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1.  A Learning-Based Approach for Biomedical Word Sense Disambiguation 
The Scientific World Journal  2012;2012:949247.
In the biomedical domain, word sense ambiguity is a widely spread problem with bioinformatics research effort devoted to it being not commensurate and allowing for more development. This paper presents and evaluates a learning-based approach for sense disambiguation within the biomedical domain. The main limitation with supervised methods is the need for a corpus of manually disambiguated instances of the ambiguous words. However, the advances in automatic text annotation and tagging techniques with the help of the plethora of knowledge sources like ontologies and text literature in the biomedical domain will help lessen this limitation. The proposed method utilizes the interaction model (mutual information) between the context words and the senses of the target word to induce reliable learning models for sense disambiguation. The method has been evaluated with the benchmark dataset NLM-WSD with various settings and in biomedical entity species disambiguation. The evaluation results showed that the approach is very competitive and outperforms recently reported results of other published techniques.
doi:10.1100/2012/949247
PMCID: PMC3361294  PMID: 22666174
2.  Evaluating contributions of natural language parsers to protein–protein interaction extraction 
Bioinformatics  2008;25(3):394-400.
Motivation: While text mining technologies for biomedical research have gained popularity as a way to take advantage of the explosive growth of information in text form in biomedical papers, selecting appropriate natural language processing (NLP) tools is still difficult for researchers who are not familiar with recent advances in NLP. This article provides a comparative evaluation of several state-of-the-art natural language parsers, focusing on the task of extracting protein–protein interaction (PPI) from biomedical papers. We measure how each parser, and its output representation, contributes to accuracy improvement when the parser is used as a component in a PPI system.
Results: All the parsers attained improvements in accuracy of PPI extraction. The levels of accuracy obtained with these different parsers vary slightly, while differences in parsing speed are larger. The best accuracy in this work was obtained when we combined Miyao and Tsujii's Enju parser and Charniak and Johnson's reranking parser, and the accuracy is better than the state-of-the-art results on the same data.
Availability: The PPI extraction system used in this work (AkanePPI) is available online at http://www-tsujii.is.s.u-tokyo.ac.jp/-100downloads/downloads.cgi. The evaluated parsers are also available online from each developer's site.
Contact: yusuke@is.s.u-tokyo.ac.jp
doi:10.1093/bioinformatics/btn631
PMCID: PMC2639072  PMID: 19073593
3.  Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologies 
Journal of biomedical informatics  2011;44(5):805-814.
Biomedical natural language processing (BioNLP) is a useful technique that unlocks valuable information stored in textual data for practice and/or research. Syntactic parsing is a critical component of BioNLP applications that rely on correctly determining the sentence and phrase structure of free text. In addition to dealing with the vast amount of domain-specific terms, a robust biomedical parser needs to model the semantic grammar to obtain viable syntactic structures. With either a rule-based or corpus-based approach, the grammar engineering process requires substantial time and knowledge from experts, and does not always yield a semantically transferable grammar. To reduce the human effort and to promote semantic transferability, we propose an automated method for deriving a probabilistic grammar based on a training corpus consisting of concept strings and semantic classes from the Unified Medical Language System (UMLS), a comprehensive terminology resource widely used by the community. The grammar is designed to specify noun phrases only due to the nominal nature of the majority of biomedical terminological concepts. Evaluated on manually parsed clinical notes, the derived grammar achieved a recall of 0.644, precision of 0.737, and average cross-bracketing of 0.61, which demonstrated better performance than a control grammar with the semantic information removed. Error analysis revealed shortcomings that could be addressed to improve performance. The results indicated the feasibility of an approach which automatically incorporates terminology semantics in the building of an operational grammar. Although the current performance of the unsupervised solution does not adequately replace manual engineering, we believe once the performance issues are addressed, it could serve as an aide in a semi-supervised solution.
doi:10.1016/j.jbi.2011.04.006
PMCID: PMC3172402  PMID: 21549857
Natural language processing; Biomedical terminology; Semantic grammar; Probabilistic parsing
4.  Classifying protein-protein interaction articles using word and syntactic features 
BMC Bioinformatics  2011;12(Suppl 8):S9.
Background
Identifying protein-protein interactions (PPIs) from literature is an important step in mining the function of individual proteins as well as their biological network. Since it is known that PPIs have distinctive patterns in text, machine learning approaches have been successfully applied to mine these patterns. However, the complex nature of PPI description makes the extraction process difficult.
Results
Our approach utilizes both word and syntactic features to effectively capture PPI patterns from biomedical literature. The proposed method automatically identifies gene names by a Priority Model, then extracts grammar relations using a dependency parser. A large margin classifier with Huber loss function learns from the extracted features, and unknown articles are predicted using this data-driven model. For the BioCreative III ACT evaluation, our official runs were ranked in top positions by obtaining maximum 89.15% accuracy, 61.42% F1 score, 0.55306 MCC score, and 67.98% AUC iP/R score.
Conclusions
Even though problems still remain, utilizing syntactic information for article-level filtering helps improve PPI ranking performance. The proposed system is a revision of previously developed algorithms in our group for the ACT evaluation. Our approach is valuable in showing how to use grammatical relations for PPI article filtering, in particular, with a limited training corpus. While current performance is far from satisfactory as an annotation tool, it is already useful for a PPI article search engine since users are mainly focused on highly-ranked results.
doi:10.1186/1471-2105-12-S8-S9
PMCID: PMC3269944  PMID: 22151252
5.  Automatic Parsing of Parental Verbal Input 
To evaluate theoretical proposals regarding the course of child language acquisition, researchers often need to rely on the processing of large numbers of syntactically parsed utterances, both from children and their parents. Because it is so difficult to do this by hand, there are currently no parsed corpora of child language input data. To automate this process, we developed a system that combined the MOR tagger, a rule-based parser, and statistical disambiguation techniques. The resultant system obtained nearly 80% correct parses for the sentences spoken to children. To achieve this level, we had to construct a particular processing sequence that minimizes problems caused by the coverage/ambiguity trade-off in parser design. These procedures are particularly appropriate for use with the CHILDES database, an international corpus of transcripts. The data and programs are now freely available over the Internet.
PMCID: PMC1880885  PMID: 15190707
6.  Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues 
BMC Bioinformatics  2006;7:334.
Background
Word sense disambiguation (WSD) is critical in the biomedical domain for improving the precision of natural language processing (NLP), text mining, and information retrieval systems because ambiguous words negatively impact accurate access to literature containing biomolecular entities, such as genes, proteins, cells, diseases, and other important entities. Automated techniques have been developed that address the WSD problem for a number of text processing situations, but the problem is still a challenging one. Supervised WSD machine learning (ML) methods have been applied in the biomedical domain and have shown promising results, but the results typically incorporate a number of confounding factors, and it is problematic to truly understand the effectiveness and generalizability of the methods because these factors interact with each other and affect the final results. Thus, there is a need to explicitly address the factors and to systematically quantify their effects on performance.
Results
Experiments were designed to measure the effect of "sample size" (i.e. size of the datasets), "sense distribution" (i.e. the distribution of the different meanings of the ambiguous word) and "degree of difficulty" (i.e. the measure of the distances between the meanings of the senses of an ambiguous word) on the performance of WSD classifiers. Support Vector Machine (SVM) classifiers were applied to an automatically generated data set containing four ambiguous biomedical abbreviations: BPD, BSA, PCA, and RSV, which were chosen because of varying degrees of differences in their respective senses. Results showed that: 1) increasing the sample size generally reduced the error rate, but this was limited mainly to well-separated senses (i.e. cases where the distances between the senses were large); in difficult cases an unusually large increase in sample size was needed to increase performance slightly, which was impractical, 2) the sense distribution did not have an effect on performance when the senses were separable, 3) when there was a majority sense of over 90%, the WSD classifier was not better than use of the simple majority sense, 4) error rates were proportional to the similarity of senses, and 5) there was no statistical difference between results when using a 5-fold or 10-fold cross-validation method. Other issues that impact performance are also enumerated.
Conclusion
Several different independent aspects affect performance when using ML techniques for WSD. We found that combining them into one single result obscures understanding of the underlying methods. Although we studied only four abbreviations, we utilized a well-established statistical method that guarantees the results are likely to be generalizable for abbreviations with similar characteristics. The results of our experiments show that in order to understand the performance of these ML methods it is critical that papers report on the baseline performance, the distribution and sample size of the senses in the datasets, and the standard deviation or confidence intervals. In addition, papers should also characterize the difficulty of the WSD task, the WSD situations addressed and not addressed, as well as the ML methods and features used. This should lead to an improved understanding of the generalizablility and the limitations of the methodology.
doi:10.1186/1471-2105-7-334
PMCID: PMC1550263  PMID: 16822321
7.  Syntactic Dependency Parsers for Biomedical-NLP 
Syntactic parsers have made a leap in accuracy and speed in recent years. The high order structural information provided by dependency parsers is useful for a variety of NLP applications. We present a biomedical model for the EasyFirst parser, a fast and accurate parser for creating Stanford Dependencies. We evaluate the models trained in the biomedical domains of EasyFirst and Clear-Parser in a number of task oriented metrics. Both parsers provide stat of the art speed and accuracy in the Genia of over 89%. We show that Clear-Parser excels at tasks relating to negation identification while EasyFirst excels at tasks relating to Named Entities and is more robust to changes in domain.
PMCID: PMC3540535  PMID: 23304280
8.  Distinguishing the species of biomedical named entities for term identification 
BMC Bioinformatics  2008;9(Suppl 11):S6.
Background
Term identification is the task of grounding ambiguous mentions of biomedical named entities in text to unique database identifiers. Previous work on term identification has focused on studying species-specific documents. However, full-length articles often describe entities across a number of species, in which case resolving the ambiguity of model organisms in entities is critical to achieving accurate term identification.
Results
We developed and compared a number of rule-based and machine-learning based approaches to resolving species ambiguity in mentions of biomedical named entities, and demonstrated that a hybrid method achieved the best overall accuracy at 71.7%, as tested on the gold-standard ITI-TXM corpora. By utilising the species information predicted by the hybrid tagger, our rule-based term identification system was improved significantly by up to 11.6%.
Conclusion
This paper shows that, in the context of identifying terms involving multiple model organisms, integration of an accurate species disambiguation system can significantly improve the performance of term identification systems.
doi:10.1186/1471-2105-9-S11-S6
PMCID: PMC2586755  PMID: 19025692
9.  A psycholinguistic model of natural language parsing implemented in simulated neurons 
Cognitive Neurodynamics  2009;3(4):317-330.
A natural language parser implemented entirely in simulated neurons is described. It produces a semantic representation based on frames. It parses solely using simulated fatiguing Leaky Integrate and Fire neurons, that are a relatively accurate biological model that is simulated efficiently. The model works on discrete cycles that simulate 10 ms of biological time, so the parser has a simple mapping to psychological parsing time. Comparisons to human parsing studies show that the parser closely approximates this data. The parser makes use of Cell Assemblies and the semantics of lexical items is represented by overlapping hierarchical Cell Assemblies so that semantically related items share neurons. This semantic encoding is used to resolve prepositional phrase attachment ambiguities encountered during parsing. Consequently, the parser provides a neurally-based cognitive model of parsing.
doi:10.1007/s11571-009-9080-6
PMCID: PMC2777190  PMID: 19301147
Fatiguing Leaky Integrate and Fire (fLIF) neurons; Natural language parsing; Timing; Prepositional phrase attachment
10.  Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches 
BMC Bioinformatics  2006;7(Suppl 3):S2.
Background
We study the adaptation of Link Grammar Parser to the biomedical sublanguage with a focus on domain terms not found in a general parser lexicon. Using two biomedical corpora, we implement and evaluate three approaches to addressing unknown words: automatic lexicon expansion, the use of morphological clues, and disambiguation using a part-of-speech tagger. We evaluate each approach separately for its effect on parsing performance and consider combinations of these approaches.
Results
In addition to a 45% increase in parsing efficiency, we find that the best approach, incorporating information from a domain part-of-speech tagger, offers a statistically significant 10% relative decrease in error.
Conclusion
When available, a high-quality domain part-of-speech tagger is the best solution to unknown word issues in the domain adaptation of a general parser. In the absence of such a resource, surface clues can provide remarkably good coverage and performance when tuned to the domain. The adapted parser is available under an open-source license.
doi:10.1186/1471-2105-7-S3-S2
PMCID: PMC1764446  PMID: 17134475
11.  A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools 
BMC Bioinformatics  2012;13:207.
Background
We introduce the linguistic annotation of a corpus of 97 full-text biomedical publications, known as the Colorado Richly Annotated Full Text (CRAFT) corpus. We further assess the performance of existing tools for performing sentence splitting, tokenization, syntactic parsing, and named entity recognition on this corpus.
Results
Many biomedical natural language processing systems demonstrated large differences between their previously published results and their performance on the CRAFT corpus when tested with the publicly available models or rule sets. Trainable systems differed widely with respect to their ability to build high-performing models based on this data.
Conclusions
The finding that some systems were able to train high-performing models based on this corpus is additional evidence, beyond high inter-annotator agreement, that the quality of the CRAFT corpus is high. The overall poor performance of various systems indicates that considerable work needs to be done to enable natural language processing systems to work well when the input is full-text journal articles. The CRAFT corpus provides a valuable resource to the biomedical natural language processing community for evaluation and training of new models for biomedical full text publications.
doi:10.1186/1471-2105-13-207
PMCID: PMC3483229  PMID: 22901054
12.  The strength of co-authorship in gene name disambiguation 
BMC Bioinformatics  2008;9:69.
Background
A biomedical entity mention in articles and other free texts is often ambiguous. For example, 13% of the gene names (aliases) might refer to more than one gene. The task of Gene Symbol Disambiguation (GSD) – a special case of Word Sense Disambiguation (WSD) – is to assign a unique gene identifier for all identified gene name aliases in biology-related articles. Supervised and unsupervised machine learning WSD techniques have been applied in the biomedical field with promising results. We examine here the utilisation potential of the fact – one of the special features of biological articles – that the authors of the documents are known through graph-based semi-supervised methods for the GSD task.
Results
Our key hypothesis is that a biologist refers to each particular gene by a fixed gene alias and this holds for the co-authors as well. To make use of the co-authorship information we decided to build the inverse co-author graph on MedLine abstracts. The nodes of the inverse co-author graph are articles and there is an edge between two nodes if and only if the two articles have a mutual author. We introduce here two methods using distances (based on the graph) of abstracts for the GSD task. We found that a disambiguation decision can be made in 85% of cases with an extremely high (99.5%) precision rate just by using information obtained from the inverse co-author graph. We incorporated the co-authorship information into two GSD systems in order to attain full coverage and in experiments our procedure achieved precision of 94.3%, 98.85%, 96.05% and 99.63% on the human, mouse, fly and yeast GSD evaluation sets, respectively.
Conclusion
Based on the promising results obtained so far we suggest that the co-authorship information and the circumstances of the articles' release (like the title of the journal, the year of publication) can be a crucial building block of any sophisticated similarity measure among biological articles and hence the methods introduced here should be useful for other biomedical natural language processing tasks (like organism or target disease detection) as well.
doi:10.1186/1471-2105-9-69
PMCID: PMC2262057  PMID: 18230174
13.  Developing a test collection for biomedical word sense disambiguation. 
Ambiguity, the phenomenon that a word has more than one sense, poses difficulties for many current Natural Language Processing (NLP) systems. Algorithms that assist in the resolution of these ambiguities, i.e. which make unambiguous a word, or more generally, a text string, will boost performance of these systems. To test such techniques in the biomedical language domain, we have developed a Word Sense Disambiguation (WSD) test collection that comprises 5,000 unambiguous instances for 50 ambiguous UMLS Metathesaurus strings.
PMCID: PMC2243574  PMID: 11825285
14.  Integrating Various Resources for Gene Name Normalization 
PLoS ONE  2012;7(9):e43558.
The recognition and normalization of gene mentions in biomedical literature are crucial steps in biomedical text mining. We present a system for extracting gene names from biomedical literature and normalizing them to gene identifiers in databases. The system consists of four major components: gene name recognition, entity mapping, disambiguation and filtering. The first component is a gene name recognizer based on dictionary matching and semi-supervised learning, which utilizes the co-occurrence information of a large amount of unlabeled MEDLINE abstracts to enhance feature representation of gene named entities. In the stage of entity mapping, we combine the strategies of exact match and approximate match to establish linkage between gene names in the context and the EntrezGene database. For the gene names that map to more than one database identifiers, we develop a disambiguation method based on semantic similarity derived from the Gene Ontology and MEDLINE abstracts. To remove the noise produced in the previous steps, we design a filtering method based on the confidence scores in the dictionary used for NER. The system is able to adjust the trade-off between precision and recall based on the result of filtering. It achieves an F-measure of 83% (precision: 82.5% recall: 83.5%) on BioCreative II Gene Normalization (GN) dataset, which is comparable to the current state-of-the-art.
doi:10.1371/journal.pone.0043558
PMCID: PMC3440407  PMID: 22984434
15.  Knowledge-based Method for Determining the Meaning of Ambiguous Biomedical Terms Using Information Content Measures of Similarity 
In this paper, we introduce a novel knowledge-based word sense disambiguation method that determines the sense of an ambiguous word in biomedical text using semantic similarity or relatedness measures. These measures quantify the degree of similarity between concepts in the Unified Medical Language System (UMLS). The objective of this work was to develop a method that can disambiguate terms in biomedical text by exploiting similarity information extracted from the UMLS and to evaluate the efficacy of information content-based semantic similarity measures, which augment path-based information with probabilities derived from biomedical corpora. We show that information content-based measures obtain a higher disambiguation accuracy than path-based measures because they weight the path based on where it exists in the taxonomy coupled with the probability of the concepts occurring in a corpus of text.
PMCID: PMC3243213  PMID: 22195148
16.  Quantitative Assessment of Dictionary-based Protein Named Entity Tagging 
Objective
Natural language processing (NLP) approaches have been explored to manage and mine information recorded in biological literature. A critical step for biological literature mining is biological named entity tagging (BNET) that identifies names mentioned in text and normalizes them with entries in biological databases. The aim of this study was to provide quantitative assessment of the complexity of BNET on protein entities through BioThesaurus, a thesaurus of gene/protein names for UniProt knowledgebase (UniProtKB) entries that was acquired using online resources.
Methods
We evaluated the complexity through several perspectives: ambiguity (i.e., the number of genes/proteins represented by one name), synonymy (i.e., the number of names associated with the same gene/protein), and coverage (i.e., the percentage of gene/protein names in text included in the thesaurus). We also normalized names in BioThesaurus and measures were obtained twice, once before normalization and once after.
Results
The current version of BioThesaurus has over 2.6 million names or 2.1 million normalized names covering more than 1.8 million UniProtKB entries. The average synonymy is 3.53 (2.86 after normalization), ambiguity is 2.31 before normalization and 2.32 after, while the coverage is 94.0% based on the BioCreAtive data set comprising MEDLINE abstracts containing genes/proteins.
Conclusion
The study indicated that names for genes/proteins are highly ambiguous and there are usually multiple names for the same gene or protein. It also demonstrated that most gene/protein names appearing in text can be found in BioThesaurus.
doi:10.1197/jamia.M2085
PMCID: PMC1561801  PMID: 16799122
17.  Concept annotation in the CRAFT corpus 
BMC Bioinformatics  2012;13:161.
Background
Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text.
Results
This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement.
Conclusions
As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.
doi:10.1186/1471-2105-13-161
PMCID: PMC3476437  PMID: 22776079
18.  The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text 
PLoS ONE  2013;8(6):e65390.
The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org.
doi:10.1371/journal.pone.0065390
PMCID: PMC3688812  PMID: 23823062
19.  PPInterFinder—a mining tool for extracting causal relations on human proteins from literature 
One of the most common and challenging problem in biomedical text mining is to mine protein–protein interactions (PPIs) from MEDLINE abstracts and full-text research articles because PPIs play a major role in understanding the various biological processes and the impact of proteins in diseases. We implemented, PPInterFinder—a web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE abstracts and consists of three phases. First, it identifies the relation keyword using a parser with Tregex and a relation keyword dictionary. Next, it automatically identifies the candidate PPI pairs with a set of rules related to PPI recognition. Finally, it extracts the relations by matching the sentence with a set of 11 specific patterns based on the syntactic nature of PPI pair. We find that PPInterFinder is capable of predicting PPIs with the accuracy of 66.05% on AIMED corpus and outperforms most of the existing systems.
Database URL: http://www.biomining-bu.in/ppinterfinder/
doi:10.1093/database/bas052
PMCID: PMC3548331  PMID: 23325628
20.  LINNAEUS: A species name identification system for biomedical literature 
BMC Bioinformatics  2010;11:85.
Background
The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.
Results
In this paper we describe an open-source species name recognition and normalization software system, LINNAEUS, and evaluate its performance relative to several automatically generated biomedical corpora, as well as a novel corpus of full-text documents manually annotated for species mentions. LINNAEUS uses a dictionary-based approach (implemented as an efficient deterministic finite-state automaton) to identify species names and a set of heuristics to resolve ambiguous mentions. When compared against our manually annotated corpus, LINNAEUS performs with 94% recall and 97% precision at the mention level, and 98% recall and 90% precision at the document level. Our system successfully solves the problem of disambiguating uncertain species mentions, with 97% of all mentions in PubMed Central full-text documents resolved to unambiguous NCBI taxonomy identifiers.
Conclusions
LINNAEUS is an open source, stand-alone software system capable of recognizing and normalizing species name mentions with speed and accuracy, and can therefore be integrated into a range of bioinformatics and text-mining applications. The software and manually annotated corpus can be downloaded freely at http://linnaeus.sourceforge.net/.
doi:10.1186/1471-2105-11-85
PMCID: PMC2836304  PMID: 20149233
21.  Anatomical entity mention recognition at literature scale 
Bioinformatics  2013;30(6):868-875.
Motivation: Anatomical entities ranging from subcellular structures to organ systems are central to biomedical science, and mentions of these entities are essential to understanding the scientific literature. Despite extensive efforts to automatically analyze various aspects of biomedical text, there have been only few studies focusing on anatomical entities, and no dedicated methods for learning to automatically recognize anatomical entity mentions in free-form text have been introduced.
Results: We present AnatomyTagger, a machine learning-based system for anatomical entity mention recognition. The system incorporates a broad array of approaches proposed to benefit tagging, including the use of Unified Medical Language System (UMLS)- and Open Biomedical Ontologies (OBO)-based lexical resources, word representations induced from unlabeled text, statistical truecasing and non-local features. We train and evaluate the system on a newly introduced corpus that substantially extends on previously available resources, and apply the resulting tagger to automatically annotate the entire open access scientific domain literature. The resulting analyses have been applied to extend services provided by the Europe PubMed Central literature database.
Availability and implementation: All tools and resources introduced in this work are available from http://nactem.ac.uk/anatomytagger.
Contact: sophia.ananiadou@manchester.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btt580
PMCID: PMC3957068  PMID: 24162468
22.  A Novel Approach to Word Sense Disambiguation Based on Topical and Semantic Association 
The Scientific World Journal  2013;2013:586327.
Word sense disambiguation (WSD) is a fundamental problem in nature language processing, the objective of which is to identify the most proper sense for an ambiguous word in a given context. Although WSD has been researched over the years, the performance of existing algorithms in terms of accuracy and recall is still unsatisfactory. In this paper, we propose a novel approach to word sense disambiguation based on topical and semantic association. For a given document, supposing that its topic category is accurately discriminated, the correct sense of the ambiguous term is identified through the corresponding topic and semantic contexts. We firstly extract topic discriminative terms from document and construct topical graph based on topic span intervals to implement topic identification. We then exploit syntactic features, topic span features, and semantic features to disambiguate nouns and verbs in the context of ambiguous word. Finally, we conduct experiments on the standard data set SemCor to evaluate the performance of the proposed method, and the results indicate that our approach achieves relatively better performance than existing approaches.
doi:10.1155/2013/586327
PMCID: PMC3833093  PMID: 24294131
23.  Complex event extraction at PubMed scale 
Bioinformatics  2010;26(12):i382-i390.
Motivation: There has recently been a notable shift in biomedical information extraction (IE) from relation models toward the more expressive event model, facilitated by the maturation of basic tools for biomedical text analysis and the availability of manually annotated resources. The event model allows detailed representation of complex natural language statements and can support a number of advanced text mining applications ranging from semantic search to pathway extraction. A recent collaborative evaluation demonstrated the potential of event extraction systems, yet there have so far been no studies of the generalization ability of the systems nor the feasibility of large-scale extraction.
Results: This study considers event-based IE at PubMed scale. We introduce a system combining publicly available, state-of-the-art methods for domain parsing, named entity recognition and event extraction, and test the system on a representative 1% sample of all PubMed citations. We present the first evaluation of the generalization performance of event extraction systems to this scale and show that despite its computational complexity, event extraction from the entire PubMed is feasible. We further illustrate the value of the extraction approach through a number of analyses of the extracted information.
Availability: The event detection system and extracted data are open source licensed and available at http://bionlp.utu.fi/.
Contact: jari.bjorne@utu.fi
doi:10.1093/bioinformatics/btq180
PMCID: PMC2881365  PMID: 20529932
24.  EXTRACTION OF GENOTYPE-PHENOTYPE-DRUG RELATIONSHIPS FROM TEXT: FROM ENTITY RECOGNITION TO BIOINFORMATICS APPLICATION 
Advances in concept recognition and natural language parsing have led to the development of various tools that enable the identification of biomedical entities and relationships between them in text. The aim of the Genotype-Phenotype-Drug Relationship Extraction from Text workshop (or GPD-Rx workshop) is to examine the current state of art and discuss the next steps for making the extraction of relationships between biomedical entities integral to the curation and knowledge management workflow in Pharmacogenomics. The workshop will focus particularly on the extraction of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships that are of interest to Pharmacogenomics. Extracting and structuring such text-mined relationships is a key to support the evaluation and the validation of multiple hypotheses that emerge from high throughput translational studies spanning multiple measurement modalities. In order to advance this agenda, it is essential that existing relationship extraction methods be compared to one another and that a community wide benchmark corpus emerges; against which future methods can be compared. The workshop aims to bring together researchers working on the automatic or semi-automatic extraction of relationships between biomedical entities from research literature in order to identify the key groups interested in creating such a benchmark.
PMCID: PMC3501138  PMID: 19904832
NLP; Pharmacogenomics; Entity Recognition; Event Extraction; Genotype-Phenotype-Drug Relationships
25.  Dependency Parser-based Negation Detection in Clinical Narratives 
Negation of clinical named entities is common in clinical documents and is a crucial factor to accurately compile patients’ clinical conditions and to further support complex phenotype detection. In 2009, Mayo Clinic released the clinical Text Analysis and Knowledge Extraction System (cTAKES), which includes a negation annotator that identifies negation status of a named entity by searching for negation words within a fixed word distance. However, this negation strategy is not sophisticated enough to correctly identify complicated patterns of negation. This paper aims to investigate whether the dependency structure from the cTAKES dependency parser can improve the negation detection performance. Manually compiled negation rules, derived from dependency paths were tested. Dependency negation rules do not limit the negation scope to word distance; instead, they are based on syntactic context. We found that using a dependency-based negation proved a superior alternative to the current cTAKES negation annotator.
PMCID: PMC3392064  PMID: 22779038

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