| bionlp-st-ge-2016-test-proteins | | Protein annotations to the benchmark test data set of the BioNLP-ST 2016 GE task.
A participant of the GE task may import the documents and annotations of this project to his/her own project, to begin with producing event annotations.
For more details, please refer to the benchmark test data set (bionlp-st-ge-2016-test).
| 4.34 K | 2023-11-27 | Released | |
| GlyCosmos600-GlycoProteins | | GlycoProtein annotations were made using the glycoprotein-name dictionary on PubDictionaries:
http://pubannotation.org/projects/GlyCosmos600-docs
The documents were imported from the GlyCosmos600-docs project:
http://pubannotation.org/projects/GlyCosmos600-docs | 3.68 K | 2023-11-27 | Testing | |
| bionlp-st-ge-2016-coref | | Coreference annotation to the benchmark data set (reference and test) of BioNLP-ST 2016 GE task.
For detailed information, please refer to the benchmark reference data set (bionlp-st-ge-2016-reference) and benchmark test data set (bionlp-st-ge-2016-test). | 853 | 2024-06-17 | Released | |
| 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 | |
| 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 | 2023-11-29 | Beta | |
| LitCovid-docs | | Updated at 2021-01-12
A comprehensive literature resource on the subject of Covid-19 is collected by NCBI:
https://www.ncbi.nlm.nih.gov/research/coronavirus/
The LitCovid project@PubAnnotation is a collection of the titles and abstracts of the LitCovid dataset, for the people who want to perform text mining analysis. Please note that if you produce some annotation to the documents in this project, and contribute the annotation back to PubAnnotation, it will become publicly available together with contribution from other people.
If you want to contribute your annotation to PubAnnotation, please refer to the documentation page:
http://www.pubannotation.org/docs/submit-annotation/
The list of the PMID is sourced from here
The 6 entries of the following PMIDs could not be included because they were not available from PubMed:32161394,
32104909,
32090470,
32076224,
32161394
32188956,
32238946.
Below is a notice from the original LitCovid dataset:
PUBLIC DOMAIN NOTICE
National Center for Biotechnology Information
This software/database is a "United States Government Work" under the
terms of the United States Copyright Act. It was written as part of
the author's official duties as a United States Government employee and
thus cannot be copyrighted. This software/database is freely available
to the public for use. The National Library of Medicine and the U.S.
Government have not placed any restriction on its use or reproduction.
Although all reasonable efforts have been taken to ensure the accuracy
and reliability of the software and data, the NLM and the U.S.
Government do not and cannot warrant the performance or results that
may be obtained by using this software or data. The NLM and the U.S.
Government disclaim all warranties, express or implied, including
warranties of performance, merchantability or fitness for any particular
purpose.
Please cite the authors in any work or product based on this material :
Chen Q, Allot A, & Lu Z. (2020) Keep up with the latest coronavirus research, Nature 579:193
| 18 | 2023-11-28 | 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 | 2023-11-28 | Developing | |
| 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 | |
| LitCovid-v1-docs | | A comprehensive literature resource on the subject of Covid-19 is collected by NCBI:
https://www.ncbi.nlm.nih.gov/research/coronavirus/
The LitCovid project@PubAnnotation is a collection of the titles and abstracts of the LitCovid dataset, for the people who want to perform text mining analysis. Please note that if you produce some annotation to the documents in this project, and contribute the annotation back to PubAnnotation, it will become publicly available together with contribution from other people.
If you want to contribute your annotation to PubAnnotation, please refer to the documentation page:
http://www.pubannotation.org/docs/submit-annotation/
The list of the PMID is sourced from here
The 6 entries of the following PMIDs could not be included because they were not available from PubMed:32161394,
32104909,
32090470,
32076224,
32161394
32188956,
32238946.
Below is a notice from the original LitCovid dataset:
PUBLIC DOMAIN NOTICE
National Center for Biotechnology Information
This software/database is a "United States Government Work" under the
terms of the United States Copyright Act. It was written as part of
the author's official duties as a United States Government employee and
thus cannot be copyrighted. This software/database is freely available
to the public for use. The National Library of Medicine and the U.S.
Government have not placed any restriction on its use or reproduction.
Although all reasonable efforts have been taken to ensure the accuracy
and reliability of the software and data, the NLM and the U.S.
Government do not and cannot warrant the performance or results that
may be obtained by using this software or data. The NLM and the U.S.
Government disclaim all warranties, express or implied, including
warranties of performance, merchantability or fitness for any particular
purpose.
Please cite the authors in any work or product based on this material :
Chen Q, Allot A, & Lu Z. (2020) Keep up with the latest coronavirus research, Nature 579:193
| 0 | 2023-11-29 | Released | |
| Glycan-GlyCosmos | | | 38.8 K | 2024-12-01 | Developing | |
