Chem2Disease - Drug Repurposing Explorer

Chem2Disease applies heterogeneous graph mining algorithms developed by Dr. Yizhou Sun at UIUC. This tool enables you to search the database for drugs like:

a) Bring me compounds which have less structural similarity and high chemical similarity; b) Bring me compounds which has high protein sharing similarity and less 3D shape; and c) Bring me some compounds which have high side effect similarity equal protein and chemical similarity.

Hierarchical Faceted Browser

Semantic web technologies help medical researchers and drug designers extract valuable information from chemical and pharmaceutical data to aid in drug research for new drug development. This tool uses the Simile Exhibit publishing framework to develop a sample hierarchical database where users can search for drugs by Anatomical Therapeutic Chemical (ATC) code. This tool provides a useful example of how linked data can be used in the chemical and pharmaceutical fields.

Muzkmesh - Semantic Music Mashups

The vision of the Semantic Web is to lift current Web into semantic repositories where heterogeneous data can be queried and different services can be mashed up. The Web becomes a platform for integrating data and services. The MuzkMesh music portal mashups existing semantic music data from the Linked Open Data (LOD) bubbles and other common APIs. It aims to demo the power of semantic integration and useful use scenarios on music retrieval and entertainment. And this tool was developed and owned by Mayank Sing.

Semantic Web Portal - A Research Group Portal (This tool is temporarily unavialable since the Longwell server is down)

Research Group portals are one of the most common portals in academic settings. Professors need to manage their research labs, centers or groups in an efficient way to conduct, disseminate and promote their research. The traditional research group websites are normally not easy to maintain, browse and search, especially when the size of groups reaches certain level. This tool demos the potential of semantic web powered portal for facet browsing and visualization. This tool was developed by Yuyin Sun, SLIS, IUB.

VIVO on VIVO (This tool is temporarily unavialable since the Longwell server is down)

VIVO on VIVO is one instance for VIVO project, which applies semantic web technology and collects both academic and non-academic people who work on project together. This instance is currently developed by IU team, including all IU VIVO people's information. It is designed by Jennifer R. S. Coffey, and programmed by Yuyin Sun, SLIS, IUB.

Faceted browser for Linked Open Data bubble

This use case demos the potential usage of semantic web to provide better browsing and searching support for Linked Open Data (LOD) bubbles. Taking chem2bio2rdf as one testing example, Faceted browser can be easily deployed to any middle-size Linked Open Data bubble sets. Demo can be found at: http://chem2bio2rdf.org/exhibit/drugbank.html. This tool was developed and owned by Chem2bio2rdf group in informatic, IUB.

EASAIER(Music Retrieval Portal)

EASAIER project (Enabling Access to Sound Archives through Integration, Enrichment and Retrieval) seeks to develop an innovative remote access system, which extends beyond standard content management and retrieval systems (EASAIER, 2008). This project is the extension of EASAIER project, which applies seven different Linked Data sources to the present study: Jamendo, Musicbrainz, MySpace, BBC playcount, Henry, Magnatune, and DBpedia. A music portal is developed here to query the RDF triples of these Linked Data through SPARQL. Welcome to go and play with this. This tool was developed by Web Science Lab, SLIS, IUB.

SPARQL Query Builder

The SPARQL query builder is an application, which helps the SPARQL query without any knowledge of SPARQL query. User can build the SPARQL query by selecting items intuitively. It automatically loads the schema of the data and shows it to user. Therefore, to some extent, it also can help user to explore the structure of the ontology. This tool was developed by Yuyin Sun, SLIS, IUB.

Semantic Association Search

The Pathfinder is an application, which uses SPARQL query to discover the relationship of two instances of semantic web data by finding the possible paths between them, and visualizes the paths in order to help users to have a better idea of the potential relationship of two instances. It employs several possible techniques to find all the paths of given length and to eliminate the loop of SPARQL query result. In addition, it uses Adobe Flex, a software development kit (SDK) released by Adobe Systems for the development and deployment of cross-platform rich Internet applications based on the Adobe Flash platform to visualize the result. The aim of Pathfinder is to help semantic web users discovering potential relationship by analyzing the paths in a data graph. This tool was developed by Yuyin Sun, SLIS, IUB. Below link shows the association between two persons: http://vivo-onto.slis.indiana.edu/pathfinder3/bin-debug/pathfinder.html.

Chem2bio2rdf

Chem2bio2rdf is a linked open data set created for biology system, which contains 18 datasets in the domain of chemical biology systems and is categorized into 5 domains, namely chemical (pubchem, ChEBI), chemogenomics (KEGG ligand, CTD chemical, BindingDB, Matador, PubChem BioAssay, QSAR, TTD, DrugBank) , biological (UNIPROT), systems (KEGG, Reactome, PPI, DIP), phenotype (OMIM, CTD disease, SIDER) and literature (PubMed). Chem2Bio2RDF is created by integrating bio2rdf and Linking Open Drug Data (LODD), allowing links between compounds, protein targets, genes and diseases to be established. We built up a Sparql EndPoint to enable RDF query (http://chem2bio2rdf.org). A user-friendly browser can be found at http://chem2bio2rdf.org/exhibit/drugbank.html. This tool was developed and owned by Chem2bio2rdf group in informatic, IUB.

   
  • One Node Search

One Node Search (Radius Pathfinder) takes one node as the center and expands it by adding its neighbours with a specific type. You can define the threshold for the distance between the center node and its neighbours to be appeared. You can also filter its neighbours by defining the ontology class of neighbours that can appear.

The Two Node Search Pathfinder is an application, which uses SPARQL query to discover the relationship of two instances of semantic web data by finding the possible paths between them, and visualizes the paths in order to help users to have a better idea of the potential relationship of two instances. It employs several possible techniques to find all the paths of given length and to eliminate the loop of SPARQL query result. In addition, it uses Adobe Flex, a software development kit (SDK) released by Adobe Systems for the development and deployment of cross-platform rich Internet applications based on the Adobe Flash platform to visualize the result. The aim of Pathfinder is to help semantic web users discovering potential relationship by analyzing the paths in a data graph. This tool was developed by Yuyin Sun, SLIS, IUB. Here are several prototypes:

http://vivo-onto.slis.indiana.edu/pathfinder/
This prototype is based on VIVO project data. It can identify semantic associations between people, event, entities, given start node and end node.

http://cheminfov.informatics.indiana.edu:8080/yuysun/hychembiospace.html
The prototype is similar as the previous one: finding the paths for given start node and end node. We try to borrow the idea Yuyin Sun from SLIS in IU and Dr. Xiao Dong from Informatics in IU discussed in group meeting to support auto-complete of the start and end node. However, this function is still under construction. Here are some examples:

   1. Links between fleroxacin (DB04576) and Bladder_cancer visualization: http://vivo-onto.slis.indiana.edu/pathfinder_A/bin-debug/pathfinder.html
2. Links between pefloxacin (DB00487) and Bladder_cancer visualization: http://vivo-onto.slis.indiana.edu/pathfinder_B/bin-debug/pathfinder.html
3. Links between fleroxacin (DB04576) and pefloxacin (DB00487) visualization: http://vivo-onto.slis.indiana.edu/pathfinder_C/bin-debug/pathfinder.html
* The maximum length of all the three case are set as the length of their shortest paths.

  • Diverse Two Node Search

Diverse path finder identifies the most semantically diverse and informative set of associations between two entities in ontology-based knowledge bases.

Three Node Search (Constraint-based diverse Pathfinder) incorporates users' preferences as constraints into the Diverse path finder, which identifies customized diverse and informative sets of semantic associations. Here is one example:

Instrument Search

This instrument search provides a way for search instrument with performer information from a hierarchical instruments list. Searching is case sensitive. Example, try "Flute", you get information of performer "Anne Evans plays instrument of "Flute-Wooden".

Country Quiz

Country Quiz is a computer-based testing system that uses Linked Open Data in RDF from Telegraphis.net along with the Jena ARQ framework to power a simple web application that quizzes users on the features of different countries. The system randomly generates multiple-choice questions based on an RDF dataset.
The Country Quiz system in its current form represents a proof of concept model. Thus far, the system demonstrates that semantic technologies can be utilized in unique ways and that they can be used to generate interactive systems that are both responsive and useful. Once the application is loaded, the user can quickly generate unique quizzes on the fly. Also, the modular construction of Country Quiz lends itself well to the integration of other data sets into the system. This tool was developed by Asik Pradhan and Bret Davidson, IUB.