Update README.md

README.md

@@ -54,4 +54,129 @@ configs:
   data_files:
   - split: train
     path: data/train-*
+license: cc-by-2.0
+task_categories:
+- text-classification
+language:
+- en
+tags:
+- biology
+- cancer
+- gene
+pretty_name: CoMAGC
+size_categories:
+- n<1K
 ---
+# Dataset Card for CoMAGC
+
+## Dataset Description
+
+- **Website:** http://biopathway.org/CoMAGC/
+- **Paper:** [CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-323)
+
+#### Dataset Summary
+
+<!-- Provide a quick summary of the dataset. -->
+**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.
+
+### Languages
+The language in the dataset is English.
+## Dataset Structure
+<!-- This section provides a description of the dataset fields, and additional information about the dataset structure such as criteria used to create the splits, relationships between data points, etc. -->
+### Dataset Instances
+An example of 'train' looks as follows:
+```json
+{
+  "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
+<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
+**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](https://github.com/phucdev)