Datasets:
Tasks:
Text Generation
Modalities:
Text
Formats:
json
Languages:
English
Size:
10K - 100K
ArXiv:
License:
| license: other | |
| license_name: common-crawl | |
| license_link: LICENSE | |
| task_categories: | |
| - text-generation | |
| language: | |
| - en | |
| pretty_name: Clinical Guidelines | |
| size_categories: | |
| - 10K<n<100K | |
| # Dataset Card for Clinical Guidelines corpus | |
| The Clinical Guidelines corpus is a new dataset of 46K clinical practice guidelines from various medical sources. This dataset is part of the original training corpus of the [Meditron](https://huggingface.co/epfl-llm/meditron-70b) LLM. | |
| <img width=50% src="guidelines.png" alt="Sources of Clinical Practice Guidelines" title="CPG sources"> | |
| We release 35K scraped articles (in both raw and cleaned form) from 8 of 16 clinical guidelines sources allowing redistribution (namely CCO, CDC, CMA, ICRC, NICE, SPOR, WHO & WikiDoc). You can scrape and clean all 16 guideline sources using our web scrapers and pre-processing code in [epfLLM/meditron](https://github.com/epfLLM/meditron). | |
| | Source | Full Name | Source tag | Total guidelines | Total words | Audience | Released | | |
| |-|-|-|-|-|-|-| | |
| | **[AAFP](https://www.aafp.org)** | American Academy of Family Physicians | `aafp` | 50 | 9.4K | Doctor | No | | |
| | **[CCO](https://www.cancercareontario.ca/en/guidelines-advice)** | Cancer Care Ontario | `cco` | 87 | 199K | Doctor | **Yes** | | |
| | **[CDC](https://www.cdc.gov/)** | Center for Disease Control and Prevention | `cdc` | 621 | 6.7M | Doctor | **Yes** | | |
| | **[CMA](https://joulecma.ca/)** | Canadian Medical Association | `cma` | 431 | 1.7M | Doctor | **Yes** | | |
| | **[CPS](https://cps.ca)** | Canadian Paediatric Society | `cps` | 54 | 133K | Doctor | No | | |
| | **[drugs.com](https://www.drugs.com/)** | Drugs.com | `drugs` | 6548 | 4.1M | Both | No | | |
| | **[GuidelineCentral](https://www.guidelinecentral.com/)** | GuidelineCentral | `gc` | 1029 | 1M | Doctor | No | | |
| | **[ICRC](http://icrc.org/)** | International Committee of the Red Cross | `icrc` | 49 | 1.2M | Doctor | **Yes** | | |
| | **[IDSA](https://www.idsociety.org/)** | Infectious Diseases Society of America | `idsa` | 47 | 646K | Doctor | No | | |
| | **[MAGIC](https://magicevidence.org/)** | Making GRADE The Irresistible Choice | `magic` | 52 | 415K | Doctor | No | | |
| | **[MayoClinic](https://www.mayoclinic.org/)** | MayoClinic | `mayo` | 1100 | 2.2M | Patient | No | | |
| | **[NICE](https://www.nice.org.uk/guidance)** | National Institute for Health and Care Excellence | `nice` | 1656 | 8.1M | Doctor | **Yes** | | |
| | **[RCH](https://www.rch.org.au/clinicalguide/about_rch_cpgs/welcome_to_the_clinical_practice_guidelines/)** | Royal Children's Hospital Melbourne | `rch` | 384 | 410K | Doctor | No | | |
| | **[SPOR](https://sporevidencealliance.ca/key-activities/cpg-asset-map/cpg-database/)** | Strategy for Patient-Oriented Research | `spor` | 217 | 1.1M | Doctor | **Yes** | | |
| | **[WHO](https://www.who.int/publications/who-guidelines)** | World Health Organization | `who` | 223 | 3.1M | Both | **Yes** | | |
| | **[WikiDoc](https://www.wikidoc.org/)** | WikiDoc | `wikidoc` | 33058 | 34M | Both | **Yes** | | |
| ## Dataset Details | |
| ### Dataset Description | |
| <!-- Provide a longer summary of what this dataset is. --> | |
| - **Curated by:** [EPFL LLM Team](https://huggingface.co/epfl-llm) | |
| - **Funded by [optional]:** [More Information Needed] | |
| - **Shared by [optional]:** [More Information Needed] | |
| - **Language(s) (NLP):** English only | |
| - **License:** [More Information Needed] | |
| ### Dataset Sources [optional] | |
| <!-- Provide the basic links for the dataset. --> | |
| - **Repository:** [epfLLM/meditron](https://github.com/epfLLM/meditron) | |
| - **Paper [optional]:** *[MediTron-70B: Scaling Medical Pretraining for Large Language Models]()* | |
| - **Demo [optional]:** [More Information Needed] | |
| ## Uses | |
| <!-- Address questions around how the dataset is intended to be used. --> | |
| ### 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 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. --> | |
| Each row of the dataset represents one clinical practice guideline article, and consists of the following string dataset fields (all strings): | |
| - `id`: Unique identifier for each article. | |
| - `source`: Source tag ('cco', 'cdc', 'cma', 'icrc', 'nice', 'spor', 'who' or 'wikidoc') | |
| - `title`: Title of the article (only for CMA, NICE and WikiDoc) | |
| - `url`: URL of the article (only for NICE and WikiDoc) | |
| - `raw_text`: Unprocessed scraped article text | |
| - `clean_text`: Cleaned and formatted article text | |
| - `overview`: Short summary of the article (only for NICE) | |
| ## Dataset Creation | |
| ### Curation Rationale | |
| <!-- Motivation for the creation of this dataset. --> | |
| Clinical practice guidelines (CPGs) are rigorously researched frameworks designed to guide healthcare practitioners and patients in making evidence-based decisions regarding diagnosis, treatment, and management. | |
| They are compiled through a systematic process of collaborative consensus between experts to establish recommendations from the latest evidence on best practices that would maximize benefit in light of practical concerns such as available resources and context. As a super-synthesis of meta-analyses, they sit atop the `evidence pyramid' and form the basis of actionable evidence-based practice. | |
| CPGs are produced at various geographic and organizational granularities, ranging from global to hospital-level initiatives directed by international professional medical associations to informal consortia, regional or national governmental bodies to individual NGOs and hospitals. | |
| Our Clinical Guidelines corpus comprises $46,469$ guideline articles from 16 globally recognized sources for clinician and patient-directed guidance across high and low-resource settings, multiple medical domains (internal medicine, pediatrics, oncology, infectious disease, etc.), and various geographic granularities. | |
| ### Source Data | |
| <!-- This section describes the source data (e.g. news text and headlines, social media posts, translated sentences, ...). --> | |
| The \guidelines corpus comprises a broad range of contexts. For instance, the geographic scope ranges from global (WHO) to national (CDC, NICE) and regional (Ontario, Melbourne) to institutional (ICRC, Mayo Clinic). The corpus also represents health care concerns from high- (Ontario, Melbourne), low- (WHO), and volatile- (ICRC) resource settings. | |
| \guidelines{} also contains a range of technical and conversational vocabulary with target audiences of clinicians or patients (or both), and is sometimes highly specialized within a theme (cancer, pediatrics, infectious disease). The peer review processes also ranged from UN bodies (WHO), institutional review boards (ICRC), professional associations (AAFP) to publicly crowdsourced knowledge bases (WikiDoc). | |
| #### Data Collection and Processing | |
| <!-- This section describes the data collection and processing process such as data selection criteria, filtering and normalization methods, tools and libraries used, etc. --> | |
| After extracting the raw text from each source, we cleaned data to exclude irrelevant or repetitive content that did not contribute to the textual content, such as URLs, references, figures, table delimiters, and ill-formatted characters. | |
| Additionally, the text was standardized to a unified format with indicated section headers, homogenous space separating paragraphs, and normalized lists. | |
| Finally, all samples were deduplicated using title matching, and articles that were too short or not English were filtered out. | |
| #### Who are the source data producers? | |
| <!-- This section describes the people or systems who originally created the data. It should also include self-reported demographic or identity information for the source data creators if this information is available. --> | |
| We employed pragmatic selection criteria over medical sources, seeking CPGs that were: | |
| - (1) open-access, | |
| - (2) systematically formatted with homogenous textual structure (i.e., in a format in which automated processes could be deployed without excessive risk of misaligning textual sequences), | |
| - (3) in the language predominantly represented by the pre-training corpus of Llama (i.e., English) | |
| - (4) covering a breadth of medical sub-domains, audiences (clinician, nurse, patient), and resource settings (high, low, and humanitarian response settings). | |
| [More Information Needed] | |
| ### Annotations [optional] | |
| <!-- If the dataset contains annotations which are not part of the initial data collection, use this section to describe them. --> | |
| #### Annotation process | |
| <!-- This section describes the annotation process such as annotation tools used in the process, the amount of data annotated, annotation guidelines provided to the annotators, interannotator statistics, annotation validation, etc. --> | |
| [More Information Needed] | |
| #### Who are the annotators? | |
| <!-- This section describes the people or systems who created the annotations. --> | |
| [More Information Needed] | |
| #### Personal and Sensitive Information | |
| <!-- State whether the dataset contains data that might be considered personal, sensitive, or private (e.g., data that reveals addresses, uniquely identifiable names or aliases, racial or ethnic origins, sexual orientations, religious beliefs, political opinions, financial or health data, etc.). If efforts were made to anonymize the data, describe the anonymization process. --> | |
| [More Information Needed] | |
| ## Bias, Risks, and Limitations | |
| <!-- This section is meant to convey both technical and sociotechnical limitations. --> | |
| [More Information Needed] | |
| ### Recommendations | |
| <!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. --> | |
| Users should be made aware of the risks, biases and limitations of the dataset. More information needed for further recommendations. | |
| ## Citation [optional] | |
| <!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. --> | |
| **BibTeX:** | |
| [More Information Needed] | |
| **APA:** | |
| [More Information Needed] | |
| ## Glossary [optional] | |
| <!-- If relevant, include terms and calculations in this section that can help readers understand the dataset or dataset card. --> | |
| [More Information Needed] | |
| ## More Information [optional] | |
| [More Information Needed] | |
| ## Dataset Card Authors [optional] | |
| [More Information Needed] | |
| ## Dataset Card Contact | |
| [More Information Needed] |