| 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 | 2023-11-28 | Developing | |
| LitCovid-sample-PD-FMA | | | 1.93 K | 2023-11-28 | Beta | |
| LitCovid-sample-PD-UBERON | | PubDictionaries annotation for UBERON terms - updated at 2020-04-30
It is annotation for anatomical entities based on Uberon.
The terms in Uberon are uploaded in PubDictionaries
(Uberon),
with which the annotations in this project are produced.
The parameter configuration used for this project is
here.
Note that it is an automatically generated dictionary-based annotation.
It will be updated periodically, as the documents are increased, and the dictionary is improved.
| 310 | 2023-11-28 | Beta | |
| Glycosmos6-GlycoEpitope | | Automatic annotation by PD-GlycoEpitope. | 19.9 K | 2023-11-28 | Developing | |
| GlyCosmos600-CLO | | | 1.73 K | 2023-11-28 | Testing | |
| pubmed-2016 | | abstracts published in 2016 | 0 | 2023-11-28 | | |
| twitter-test | | | 13 | 2023-11-28 | Developing | |
| LitCovid-sample-Pubtator | | | 3.86 K | 2023-11-28 | Uploading | |
| uniprot-mouse | | Protein annotation based on UniProt | 11.5 K | 2023-11-28 | Developing | |
| 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 K | 2023-11-28 | Released | |
