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Datasets:
EMBO
/
SourceData

Tasks:
Token Classification
Languages:
English
Size:
10K<n<100K
ArXiv:
Tags:
biology
medical
NER
NEL
DOI:
License:
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5
drAbreu commited on
Commit
f1c6bcc
•
1 Parent(s): dc9edd9

Adding information extraction data from neo4j

Browse files
Files changed (20) hide show
  1. .gitattributes +20 -0
  2. README.md +24 -0
  3. information_extraction/assayed_entities.csv +3 -0
  4. information_extraction/assayed_entities.json +3 -0
  5. information_extraction/chemicals.csv +3 -0
  6. information_extraction/chemicals.json +3 -0
  7. information_extraction/controlled_entities.csv +3 -0
  8. information_extraction/controlled_entities.json +3 -0
  9. information_extraction/diseases.csv +3 -0
  10. information_extraction/diseases.json +3 -0
  11. information_extraction/experimental_assay.csv +3 -0
  12. information_extraction/experimental_assay.json +3 -0
  13. information_extraction/hypothesis_tested.csv +3 -0
  14. information_extraction/hypothesis_tested.json +3 -0
  15. information_extraction/is_experiment.csv +3 -0
  16. information_extraction/is_experiment.json +3 -0
  17. information_extraction/ncbi_gene_linking.csv +3 -0
  18. information_extraction/ncbi_gene_linking.json +3 -0
  19. information_extraction/where_was_tested.csv +3 -0
  20. information_extraction/where_was_tested.json +3 -0
.gitattributes CHANGED
@@ -141,3 +141,23 @@ token_classification/roles_small_mol/train.jsonl filter=lfs diff=lfs merge=lfs -
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  token_classification/roles_small_mol/validation.jsonl filter=lfs diff=lfs merge=lfs -text
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  image_segmentation/train/labels.cache filter=lfs diff=lfs merge=lfs -text
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  image_segmentation/clip_panel_image_captions/ filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  token_classification/roles_small_mol/validation.jsonl filter=lfs diff=lfs merge=lfs -text
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  image_segmentation/train/labels.cache filter=lfs diff=lfs merge=lfs -text
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  image_segmentation/clip_panel_image_captions/ filter=lfs diff=lfs merge=lfs -text
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+ . filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/ filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/experimental_assay.json filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/hypothesis_tested.json filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/is_experiment.json filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/ncbi_gene_linking.csv filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/where_was_tested.csv filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/where_was_tested.json filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/controlled_entities.json filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/diseases.json filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/chemicals.csv filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/is_experiment.csv filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/diseases.csv filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/experimental_assay.csv filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/assayed_entities.csv filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/controlled_entities.csv filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/hypothesis_tested.csv filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/ncbi_gene_linking.json filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/assayed_entities.json filter=lfs diff=lfs merge=lfs -text
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+ information_extraction/chemicals.json filter=lfs diff=lfs merge=lfs -text
README.md CHANGED
@@ -172,6 +172,30 @@ The text in the dataset is English.
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  })
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  ```
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  ## Dataset Creation
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  ### Curation Rationale
 
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  })
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  ```
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+ ### Information Extraction
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+
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+ This folder contains `caption` `answer` pairse intended to be used for information extraction. Each of the files contains answers to given questions about the captions.
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+ Each file is provided in `csv` and `json` format for convinience for different cases.
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+ The list of files and questions they answer are shown below:
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+
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+ * `assayed_entities`: What is the assayed/measured entity?
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+
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+ * `chemicals`: Are there any chemical compounds or small molecules mentioned?
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+
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+ * `diseases`: Is there any disease term mentioned, or can be infered, in the figure legend?
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+
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+ * `experimental_assay`: What kind of experimental assay was used for this experiment?
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+
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+ * `hypothesis_tested`: Can you formulate the hypothesis that this experiment has tested.
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+
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+ * `is_experiment`: Does the legend describe an experiment or not?
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+
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+ * `ncbi_gene_linking`: Can you link the identified genes to their NCBI gene identifiers?
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+
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+ * `where_was_tested`: In what kind of cell/tissue/organism/subcellular component was the experiment performed?
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+
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+ We refer the interested reader to the [cypher queries](https://github.com/source-data/soda-data/blob/master/src/soda_data/sdneo/info_extraction_queries.py) used to generate this data for further information.
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+
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  ## Dataset Creation
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  ### Curation Rationale
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