Dataset Card for CoMAGC

Dataset Summary

CoMAGC Dataset Summary:

CoMAGC is a corpus with multi-faceted annotations of gene-cancer relations. CoMAGC consists of 821 sentences collected from MEDLINE abstracts, and the sentences are about three different types of cancers, or prostate, breast and ovarian cancers. In CoMAGC, a piece of annotation is composed of four semantically orthogonal concepts that together express 1) how a gene changes, 2) how a cancer changes and 3) the causality between the gene and the cancer. The four concepts that constitute the multi-faceted annotation scheme are Change in Gene Expression (CGE), Change in Cell State (CCS), Proposition Type (PT) and Initial Gene Expression level (IGE).

• CGE captures whether the expression level of a gene is increased or decreased in a cell
• CCS captures the way how the cell changes together with a gene expression level change
  • normalTOnormal: The cell or tissue remains as normal after the change in the gene’s expression level.
  • normalTOcancer: The cell or tissue acquires cancerous properties as the gene expression level changes; some cancerous properties are strengthened.
  • cancerTOcancer: There's no change in the cancerous properties of the cell or tissue despite the change in the expression level of the gene.
  • cancerTOnormal: The cell or tissue loses some cancerous properties as the gene expression level changes; some cancerous properties are weakened.
  • unidentifiable: The information about whether or not the gene expression level change accompanies cell or tissue state change is not provided.
• PT captures whether the causality between the gene expression change and the cell property change
  • observation: Cell or tissue change accompanied by the gene expression level change is reported as observed but the causality between the two is not claimed. |
  • causality: The causality between the gene expression level change and the cell or tissue change is claimed.
• IGE captures the initial expression level of a gene before the change in its expression level
  • up-regulated: The initial gene expression level is higher than the expression level of the gene in the normal state.
  • down-regulated: The initial gene expression level is lower than the expression level of the gene in the normal state.
  • unchanged: The initial gene expression level is comparable to the expression level of the gene in the normal state.
  • unidentifiable: The information about the initial gene expression level is not provided. |

The original dataset in XML format is available here: http://biopathway.org/CoMAGC/

We converted the dataset to a JSONL format before pushing the data to the hub.

Languages

The language in the dataset is English.

Dataset Structure

Dataset Instances

An example of 'train' looks as follows:

{
  "pmid": "11722842.s0",
  "sentence": "Isolation and characterization of the major form of human MUC18 cDNA gene and correlation of MUC18 over-expression in prostate cancer cell lines and tissues with malignant progression.",
  "cancer_type": "prostate",
  "gene": {
    "name": "MUC18",
    "pos": [93, 97]
  },
  "cancer": {
    "name": "prostate cancer",
    "pos": [118, 132]
  },
  "CGE": "increased",
  "CCS": "normalTOcancer",
  "PT": "observation",
  "IGE": "unchanged",
  "expression_change_keyword_1": {
    "name": "over-expression",
    "pos": [99, 113],
    "type": "Gene_expression"
  },
  "expression_change_keyword_2": {
    "name": "over-expression",
    "pos": [99, 113],
    "type": "Positive_regulation"
  }
}

Data Fields

• pmid: the id of this sentence, a string feature.
• sentence: the text of this sentence, a string feature.
• cancer_type: the type of cancer in this sentence, a string feature.
• gene: gene entity
  • pos: character offsets of the gene entity, a list of int32 features.
  • name: gene entity text, a string feature.
• cancer: cancer entity
  • pos: character offsets of the cancer entity, a list of int32 features.
  • name: cancer entity text, a string feature.
• CGE: change in gene expression, a string feature.
• CCS: change in cell state, a string feature.
• PT: proposition type, a string feature.
• IGE: initial gene expression, a string feature.
• expression_change_keyword_1: a dict
  • name: keyword text, a string feature.
  • pos: character offsets of the keyword, a list of int32 features.
  • type: type of the expression change keyword, a string feature.
• expression_change_keyword_2: a dict
  • name: keyword text, a string feature.
  • pos: character offsets of the keyword, a list of int32 features.
  • type: type of the expression change keyword, a string feature.

Citation

BibTeX:

@article{lee2013comagc,
  title={CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations},
  author={Lee, Hee-Jin and Shim, Sang-Hyung and Song, Mi-Ryoung and Lee, Hyunju and Park, Jong C},
  journal={BMC bioinformatics},
  volume={14},
  pages={1--17},
  year={2013},
  publisher={Springer}
}

APA:

• Lee, H. J., Shim, S. H., Song, M. R., Lee, H., & Park, J. C. (2013). CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations. BMC bioinformatics, 14, 1-17.

Dataset Card Authors

@phucdev