-eval | | | 426 | | Jin-Dong Kim | 2019-05-01 | Testing | |
| DisGeNet-2017-sample | | | 2.93 K | | Jin-Dong Kim | 2017-09-25 | Testing | |
| ICD10 | | Annotation for disease names as defined in ICD10 | 1.6 K | DBCLS | Jin-Dong Kim | 2016-05-04 | Developing | |
| pubtator-sample | | Sample annotation of PubTator produced by Zhiyong Lu et al. | 28 | Zhiyong Lu | Jin-Dong Kim | 2016-01-19 | Testing | |
| EDAM-DFO | | annotation for EDAM terms for data, formats, and operations | 12.5 K | | Jin-Dong Kim | 2016-09-21 | Testing | |
| bionlp-st-ge-2016-uniprot | | UniProt protein annotation to the benchmark data set of BioNLP-ST 2016 GE task: reference data set (bionlp-st-ge-2016-reference) and test data set (bionlp-st-ge-2016-test).
The annotations are produced based on a dictionary which is semi-automatically compiled for the 34 full paper articles included in the benchmark data set (20 in the reference data set + 14 in the test data set).
For detailed information about BioNLP-ST GE 2016 task data sets, please refer to the benchmark reference data set (bionlp-st-ge-2016-reference) and benchmark test data set (bionlp-st-ge-2016-test).
| 16.2 K | DBCLS | Jin-Dong Kim | 2016-05-22 | Beta | |
| GlyCosmos600-MAT | | | 863 | | Jin-Dong Kim | 2019-07-10 | Testing | |
| pmc-enju-pas | | Predicate-argument structure annotation produced by Enju.
This data set is initially produced as a supporting resource for BioNLP-ST 2016 GE task.
As so, it currently includes the 34 full paper articles that are in the benchmark data sets of GE 2016 task, reference data set (bionlp-st-ge-2016-reference) and test data set (bionlp-st-ge-2016-test), but will be extended to include more papers from the PubMed Central Open Access subset (PMCOA).
| 205 K | DBCLS | Jin-Dong Kim | 2017-11-07 | Developing | |
| GlycoBiology-FMA | | FMA ontology-based annotation to GlycoBiology abstracts | 96.3 K | | Jin-Dong Kim | 2020-02-05 | Testing | |
| DisGeNET | | Disease-Gene association annotation. | 3.12 M | Nuria Queralt | Jin-Dong Kim | 2016-01-28 | Beta | |
| BioASQ-sample | | collection of PubMed articles which appear in the BioASQ sample data set. | 0 | BioASQ | Jin-Dong Kim | 2015-10-13 | Testing | |
| EDAM-topics | | annotation for EDAM topics | 11.6 K | | Jin-Dong Kim | 2016-09-21 | Testing | |
| uniprot-mouse | | Protein annotation based on UniProt | 11.5 K | | Jin-Dong Kim | 2016-04-27 | Developing | |
| sentences | | Sentence segmentation annotation | 1.27 M | DBCLS | Jin-Dong Kim | 2019-07-11 | Testing | |
