Currently, you are not logged in to my.chemeurope.com. Therefore, you can remember a maximum of 5 contents.
State-of-the-art text mining technologies for chemistry
The Biological Text Mining Unit at the Spanish National Cancer Research Centre (CNIO) together with with researchers at the Center for Applied Medical Research (CIMA), of the University of Navarra, in Pamplona, and the Barcelona Supercomputing Centre (BSC-CNS) have published the first exhaustive revision of the state-of-the-art methodologies underlying chemical search engines, named entity recognition and text mining systems.
The rapidly growing field of big data applications in biomedical research together with the use of machine learning and artificial intelligence technologies for text data mining has resulted in promising tools. "This review -state the authors- is organised to serve as a practical guide to researchers entering in this field but also to help them to envision the next steps in this emerging data science field".
"Through the release of Gold Standard datasets and the organisation of several community challenge benchmark events, the Biological Text Mining Unit has played a critical role in the development and evaluation of current chemical text mining systems, as highlighted in this article," explains Martin Krallinger, head of the Unit and co-first author of the review.
A huge amount of unstructured data
A considerable fraction of biomedical-relevant data is only available in the form of unstructured data. This type of data includes the rapidly growing scientific literature, medicinal chemistry patents, electronic health records or clinical trial documents. In fact, every year, over 20,000 new compounds are published in medicinal and biological chemistry journals.
Being able to transform unstructured biomedical research data into structured databases that can be more efficiently processed by machines or queried by humans is becoming critical for a range of very heterogeneous applications. These include the identification of new drug targets and chemical probes to validate/discard those new potential targets, re-purposing of approved drugs, the identification of adverse drug events or retrieval of systems biology associated with chemical-disease or chemical-gene networks.
Chemical compounds constitute a key entity type of critical relevance for biomedical research; as a therapeutic strategy to treat medical needs. In fact, "the construction of large chemical knowledge bases, integrating chemical information with biological and clinical data, is crucial to identify and validate new therapeutic targets for unmet medical needs as well as to speed up the drug discovery process" explains Julen Oyarzabal, Director of Translational Sciences at CIMA and co-leader of this report.
Centro Nacional de Investigaciones Oncológicas (CNIO)
- Text Mining
- systems biology
- medicinal chemistry
- drug discovery
- data mining
- biological chemistry
- big data
- artificial intelligence
- 1Researchers use light to convert abundant lignin into plastic that can be continually recycled
- 2This ‘Harry Potter’ light sensor achieves magically high efficiency of 200 per cent
- 3Crab shells could help power the next generation of rechargeable batteries
- 4Toilet paper is an unexpected source of PFAS in wastewater
- 5A greener alternative for aviation fuel
- 6IFF Announces the Sale of Flavor Specialty Ingredients Business to Exponent
- 7An international team presents a potentially groundbreaking discovery for nitrogen chemistry
- 8New corrosion protection that repairs itself
- 9Efficient recovery of lithium from end-of-life batteries and battery production scrap
- 10BASF to invest in its aroma ingredients business by expanding its global production footprint with new plants in China and Germany
- Covestro successfully starts up a new world-scale chlorine plant in Tarragona
- A new way to decontaminate water and gas with a new 3D extra-large pore zeolite
- Microplastics deposited on the seafloor triple in 20 years
- New X-ray imaging technique to study the transient phases of quantum materials
- New approaches to the mystery of why ice is slippery