Mining Images in Biomedical Publications: Detection and Analysis of Gel Diagrams

Authors of biomedical publications use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a concise way to communicate such findings, not all of which need to be explicitly discussed in the article text. This fact together with the abundance of gel images and their shared common patterns makes them prime candidates for automated image mining and parsing. We introduce an approach for the detection of gel images, and present a workflow to analyze them. We are able to detect gel segments and panels at high accuracy, and present preliminary results for the identification of gene names in these images. While we cannot provide a complete solution at this point, we present evidence that this kind of image mining is feasible.Comment: arXiv admin note: substantial text overlap with arXiv:1209.148

Do peers see more in a paper than its authors?

Recent years have shown a gradual shift in the content of biomedical publications that is freely accessible, from titles and abstracts to full text. This has enabled new forms of automatic text analysis and has given rise to some interesting questions: How informative is the abstract compared to the full-text? What important information in the full-text is not present in the abstract? What should a good summary contain that is not already in the abstract? Do authors and peers see an article differently? We answer these questions by comparing the information content of the abstract to that in citances-sentences containing citations to that article. We contrast the important points of an article as judged by its authors versus as seen by peers. Focusing on the area of molecular interactions, we perform manual and automatic analysis, and we find that the set of all citances to a target article not only covers most information (entities, functions, experimental methods, and other biological concepts) found in its abstract, but also contains 20% more concepts. We further present a detailed summary of the differences across information types, and we examine the effects other citations and time have on the content of citances

Information Extraction from Biomedical Texts

V poslední době bylo vynaloženo velké úsilí k tomu, aby byly biomedicínské znalosti, typicky uložené v podobě vědeckých článků, snadněji přístupné a bylo možné je efektivně sdílet. Ve skutečnosti ale nestrukturovaná podstata těchto textů způsobuje velké obtíže při použití technik pro získávání a vyvozování znalostí. Anotování entit nesoucích jistou sémantickou informaci v textu je prvním krokem k vytvoření znalosti analyzovatelné počítačem. V této práci nejdříve studujeme metody pro automatickou extrakci informací z textů přirozeného jazyka. Dále zhodnotíme hlavní výhody a nevýhody současných systémů pro extrakci informací a na základě těchto znalostí se rozhodneme přijmout přístup strojového učení pro automatické získávání exktrakčních vzorů při našich experimentech. Bohužel, techniky strojového učení často vyžadují obrovské množství trénovacích dat, která může být velmi pracné získat. Abychom dokázali čelit tomuto nepříjemnému problému, prozkoumáme koncept tzv. bootstrapping techniky. Nakonec ukážeme, že během našich experimentů metody strojového učení pracovaly dostatečně dobře a dokonce podstatně lépe než základní metody. Navíc v úloze využívající techniky bootstrapping se podařilo významně snížit množství dat potřebných pro trénování extrakčního systému.Recently, there has been much effort in making biomedical knowledge, typically stored in scientific articles, more accessible and interoperable. As a matter of fact, the unstructured nature of such texts makes it difficult to apply  knowledge discovery and inference techniques. Annotating information units with semantic information in these texts is the first step to make the knowledge machine-analyzable.  In this work, we first study methods for automatic information extraction from natural language text. Then we discuss the main benefits and disadvantages of the state-of-art information extraction systems and, as a result of this, we adopt a machine learning approach to automatically learn extraction patterns in our experiments. Unfortunately, machine learning techniques often require a huge amount of training data, which can be sometimes laborious to gather. In order to face up to this tedious problem, we investigate the concept of weakly supervised or bootstrapping techniques. Finally, we show in our experiments that our machine learning methods performed reasonably well and significantly better than the baseline. Moreover, in the weakly supervised learning task we were able to substantially bring down the amount of labeled data needed for training of the extraction system.

Building a semantically annotated corpus of clinical texts

In this paper, we describe the construction of a semantically annotated corpus of clinical texts for use in the development and evaluation of systems for automatically extracting clinically significant information from the textual component of patient records. The paper details the sampling of textual material from a collection of 20,000 cancer patient records, the development of a semantic annotation scheme, the annotation methodology, the distribution of annotations in the final corpus, and the use of the corpus for development of an adaptive information extraction system. The resulting corpus is the most richly semantically annotated resource for clinical text processing built to date, whose value has been demonstrated through its use in developing an effective information extraction system. The detailed presentation of our corpus construction and annotation methodology will be of value to others seeking to build high-quality semantically annotated corpora in biomedical domains

MLA for Identifying Disease-Treatment

The Machine Learning is pictured as a tool by which computer-based systems can be unified in the healthcare field in order to get a better, more efficient medical care. This paper describes a Machine Learning based methodology for building an application and scattering healthcare information. It extracts sentences from published medical papers that mention diseases and treatments, and identifies relation between meanings that exist between diseases and treatment

From Questions to Effective Answers: On the Utility of Knowledge-Driven Querying Systems for Life Sciences Data

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data. These interfaces could be seen as implementing a set of "pre-canned" queries commonly used by the life science researchers that we study. The second approach is based on semantic Web technologies and is knowledge (model) driven. It utilizes a large OWL ontology and same datasets as before but associated as RDF instances of the ontology concepts. An intuitive interface is provided that allows the formulation of RDF triples-based queries. Both these approaches are being used in parallel by a team of cell biologists in their daily research activities, with the objective of gradually replacing the conventional approach with the knowledge-driven one. This provides us with a valuable opportunity to compare and qualitatively evaluate the two approaches. We describe several benefits of the knowledge-driven approach in comparison to the traditional way of accessing data, and highlight a few limitations as well. We believe that our analysis not only explicitly highlights the specific benefits and limitations of semantic Web technologies in our context but also contributes toward effective ways of translating a question in a researcher's mind into precise computational queries with the intent of obtaining effective answers from the data. While researchers often assume the benefits of semantic Web technologies, we explicitly illustrate these in practice

The biomedical discourse relation bank

<p>Abstract</p> <p>Background</p> <p>Identification of discourse relations, such as causal and contrastive relations, between situations mentioned in text is an important task for biomedical text-mining. A biomedical text corpus annotated with discourse relations would be very useful for developing and evaluating methods for biomedical discourse processing. However, little effort has been made to develop such an annotated resource.</p> <p>Results</p> <p>We have developed the Biomedical Discourse Relation Bank (BioDRB), in which we have annotated explicit and implicit discourse relations in 24 open-access full-text biomedical articles from the GENIA corpus. Guidelines for the annotation were adapted from the Penn Discourse TreeBank (PDTB), which has discourse relations annotated over open-domain news articles. We introduced new conventions and modifications to the sense classification. We report reliable inter-annotator agreement of over 80% for all sub-tasks. Experiments for identifying the sense of explicit discourse connectives show the connective itself as a highly reliable indicator for coarse sense classification (accuracy 90.9% and F1 score 0.89). These results are comparable to results obtained with the same classifier on the PDTB data. With more refined sense classification, there is degradation in performance (accuracy 69.2% and F1 score 0.28), mainly due to sparsity in the data. The size of the corpus was found to be sufficient for identifying the sense of explicit connectives, with classifier performance stabilizing at about 1900 training instances. Finally, the classifier performs poorly when trained on PDTB and tested on BioDRB (accuracy 54.5% and F1 score 0.57).</p> <p>Conclusion</p> <p>Our work shows that discourse relations can be reliably annotated in biomedical text. Coarse sense disambiguation of explicit connectives can be done with high reliability by using just the connective as a feature, but more refined sense classification requires either richer features or more annotated data. The poor performance of a classifier trained in the open domain and tested in the biomedical domain suggests significant differences in the semantic usage of connectives across these domains, and provides robust evidence for a biomedical sublanguage for discourse and the need to develop a specialized biomedical discourse annotated corpus. The results of our cross-domain experiments are consistent with related work on identifying connectives in BioDRB.</p