A dataset for Named Entity Recognition for rice gene
- Find the project page on PubAnnotation repository: http://pubannotation.org/projects/OryzaGP
- Find the development project page http://pubannotation.org/projects/OryzaGP_2021
- Dowload the OryzaGP datatset http://pubannotation.org/projects/OryzaGP_2021/annotations.tgz
Please cite with the following reference:
- Pierre Larmande, Huy Do, Yue Wang. OryzaGP: rice gene and protein dataset for named-entity recognition. Genomics Inform. 2019;17(2):e17. DOI: https://doi.org/10.5808/GI.2019.17.2.e17
The aim of this projet is to :
- update the datasets with new pubmed entries
- process annotation on gene/protein entities
- Downloaded Oryza reference dataset from Oryzabase database https://shigen.nig.ac.jp/rice/oryzabase/.
- Oryzabase provides manually curated dataset for new rice related pubmed entries
- A list of pubmedid have been created and uploaded on http://pubannotation.org/projects/OryzaGP_2021
- Corresponding abstracts have been retrieved
- In order to create or use ER tools, we need to setup a dictionary of gene/protein entities
- a first file named pub_dictionnary.txt was created from the Oryzabase gene dataset
- https://shigen.nig.ac.jp/rice/oryzabase/download/gene.
- it contains a label/gene name/symbol/synonyms [TAB] Oryzabase database URI
- a second pub_dictionnary_with_rapdb_URI.txt was created from the same dataset
- it contains a label/gene name/symbol/synonyms [TAB] RAP-DB database URI
- a third pub_dictionnary_with_msu.txt was created from the same dataset
- it contains a label/gene name/symbol/synonyms [TAB] MSU database URI
- we created 2 annotators for each pub dictionary ( single and batch mode)