Update README.md

README.md

@@ -20,13 +20,11 @@ configs:
     path: data/train-*
 language:
 - en
+
 ---
 
 # Dataset Card for Dataset Name
 
-<!-- Provide a quick summary of the dataset. -->
-
-This dataset card aims to be a base template for new datasets. It has been generated using [this raw template](https://github.com/huggingface/huggingface_hub/blob/main/src/huggingface_hub/templates/datasetcard_template.md?plain=1).
 
 
 ### Dataset Description
@@ -37,116 +35,100 @@ This dataset has been extracted from [Europe PMC (EPMC)](https://europepmc.org/)
 ## Dataset Details
 The dataset focuses on mentions of cell lines and related entities in biomedical text, making it a valuable resource for advancing natural language processing (NLP) tasks in the biomedical domain.
 
-### Uses: NLP Tasks Supported
-Named Entity Recognition (NER):
+### Intended Uses: NLP Tasks Supported
+- **Named Entity Recognition (NER**):
 Identify and classify mentions of cell lines or related entities appearing in biomedical contexts.
 
-Relationship Extraction:
+- **Relationship Extraction**:
 Extract relationships between cell lines and other biomedical entities, such as genes, diseases, or drugs.
 
-Text Classification:
+- **Text Classification**:
 Classify sentences or articles based on their relevance to specific cell lines, particularly in cancer research or drug development.
 
-Sentiment Analysis:
+- **Sentiment Analysis**:
 Analyze the sentiment or tone of texts discussing cell lines, such as the evaluation of experimental results (positive or negative).
 
-Information Retrieval:
+- **Information Retrieval**:
 Develop systems to retrieve articles or specific mentions of cell lines based on user queries.
 
-Entity Linking:
+- **Entity Linking**:
 Link cell line mentions in text to standardized identifiers in cell line ontologies or databases.
 
-Question Answering (QA):
+- **Question Answering (QA)**:
 Build systems that can answer specific questions about cell lines, such as their role in particular diseases or experiments.
 
-Topic Modeling:
+- **Topic Modeling**:
 Analyze the dataset to uncover major themes or trends in research involving cell lines.
 
-Text Summarization:
+- **Text Summarization**:
 Automatically generate summaries of articles or sections discussing cell lines.
 
 
 
+### Who funded the creation of the dataset?
 
-- **Curated by:** [More Information Needed]
-- **Funded by [optional]:** [More Information Needed]
-- **Shared by [optional]:** [More Information Needed]
-- **Language(s) (NLP):** [More Information Needed]
-- **License:** [More Information Needed]
-
-### Dataset Sources [optional]
-
-<!-- Provide the basic links for the dataset. -->
-
-- **Repository:** [More Information Needed]
-- **Paper [optional]:** [More Information Needed]
-- **Demo [optional]:** [More Information Needed]
-
-
-### Direct Use
-
-<!-- This section describes suitable use cases for the dataset. -->
-
-[More Information Needed]
-
-### Out-of-Scope Use
-
-<!-- This section addresses misuse, malicious use, and uses that the dataset will not work well for. -->
-
-[More Information Needed]
-
-## Dataset Features
-
-Text: Full-text sentences or abstracts extracted from EPMC articles.
-Annotations: Mentions of cell lines and other related entities, along with their contextual roles.
-Metadata: Includes article identifiers (e.g., PMCID), titles, and publication types
-
-[More Information Needed]
-
-## Dataset Creation
-
-### Curation Rationale
 
-The dataset was curated to support research in biomedical NLP, focusing on cell lines—a critical component in experimental biology and drug discovery.
+### Any other comments?
+The dataset aims to provide a foundational resource for advancing NLP in biomedicine.
 
-[More Information Needed]
+## Dataset Composition
 
-### Source Data
+- **What are the instances?**
+Instances consist of metadata and textual data from biomedical articles, including columns for PMCID, title, year, and publication type.
 
-<!-- This section describes the source data (e.g. news text and headlines, social media posts, translated sentences, ...). -->
+- **Are there multiple types of instances?**
+The dataset currently focuses on metadata and abstracts but can be extended to include relationships between entities or other structured annotations.
 
-#### Data Collection and Processing
+- **What experiments were initially run on this dataset?**
+No experiments have been conducted yet. Updates will follow as they occur.
 
-<!-- This section describes the data collection and processing process such as data selection criteria, filtering and normalization methods, tools and libraries used, etc. -->
+## Data Collection Process
 
+- **How was the data collected?**
+The dataset was collected using the Europe PMC API. Articles marked as "open access" were retrieved, and those labeled as "retraction of publication" were excluded. Duplicate entries were filtered by ensuring unique PMCIDs.
 
+- **Who was involved in the data collection process?**
+The data collection process was carried out by researchers at EMBL-EBI, leveraging automated tools for querying and processing the Europe PMC repository.
 
-## Citation [optional]
+- **Are there any known errors, sources of noise, or redundancies in the data?**
+None have been identified yet.
 
-<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
+## Data Preprocessing
 
-**BibTeX:**
+**What preprocessing/cleaning was done?**
+- Only open-access articles were retrieved.
+- Articles labeled as "retraction of publication" were excluded.
+- Duplicate entries based on the PMCID column were removed.
 
-[More Information Needed]
+## Dataset Distribution
 
-**APA:**
+- **How is the dataset distributed?**
+The dataset is freely available for use and reproduction. Proper citation of the authors is required(Information to be updated).
 
-[More Information Needed]
+- **When will the dataset be released/first distributed?**
+To be updated.
 
-## Glossary [optional]
+## Dataset Maintenance
 
-<!-- If relevant, include terms and calculations in this section that can help readers understand the dataset or dataset card. -->
+### Who is supporting/hosting/maintaining the dataset?
+Europe PMC, and ChEMBL team responsible for the dataset's maintenance.
 
-[More Information Needed]
+### How does one contact the owner/curator/manager of the dataset?
+Contact can be made via the community discussion forums on GitHub or Hugging Face.
 
-## More Information [optional]
+### Will the dataset be updated?
+Yes, updates will occur as the project progresses.
 
-[More Information Needed]
+### How often and by whom?
+Updates will be carried out periodically by the team.
 
-## Dataset Card Authors [optional]
+### How will updates/revisions be documented and communicated?
+Updates will be documented via GitHub, using version tags.
 
-[More Information Needed]
+### Is there a repository to link to any/all papers/systems that use this dataset?
+Yes, a GitHub repository will track publications and systems using this dataset.
 
-## Dataset Card Contact
+### If others want to extend/augment/build on this dataset, is there a mechanism for them to do so?
+Yes, contributions are encouraged via GitHub. Quality will be assessed through pull requests, and accepted contributions will be communicated to users via version tags and release notes.
 
-[More Information Needed]
+---