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README.md
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## Training corpora and preprocessing
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The training corpus is composed of several biomedical corpora in Spanish, collected from publicly available corpora and crawlers
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| Name | No. tokens | Description |
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|-----------------------------------------------------------------------------------------|-------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| [Medical crawler](https://zenodo.org/record/4561971#.YTtwM32xXbQ) | 745,705,946 | Crawler of more than 3,000 URLs belonging to Spanish biomedical and health domains. |
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| [Scielo](https://github.com/PlanTL-SANIDAD/SciELO-Spain-Crawler) | 60,007,289 | Publications written in Spanish crawled from the Spanish SciELO server in 2017. |
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| [BARR2_background](https://temu.bsc.es/BARR2/downloads/background_set.raw_text.tar.bz2) | 24,516,442 | Biomedical Abbreviation Recognition and Resolution (BARR2) containing Spanish clinical case study sections from a variety of clinical disciplines. |
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| Wikipedia_life_sciences | 13,890,501 | Wikipedia articles
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| Patents | 13,463,387 | Google Patent in Medical Domain for Spain (Spanish). The accepted codes (Medical Domain) for Json files of patents are: "A61B", "A61C","A61F", "A61H", "A61K", "A61L","A61M", "A61B", "A61P". |
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| [EMEA](http://opus.nlpl.eu/download.php?f=EMEA/v3/moses/en-es.txt.zip) | 5,377,448 | Spanish-side documents extracted from parallel corpora made out of PDF documents from the European Medicines Agency. |
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| [mespen_Medline](https://zenodo.org/record/3562536#.YTt1fH2xXbR) | 4,166,077 | Spanish-side articles extracted from a collection of Spanish-English parallel corpus consisting of biomedical scientific literature. The collection of parallel resources are aggregated from the MedlinePlus source. |
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| PubMed | 1,858,966 | Open-access articles from the PubMed repository crawled in 2017. |
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To obtain a high-quality training corpus, a cleaning pipeline with the following operations has been applied:
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- data parsing in different formats
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- sentence splitting
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- language detection
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- filtering of ill-formed sentences
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- deduplication of repetitive contents
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- keep the original document boundaries
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Finally, the corpora are concatenated and further global deduplication among the corpora have been applied.
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The result is a medium-size biomedical corpus for Spanish composed of about 860M tokens.
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## Evaluation and results
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## Training corpora and preprocessing
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+
The training corpus is composed of several biomedical corpora in Spanish, collected from publicly available corpora and crawlers.
|
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+
To obtain a high-quality training corpus, a cleaning pipeline with the following operations has been applied:
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+
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+
- data parsing in different formats
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+
- sentence splitting
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+
- language detection
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+
- filtering of ill-formed sentences
|
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+
- deduplication of repetitive contents
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+
- keep the original document boundaries
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+
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+
Finally, the corpora are concatenated and further global deduplication among the corpora have been applied.
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The result is a medium-size biomedical corpus for Spanish composed of about 860M tokens. The table below shows some basic statistics of the individual cleaned corpora:
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| Name | No. tokens | Description |
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|-----------------------------------------------------------------------------------------|-------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| [Medical crawler](https://zenodo.org/record/4561971#.YTtwM32xXbQ) | 745,705,946 | Crawler of more than 3,000 URLs belonging to Spanish biomedical and health domains. |
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| [Scielo](https://github.com/PlanTL-SANIDAD/SciELO-Spain-Crawler) | 60,007,289 | Publications written in Spanish crawled from the Spanish SciELO server in 2017. |
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| [BARR2_background](https://temu.bsc.es/BARR2/downloads/background_set.raw_text.tar.bz2) | 24,516,442 | Biomedical Abbreviation Recognition and Resolution (BARR2) containing Spanish clinical case study sections from a variety of clinical disciplines. |
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| Wikipedia_life_sciences | 13,890,501 | Wikipedia articles crawled 04/01/2021 with the [Wikipedia API python library](https://pypi.org/project/Wikipedia-API/) starting from the "Ciencias\_de\_la\_vida" category up to a maximum of 5 subcategories. Multiple links to the same articles are then discarded to avoid repeating content. |
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| Patents | 13,463,387 | Google Patent in Medical Domain for Spain (Spanish). The accepted codes (Medical Domain) for Json files of patents are: "A61B", "A61C","A61F", "A61H", "A61K", "A61L","A61M", "A61B", "A61P". |
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| [EMEA](http://opus.nlpl.eu/download.php?f=EMEA/v3/moses/en-es.txt.zip) | 5,377,448 | Spanish-side documents extracted from parallel corpora made out of PDF documents from the European Medicines Agency. |
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| [mespen_Medline](https://zenodo.org/record/3562536#.YTt1fH2xXbR) | 4,166,077 | Spanish-side articles extracted from a collection of Spanish-English parallel corpus consisting of biomedical scientific literature. The collection of parallel resources are aggregated from the MedlinePlus source. |
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| PubMed | 1,858,966 | Open-access articles from the PubMed repository crawled in 2017. |
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## Evaluation and results
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