Spanish Biomedical Corpus

Embeddings
This repository contains the word embeddings generated from biomedical Spanish texts corpora.

Corpus detail
The corpus was gathered from Spanish biomedical texts from different multilingual biomedical sources:

IBECS (Spanish Bibliographical Index in Health Sciences): corpus that collects scientific journals covering multiple fields in health sciences. Contains titles and abstracts from 168,198 records in English and Spanish.
SciELO (Scientific Electronic Library Online): corpus gathers electronic publications of complete full-text articles from scientific journals of Latin America, South Africa, and Spain. Contains titles and abstracts from 161,710 records in English and Spanish.
Pubmed: free search engine used to access the MedlineNLM (https://www.ncbi.nlm.nih.gov/pubmed/). Contains titles and abstracts from 127,619 records.
MedlinePlus: corpus with health topics, drugs and supplements, laboratory test information, and medical encyclopedia texts contains 7,033 articles in English and Spanish.
UFAL Medical Corpus is a collection of parallel corpora of medical and general domain texts.
All corpus data files can be found in the next link: http://temu.bsc.es/mespen/

Pre-trained Models
FastText
We used the FastText (Bojanowski et al., 2016) implementation to training our word embeddings using the preprocessed Spanish Biomedical corpus (FastText-SBC). Moreover, we trained a concept embedding model replacing biomedical concepts in the Spanish Biomedical corpus with their unique SNOMED-CT Spanish Edition iden-tifier (SNOMED-SBC). We used the PyMedTer-mino library (Lamy et al., 2015) for concept indexing using full-text search and fuzzy search with threshold.

Train Parameters
Dimension = 300
epoch=10,20
min_count=20
neg=20
t=6e-5
thread=7
encoding='utf8'
min subword-ngram = 3
max subword-ngram = 6

Links to the embeddings
FastText-SBC, epoch 10
FastText-SBC, epoch 20
SNOMED-SBC