The amount of biomedical literature available is increasing at an exponential rate and is becoming increasingly difficult to navigate. Text-mining methods can potentially mitigate this problem, through the systematic and large-scale extraction of structured information from inherently unstructured biomedical text. This thesis reports the development of four text-mining systems that, by building on each other, has enabled the extraction of information about a large number of published statements in the biomedical literature. The first system, LINNAEUS, enables highly accurate detection ('recognition') and identification ('normalization') of species names in biomedical articles. Building on LINNAEUS, we implemented a range of improvements in the GNAT system, enabling high-throughput gene/protein detection and identification. Using gene/protein identification from GNAT, we developed the Gene Expression Text Miner (GETM), which extracts information about gene expression statements. Finally, building on GETM as a pilot project, we constructed the BioContext integrated event extraction system, which was used to extract information about over 11 million distinct biomolecular processes in 10.9 million abstracts and 230,000 full-text articles. The ability to detect negated statements in the BioContext system enables the preliminary analysis of potential contradictions in the biomedical literature. All tools (LINNAEUS, GNAT, GETM, and BioContext) are available under open-source software licenses, and LINNAEUS and GNAT are available as online web-services. All extracted data (36 million BioContext statements, 720,000 GETM statements, 72,000 contradictions, 37 million mentions of species names, 80 million mentions of gene names, and 57 million mentions of anatomical location names) is available for bulk download. In addition, the data extracted by GETM and BioContext is also available to biologists through easy-to-use search interfaces.

The purpose of this thesis is to contribute a corpus for sentence level interpretation of biomedical language. The available corpora for the biomedical domain are small in terms of amount of text and predicates. Besides that these corpora are developed rather intuitively. In this effort which we call BioOntoFN, we created a corpus from the domain knowledge provided by an ontology. By doing this we believe that we can provide a rough set of rules to create corpora from ontologies. Besides that we also designed an annotation tool specifically for building our corpus. We built a corpus for biological transport events. The ontology we used is the piece of Gene Ontology pertaining to transport, the term transport GO: 0006810 and all of its child concepts, which could be called a sub-ontology. The annotation of the corpus follows the rules of FrameNet and the output is annotated text that is in an XML format similar to that of FrameNet. The text for the corpus is taken from abstracts of MEDLINE articles. The annotation tool is a GUI created using Java.

Experimentally determining the biological function of a protein is a process known as protein characterization. Establishing the role a specific protein plays is a vital step toward fully understanding the biochemical processes that drive life in all its forms. In order for researchers to efficiently locate and benefit from the results of protein characterization experiments, the relevant information is compiled into public databases. To populate such databases, curators, who are experts in the biomedical domain, must search the literature to obtain the relevant information, as the experiment results are typically published in scientific journals. The database curators identify relevant journal articles, read them, and then extract the required information into the database. In recent years the rate of biomedical research has greatly increased, and database curators are unable to keep pace with the number of articles being published. Consequently, maintaining an up-to-date database of characterized proteins, let alone populating a new database, has become a daunting task. In this thesis, we report our work to reduce the effort required from database curators in order to create and maintain a database of characterized proteins. We describe a system we have designed for automatically identifying relevant articles that discuss the results of protein characterization experiments. Classifiers are trained and tested using a large dataset of abstracts, which we collected from articles referenced in public databases, as well as small datasets of manually labeled abstracts. We evaluate both a standard and a modified naïve Bayes classifier and examine several different feature sets for representing articles. Our findings indicate that the resulting classifier performs well enough to be considered useful by the curators of a characterized protein database. / Thesis (Master, Computing) -- Queen's University, 2010-01-28 18:45:17.249

Biomedical literature such as MEDLINE articles are rich resources for discovering and tracking disease and drug knowledge. For example, information regarding the drugs that are used with a particular disease or the changes in drug usage over time is valulable. However, this information is buried in thousands of MEDLINE articles. Acquiring knowledge from these articles requires complex processes depending on the biomedical text mining techniques. Today, parasitic and bacterial diseases affect hundreds of millions of people worldwide. They result in significant mortality and devastating social and economic consequences. There are many control and eradication programs conducted in the world. Also, many drugs are developed for diseases caused from parasites and bacteria. In this study, research was conducted of parasites (bacteria affecting the liver) and treatment drugs were tested. Also, relationships between these diseases and genes, along with parasites and bacteria were searched through data and biomedical text mining techniques. This study reveals that the treatment of parasites and bacteria seems to be stable over the last four decades. The methodology introduced in this study also presents a reference model to acquire medical knowledge from the literature.

Τα τελευταία χρόνια, υπάρχει ένα αυξανόμενο ενδιαφέρον για την αυτόματη εξόρυξη κειμένων (Text Mining) με βιοϊατρικό περιεχόμενο, λόγω της ραγδαίας αύξησης των δημοσιεύσεων που είναι αποθηκευμένες σε ηλεκτρονική μορφή σε Βάσεις Δεδομένων του Παγκόσμιου Ιστού, όπως το PubMed και το Springerlink. Το βασικό πρόβλημα που κάνει αυτό τον στόχο περισσότερο προκλητικό και δύσκολο είναι η αδυναμία της επεξεργασίας της διαθέσιμης αυτής πληροφορίας και της εξαγωγής χρήσιμων συνδέσεων και συμπερασμάτων. Κρίνεται, επομένως, επιτακτική η ανάπτυξη νέων εργαλείων που θα διευκολύνουν την εξόρυξη γνώσης από κείμενα βιολογικού περιεχομένου. Σκοπός της παρούσας διπλωματικής εργασίας είναι αρχικά η παρουσίαση γνωστών μεθόδων εξόρυξης δεδομένων από κείμενα αλλά και η ανάπτυξη ενός εργαλείου για την αποδοτική και αξιόπιστη ανακάλυψη γνώσεων από βιοϊατρική βιβλιογραφία που να βασίζεται σε προηγμένες τεχνικές εξόρυξης γνώσης από κείμενα. Πιο συγκεκριμένα, η προσπάθειά μας επικεντρώνεται στην ανάπτυξη ενός αποδοτικού αλγόριθμου συσταδοποίησης και τη χρήση αποδοτικών τεχνικών που αξιολογούν τα αποτελέσματα της συσταδοποίησης, έτσι ώστε να παρέχεται βοήθεια στον χρήστη στην προσπάθεια αναζήτησης του για πληροφορία βιολογικού περιεχομένου. Ο προτεινόμενος αλγόριθμος βασίζεται σε διαφορετικές τεχνικές συσταδοποίησης, όπως ο Ιεραρχικός Αλγόριθμος και ο Spherical K-means Αλγόριθμος και εφαρμόζει μια τελική ταξινόμηση με βάση το Impact Factor των κειμένων που ανακτήθηκαν. Τα βασικά βήματα που περιλαμβάνει ο αλγόριθμος είναι: η προεπεξεργασία των κειμένων, η αναπαράσταση των κειμένων σε διανυσματική μορφή με χρήση του Διανυσματικού Μοντέλου (Vector Space Model), η εφαρμογή της Λανθάνουσας Σημασιολογικής Δεικτοδότησης (Latent Semantic Indexing), η Ασαφής Συσταδοποίηση (Fuzzy Clustering), ο Ιεραρχικός Αλγόριθμος (Hierarchical Algorithm), o Spherical K-means Αλγόριθμος, η επιλογή της καλύτερης συστάδας και τέλος η ταξινόμηση με βάση το Impact Factor των κειμένων που ανακτήθηκαν. Η εφαρμογή που υλοποιούμε βασίζεται στον παραπάνω αλγόριθμο και προσφέρει δύο τρόπους αναζήτησης: 1) σε τρέχοντα ερωτήματα του χρήστη, τα οποία αποθηκεύονται στη βάση δεδομένων και επομένως λειτουργεί ως μέσο συμπιεσμένης αποθήκευσης των προηγούμενων ερωτημάτων του χρήστη, 2) αναζήτηση μέσα από μία λίστα προκαθορισμένων Topic βιολογικού περιεχομένου και επομένως παρέχει στο χρήστη μια επιπλέον βοήθεια σε ένα ευρύ φάσμα ερωτημάτων. Επιπλέον, η εφαρμογή εξάγει χρήσιμες συσχετίσεις όρων χρησιμοποιώντας τις τελικές συστάδες. / There is an increasing interest in automatic text mining in biomedical texts due to the increasing number of electronically available publications stored in databases such as PubMed and SpringerLink. The main problem that makes this goal more challenging and difficult is the inability of processing the available information and extracting useful connections and assumptions. Therefore, there is an urgent need for new text-mining tools to facilitate the process of text mining from biomedical documents. The goal of the present diploma thesis is to present known methods of text mining, and to develop an application that provides reliable knowledge from biomedical literature based on efficient text mining techniques. In particular, our attempt is mainly focused on developing an efficient clustering algorithm and using techniques for evaluating the results of clustering, in order to assist the users in their biological information seeking activities. The proposed algorithm involves different clustering techniques, such as Hierarchical Algorithm, Spherical K-means Algorithm and employs a final ranking according to Impact Factor of retrieved documents. The basic steps of our algorithm are: preprocessing of text’s content, representation with the vector space model, applying Latent Semantic Indexing (LSI), fuzzy clustering, hierarchical clustering, spherical k-means clustering, selection of the best cluster and ranking of biomedical documents according to their impact factor. The application that we implement is based on the above algorithm and provides two search methods: 1) search with user’s queries, which are saved in the database and thus playing the role of a compacted storage of his past search activities, 2) search through a list of pre-specified biological Topics, and thus providing the user with an extra assistance in his various queries. Moreover the whole scheme can mine useful associations between terms by exploiting the nature of the formed clusters.

With the constantly growing amount of biomedical literature, methods for automatically distilling information from unstructured data, collectively known as information extraction, have become indispensable. Whilst most biomedical information extraction efforts in the last decade have focussed on the identification of gene products and interactions between them, the biomedical text mining community has recently extended their scope to capture associations between biomedical and chemical entities with the aim of supporting applications in drug discovery. This thesis is the first comprehensive study focussing on information extraction from pharmaceutical chemistry literature. In this research, we describe our work on (1) recognising names of chemical compounds and drugs, facilitated by the incorporation of domain knowledge; (2) exploring different coreference resolution paradigms in order to recognise co-referring expressions given a full-text article; and (3) defining drug-target interactions as events and distilling them from pharmaceutical chemistry literature using event extraction methods.

With the advent of online publishing of scientific research came an avalanche of electronic resources and repositories containing knowledge encoded in some form or another. In the domain of biomedical sciences, research is now being published at a faster-than-ever pace, with several thousand articles per day. It is impossible for any human being to process that amount of information in due time, let alone apply it to their own needs. Thus appeared the necessity of being able to automatically retrieve relevant documents and extract useful information from text. Although it is now possible to distil essential factual knowledge from text, it is difficult to interpret the connections between the extracted facts. These connections, also known as discourse relations, make the text coherent and cohesive, and their automatic discovery can lead to a better understanding of the conveyed knowledge. One fundamental discourse relation is causality, as it is the one which explains reasons and allows for inferences to be made. This thesis is the first comprehensive study which focusses on recognising discourse causality in biomedical scientific literature. We first construct a manually annotated corpus of discourse causality and analyse its characteristics. Then, a methodology for automatically recognising causal relations using text mining and natural language processing techniques is presented. Furthermore, we investigate the automatic identification of additional information about the polarity, certainty, knowledge type and source of causal relations. The entire methodology is evaluated by empirical experiments, whose results show that it is possible to successfully extract causal relations from biomedical literature. Finally, we provide an example of a direct application of our research and offer ideas for further research directions and possible improvements to our methodology.

This thesis examines biomedical text mining with an application in bone biology. A special thanks is extended to Anita Park and Mark Jaeger from the Purdue University Graduate School Office, who acted as invaluable assets in the formatting of the thesis. IUPUI and every other university would be fortunate to have staff that respond in such a timely, corteous, and professional manner. / Indiana University-Purdue University Indianapolis (IUPUI) / The biological literature is a huge and constantly increasing source of information which the biologist may consult for information about their field, but the vast amount of data can sometimes become overwhelming. Medline, which makes a great amount of biological journal data available online, makes the development of automated text mining systems and hence “data-driven discovery” possible. This thesis examines current work in the field of text mining and biological literature, and then aims to mine documents pertaining to bone biology. The documents are retrieved from PubMed, and then direct associations between the terms are computers. Potentially novel transitive associations among biological objects are then discovered using the transitive closure algorithm and the maximum flow algorithm. The thesis discusses in detail the extraction of biological objects from the collected documents and the co-occurrence based text mining algorithm, the transitive closure algorithm, and the maximum network flow which were then run to extract the potentially novel biological associations. Generated hypotheses (novel associations) were assigned with significance scores for further validation by a bone biologist expert. Extension of the work in to hypergraphs for enhanced meaning and accuracy is also examined in the thesis.

The main archive of life sciences literature currently contains more than 18,000,000 references, and it is virtually impossible for any human to stay up-to-date with this large number of papers, even in a specific sub-domain. Not every fact that is reported in the literature is novel and distinct. Scientists report repeat experiments, or refer to previous findings. Given the large number of publications, it is not surprising that information on certain topics is repeated over a number of publications. From consensus to contradiction, there are all shades of agreement between the claimed facts in the literature, and considering the volume of the corpus, conflicting findings are not unlikely. Finding such claims is particularly interesting for scientists, as they can present opportunities for knowledge consolidation and future investigations. In this thesis we present a method to extract and contextualise statements about molecular events as expressed in the biomedical literature, and to find those that potentially conflict each other. The approach uses a system that detects event negations and speculation, and combines those with contextual features (e.g. type of event, species, and anatomical location) to build a representational model for establishing relations between different biological events, including relations concerning conflicts. In the detection of negations and speculations, rich lexical, syntactic, and semantic features have been exploited, including the syntactic command relation. Different parts of the proposed method have been evaluated in a context of the BioNLP 09 challenge. The average F-measures for event negation and speculation detection were 63% (with precision of 88%) and 48% (with precision of 64%) respectively. An analysis of a set of 50 extracted event pairs identified as potentially conflicting revealed that 32 of them showed some degree of conflict (64%); 10 event pairs (20%) needed a more complex biological interpretation to decide whether there was a conflict. We also provide an open source integrated text mining framework for extracting events and their context on a large-scale basis using a pipeline of tools that are available or have been developed as part of this research, along with 72,314 potentially conflicting molecular event pairs that have been generated by mining the entire body of accessible biomedical literature. We conclude that, whilst automated conflict mining would need more comprehensive context extraction, it is feasible to provide a support environment for biologists to browse potential conflicting statements and facilitate data and knowledge consolidation.