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README.md
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<!-- Si queréis incluir una versión de la Dataset Card en español, enlazarla aquí al principio (e.g. `README_es.md`).-->
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This dataset groups and organizes several datasets present in hugginface (e.g.: PlanTL-GOB-ES/cantemist-ner, PlanTL-GOB-ES/pharmaconer)
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## Uses
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<!-- Address questions around how the dataset is intended to be used. -->
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### Direct Use
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### Out-of-Scope Use
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<!-- This section addresses misuse, malicious use, and uses that the dataset will not work well for. -->
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## Dataset Structure
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<!-- En esta sección podéis enumerar y explicar cada columna del corpus. Para cada columna que sea de tipo "categoría" podéis indicar el porcentaje de ejemplos. -->
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- **question (raw_text)**:
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- **answer (topic)**: (
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- **speciality**: (
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- **raw_text_type**: (
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- **topic_type**: (
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- **source**:
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- **country**:
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- **document_id**:
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<!-- - **idioma**: (Variedad geográfica) código ISO del idioma -->
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<!--- **registro** (Variedad funcional): Siempre es `medio`. -->
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<!-- - **periodo** (Variedad histórica): Siempre es `actual`. -->
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<!-- - **tarea**: `pregunta` | `resumen` | `open_text` | `clinic_case`. -->
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<!-- - **país_origen**: País de origen de los datos. -->
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- **Id**:
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- **Tokens**:
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- **Licencia**:
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Apache 2
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## Dataset Creation
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### Curation Rationale
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<!-- Motivation for the creation of this dataset. -->
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### Source Data
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<!-- This section describes the source data (e.g. news text and headlines, social media posts, translated sentences, ...). -->
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| --- | ----------- | ----------- | ----------- | ----------- | ----------- | ----------- |
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| 1 | Cantemist corpus: gold standard of oncology clinical cases annotated with CIE-O 3 terminology | 349287 | 9157 kB | [CC Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/) | https://huggingface.co/datasets/bigbio/cantemist/viewer/cantemist_bigbio_kb | es |
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| 2 | MedlinePlus Spanish (National Library of Medicine, NLM) | 7757337 | 35 MB | | https://medlineplus.gov/spanish/ | es |
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**Sugerencias:**
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#### Who are the source data producers?
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<!-- 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. -->
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#### Annotation process
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<!-- Enlazar aquí el notebook utilizado para crear el espacio de anotación de Argilla y la guía de anotación. -->
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#### Who are the annotators?
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<!-- This section describes the people or systems who created the annotations. -->
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#### Personal and Sensitive Information
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<!-- 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. -->
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<!-- In the construction process, it was taken into account that sensitive user data was not included in any of the cases (e.g., clinical cases). -->
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<!-- Aquí podéis mencionar los posibles sesgos heredados según el origen de los datos y de las personas que lo han anotado, hablar del balance de las categorías representadas, los esfuerzos que habéis hecho para intentar mitigar sesgos y riesgos. -->
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En el caso de necesitar filtrar por fuente de datos u otro criterio usted puede auxiliarse de las propiedades de la estructura de datos `Dataset` del marco de trabajo
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Hugginface. En el siguiente ejemplo de código se obtienen del conjunto de datos las entradas que tienen un tipo de tópico sobre diagnóstico medico o un tópico médico:
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```
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Users should be made aware of the risks, biases and limitations of the dataset. More information needed for further recommendations. -->
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`medical_diagnostic`, `answer`, `natural_medicine_topic`.
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In case of using this dataset for the LLM training or finetuning for natural language generating with a production
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<!-- Si queréis incluir una versión de la Dataset Card en español, enlazarla aquí al principio (e.g. `README_es.md`).-->
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This dataset groups and organizes several datasets present in hugginface (e.g.: PlanTL-GOB-ES/cantemist-ner, PlanTL-GOB-ES/pharmaconer)
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and other public resources created by researchers with different formats (e.g.; MedLexSp )
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to allow it to be a source of knowledge of large language models in Spanish for the medical domain.
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This dataset groups and organizes several datasets present in hugginface (e.g.: PlanTL-GOB-ES/cantemist-ner, PlanTL-GOB-ES/pharmaconer)
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## Uses
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<!-- Address questions around how the dataset is intended to be used. -->
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The use of this dataset is suggested to achieve self-tuning and pre-training of LLM for the medical domain with information in Spanish.
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### Direct Use
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### Out-of-Scope Use
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<!-- This section addresses misuse, malicious use, and uses that the dataset will not work well for. -->
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The creators of the dataset are not responsible for harmful results that the models may generate when trained with this information.
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A rigorous evaluation process with specialists of the results generated by trained LLM models is suggested.
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## Dataset Structure
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<!-- En esta sección podéis enumerar y explicar cada columna del corpus. Para cada columna que sea de tipo "categoría" podéis indicar el porcentaje de ejemplos. -->
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For each entry or document in the information source, organize it in a Hugginface dataset as follows:
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- **question (raw_text)**: Text associated with the document, question, clinical case or other type of information.
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- **answer (topic)**: (Text associated with medical treatment (healthcare_treatment), diagnosis (healthcare_diagnosis),
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health topic (topic), answer to a question (answer), other, or be empty e.g. in the open text)
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- **speciality**: (Medical specialty to which the raw_text relates, e.g. cardiology, surgery, others)
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- **raw_text_type**: (Can be clinic_case, open_text, question or empty)
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- **topic_type**: (It can be medical topic, medical diagnosis, answer, natural medicine topic, other, or empty)
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- **source**: Identifier of the source associated with the document that appears in the README and description of the dataset.
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- **country**: Identifier of the country of origin of the source (e.g.; ch, es) using the ISO 3166-1 alpha-2 standard (Two-letter country codes).
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- **document_id**: Document identifier in the source dataset, this value can be empty in case it is not known.
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<!-- - **idioma**: (Variedad geográfica) código ISO del idioma -->
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<!--- **registro** (Variedad funcional): Siempre es `medio`. -->
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<!-- - **periodo** (Variedad histórica): Siempre es `actual`. -->
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<!-- - **tarea**: `pregunta` | `resumen` | `open_text` | `clinic_case`. -->
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<!-- - **país_origen**: País de origen de los datos. -->
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At the beginning of this construction process, the table in the [Source Data](#source_data) section must be updated.
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description of the source of information with the following data:
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- **Id**: This will be a number so that the source of information can be referenced in each entry of the data set.
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- **Name**: Name of the source from which it comes.
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- **Tokens**: Number of tokens it contains.
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- **Memory**: Memory size of the dataset generated for huggingface
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- **Licencia**: In this case, if it is only for research or if you have another license such as MIT,
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Apache 2 or others
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- **Address**: URL from where the information can be downloaded or consulted.
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- **Country**: Information source country of the using the [ISO 3166-1 standard](https://es.wikipedia.org/wiki/ISO_3166-1) alpha-2 code: 2-letter ISO code assigned to that country or territory.
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## Dataset Creation
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### Curation Rationale
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<!-- Motivation for the creation of this dataset. -->
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More than 600 million Spanish speakers need resources, such as LLMs, to obtain medical information freely
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and safe, complying with the millennium objectives: Health and Wellbeing, Education and Quality, End of Poverty proposed by the UN.
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There are few resources or data sets from the medical domain for training or self-tuning for an LLM in the Spanish language.
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To train an LLM autotuner in the domain of medicine and healthcare, a large amount of data from this context is needed.
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To create a data set in the medical domain, some certification by specialists in corpus construction is necessary.
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### Source Data
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<!-- This section describes the source data (e.g. news text and headlines, social media posts, translated sentences, ...). -->
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| Id | Name | Tokens | Memory | Licencia | Address | Country |
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| --- | ----------- | ----------- | ----------- | ----------- | ----------- | ----------- |
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| 1 | Cantemist corpus: gold standard of oncology clinical cases annotated with CIE-O 3 terminology | 349287 | 9157 kB | [CC Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/) | https://huggingface.co/datasets/bigbio/cantemist/viewer/cantemist_bigbio_kb | es |
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| 2 | MedlinePlus Spanish (National Library of Medicine, NLM) | 7757337 | 35 MB | | https://medlineplus.gov/spanish/ | es |
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**Sugerencias:**
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- In [BioMistral/BioInstructQA](https://huggingface.co/datasets/BioMistral/BioInstructQA) the information was used in Spanish. For more information consult the article [BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains](https://arxiv.org/pdf/2402.10373.pdf?trk=public_post_comment-text).
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- In [Cantemist](https://huggingface.co/datasets/bigbio/cantemist/viewer/cantemist_bigbio_kb) a search was made for the code associated with the pathology and it was established as a topic.
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- In [CARES](https://huggingface.co/datasets/chizhikchi/CARES) the associated type was searched in the established code table.
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#### Who are the source data producers?
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<!-- 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. -->
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Different events, NLP competitions or the construction of data sets for LLM such as BioMistral. See [table in Source Data section](#Source)
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#### Annotation process
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<!-- Enlazar aquí el notebook utilizado para crear el espacio de anotación de Argilla y la guía de anotación. -->
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The annotation process was automatic, converting the data sources to the attributes of the new data set.
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#### Who are the annotators?
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<!-- This section describes the people or systems who created the annotations. -->
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See the section [Team](#Team)
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#### Personal and Sensitive Information
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<!-- 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. -->
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In the construction process, it was taken into account that sensitive user data was not included in any of the cases (e.g., clinical cases).
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<!-- In the construction process, it was taken into account that sensitive user data was not included in any of the cases (e.g., clinical cases). -->
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<!-- Aquí podéis mencionar los posibles sesgos heredados según el origen de los datos y de las personas que lo han anotado, hablar del balance de las categorías representadas, los esfuerzos que habéis hecho para intentar mitigar sesgos y riesgos. -->
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It is suggested to take into account the scope of the license of each of the sources (e.g., review the source and License field in the previous table).
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If you need to filter by data source or other criteria, you can use the properties of the `Dataset` data structure of the framework.
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Hugginface. In the following code example, the entries that have a topic type about medical diagnosis or a medical topic are obtained from the data set:
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```
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Users should be made aware of the risks, biases and limitations of the dataset. More information needed for further recommendations. -->
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Personnel using this dataset must be aware of the risks, biases and limitations of the dataset.
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For the autotuning of an LLM, it is suggested to take into account the rows where the topic type (ed., topic_type field) has values: `medical_topic`,
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`medical_diagnostic`, `answer`, `natural_medicine_topic`. Because it indicates that this field is not empty and has value for the creation of instructions of the
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question and answer form.
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For LLM pre-training, it is suggested to take into account when the `raw_text_type` field is equal to `open_text`. This indicates that the text
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is not part of a question/answer format but has important value for LLM pre-training.
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<!--
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In case of using this dataset for the LLM training or finetuning for natural language generating with a production
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