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Welcome to PDBWiki - A community annotated knowledge base of biological molecular structures

Systems Biology Linker (Sybil) is a platform for the integration of BioPAX and SBML. It is part of the Virtual Cell but also a useful tool for any SBML and BioPAX integration, in other words for any one who wants to use BioPAX with an SBML-capable platform or vice versa. While Sybil can be used as an intelligent conversion tool between SBML and BioPAX, it is primarily intended for building a joint repository for SBML and BioPAX data, where links between SBML elements and BioPAX objects are maintained by SBPAX. Sybil uses SYBREAM for most of the intelligent work involved in building the SBML-SBPAX-BioPAX joint repository.

novo|seek is a search engine for biomedical literature in Medline

NCBO Seminar Series talks occur via the Web and teleconference at 10:00AM, Pacific time, the 1st and 3rd Wednesday of every month. This series aims to showcase new projects, technologies and ideas in biomedical ontology by featuring the work of a different collaborator each session. It is open to anyone interested, regardless of location or affiliation.

Primary Objectives * Build a demo that spans from bench to bedside using RDF and OWL. * Explore the effectiveness of current tools. * Document our finding to help accelerate adoption of the Semantic Web.

# The primary intention of creating aTags is not the categorization of the document, but the representation of the key facts inside the document. Key facts in the biomedical domain might be, for example, "Protein A interacts with protein B" or "Overexpression of protein A in tissue B is the cause of disease C". # An aTag is comprised of a set of associated entities. The size of the set is arbitrary, but will typically lie between 2 and 5 entities. For example, the fact "Protein A binds to protein B" can be represented with an aTag comprising of the three entities "Protein A", "Molecular interaction" and "Protein B". Similarly, the fact "Overexpression of protein A in tissue B is the cause of disease C" can be represented with an aTag comprising of the four entities "Overexpression", "Protein A", "Tissue B" and "Disease C". # Each document or database entry can be described with an arbitrary number of such aTags. Each aTag can be associated with the relevant portions of text or data in a fine granularity. # The entities in an aTag are not simple strings, but resources that are part of ontologies and RDF/OWL-enabled databases. For example, "Protein A" and "Protein B" are resources that are defined in the UniProt database, whereas "Molecular Interaction" is a class in the branch of biological processes of the Gene Ontology. They are identified with their URIs.

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit.

Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust. This site provides free access to all the data and software from the Ensembl project. Click on a species name to browse the data.

SWAN (Semantic Web Applications in Neuromedicine) is a project to develop knowledge bases for the neurodegenerative disease research communities, using the energy and self-organization of that community enabled by Semantic Web technology. Created in collaboration with the Alzforum and other partners. Read more about the SWAN project here.

The Society for Integrative and Comparative Biology (SICB) is one of the largest and most prestigious professional associations of its kind. Formed as the American Society of Zoologists through a 1902 merger of two societies, the Central Naturalists and the American Morphological Society, its focus has remained to integrate the many fields of specialization which occur in the broad field of biology. Throughout most of its history the society was known as the American Society of Zoologists and changed its name to the Society for Integrative and Comparative Biology in 1996 to reflect the scientific breadth, integrative approaches, and interests of its membership across all disciplines of biology. The SICB is organized around disciplinary divisions, each relevant to a major segment of biology.

BiOS is a response to inequities in food security, nutrition, health, natural resource management and energy. Our goal is to democratise problem solving to enable diverse solutions through decentralised innovation. Open Source We promote an innovation paradigm that focuses on a distinction between the tools of innovation and the products. We promote licenses that couple rights with responsibilities to foster efficient development, improvement, sharing and use of technology. Open Science We create and share new biological enabling technologies and platforms that can be used to deliver innovations. We develop new licensing and distributive collaboration mechanisms that have resonance with the open source software movement, but are tailored for biological innovation. Open Society We enhance the transparency, accessibility and capability to use all the tools of science, whether patented, open access or public domain.

The ISCB is a scholarly society dedicated to advancing the scientific understanding of living systems through computation

Cyberinfrastructure for Phylogenetic Research (CIPRES) project is an open collaboration funded by the National Science Foundation. The group is led by Tandy Warnow and involves researchers (biologists, computer scientists, statisticians, and mathematicians) at sixteen institutions. The goal of the CIPRES project is to enable large-scale phylogenetic reconstructions on a scale that will enable analyses of huge data sets containing hundreds of thousands of bio molecular sequences. To achieve this goal we have brought together a group of researchers involved in phylogeny estimation, statistics, and computer science to create new solutions for the difficult computational problems that arise in inferring evolutionary relationships.

See also http://www.cs.utexas.edu/~tandy/ SATe bio tree software and data