GeneNotes – A novel information management software for biologists

BACKGROUND: Collecting and managing information is a challenging task in a genome-wide profiling research project. Most databases and online computational tools require a direct human involvement. Information and computational results are presented in various multimedia formats (e.g., text, image, PDF, word files, etc.), many of which cannot be automatically processed by computers in biologically meaningful ways. In addition, the quality of computational results is far from perfect and requires nontrivial manual examination. The timely selection, integration and interpretation of heterogeneous biological information still heavily rely on the sensibility of biologists. Biologists often feel overwhelmed by the huge amount of and the great diversity of distributed heterogeneous biological information. DESCRIPTION: We developed an information management application called GeneNotes. GeneNotes is the first application that allows users to collect and manage multimedia biological information about genes/ESTs. GeneNotes provides an integrated environment for users to surf the Internet, collect notes for genes/ESTs, and retrieve notes. GeneNotes is supported by a server that integrates gene annotations from many major databases (e.g., HGNC, MGI, etc.). GeneNotes uses the integrated gene annotations to (a) identify genes given various types of gene IDs (e.g., RefSeq ID, GenBank ID, etc.), and (b) provide quick views of genes. GeneNotes is free for academic usage. The program and the tutorials are available at: . CONCLUSIONS: GeneNotes provides a novel human-computer interface to assist researchers to collect and manage biological information. It also provides a platform for studying how users behave when they manipulate biological information. The results of such study can lead to innovation of more intelligent human-computer interfaces that greatly shorten the cycle of biology research

Pathway curator: an online webserver extracting genes and interactions from figures

In the biomedical literature, gene pathways are frequently included. Many high-quality gene pathways are illustrated in the form of visuals and text, making them valuable study tools for biological processes and precision medicine. Pathway maps and literature texts provide researchers with access to a huge number of new biological treatments. For general usage, these pathway maps should be logically ordered, coordinated, and converted into a computer-readable format. Currently, keeping up with the rapid increase of the literature requires laborious extraction of information from a publication at a time. A gene pathway map recognition system is devised and implemented in this study. Based on the pathway map and relevant information supplied by users, the system extracts gene identity and gene interaction information, and the automated extraction from pathway maps is efficient. Furthermore, the tool offers users with a full view of a certain illness's pathway, which is useful for researchers and can speed up the research process in a variety of biomedical applications. This thesis first explains the project's goal and provides the background information. The project's design ideas are then presented, as well as an analysis of the system and introductions to related platforms. After that, the system's implementations are described one by one, together with the deployment and testing processes. Finally, potential improvements and future work are discussed.Includes bibliographical references

Commentary. Common criteria among States for storage and use of dried blood spot specimens after newborn screening

Biological samples collected in biobanks are a resource with significant research potential. The Italian Joint Group cNB - cNBBSV (National committee of Bioethics - National committee for Biosecurity, Biotechnologies and Life Sciences) published a document reporting recommendations on storage and use of dried blood spot (DBS) and on the development of a National Network of Regional Newborn Screening Repositories for collection of residual DBS. Several ethical questions (about consent, possible use of genetic information, unanticipated possible usages for research purposes) rise from residual newborn screening specimens collections. Moreover, legal and ethical controversies are accentuated by the conflicts between the interests of sample donors, biobank holders, researchers and the public. To overcome these difficulties the identification of a few criteria for storage and research usage of DBS is crucial

Extracting human protein information from MEDLINE using a full-sentence parser

Today, a fair number of systems are available for the task of processing biological data. The development of effective systems is of great importance since they can support both the research and the everyday work of biologists. It is well known that biological databases are large both in size and number, hence data processing technologies are required for the fast and effective management of the contents stored in databases like MEDLINE. A possible solution for content management is the application of natural language processing methods to help make this task easier. With our approach we would like to learn more about the interactions of human genes using full-sentence parsing. Given a sentence, the syntactic parser assigns to it a syntactic structure, which consists of a set of labelled links connecting pairs of words. The parser also produces a constituent representation of a sentence (showing noun phrases, verb phrases, and so on). Here we show experimentally that using the syntactic information of each abstract, the biological interactions of genes can be predicted. Hence, it is worth developing the kind of information extraction (IE) system that can retrieve information about gene interactions just by using syntactic information contained in these text. Our IE system can handle certain types of gene interactions with the help of machine learning (ML) methodologies (Hidden Markov Models, Artificial Neural Networks, Decision Trees, Support Vector Machines). The experiments and practical usage show clearly that our system can provide a useful intuitive guide for biological researchers in their investigations and in the design of their experiments

An Immune Inspired Approach to Anomaly Detection

The immune system provides a rich metaphor for computer security: anomaly detection that works in nature should work for machines. However, early artificial immune system approaches for computer security had only limited success. Arguably, this was due to these artificial systems being based on too simplistic a view of the immune system. We present here a second generation artificial immune system for process anomaly detection. It improves on earlier systems by having different artificial cell types that process information. Following detailed information about how to build such second generation systems, we find that communication between cells types is key to performance. Through realistic testing and validation we show that second generation artificial immune systems are capable of anomaly detection beyond generic system policies. The paper concludes with a discussion and outline of the next steps in this exciting area of computer security.Comment: 19 pages, 4 tables, 2 figures, Handbook of Research on Information Security and Assuranc

Security-oriented data grids for microarray expression profiles

Microarray experiments are one of the key ways in which gene activity can be identified and measured thereby shedding light and understanding for example on biological processes. The BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project has developed an infrastructure which allows post-genomic life science researchers to ask and answer the following questions: who has undertaken microarray experiments that are in some way similar or relevant to mine; and how similar were these relevant experiments? Given that microarray experiments are expensive to undertake and may possess crucial information for future exploitation (both academically and commercially), scientists are wary of allowing unrestricted access to their data by the wider community until fully exploited locally. A key requirement is thus to have fine grained security that is easy to establish and simple (or ideally transparent) to use across inter-institutional virtual organisations. In this paper we present an enhanced security-oriented data Grid infrastructure that supports the definition of these kinds of queries and the analysis and comparison of microarray experiment results

WikiPathways: building research communities on biological pathways.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further

Leveling the Field: Talking Levels in Cognitive Science

Talk of levels is everywhere in cognitive science. Whether it is in terms of adjudicating longstanding debates or motivating foundational concepts, one cannot go far without hearing about the need to talk at different ‘levels’. Yet in spite of its widespread application and use, the concept of levels has received little sustained attention within cognitive science. This paper provides an analysis of the various ways the notion of levels has been deployed within cognitive science. The paper begins by introducing and motivating discussion via four representative accounts of levels. It then turns to outlining and relating the four accounts using two dimensions of comparison. The result is the creation of a conceptual framework that maps the logical space of levels talk, which offers an important step toward making sense of levels talk within cognitive science