Posts from August 2019

While Natural Language Processing (NLP)-based text mining has become a widely used technology within pharma, biotech and healthcare organizations, some still view NLP use as esoteric, only for experts. At AbbVie, however, the use of NLP has been democratized for researchers with the provision of broad-access web portals.

One project to illustrate their approach to broaden access to NLP was presented earlier this year at a Linguamatics NLP seminar. Abhik Seal, from the data science team at AbbVie, described an innovative web portal developed to provide a more effective search for pharmacokinetic and pharmacodynamic parameters, for pharmacometricians and chemists within the Clinical Pharmacology and Pharmacometrics (CPPM) group. Manual search of scientific abstracts and full-text papers is typically slow and laborious, particularly when extracting key pk/pd numerics and units, such as drug concentrations, exposures, efficacies, dosages and more.

The platform Seal’s team developed is known as PharMine (Figure 1). They have implemented a workflow (Figure 2) that takes in Medline abstracts and uses a suite of NLP queries to extract key information including:


Bone deformities, hearing loss, frequent respiratory infections, cognitive impairment and chronic heart and liver disorders are symptoms suffered by infants with Hunter syndrome (also known as Mucopolysaccharidosis II). This blog follows our previous research on associations between genotype and phenotype in very rare diseases, in collaboration with Shire. 

Shire, now part of Takeda, provides an enzyme replacement therapy for Hunter Syndrome. However, in order to ameliorate the neurocognitive effects, the enzyme replacement molecule needs to be delivered to the central nervous system (CNS) via an innovative implant device, which is an invasive procedure.