Question: When compared to NER in the domain of general text, what are the characteristic challenges of the biomedical domain?
Evidence: Named Entity Recognition (NER) in the Biomedical domain usually includes recognition of entities such as proteins, genes, diseases, treatments, drugs, etc. Fact extraction involves extraction of Named Entities from a corpus, usually given a certain ontology. When compared to NER in the domain of general text, the biomedical domain has some characteristic challenges:
Some of the earliest systems were heavily dependent on hand-crafted features. The method proposed in BIBREF4 for recognition of protein names in text does not require any prepared dictionary. The work gives examples of diversity in protein names and lists multiple rules depending on simple word features as well as POS tags.
 BIBREF5 adopt a machine learning approach for NER. Their NER system extracts medical problems, tests and treatments from discharge summaries and progress notes. They use a semi-Conditional Random Field (semi-CRF) BIBREF6 to output labels over all tokens in the sentence. They use a variety of token, context and sentence level features. They also use some concept mapping features using existing annotation tools, as well as Brown clustering to form 128 clusters over the unlabelled data. The dataset used is the i2b2 2010 challenge dataset. Their system achieves an F-Score of 0.85. BIBREF7 is an incremental paper on NER taggers. It uses 3 types of word-representation techniques (Brown clustering, distributional clustering, word vectors) to improve performance of the NER Conditional Random Field tagger, and achieves marginal F-Score improvements.
 BIBREF8 propose a boostrapping mechanism to bootstrap biomedical ontologies using NELL BIBREF9 , which uses a coupled semi-supervised bootstrapping approach to extract facts from text, given an ontology and a small number of “seed” examples for each category. This interesting approach (called BioNELL) uses an ontology of over 100 categories. In contrast to NELL, BioNELL does not contain any relations in the ontology. BioNELL is motivated by the fact that a lot of scientific literature available online is highly reliable due to peer-review. The authors note that the algorithm used by NELL to bootstrap fails in BioNELL due to ambiguities in biomedical literature, and heavy semantic drift. One of the causes for this is that often common words such as “white”, “dad”, “arm” are used as names of genes- this can easily result in semantic drift in one iteration of the bootstrapping. In order to mitigate this, they use Pointwise Mutual Information scores for corpus level statistics, which attributes a small score to common words. In addition, in contrast to NELL, BioNELL only uses high instances as seeds in the next iteration, but adds low ranking instances to the knowledge base. Since evaluation is not possible using Mechanical Turk or a small number of experts (due to the complexity of the task), they use Freebase BIBREF10 , a knowledge base that has some biomedical concepts as well. The lexicon learned using BioNELL is used to train an NER system. The system shows a very high precision, thereby showing that BioNELL learns very few ambiguous terms.
More recently, deep learning techniques have been developed to further enhance the performance of NER systems. BIBREF11 explore recurrent neural networks for the problem of NER in biomedical text.
When compared to NER in the domain of general text, the biomedical domain has some characteristic challenges: 1. Synonymy: the same biomedical entity is often known by different names. E.g. “cyclin-dependent kinase inhibitor p27” and “p27kip1” are the same proteins, “heart attack” and “myocardial infarcation” refer to the same medical problem. 2. Abbreviations: The literature is rich with ambiguous abbreviations: “RA” can refer to “right atrium”, “rheumatoid arthritis”, “renal artery” or several other concepts (Pakhomov, 2002) 3. Entity names are subject to many variants, and also change over time.
Answer: There are synonymy,  abbreviations in the biomedical domain and entity names are subject to many variants, and also change over time.