A web based framework that takes advantage of domain specific ontologies, and Natural Language Processing, aiming to empower exploration of biomedical resources via semantic-based querying and search. The NLP engine analyzes the input free-text query and translates it into targeted queries with terms from the underlying ontology. Each query is passed to the semantically-annotated tools repository, and based on similarity matches, it ranks the available resources.
Project: EC | SOUND (633974), NIH | Accelerating Cancer Genom... (1U01CA214846-01), NIH | Bioconductor: An Open Com... (5U41HG004059-10), NIH | ADDRESSING THE ISSUE OF G... (1R01HG002020-01), NIH | Cancer Genomics:Integrati... (5U24CA180996-05)
Package that facilitates access to extensive metadata in computable form covering the Bioconductor package ecosystem, facilitating downstream applications such as custom reporting, data and text mining of Bioconductor package text descriptions, graph analytics over package dependencies, and custom search approaches.
WHOSe Heritage: Classification of UNESCO World Heritage "Outstanding Universal Value" Documents with Smoothed Labels This repository provides the supplemental materials for reproducing the results of the above-mentioned paper as submitted to arXiv preprint server, including both models and results.
ORGANISMS is a weekly updated web resource that facilitates taxonomy-aware search and retrieval of articles. To this end, the the resource performs named entity recognition of terms from the NCBI Taxonomy on PubMed abstracts. The resource further provides download files of organism-disease and organism-tissue associations extracted through automatic text mining.
DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. We further unify the evidence by assigning confidence scores that facilitate comparison of the different types and sources of evidence.