Biomedical Knowledge Engineering Group Wiki (Main page)

This is the top level page for the Wiki for (the Biomedical Knowledge Engineering Group @ ISI). This is a general discussion wiki designed to house notes, minutes and working documentation for the projects we are currently working on. This is a fluid set of documents, prone to change (and team members are encouraged to correct and edit these pages as they see fit).

Please maintain pages that you are responsible for. Keep them up to date and make sure that they don't get stale.

Note that this web is publicly accessible and provides access to generally-accessible information for any potential collaborators or users of our technology. Each of the other webs contain in-house information that is only available to the software development teams working on that project. If you would like to join one of these teams, please contact GullyBurns. We welcome active collaborations.

Read our statement concerning our SoftwareEngineeringParadigm.

Here are the SoftwareLibrariesAndTools that we use (including information and documentation about using these technologies where relevant).

Actively Funded Projects

BioScholar: lightweight client-side knowledge manangement software

The BioScholar project is the next phase of the 'NeuroScholar' project. NeuroScholar is a knowledge management and engineering platform for neuroscientists to be able to keep track of what they have read by annotating PDF files. We are now developing this system to be more in-line with current semantic web technology and to provide a platform for developing lightweight knowledge bases that leverage the information extraction technology we are developing. We submitted an RO1 application to NIH on this topic in May to support this project.

Packages from the NeuroScholar website have been downloaded over 4000 times since October 2005. It is our responsibility to provide support and documentation for anyone using this technology. Current development and support for the NeuroScholar system is frozen. Note: for future developments of this technology see the BioScholar web.

TopicMapping: Topic Mapping architecture using LDA

We are working with colleagues at UCI and IU to build statistical models of the biomedical literature that can be mapped using cutting edge visualization techniques.

KEfED: 'Knowledge Engineering from Experimental Design'

This project is not funded separately but is an active component of many of the other, higher-level projects described here. The design of the target knowledge representations we are constructing for our purposes (knowledge engineering and computation according to specific knowledge-intensive application) are potentially complex and a good design is essential to be able to address specific problems. We are currently developing a completely generic representation based on experimental design (called 'Knowledge Engineering from Experimental Design' or 'KE-f-ED') which we are currently developing as a paper. When this work is complete, then we will publish complete specifications here for use by our collaborators.

Projects that are in-process that are currently unfunded

BiocurationTools: Biocuration methods and services

We are developing biocuration user interfaces and approaches to assist biocurators with their task of converting data found in text into meaningful computational, structured data. Biocurators are targeted as our primary user group. Here we describe our interactions with biocuration teams and encourage these teams to constribute and discuss their efforts on this web. We are pursuing collaborations with the Jackson Laboratory and the NCBO with RO1 submissions to pursue this.

IEWorkFlow: Information Extraction workflow

We are proposing to mine the text of one million scientific articles according to the KE-f-ED framework (see below). We have submitted a proposal to the BD&I initiative at NSF to support this effort.

NeuARt: Neuroanatomical mapping software

Here we develop the NeuARt II project. This was previously developed with the Brain Archtiecture Center at USC to provide a way of displaying and managing neuroanatomical maps that had been drawn over a brain atlas. We are seeking RO1 funding for this project and are engaged in developing a collaboration with the BrainMaps project at UC Davis to develop this further.

Some conceptual maps of the structure of projects and work within BMKEG

• 'Vision' of the essential components of the high-level infrastructure

• A high-level map of our activities, instantiated for specific projects:
  

Web Utilities for the Main web

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• WebTopicList - all topics in alphabetical order
• WebChanges - recent topic changes in this web
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• WebRss, WebAtom - RSS and ATOM news feeds of topic changes
• WebStatistics - listing popular topics and top contributors
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