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README.md

@@ -1,102 +1,259 @@
----
-license: cc-by-4.0
-dataset_info:
-  features:
-  - name: hgnc_id
-    dtype: string
-  - name: symbol
-    dtype: string
-  - name: name
-    dtype: string
-  - name: locus_group
-    dtype: string
-  - name: locus_type
-    dtype: string
-  - name: status
-    dtype: string
-  - name: location
-    dtype: string
-  - name: alias_symbol
-    sequence: string
-  - name: alias_name
-    sequence: string
-  - name: prev_symbol
-    sequence: string
-  - name: prev_name
-    sequence: string
-  - name: gene_group
-    sequence: string
-  - name: gene_group_id
-    sequence: int64
-  - name: date_approved_reserved
-    dtype: string
-  - name: date_symbol_changed
-    dtype: string
-  - name: date_name_changed
-    dtype: string
-  - name: date_modified
-    dtype: string
-  - name: entrez_id
-    dtype: string
-  - name: ensembl_gene_id
-    dtype: string
-  - name: vega_id
-    dtype: string
-  - name: ucsc_id
-    dtype: string
-  - name: ena
-    sequence: string
-  - name: refseq_accession
-    sequence: string
-  - name: ccds_id
-    sequence: string
-  - name: uniprot_ids
-    sequence: string
-  - name: pubmed_id
-    sequence: int64
-  - name: mgd_id
-    sequence: string
-  - name: rgd_id
-    sequence: string
-  - name: lsdb
-    sequence: string
-  - name: cosmic
-    dtype: string
-  - name: omim_id
-    sequence: string
-  - name: bioparadigms_slc
-    dtype: string
-  - name: orphanet
-    dtype: float64
-  - name: merops
-    dtype: string
-  - name: iuphar
-    dtype: string
-  - name: cd
-    dtype: string
-  - name: enzyme_id
-    sequence: string
-  - name: agr
-    dtype: string
-  - name: mane_select
-    sequence: string
-  - name: gencc
-    dtype: string
-  - name: uuid
-    dtype: string
-  - name: rna_central_id
-    sequence: string
-  - name: curator_notes
-    sequence: string
-  splits:
-  - name: train
-    num_bytes: 65361
-    num_examples: 87
-  download_size: 58173
-  dataset_size: 65361
-configs:
-- config_name: default
-  data_files:
-  - split: train
-    path: data/train-*
----
+---
+license: cc-by-4.0
+dataset_info:
+  features:
+  - name: hgnc_id
+    dtype: string
+  - name: symbol
+    dtype: string
+  - name: name
+    dtype: string
+  - name: locus_group
+    dtype: string
+  - name: locus_type
+    dtype: string
+  - name: status
+    dtype: string
+  - name: location
+    dtype: string
+  - name: alias_symbol
+    sequence: string
+  - name: alias_name
+    sequence: string
+  - name: prev_symbol
+    sequence: string
+  - name: prev_name
+    sequence: string
+  - name: gene_group
+    sequence: string
+  - name: gene_group_id
+    sequence: int64
+  - name: date_approved_reserved
+    dtype: string
+  - name: date_symbol_changed
+    dtype: string
+  - name: date_name_changed
+    dtype: string
+  - name: date_modified
+    dtype: string
+  - name: entrez_id
+    dtype: string
+  - name: ensembl_gene_id
+    dtype: string
+  - name: vega_id
+    dtype: string
+  - name: ucsc_id
+    dtype: string
+  - name: ena
+    sequence: string
+  - name: refseq_accession
+    sequence: string
+  - name: ccds_id
+    sequence: string
+  - name: uniprot_ids
+    sequence: string
+  - name: pubmed_id
+    sequence: int64
+  - name: mgd_id
+    sequence: string
+  - name: rgd_id
+    sequence: string
+  - name: lsdb
+    sequence: string
+  - name: cosmic
+    dtype: string
+  - name: omim_id
+    sequence: string
+  - name: bioparadigms_slc
+    dtype: string
+  - name: orphanet
+    dtype: float64
+  - name: merops
+    dtype: string
+  - name: iuphar
+    dtype: string
+  - name: cd
+    dtype: string
+  - name: enzyme_id
+    sequence: string
+  - name: agr
+    dtype: string
+  - name: mane_select
+    sequence: string
+  - name: gencc
+    dtype: string
+  - name: uuid
+    dtype: string
+  - name: rna_central_id
+    sequence: string
+  - name: curator_notes
+    sequence: string
+  splits:
+  - name: train
+    num_bytes: 65361
+    num_examples: 87
+  download_size: 58173
+  dataset_size: 65361
+configs:
+- config_name: default
+  data_files:
+  - split: train
+    path: data/train-*
+tags:
+- biology
+- chemistry
+- medical
+---
+
+# Dataset Card for **Synthetic Lethal Tumor Suppressor Genes (SL TSG)**
+
+This dataset was created with the goal of providing cancer researchers and bioinformaticians with a comprehensive resource for studying **synthetic lethality** in **tumor suppressor genes (TSGs)**. By identifying genetic interactions that lead to cancer cell death when both a tumor suppressor gene and its synthetic lethal partner are mutated or deactivated, this dataset aims to support the development of novel cancer therapeutics.
+
+It is currently a highly filtered list of ~90 genes and intended to be used in combination with the [dwb2023/pmc_35559673_table_s6](https://huggingface.co/datasets/dwb2023/pmc_35559673_table_s6) dataset.
+
+In creating this dataset, we are grateful for the rich, publicly available data curated by the **HUGO Gene Nomenclature Committee (HGNC)**. Their dedication to maintaining high-quality gene data has been instrumental to this work.
+
+## Dataset Details
+
+### Dataset Description
+
+This dataset consists of curated information on synthetic lethal interactions involving tumor suppressor genes. The fields in this dataset include gene symbols, gene IDs, and additional metadata sourced from public bioinformatics databases, including **HGNC**, **ENSEMBL**, **NCBI Entrez**, and others. Researchers can leverage this dataset to study gene-gene interactions in cancer biology, particularly those that lead to synthetic lethality, an emerging therapeutic strategy in cancer treatment.
+
+We would like to acknowledge **HGNC** as the primary source of the gene nomenclature and ID data used in this dataset. **HGNC** provides freely accessible gene data under the **Creative Commons Public Domain (CC0)** license. While attribution is not required, we believe in giving credit to the dedicated curators who make such valuable resources available.
+
+### Dataset Sources
+
+- **Source File:** [HGNC Complete Set JSON](https://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json)
+- **Paper:** [Genenames.org: the HGNC resources in 2023](https://academic.oup.com/nar/article/51/D1/D1003/6761747) by Ruth L. Seal, et al.
+
+## Uses
+
+### Direct Use
+
+This dataset is primarily intended for use in **cancer research**. Specifically, it supports the study of **synthetic lethal interactions** involving tumor suppressor genes, helping researchers:
+- Identify potential therapeutic targets in cancer cells harboring TSG mutations.
+- Explore gene-gene dependencies that may reveal vulnerabilities in cancer cells.
+- Integrate synthetic lethal interactions with other cancer data to guide precision medicine.
+
+### Out-of-Scope Use
+
+- This dataset is not designed for clinical decision-making or to predict individual genetic predispositions to diseases.
+- Using the dataset for commercial purposes without proper validation and clinical trials is discouraged.
+
+## Dataset Structure
+
+The dataset contains the following fields, each of which is essential for understanding the synthetic lethal interactions and genetic relationships in cancer:
+
+| Field Name | Description |
+|------------|-------------|
+| hgnc_id | HGNC ID. A unique ID created by the HGNC for every approved symbol. |
+| symbol | The HGNC approved gene symbol. Equates to the "Approved symbol" field within the gene symbol report. |
+| name | HGNC approved name for the gene. Equates to the "Approved name" field within the gene symbol report. |
+| locus_group | A group name for a set of related locus types as defined by the HGNC (e.g. non-coding RNA). |
+| locus_type | The locus type as set by the HGNC. |
+| status | Status of the symbol report, which can be either "Approved" or "Entry Withdrawn". |
+| location | Cytogenetic location of the gene (e.g. 2q34). |
+| alias_symbol | Other symbols used to refer to this gene as seen in the "Alias symbols" field in the gene symbol report. |
+| alias_name | Other names used to refer to this gene as seen in the "Alias names" field in the gene symbol report. |
+| prev_symbol | Gene symbols previously approved by the HGNC for this gene. Equates to the "Previous symbols" field within the gene symbol report. |
+| prev_name | Gene names previously approved by the HGNC for this gene. Equates to the "Previous names" field within the gene symbol report. |
+| gene_group | The gene group name as set by the HGNC and seen at the top of the gene group reports. |
+| gene_group_id | ID used to designate a gene group the gene has been assigned to. |
+| date_approved_reserved | The date the entry was first approved. |
+| date_symbol_changed | The date the approved symbol was last changed. |
+| date_name_changed | The date the approved name was last changed. |
+| date_modified | Date the entry was last modified. |
+| entrez_id | NCBI gene ID. Found within the "Gene resources" section of the gene symbol report. |
+| ensembl_gene_id | Ensembl gene ID. Found within the "Gene resources" section of the gene symbol report. |
+| vega_id | Vega gene ID. Found within the "Gene resources" section of the gene symbol report. |
+| ucsc_id | UCSC gene ID. Found within the "Gene resources" section of the gene symbol report. |
+| ena | International Nucleotide Sequence Database Collaboration (GenBank, ENA and DDBJ) accession number(s). Found within the "Nucleotide resources" section of the gene symbol report. |
+| refseq_accession | RefSeq nucleotide accession(s). Found within the "Nucleotide resources" section of the gene symbol report. |
+| ccds_id | Consensus CDS ID. Found within the "Nucleotide resources" section of the gene symbol report. |
+| uniprot_ids | UniProt protein accession. Found within the "Protein resource" section of the gene symbol report. |
+| pubmed_id | Pubmed and Europe Pubmed Central PMID(s). |
+| mgd_id | Mouse genome informatics database ID. Found within the "Homologs" section of the gene symbol report. |
+| rgd_id | Rat genome database gene ID. Found within the "Homologs" section of the gene symbol report. |
+| lsdb | The name of the Locus Specific Mutation Database and URL for the gene separated by a | character. |
+| cosmic | Symbol used within the Catalogue of somatic mutations in cancer for the gene. (No longer updated!). |
+| omim_id | Online Mendelian Inheritance in Man (OMIM) ID |
+| bioparadigms_slc | Symbol used to link to the SLC tables database at bioparadigms.org for the gene |
+| orphanet | Orphanet ID |
+| merops | ID used to link to the MEROPS peptidase database |
+| iuphar | The objectId used to link to the IUPHAR/BPS Guide to PHARMACOLOGY database. |
+| cd | Symbol used within the Human Cell Differentiation Molecule database for the gene |
+| enzyme_id | ENZYME EC accession number |
+| agr | The HGNC ID that the Alliance of Genome Resources (AGR) have linked to their record of the gene. |
+| mane_select | NCBI and Ensembl transcript IDs/acessions including the version number for one high-quality representative transcript per protein-coding gene. |
+| gencc | The HGNC ID used within the GenCC database as the unique identifier of their gene reports within the GenCC database. |
+| uuid | Unique identifier (not in original description, but present in the JSON list) |
+| rna_central_id | RNA Central ID (not in original description, but present in the JSON list) |
+| curator_notes | Curator notes (not in original description, but present in the JSON list) |
+
+## Dataset Creation
+
+### Curation Rationale
+
+The curation of this dataset was driven by a need for a well-organized, comprehensive source of synthetic lethal interactions in tumor suppressor genes. These relationships offer a promising avenue for cancer therapies that specifically target cancer cells, leaving healthy cells unaffected.
+
+### Source Data
+
+#### Data Collection and Processing
+
+The data was collected from multiple publicly available sources, including:
+- **HGNC**: Providing gene nomenclature and IDs.
+- **ENSEMBL**: Offering curated genomic annotations.
+- **NCBI Entrez**: Supplying cross-referenced gene IDs.
+
+Data was processed to ensure consistency across gene symbols and IDs, with normalization steps applied to ensure accuracy and usability in bioinformatics workflows.
+
+#### Who are the source data producers?
+
+- **HGNC (HUGO Gene Nomenclature Committee)**: Providing standardized gene symbols and IDs (https://www.genenames.org/)
+- **ENSEMBL**: Offering detailed genome annotations (https://www.ensembl.org/)
+- **NCBI Entrez**: Supplying gene-related data (https://www.ncbi.nlm.nih.gov/gene/)
+
+### Annotations [optional]
+
+No manual annotations were added to the dataset.
+
+## Bias, Risks, and Limitations
+
+### Recommendations
+
+This dataset is intended for research purposes only. Users should be aware that synthetic lethal interactions are still under active research, and many interactions need experimental validation. Users are encouraged to critically evaluate the dataset before applying it in any therapeutic development context.
+
+## Citation
+
+Please cite the original dataset using the following format:
+
+**BibTeX:**
+```
+@article{10.1093/nar/gkac888,
+    author = {Seal, Ruth L and Braschi, Bryony and Gray, Kristian and Jones, Tamsin E M and Tweedie, Susan and Haim-Vilmovsky, Liora and Bruford, Elspeth A},
+    title = "{Genenames.org: the HGNC resources in 2023}",
+    journal = {Nucleic Acids Research},
+    volume = {51},
+    number = {D1},
+    pages = {D1003-D1009},
+    year = {2022},
+    month = {10},
+    abstract = "{The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes. The HGNC database (www.genenames.org) currently contains over 43 000 approved gene symbols, over 19 200 of which are assigned to protein-coding genes, 14 000 to pseudogenes and nearly 9000 to non-coding RNA genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC nomenclature advisors and links to related genomic, clinical, and proteomic information. Here, we describe updates to our resource, including improvements to our search facility and new download features.}",
+    issn = {0305-1048},
+    doi = {10.1093/nar/gkac888},
+    url = {https://doi.org/10.1093/nar/gkac888},
+    eprint = {https://academic.oup.com/nar/article-pdf/51/D1/D1003/48441239/gkac888.pdf},
+}
+```
+
+## Dataset Card Authors
+
+- **Author:** dwb2023
+
+## Dataset Card Contact
+
+- **Contact:** dwb2023
+
+---
+
+This card now includes proper attribution for **HGNC** and other contributors, aligning with their recommendations for proper citation and respecting their curation efforts. Let me know if there are any final adjustments!